@article {1124517, title = {The role of progenesis in the diversification of the interstitial annelid lineage Psammodrilidae}, journal = {Invertebrate Systematics.}, year = {In Press}, author = {Worsaae, K. and Giribet, G. and Mart{\'\i}nez, A.} } @article {1124516, title = {. A phylotranscriptomic backbone of the orb-weaving spider family Araneidae (Arachnida, Araneae) supported by multiple methodological approaches. }, journal = {Molecular Phylogenetics and Evolution.}, year = {In Press}, author = {Kallal, R. J. and Fern{\'a}ndez, R. and Giribet, G. and Hormiga, G.} } @article {1124514, title = {The "Peripatos" in Eurogondwana?-Lack of evidence that southeast Asian onychophorans walked through Europe. }, year = {In Press}, author = {Giribet, G. and Buckman-Young, R. and Sampaio Costa, C. and Baker, C.M. and Benavides, L. R. and Branstetter, M. G. and Daniels, S. R. and R. Pinto-da-Rocha} } @book {1226107, title = {The Invertebrate Tree of Life.}, year = {Forthcoming}, publisher = {Princeton University Press}, organization = {Princeton University Press}, address = {March 2020}, author = {Giribet, G. and G.D. Edgecombe} } @article {1226099, title = { Resolving the relationships of clams and cockles: dense transcriptome sampling drastically improves the bivalve tree of life }, journal = {Proceedings of the Royal Society B: Biological Sciences }, volume = {286}, year = {2019}, pages = {20182684}, abstract = {Bivalvia has been the subject of extensive recent phylogenetic work to attempt resolving either the backbone of the bivalve tree using transcriptomic data, or the tips using morpho-anatomical data and up to five genetic markers. Yet the first approach lacked decisive taxon sampling and the second failed to resolve many interfamilial relationships, especially within the diverse clade Imparidentia. Here we combine dense taxon sampling with 108 deep-sequenced Illumina-based transcriptomes to provide resolution in nodes that required additional study. We designed specific data matrices to address the poorly resolved relationships within Imparidentia. Our results support the overall backbone of the bivalve tree, the monophyly of Bivalvia and all its main nodes, although the monophyly of Protobranchia remains less clear. Likewise, the inter-relationships of the six main bivalve clades were fully supported. Within Imparidentia, resolution increases when analysing Imparidentia-specific matrices. Lucinidae, Thyasiridae and Gastrochaenida represent three early branches. Gastrochaenida is sister group to all remaining imparidentians, which divide into six orders. Neoheterodontei is always fully supported, and consists of Sphaeriida, Myida and Venerida, with the latter now also containing Mactroidea, Ungulinoidea and Chamidae, a family particularly difficult to place in earlier work. Overall, our study, by using densely sampled transcriptomes, provides the best-resolved bivalve phylogeny to date.}, author = {Lemer, S. and Bieler, R., and Giribet, G.} } @article {1226098, title = {Revisiting metazoan phylogeny with genomic sampling of all phyla}, journal = {Proceedings of the Royal Society B: Biological Sciences}, volume = {286}, year = {2019}, pages = {20190831}, abstract = {Proper biological interpretation of a phylogeny can sometimes hinge on the placement of key taxa-or fail when such key taxa are not sampled. In this light, we here present the first attempt to investigate (though not conclusively resolve) animal relationships using genome-scale data from all phyla. Results from the site-heterogeneous CAT + GTR model recapitulate many established major clades, and strongly confirm some recent discoveries, such as a monophyletic Lophophorata, and a sister group relationship between Gnathifera and Chaetognatha, raising continued questions on the nature of the spiralian ancestor. We also explore matrix construction with an eye towards testing specific relationships; this approach uniquely recovers support for Panarthropoda, and shows that Lophotrochozoa (a subclade of Spiralia) can be constructed in strongly conflicting ways using different taxon- and/or orthologue sets. Dayhoff-6 recoding sacrifices information, but can also reveal surprising outcomes, e.g. full support for a clade of Lophophorata and Entoprocta + Cycliophora, a clade of Placozoa + Cnidaria, and raising support for Ctenophora as sister group to the remaining Metazoa, in a manner dependent on the gene and/or taxon sampling of the matrix in question. Future work should test the hypothesis that the few remaining uncertainties in animal phylogeny might reflect violations of the various stationarity assumptions used in contemporary inference methods.}, author = {Laumer, C.E., and Fern{\'a}ndez, R., and Lemer, S., and Combosch, D. J., and Kocot, K., and Andrade, S. C. S., and Sterrer, W., and S{\o}rensen, M.V. and Giribet, G.} } @article {1226080, title = {The phylogeny and evolutionary history of arthropods}, journal = {Current Biology}, volume = {29}, year = {2019}, pages = {R592-R602}, abstract = {Arthropods are the most diverse animal phylum, and their phylogenetic relationships have been debated for centuries. With the advent of molecular phylogenetics, arthropods were found to be monophyletic and placed within a clade of molting animals, the ecdysozoans, with nematodes and six other phyla. Molecular phylogenetics also provided a new framework for relationships between the major arthropod groups, such as the clade Pancrustacea, which comprises insects and crustaceans. Phylogenomics based on second-generation genomics and transcriptomics has further resolved puzzles such as the exact position of myriapods or the closest crustacean relatives of hexapods. It is now broadly recognized that extant arthropods are split into chelicerates and mandibulates, and relationships within the two mandibulate clades (myriapods and pancrustaceans) are stabilizing. Notably, the phylogeny of insects is now understood with considerable confidence, whereas relationships among chelicerate orders remain poorly resolved. The evolutionary history of arthropods is illuminated by a rich record of fossils, often with exquisite preservation, but current analyses conflict over whether certain fossil groups are stem- or crown-group arthropods. Molecular time-trees calibrated with fossils estimate the origins of arthropods to be in the Ediacaran, while most other deep nodes date to the Cambrian. The earliest stem-group arthropods were lobopodians, worm-like animals with annulated appendages. Confidently placing some key extinct clades on the arthropod tree of life may require less ambiguous interpretation of fossil structures and better integration of morphological data into the phylogeny.}, author = {Giribet, G. and G.D. Edgecombe} } @article {1226077, title = {Further discussion on the Eocene drowning of New Caledonia: discordances from the point of view of zoology}, journal = {Journal of Biogeography }, volume = {46}, year = {2019}, pages = {1912-1918}, abstract = {We discuss the fauna of New Caledonia in the context of the prolonged submergence of Grande Terre until its re-emergence around 37 million years ago and whether the resulting fauna can be entirely explained by over-water dispersal. The current literature discussing the predominant neoendemism in New Caledonia is reviewed, questioning some of the discourse about how the fact that most animal and plant lineages are neoendemics should weigh in to disregard the fewer cases of paleoendemism (clades that have persisted and diversified in New Caledonia for over 37 million years). We argue that many of the examples used in the literature, selected for other purposes, were not chosen to test this particular hypothesis, but several old lineages of non-vagile animals show that a non-trivial number of clades have a history that predates the supposed emergence of New Caledonia. We conclude by posing the question of how much additional evidence should be needed to demonstrate a discordance between the geological history of the archipelago and the evolutionary history of its biota.}, author = {Giribet, G. and Baker, C.M.} } @article {1226076, title = {Sequence capture phylogenomics of historical ethanol-preserved museum specimens: unlocking the rest of the vault}, journal = {Molecular Ecology Resources}, volume = {00}, year = {2019}, pages = {1-14}, abstract = {Natural history collections play a crucial role in biodiversity research, and museum specimens are increasingly being incorporated into modern genetics-based studies. Sequence capture methods have proven incredibly useful for phylogenomics, providing the additional ability to sequence historical museum specimens with highly degraded DNA, which until recently have been deemed less valuable for genetic work. The successful sequencing of ultraconserved elements (UCEs) from historical museum specimens has been demonstrated on multiple tissue types including dried bird skins, formalin-fixed squamates and pinned insects. However, no study has thoroughly demonstrated this approach for historical ethanol-preserved museum specimens. Alongside sequencing of {\textquotedblleft}fresh{\textquotedblright} specimens preserved in \>95\% ethanol and stored at -80{\textdegree}C, we used extraction techniques specifically designed for degraded DNA coupled with sequence capture protocols to sequence UCEs from historical museum specimens preserved in 70\%{\textendash}80\% ethanol and stored at room temperature, the standard for such ethanol-preserved museum collections. Across 35 fresh and 15 historical museum samples of the arachnid order Opiliones, an average of 345 UCE loci were included in phylogenomic matrices, with museum samples ranging from six to 495 loci. We successfully demonstrate the inclusion of historical ethanol-preserved museum specimens in modern sequence capture phylogenomic studies, show a high frequency of variant bases at the species and population levels, and from off-target reads successfully recover multiple loci traditionally sequenced in multilocus studies including mitochondrial loci and nuclear rRNA loci. The methods detailed in this study will allow researchers to potentially acquire genetic data from millions of ethanol-preserved museum specimens held in collections worldwide.}, author = {Derkarabetian, S and Benavides, L. R. and Giribet, G.} } @article {1226074, title = {A congruent topology for deep gastropod relationships}, journal = {Proceedings of the Royal Society B: Biological Sciences}, volume = {286}, year = {2019}, pages = {20182776}, abstract = {Gastropod molluscs are among the most diverse and abundant animals in the oceans, and are successful colonizers of terrestrial and freshwater environments. Past phylogenetic efforts to resolve gastropod relationships resulted in a range of conflicting hypotheses. Here, we use phylogenomics to address deep relationships between the five major gastropod lineages{\textemdash}Caenogastropoda, Heterobranchia, Neritimorpha, Patellogastropoda and Vetigastropoda{\textemdash}and provide one congruent and well-supported topology. We substantially expand taxon sampling for outgroups and for previously underrepresented gastropod lineages, presenting new transcriptomes for neritimorphs and patellogastropods. We conduct analyses under maximum-likelihood, Bayesian inference and a coalescent-based approach, accounting for the most pervasive sources of systematic errors in large datasets: compositional heterogeneity, site heterogeneity, heterotachy, variation in evolutionary rates among genes, matrix completeness, outgroup choice and gene tree conflict. We find that vetigastropods and patellogastropods are sister taxa, and that neritimorphs are the sister group to caenogastropods and heterobranchs. We name these two major unranked clades Psilogastropoda and Angiogastropoda, respectively. We additionally provide the first genomic-scale data for internal relationships of neritimorphs and patellogastropods. Our results highlight the need for reinterpreting the evolution of morphological and developmental characters in gastropods, especially for inferring their ancestral states.}, author = {Cunha, T. J. and Giribet, G.} } @article {1226073, title = { Phylogeny, evolution and systematic revision of the mite harvestman family Neogoveidae (Opiliones Cyphophthalmi)}, journal = {Invertebrate Systematics}, volume = {33}, year = {2019}, pages = {101-180}, abstract = {Mite harvestmen of the family Neogoveidae have a tropical trans-Atlantic distribution with representatives in equatorial West Africa and the Neotropics, specifically in the south-east region of the USA and in northern South America, being conspicuously absent from Central America. We provide a comprehensive molecular phylogeny of the family including representatives of all genera but the monotypic Tucanogovea Karaman, 2013, and new information on the type species described by Jochen Martens in 1969 that were unavailable for molecular study until now: Brasiliogovea microphaga, Metagovea oviformis and {\textquoteleft}? Gen. enigmaticus{\textquoteright}. Additionally, we revisit the somatic and male genitalic morphology of representatives of all genera by means of scanning electron microscopy and confocal laser scanning microscopy, and describe the new genera Leggogovia Benavides \& Giribet, gen. nov., Microgovia Benavides, Hormiga \& Giribet, gen. nov., Waiwaigovia Benavides, Hormiga \& Giribet, gen. nov. and 13 new species: Brasiliogovea aphantostylus Benavides, Hormiga \& Giribet, sp. nov., Brasiliogovea microstylus Benavides, Hormiga \& Giribet, sp. nov., Brasiliogovea yacambuensis Benavides, Hormiga \& Giribet, sp. nov., Metagovea matapi Benavides, Hormiga \& Giribet, sp. nov., Metagovea planada Benavides, Hormiga \& Giribet, sp. nov., Microgovia chenepau Benavides, Hormiga \& Giribet, sp. nov., Neogovea branstetteri Benavides, Hormiga \& Giribet, sp. nov., Neogovea enigmatica Martens, sp. nov., Neogovea matawai Benavides, Hormiga \& Giribet, sp. nov., Parogovia montealensis Benavides \& Giribet, sp. nov., Parogovia prietoi Benavides \& Giribet, sp. nov., Parogovia putnami Benavides \& Giribet, sp. nov. and Waiwaigovia schultzi Benavides, Hormiga \& Giribet, sp. nov. Phylogenetic analyses based on maximum likelihood, parsimony and Bayesian inference support the monophyly of Neogoveidae and a sister group relationship of Neogoveidae + Ogoveidae with Troglosironidae (a clade named Sternophthalmi). Relationships among neogoveid genera are largely congruent between methods as follows: ((Leggogovia gen. nov., Metasiro), (Parogovia, ((Canga, Microgovia gen. nov.), ((Brasiliogovea, Neogovea), (Huitaca, (Waiwaigovia gen. nov., Metagovea)))))). In light of our results, the following taxonomic changes are proposed: Metagovea oviformis Martens, 1969 is transferred to Microgovia, gen. nov.; Parogovia pabsgarnoni Legg, 1990 is transferred to Leggogovia, gen. nov.; {\textquoteleft}? Gen. enigmaticus Martens, 1969{\textquoteright} is an invalid name according to the ICZN; the corresponding taxon is redescribed and formally named as Neogovea enigmatica Martens, sp. nov.}, author = {Benavides, L. R. and Hormiga, G. and Giribet, G.} } @article {1226068, title = {Phylogenomic interrogation resolves the backbone of the Pseudoscorpiones Tree of Life}, journal = {Molecular Phylogenetics and Evolution}, volume = {139}, year = {2019}, pages = {106509}, abstract = {Pseudoscorpiones, with nearly 3700 described species, are an ancient and globally distributed group of arachnids with a fossil record dating back to the Middle Devonian. Previous attempts to reconstruct their phylogenetic history have used morphology or a few amplicons, mostly of rRNAs and mitochondrial genes, which have not been able to completely resolve family-level relationships nor the earliest nodes in the pseudoscorpion tree{\textemdash}those which are most informative about the origins of key characters like venoms and silk. Here we undertake a phylogenetic approach using 41 pseudoscorpion transcriptomes and a series of analyses that account for many of the common pitfalls faced in large phylogenomic analyses. All analyses, using concatenation methods and coalescent approaches, supported monophyly of Iocheirata (the venomous pseudoscorpions), which diversified mostly during the Mesozoic, but paraphyly of Epiocheirata, with a sister group relationship of Feaelloidea to Iocheirata, with Chthonioidea as their sister group. These three main lineages were established during the mid-to-late Paleozoic. Our phylogenetic scheme is consistent with the prior hypothesis that the lack of venom in Pseudoscorpiones is plesiomorphic and not a synapomorphy of Epiocheirata. Based on the results of this study, a new classification is proposed for Pseudoscorpiones including the following new nomenclatural and taxonomic acts: the new suborders Palaeosphyronida Harvey and Atoposphyronida Harvey for Dracochelidae and Feaelloidea, respectively; the newly recognized superfamily Garypinoidea for Garypinidae and Larcidae; the revised rank for Lechytiidae and Tridenchthoniidae, which are regarded as subfamilies of Chthoniidae; the revised rank for Tridenchthoniini and Verrucadithini which are regarded as tribes of Tridenchthoniinae; and the elevation of Hesperolpiinae as a distinct family, Hesperolpiidae.}, author = {Benavides, L. R. and Cosgrove, J. G. and Harvey, M. S. and Giribet, G.} } @article {1124511, title = {A revised dated phylogeny of scorpions: Phylogenomic support for ancient divergence of the temperate Gondwanan family Bothriuridae. }, journal = {Molecular Phylogenetics and Evolution }, volume = {122}, year = {2018}, pages = {37-45.}, abstract = {The scorpion family Bothriuridae occupies a subset of landmasses formerly constituting East and West temperate Gondwana, but its relationship to other scorpion families is in question. Whereas morphological data have strongly supported a sister group relationship of Bothriuridae and the superfamily Scorpionoidea, a recent phylogenomic analysis recovered a basal placement of bothriurids within Iurida, albeit sampling only a single exemplar. Here we reexamined the phylogenetic placement of the family Bothriuridae, sampling six bothriurid exemplars representing both East and West Gondwana, using transcriptomic data. Our results demonstrate that the sister group relationship of Bothriuridae to the clade ("Chactoidea" + Scorpionoidea) is supported by the inclusion of additional bothriurid taxa, and that this placement is insensitive to matrix completeness or partitioning by evolutionary rate. We also estimated divergence times within the order Scorpiones using multiple fossil calibrations, to infer whether the family Bothriuridae is sufficiently old to be characterized as a true Gondwanan lineage. We show that scorpions underwent ancient diversification between the Devonian and early Carboniferous. The age interval of the bothriurids sampled (a derived group that excludes exemplars from South Africa) spans the timing of breakup of temperate Gondwana.}, author = {Sharma, P. P. and Baker, C. and Cosgrove, J. G. and Johnson, J. and Oberski, J. and Raven, R. and Harvey, M. and Boyer, S. and Giribet, G.} } @article {1124510, title = {Origin of spiders and their spinning organs illuminated by mid-Cretaceous amber fossils. }, journal = {Nature Ecology \& Evolution}, volume = { 2}, year = {2018}, pages = {623-627.}, author = {Huang, D. and Hormiga, G. and Xia, F. and Cai, C. and Yin, Z. and Su, Y. and Giribet, G.} } @article {1124508, title = {Phylogenomics resolves the evolutionary chronicle of our squirting closest relatives}, journal = {BMC Biology}, year = {2018}, abstract = {A recent paper in BMC Biology has resolved the family relationships of sea squirts, one of our closest invertebrate relatives, by using a large phylogenomic data set derived from available genomes and newly generated transcriptomes. The work confirms previous ideas that ascidians (the sea squirts) are not monophyletic, as they include some pelagic jelly-like relatives, and proposes a chronogram for a group that has been difficult to resolve due to their accelerated genome evolution.}, author = {Giribet, G.} } @article {1124507, title = {Current views on chelicerate phylogeny{\textemdash}A tribute to Peter Weygoldt}, journal = {Zoologischer Anzeiger }, volume = {273,}, year = {2018}, pages = { 7-13.}, author = {Giribet, G.} } @article {1124505, title = {Putative adhesive setae on the walking legs of the Paleotropical harvestman Metibalonius sp. (Arachnida: Opiliones: Podoctidae). }, journal = {Journal of Arachnology }, volume = {46}, year = {2018}, pages = {62-68}, abstract = {We provide a first scanning electron microscopy examination of the Paleotropical harvestman family Podoctidae (Opiliones: Laniatores), focusing on the distitarsus of the legs of Metibalonius sp. Distitarsi I and II are mostly equipped with olfactory sensilla chaetica with wall pores, while those of legs III and IV have gustatory sensilla chaetica with a tip pore, ventral trichomes with ovate tips (non-sensory) and a type of spatulate seta. Spatulate setae are present in adults of both sexes, with no apparent sexual dimorphism, but they are absent in the nymph. Seven of these setae are inserted on the frontal surface of the last tarsomere of legs III and IV, with the tips oriented ventrally. Each seta has an s-shaped socketed shaft, which terminates distally in a spatula-shaped structure. The distribution of spatulate setae, restricted to legs III and IV (walking legs), the position on the distitarsi, and the typical spatulate shape suggest an adhesive function for these structures. Morphology and position suggest that the socketed spatulate setae of Metibalonius sp. and the previously reported scopular spatulate setae of other harvestmen constitute two distinct types of adhesive structures, highlighting the diversity of adhesive structures in Laniatores. Future investigations about the natural history of this species and internal morphology of spatulate setae are necessary to test further functional hypotheses and to determine their behavioral role.}, author = {Gainett, G. and Sharma, P. P. and Giribet, G. and Willemart, R. H.} } @article {1124504, title = {Phylogenomics, diversification dynamics and comparative transcriptomics across the Spider Tree of Life. }, journal = {Current Biology}, year = {2018}, author = {Fern{\'a}ndez, R. and Kallal, R. J. and D. Dimitrov and Ballesteros, J. A. and Arnedo, M. A. and Giribet, G. and Hormiga, G.} } @article {1124502, title = {Phylogenomics illuminates the backbone of the Myriapoda Tree of Life and reconciles morphological and molecular phylogenies. }, journal = {Scientific Reports }, volume = {8}, year = {2018}, pages = {83}, abstract = {The interrelationships of the four classes of Myriapoda have been an unresolved question in arthropod phylogenetics and an example of conflict between morphology and molecules. Morphology and development provide compelling support for Diplopoda (millipedes) and Pauropoda being closest relatives, and moderate support for Symphyla being more closely related to the diplopod-pauropod group than any of them are to Chilopoda (centipedes). In contrast, several molecular datasets have contradicted the Diplopoda{\textendash}Pauropoda grouping (named Dignatha), often recovering a Symphyla{\textendash}Pauropoda group (named Edafopoda). Here we present the first transcriptomic data including a pauropod and both families of symphylans, allowing myriapod interrelationships to be inferred from phylogenomic data from representatives of all main lineages. Phylogenomic analyses consistently recovered Dignatha with strong support. Taxon removal experiments identified outgroup choice as a critical factor affecting myriapod interrelationships. Diversification of millipedes in the Ordovician and centipedes in the Silurian closely approximates fossil evidence whereas the deeper nodes of the myriapod tree date to various depths in the Cambrian-Early Ordovician, roughly coinciding with recent estimates of terrestrialisation in other arthropod lineages, including hexapods and arachnids.}, author = {Fern{\'a}ndez, R. and G.D. Edgecombe and Giribet, G.} } @article {1124501, title = {Advancing genomics through the Global Invertebrate Genomics Alliance (GIGA}, journal = {Invertebrate Systematics }, volume = {31}, year = {2017}, pages = {1-7.}, abstract = {The Global Invertebrate Genomics Alliance (GIGA), a collaborative network of diverse scientists, marked its second anniversary with a workshop in Munich, Germany in 2015, where international attendees focused on discussing current progress, milestones and bioinformatics resources. The community determined the recruitment and training of talented researchers as one of the most pressing future needs and identified opportunities for network funding. GIGA also promotes future research efforts to prioritise taxonomic diversity and create new synergies. Here, we announce the generation of a central and simple data repository portal with a wide coverage of available sequence data, via the compagen platform, in parallel with more focused and specialised organism databases to globally advance invertebrate genomics. This article serves the objectives of GIGA by disseminating current progress and future prospects in the science of invertebrate genomics with the aim of promotion and facilitation of interdisciplinary and international research.}, author = {Voolstra, C. and Adamski, M. and Agrawal, S. and Antunes, A. and Aranda, M. and Baxevanis, A., and Blaxter, M. and Bosch, T. and Bracken-Grissom, H. and Coddington, J.} } @article {1124500, title = {A phylogenomic solution to the origin of insects by resolving crustacean-hexapod relationships}, journal = {Current Biology }, volume = {27}, year = {2017}, pages = {1818-1824.}, abstract = {Insects, the most diverse group of organisms, are nested within crustaceans, arguably the most abundant group of marine animals. However, to date, no consensus has been reached as to which crustacean taxon is the closest relative of hexapods. A majority of\ studies have proposed that Branchiopoda (e.g., fairy shrimps) is the sister group of Hexapoda [1-7].\ However, these investigations largely excluded two\ equally important taxa, Remipedia and Cephalocarida. Other studies suggested Remipedia [8-11] or\ Remipedia\ + Cephalocarida [12, 13] as potential sister groups of hexapods, but they either did not\ include Cephalocarida or used only Sanger sequence data and morphology [9, 12]. Here we present the first phylogenomic study specifically addressing the origins of hexapods, including transcriptomes for two species each of Cephalocarida and Remipedia. Phylogenetic analyses of selected matrices, ranging from 81 to 1,675 orthogroups and up to 510,982 amino acid positions, clearly reject a\ sister-group relationship between Hexapoda and Branchiopoda [1-7]. Nonetheless, support for a hexapod sister-group relationship to Remipedia or to Cephalocarida-Remipedia was highly dependent on the employed analytical methodology. Further analyses assessing the effects of gene evolutionary rate and targeted taxon exclusion\ support Remipedia as the sole sister taxon of Hexapoda and suggest that the prior grouping of Remipedia\ + Cephalocarida is an artifact, possibly due to long branch attraction and compositional heterogeneity. We further conclude that terrestrialization of Hexapoda probably occurred in the late Cambrian to early Ordovician, an estimate that is independent of their proposed sister group [4, 8, 12, 14].}, author = {Schwentner, M. and Combosch, D.J. and Nelson, J. P. and Giribet, G.} } @article {1124497, title = {Genetic variation and geographic differentiation in the marine triclad Bdelloura candida (Platyhelminthes, Tricladida, Maricola), ectocommensal on the American horseshoe crab Limulus polyphemus. }, journal = {Marine Biology }, volume = {164}, year = {2017}, pages = {111.}, abstract = {Bdelloura candida (Platyhelminthes, Tricladida, Maricola) is an ectocommensal symbiont on the American horseshoe crab Limulus polyphemus, living on the book gills and appendages, where it spends its entire life. Given its limited dispersal capabilities and its inability to live outside of the host, we hypothesized a genetic structure that parallels that of its host. We obtained 84 planarian individuals from 19 horseshoe crabs collected from 10 sites from Massachusetts to Florida. We amplified the mitochondrial 16S rRNA and the nuclear internal transcribed spacer 2 and conducted phylogeographic and population genetic analyses, which show a clear and strong genetic break between the populations in the Atlantic and the Gulf coasts. Among the Atlantic populations, two additional, weaker barriers located along Cape Hatteras and Cape Cod restrict gene flow. Even though previous studies have suggested that the populations of the host may be in decline, those of B. candida remain stable, and some even shows signatures of expansion. Our results indicate that the phylogeography of these marine ectocommensal triclads closely mirrors that of its Limulus host, and highlight the challenges to both host and symbiont to genetically connect populations across their distribution.}, author = {Riesgo, A. and Burke, E. A. and Laumer, C. and Giribet, G.} } @article {1124454, title = {Phylogenetic relationships within Adiaphanida (phylum Platyhelminthes) and the status of the crustacean-parasitic genus Genostoma.}, journal = {Invertebrate Biology }, volume = {136 }, year = {2017}, pages = {184-198.}, abstract = {The existence of the platyhelminth clade Adiaphanida{\textemdash}an assemblage comprising the well-studied order Tricladida as well as two lesser known taxa, Prolecithophora and the obligate parasitic Fecampiida{\textemdash}is among the more surprising results of flatworm molecular systematics. Each of these three clades is itself largely well-defined from a morphological point of view, although Adiaphanida at large, despite its strong support in molecular phylogenetic analyses, lacks known morphological synapomorphies. However, one taxon, the genus Genostoma, a parasite of the leptostracan crustacean Nebalia, rests uneasily within its current classification within the fecampiid family Genostomatidae; ultrastructural investigations on this taxon have uncovered a spermatogenesis reminiscent of Kalyptorhynchia, and a dorsal syncytium resembling the neodermatan tegument. Here, we provide molecular sequence data (nearly complete 18S and 28S rRNA) from a representative of Genostoma, with which we test hypotheses on the phylogenetic position of this taxon within Platyhelminthes, expanding upon a recently published phylum-wide analysis, and applying novel alignment algorithms and substitution models. These analyses unequivocally position Genostoma as the sister group of Prolecithophora. However, even in taxon-rich analyses, support for the position of the root of Adiaphanida is lacking, highlighting the need for new data types to study the phylogeny of this clade. Interestingly, our analyses also do not recover the monophyly of several taxa previously proposed, notably Continenticola within Tricladida and Protomonotresidae within Prolecithophora. In light of this phylogeny and the distinctive morphology (especially, spermatogenesis) of Genostoma, we advocate for a redefinition of the family Genostomatidae, outside of both Fecampiida and Prolecithophora, to encompass the members of this unique genus of parasites. Within Fecampiida, the family Piscinquilinidae fam. nov. is erected to accommodate the vertebrate-parasitic Piscinquilinus, formerly Genostomatidae.}, author = {Laumer, C. E. and Giribet, G.} } @article {1123837, title = {Sperm ultrastructure of the Protobranchia: comparison with other bivalve mollusks and potential taxonomic and phylogenetic significance. }, journal = {Fieldiana Zoology }, volume = {11}, year = {2017}, pages = {1-28}, abstract = {Sperm ultrastructure of nine species of protobranch bivalves, representing three of four extant orders (Solemyida, Nuculida, Nuculanida), is discussed. Greatest diversity occurs in Solemyida (acrosomal vesicle low-conical, tall-conical, or very elongate, with radial plates; nucleus rod-shaped, teardrop-shaped, or very elongate; four, five, or six mitochondria) and the least in Nuculida (acrosomal vesicle low- to tall-conical; lacking radial plates; nucleus rod-shaped, five or six mitochondria) followed by Nuculanida (short, conical acrosomal vesicle with radial plates; spheroidal nucleus; four or five mitochondria). The wide variety of shapes in Solemyidae suggests taxonomic potential, especially in resolution and/or recognition of supraspecific taxa, but no diagnostic family characters were identified. Taxonomic potential exists for Nuculida (acrosomal shape) and Nuculanida (mitochondrial number). Protobranch sperm is highly diverse, and no defining character of the whole group was found. Support was found for the Nuculida and Nuculanida as natural groups but not for their close relationship. Nuculanida and Solemyida exhibit radial plates in the acrosomal vesicle but otherwise share no derived characters. The striking similarity of most sperm features of Nuculanida with certain pteriomorphians, especially Pectinoidea, a relationship also suggested by some mitochondrial DNA sequence data, poses interesting questions concerning their relationships and/or shared functional constraints.}, author = {Healy, J. M. and Mikkelsen, P. M. and Giribet, G. and Bieler, R.} } @article {1123833, title = { The biogeography of Australasian arachnids. }, journal = {Ebach, M. C. (Ed.) Handbook of Australasian Biogeography. CRC/Taylor and Francis Group}, year = {2017}, pages = {241-267}, author = {Harvey, M. S. and Rix, M. G. and Harms, D. and Giribet, G. and Vink, C. J. and Walter, D. E.} } @article {1123830, title = {Current understanding of Ecdysozoa and its internal phylogenetic relationships. }, journal = {Integrative and Comparative Biology }, volume = {57}, year = {2017}, pages = {455-466}, author = {Giribet, G. and Edgecombe, Gregory D.} } @article {1123827, title = {The systematics and biogeography of the mite harvestman family Sironidae (Arachnida : Opiliones : Cyphophthalmi) with the description of five new species. }, journal = {Invertebrate Systematics }, volume = {31}, year = {2017}, pages = {456-491}, abstract = {Sironidae, the first described family of Cyphophthalmi, is among the least understood phylogenetically. After examining recent collections across their distribution range, we provide the first comprehensive treatment of Sironidae by including molecular data from most of the known species, and all genera except for the monotypic Odontosiro Juberthie, 1961. We also revisit the male genitalic morphology for most genera by using confocal laser scanning microscopy and provide descriptions of five new species belonging to Iberosiro de Bivort \& Giribet, 2004 (monotypic until now), Paramiopsalis Juberthie, 1962 and Siro Latreille, 1802. While the monophyly of Sironidae remains poorly supported using traditional Sanger-based markers, with the Mediterranean Parasiro Hansen \& S{\o}rensen, 1904 and the Japanese Suzukielus Juberthie, 1970b sometimes branching basally with respect to the other sironids, the remaining genera form a well-supported Laurentian/Laurasian clade. This group divides into a Western European/North American clade of Siro and the remaining genera, Iberosiro, Paramiopsalis and Cyphophthalmus Joseph, 1868. Iberosiro and Paramiopsalis form a well-supported clade from the NW corner of the Iberian Peninsula, while Cyphophthalmus is widespread in the Balkan region and Eastern Mediterranean. Finally, the following new taxa are described: Iberosiro rosae Giribet, Merino-S{\'a}inz \& Benavides, sp. nov., Paramiopsalis anadonae Giribet, Merino-S{\'a}inz \& Benavides, sp. nov., Paramiopsalis ramblae Benavides \& Giribet, sp. nov., Siro ligiae Giribet, sp. nov., and Siro richarti Benavides \& Giribet, sp. nov.}, author = {Giribet, G. and Benavides, L. R. and Merino-S{\'a}inz, I.} } @article {1123819, title = { Nacre tablet thickness records formation temperature in modern and fossil shells. }, journal = {Earth and Planetary Science Letters }, volume = {460}, year = {2017}, pages = {281-292.}, abstract = {{\textcopyright} 2016 Elsevier B.V. Nacre, the iridescent outer lining of pearls and inner lining of many mollusk shells, is composed of periodic, parallel, organic sheets alternating with aragonite (CaCO 3 ) tablet layers. Nacre tablet thickness (TT) generates both nacre{\textquoteright}s iridescence and its remarkable resistance to fracture. Despite extensive studies on how nacre forms, the mechanisms controlling TT remain unknown, even though they determine the most conspicuous of nacre{\textquoteright}s characteristics, visible even to the naked eye. Thermodynamics predicts that temperature (T) will affect both physical and chemical components of biomineralized skeletons. The chemical composition of biominerals is well-established to record environmental parameters, and has therefore been extensively used in paleoclimate studies. The physical structure, however, has been hypothesized but never directly demonstrated to depend on the environment. Here we observe that the physical TT in nacre from modern and fossil shallow-water shells of the bivalves Pinna and Atrina correlates with T as measured by the carbonate clumped isotope thermometer. Based on the observed TT vs. T correlation, we anticipate that TT will be used as a paleothermometer, useful to estimate paleotemperature in shallow-water paleoenvironments. Here we successfully test the proposed new nacre TT thermometer on two Jurassic Pinna shells. The increase of TT with T is consistent with greater aragonite growth rate at higher T, and with greater metabolic rate at higher T. Thus, it reveals a complex, T-dependent biophysical mechanism for nacre formation.}, author = {P.U.P.A. Gilbert and Bergmann, K. D. and Myers, C. E. and Marcus, M. A. and DeVol, R. T. and Sun, C.-Y. and Blonsky, A. Z. and Zhao, J. and Karan, E. A. and Tamre, E.} } @article {1123808, title = {Putative thermo-/hygroreceptive tarsal sensilla on the sensory legs of an armored harvestman (Arachnida, Opiliones).}, journal = { Zoologischer Anzeiger }, volume = {270}, year = {2017}, pages = {81-97.}, abstract = {Most harvestman species are dependent on high humidity levels and amenable temperatures for homeostasis. While they are known to actively choose environments with these conditions, no thermo-/hygroreceptor has yet been identified in harvestmen. Using electron microscopy, we investigated the ultrastructure of two types of hair sensilla of the armored harvestman Heteromitobates discolor (Laniatores, Gonyleptidae): namely the sensillum basiconicum and the hooded sensillum. Both structures occur in small numbers (sensilla basiconica: 28 units; hooded sensilla: 4 units) and are distributed on the distal parts of the legs. On the distalmost tarsomeres I and II, the receptor cells of paired sensilla basiconica and single hooded sensillum form a common axon bundle proceeding towards the tarsal nerve. The sensillum basiconicum is innervated by 3-4 dendrites and has a longitudinal slit giving the impression of a shaft with two flaps, resembling a beak. The slit probably allows for evaporation of sensillum lymph. The hooded sensillum is innervated by two bundles of three dendrites each, has two pore-like structures on its tip and displays an unusual reticulate cuticle of the shaft. Details of shaft cuticle, the evidence of evaporation of sensillum lymph, and specific innervation patterns support our hypothesis that sensilla basiconica are thermo- and/or hygroreceptors. Even though the definite function of hooded sensilla remains unclear, its putative receptor modalities are assessed by means of specific ultrastructures. Moreover, we discuss with regard to functional ultrastructures as to whether the evaporation system of sensilla basiconica fits mechanisms of hygroreception as known from current literature. Finally, we discuss potentials and purpose given by spatial coherence of both types of sensilla at the tip of the sensory appendages.
Putative thermo-/hygroreceptive tarsal... (PDF Download Available). Available from: https://www.researchgate.net/publication/320319517_Putative_thermo-hygroreceptive_tarsal_sensilla_on_the_sensory_legs_of_an_armored_harvestman_Arachnida_Opiliones [accessed Apr 24 2018].}, author = {Gainett, G. and Michalik, P. and M{\"u}ller, C. H. G. and Giribet, G. and Talarico, G and Willemart, R. H.} } @article {1123760, title = {Ultrastructure of chemoreceptive tarsal sensilla in an armored harvestman and evidence of olfaction across Laniatores (Arachnida, Opiliones.)}, journal = {Arthropod Structure \& Development}, volume = {46}, year = {2017}, pages = {178-195.}, abstract = {Harvestmen (Arachnida, Opiliones) are especially dependent on chemical cues and are often regarded as animals that rely mainly on contact chemoreception. Information on harvestman sensilla is scarce when compared to other arachnid orders, especially concerning internal morphology. Using scanning (SEM) and transmission (TEM) electron microscopy, we investigated tarsal sensilla on the distal tarsomeres (DT) of all leg pairs in Heteromitobates discolor (Laniatores, Gonyleptidae). Furthermore, we explored the typological diversity of sensilla present on the DT I and II in members of the suborder Laniatores, which include two thirds of the formally described opilionid fauna, using species from 17 families representing all main laniatorian lineages. Our data revealed that DT I and II of H.\ discolor are equipped with wall-pored falciform hairs (two types), wall-pored sensilla chaetica (two types) and tip-pored sensilla chaetica, while DT III and IV are mainly covered with trichomes (non-sensory) and tip-pored sensilla chaetica. The ultrastructural characteristics support an olfactory function for all wall-pored sensilla and a dual gustatory/mechanoreceptive function for tip-pored sensilla chaetica. Based on our comparative SEM survey, we show that wall-pored sensilla occur in all investigated Laniatores, demonstrating their widespread occurrence in the suborder and highlighting the importance of both legs I and II as the sensory appendages of laniatorean harvestmen. Our results provide the first morphological evidence for olfactory receptors in Laniatores and suggest that olfaction is more important for harvestmen than previously thought.}, author = {Gainett, G. and Michalik, P., and M{\"u}ller, C. H. G. and Giribet, G. and Talarico, G. and Willemart, R. H.} } @article {1123757, title = {The Opiliones tree of life: Shedding light on harvestmen relationships through transcriptomics. }, journal = {Proceedings of the Royal Society B: Biological Sciences }, volume = {284}, year = {2017}, pages = {20162340}, abstract = {Opiliones are iconic arachnids with a Palaeozoic origin and a diversity that reflects ancient biogeographic patterns dating back at least to the times of Pangea. Owing to interest in harvestman diversity, evolution and biogeography, their relationships have been thoroughly studied using morphology and PCR-based Sanger approaches to infer their systematic relationships. More recently, two studies utilized transcriptomics-based phylogenomics to explore their basal relationships and diversification, but sampling was limiting for understanding deep evolutionary patterns, as they lacked good taxon representation at the family level. Here, we analysed a set of the 14 existing transcriptomes with 40 additional ones generated for this study, representing approximately 80\% of the extant familial diversity in Opiliones. Our phylogenetic analyses, including a set of data matrices with different gene occupancy and evolutionary rates, and using a multitude of methods correcting for a diversity of factors affecting phylogenomic data matrices, provide a robust and stable Opiliones tree of life, where most families and higher taxa are precisely placed. Our dating analyses using alternative calibration points, methods and analytical parameters provide well-resolved old divergences, consistent with ancient regionalization in Pangea in some groups, and Pangean vicariance in others. The integration of state-of-the-art molecular techniques and analyses, together with the broadest taxonomic sampling to date presented in a phylogenomic study of harvestmen, provide new insights into harvestmen interrelationships, as well as an overview of the general biogeographic patterns of this ancient arthropod group.}, author = {Fern{\'a}ndez, R. and Sharma, P. P. and Tourinho, A. L. and Giribet, G.} } @article {1123753, title = {Rounding up the usual suspects: a standard target-gene approach for resolving the interfamilial phylogenetic relationships of ecribellate orb-weaving spiders with a new family-rank classification (Araneae, Araneoidea). }, journal = {Cladistics }, volume = {33}, year = {2017}, pages = {221-250}, abstract = {We test the limits of the spider superfamily Araneoidea and reconstruct its interfamilial relationships using standard molecular markers. The taxon sample (363 terminals) comprises for the first time representatives of all araneoid families, including the first molecular data of the family Synaphridae. We use the resulting phylogenetic framework to study web evolution in araneoids. Araneoidea is monophyletic and sister to Nicodamoidea rank. n. Orbiculariae are not monophyletic and also include the RTA clade, Oecobiidae and Hersiliidae. Deinopoidea is paraphyletic with respect to a lineage that includes the RTA clade, Hersiliidae and Oecobiidae. The cribellate orb-weaving family Uloboridae is monophyletic and is sister group to a lineage that includes the RTA Clade, Hersiliidae and Oecobiidae. The monophyly of most Araneoidea families is well supported, with a few exceptions. Anapidae includes holarchaeids but the family remains diphyletic even if Holarchaea is considered an anapid. The orb-web is ancient, having evolved by the early Jurassic; a single origin of the orb with multiple {\textquotedblleft}losses{\textquotedblright} is implied by our analyses. By the late Jurassic, the orb-web had already been transformed into different architectures, but the ancestors of the RTA clade probably built orb-webs. We also find further support for a single origin of the cribellum and multiple independent losses. The following taxonomic and nomenclatural changes are proposed: the cribellate and ecribellate nicodamids are grouped in the superfamily Nicodamoidea rank n. (Megadictynidae rank res. and Nicodamidae stat. n.). Araneoidea includes 17 families with the following changes: Araneidae is re-circumscribed to include nephilines, Nephilinae rank res., Arkyidae rank n., Physoglenidae rank n., Synotaxidae is limited to the genus Synotaxus, Pararchaeidae is a junior synonym of Malkaridae (syn. n.), Holarchaeidae of Anapidae (syn. n.) and Sinopimoidae of Linyphiidae (syn. n.).}, author = {D. Dimitrov and Benavides, L. R. and Arnedo, M. A. and Giribet, G. and Griswold, C.E. and Scharff, N. and Hormiga, G.} } @article {1123749, title = {Insights into the origin of parthenogenesis in oligochaetes: strong genetic structure in a cosmopolitan earthworm is not related to reproductive mode. }, journal = {European Journal of Soil Biology }, volume = {81}, year = {2017}, pages = {31-38.}, author = {De Sosa, I. and Fern{\'a}ndez-March{\'a}n, D. and Novo, M., and D{\'\i}az Cos{\'\i}n, D. J. and Giribet, G. and Fern{\'a}ndez, R.} } @article {1123748, title = {Genomic signatures of evolution in Nautilus{\textemdash}an endangered living fossil.}, journal = {Molecular Ecology }, volume = {26}, year = {2017}, pages = {5923-5938}, abstract = {Living fossils are survivors of previously more diverse lineages that originated millions of years ago and persisted with little morphological change. Therefore, living fossils are model organisms to study both long-term and ongoing adaptation and speciation processes. However, many aspects of living fossil evolution and their persistence in the modern world remain unclear. Here, we investigate three major aspects of the evolutionary history of living fossils: cryptic speciation, population genetics and effective population sizes, using members of the genera Nautilus and Allonautilus as classic examples of true living fossils. For this, we analysed genomewide ddRAD-Seq data for all six currently recognized nautiloid species throughout their distribution range. Our analyses identified three major allopatric Nautilus clades: a South Pacific clade, subdivided into three subclades with no signs of admixture between them; a Coral Sea clade, consisting of two genetically distinct populations with significant admixture; and a widespread Indo-Pacific clade, devoid of significant genetic substructure. Within these major clades, we detected five Nautilus groups, which likely correspond to five distinct species. With the exception of Nautilus macromphalus, all previously described species are at odds with genomewide data, testifying to the prevalence of cryptic species among living fossils. Detailed FST analyses further revealed significant genome-wide and locus-specific signatures of selection between species and differentiated populations, which is demonstrated here for the first time in a living fossil. Finally, approximate Bayesian computation (ABC) simulations suggest large effective population sizes, which may explain the low levels of population differentiation commonly observed in living fossils.}, author = {Combosch, D. J and Lemer, S., and Ward, P. D., and Landman, N. H., and Giribet, G.} } @article {1123744, title = {A family-level Tree of Life for bivalves based on a Sanger-sequencing approach. }, journal = {Molecular Phylogenetics and Evolution }, volume = {107}, year = {2017}, pages = { 191-208}, author = {Combosch, D.J. and Collins, T. M. and Glover, E. A. and Graf, D. L. and Harper, E. M. and Healy, J. M. and Kawauchi, G. Y. and Lemer, S. and McIntyre, E. and Strong, E. E.} } @article {1123739, title = {First global molecular phylogeny and biogeographical analysis of two arachnid orders (Schizomida and Uropygi) supports a tropical Pangean origin and mid-Cretaceous diversification.}, journal = {Journal of Biogeography }, volume = {44}, year = {2017}, pages = {2660-2672}, author = {Clouse, R. M and Branstetter, M. G. and Buenavente, P. A. C. and Crowley, L. M. and Czekanski-Moir, J. and General, D. E. M. and Giribet, G. and Harvey, M. S and Janies, D. A. and Mohagan, A. B} } @article {1123734, title = {Molecular phylogenetic analysis of "pirate spiders" (Araneae, Mimetidae) with the description of a new African genus and the first report of maternal care in the family. }, journal = {Cladistics }, volume = {33}, year = {2017}, pages = {375-405}, abstract = {We investigate the phylogeny of {\textquotedblleft}pirate spiders{\textquotedblright} (Mimetidae), a family of araneophagic spiders known for their use of aggressive mimicry as a foraging strategy, but poorly understood phylogenetically. Relationships are inferred by including molecular data from six loci for 92 mimetid terminals spanning four genera, and 119 outgroups representing 12 families. Phylogenetic analyses based on parsimony, maximum-likelihood and Bayesian approaches, as well as static and dynamic homology, robustly support monophyly of Mimetidae and a sister-group relationship to a clade comprising Tetragnathidae\ +\ Arkyidae. Relationships among the mimetid genera are largely congruent across methods, as follows: (Gelanor (Ero (Anansi n. gen. (Australomimetus, Mimetus)))). Diversification of Mimetidae is estimated to be around 114\ Ma, in the Early Cretaceous. In light of the results of our phylogenetic analyses, we erect Anansi n. gen. to include a clade of mimetids from West Africa that contains at least four species, including the newly described A.\ luki n. sp. We present the first report of maternal care in Mimetidae based on novel field observations.}, author = {Benavides, L. R and Giribet, G. and Hormiga, G.} } @article {1123730, title = { Straightening the striped chaos: systematics and evolution of Trypanosyllis and the case of its pseudo-cryptic type species Trypanosyllis krohnii (Annelida, Syllidae). }, journal = {Zoological Journal of the Linnean Society}, volume = {179}, year = {2017}, pages = {492-540}, abstract = {All members of the syllid genus Trypanosyllis show distinctive flattened, ribbon-like bodies and a pharynx armed with a trepan; however, the phylogenetic relationships within this genus remain unsettled, especially with respect to the genera Eurysyllis and Xenosyllis (morphologically similar). To resolve this systematic uncertainty we analysed the phylogenetic relationships of a worldwide sampling of specimens of Trypanosyllis and three related genera using multiple molecular markers. We show that Trypanosyllis as presently construed is paraphyletic, and identify a clade of striped species that were previously all considered to be Trypanosyllis zebra (Grube, 1860). We outline the case to consider Trypanosyllis krohnii Claparede, 1864 as the type species of the genus, instead of Trypanosyllis zebra. Trypanosyllis krohnii (interpreted as Trypanosyllis zebra by recent authors) was previously believed to be cosmopolitan, but we show that it includes at least seven cryptic and pseudocryptic species, five of which are described herein: Trypanosyllis kalkin sp. nov., Trypanosyllis californiensis sp. nov., Trypanosyllis luquei sp. nov., Trypanosyllis leivai sp. nov., and Trypanosyllis taboadai sp. nov. In addition, Trypanedenta gemmipara (Johnson, 1901) comb. nov. and Trypanedenta gigantea (McIntosh, 1885) comb. nov., previously included in Trypanosyllis, are here transferred to Trypanedenta Imajima \& Hartman, 1964, and Pseudosyllis brevipennis Grube, 1863 [previously named Trypanosyllis coeliaca (Claparede, 1868)] is transferred to the resurrected genus Pseudosyllis Grube, 1863. Overall our results show a complex scenario of speciation, with cases of pseudocryptic species that correspond to geographically restricted lineages. (C) 2017 The Linnean Society of London, Zoological Journal of the Linnean Society, 2017}, author = {{\'A}lvarez-Campos, P and Giribet, G. and San Mart{\'\i}n, G and Rouse, G. W. and Riesgo, A.} } @article {1123729, title = {The Syllis gracilis species complex: a molecular approach to a difficult taxonomic problem (Annelida, Syllidae).}, journal = {Molecular Phylogenetics and Evolution}, volume = {109}, year = {2017}, pages = {138-150}, abstract = {Syllis gracilis is an emblematic member of the subfamily Syllinae (Syllidae, Annelida), which inhabits shallow, temperate coastal waters and can be found on algae, coral rubble, and sponges. Their distinctive ypsiloid chaetae, usually found in specimens from populations all around the world, led to the consideration of the species as cosmopolitan, even though four other species have similar chaetae: Syllis magellanica, S. picta, S. mayeri and S. ypsiloides. The discovery of deeply divergent lineages in the Mediterranean Sea, that were morphologically similar, questioned the cosmopolitanism of S. gracilis and suggested the possibility of it being a species complex. In order to assess the speciation patterns within the putative S. gracilis complex, we undertook species delimitation and phylogenetic analyses on 61 specimens morphologically ascribed to Syllis gracilis and closely related species using a multilocus molecular dataset (two mitochondrial and two nuclear markers). Our results suggest high levels of genetic differentiation between the S. gracilis populations analyzed, some of which have morphologically distinctive features. Five to eight distinct lineages (depending on the analysis) were identified, all with geographically restricted distributions. Although the presence of ypsiloid chaetae has been traditionally considered the main character to identify S. gracilis, we conclude that this feature is homoplastic. Instead, we propose that characters such as the degree of fusion of blades and shafts in chaetae, the morphology of the posterior chaetae or the animal color pattern should be considered to differentiate lineages within the S. gracilis species complex. Our study does not support the cosmopolitanism of S. gracilis, and instead provides morphological and molecular evidence of the existence of a complex of pseudo-cryptic species.}, author = {{\'A}lvarez-Campos, P. and Giribet, G. and Riesgo, A.} } @article {1065051, title = {When predator becomes prey: investigating the salivary transcriptome of the shark-feeding leech Pontobdella macrothela (Hirudinea: Piscicolidae)}, journal = {Zoological Journal of the Linnean Society}, volume = {179}, year = {2017}, pages = {725{\textendash}737}, abstract = {Although several leech species have recently been screened for anticoagulation factors, piscicolids represent a major gap in our knowledge of the distribution of these proteins across the phylogeny of leeches. Piscicolidae is predominantly a marine family and its members feed on a variety of fish species. The pontobdelline species\ Pontobdella macrothela\ has evolved a preference for feeding on elasmobranch blood and, because of this, may have a divergent anticoagulant repertoire, compared to its mammal-, reptile- and amphibian-feeding counterparts. Representing the first piscicolid leech comprehensively investigated, here we convey results from a salivary transcriptome sequencing effort of\ P. macrothela\ collected from a blacktip shark (Carcharinus limbatus) in Veracruz, Mexico (Western Gulf of Mexico). Following orthology determination based on phylogenetic inference, amino acid conservation and a series of BLAST searches against the UniProtKB database, as well as searches of Pfam domains, we identified matches against ten known anticoagulants in the\ P. macrothela\ transcriptome. In addition, 13 hits were recovered against proteins that have previously been linked to anticoagulation but whose functions within leeches are not unequivocally understood. Finally, we discuss the largely untested hypothesis that prey choice in leeches impacts the diversity of anticoagulants.}, url = {https://academic.oup.com/zoolinnean/article/179/4/725/3076078/When-predator-becomes-prey-investigating-the}, author = {S. Kvist and Oceguera-Figueroa, A. and Tessler, M. and Jim{\'e}nez-Armenta, J. and Freeman, R.M. and Giribet, G. and Siddall, M.E.} } @inbook {1065126, title = {Molecular data in systematics: a promise fulfilled, a future beckoning}, booktitle = {The Future of Phylogenetic Systematics: The Legacy of Willi Hennig}, volume = {13}, year = {2016}, pages = {229-343}, publisher = {Cambridge University Press}, organization = {Cambridge University Press}, author = {W.C. Wheeler and Giribet, G.} } @article {1065121, title = {Taxonomic Notes on Mesoperipatus tholloni (Onychophora: Peripatidae), an Elusive Velvet Worm from Gabon}, journal = {Breviora}, volume = {552}, year = {2016}, pages = {1-10}, abstract = {The velvet worm\ Mesoperipatus tholloni\ (Bouvier, 1898) is among the least understood of the velvet worms, the only species in the genus\ MesoperipatusEvans, 1901, and the only African Peripatidae. Despite its biogeographic and phylogenetic uniqueness, originally thought to be an intermediate between Peripatidae and Peripatopsidae, little work has been published since its original treatment in a series of papers in the late 1800s and early 1900s. Here, we provide a redescription of this species based on new material collected during a 2009 Museum of Comparative Zoology (MCZ) expedition to Gabon and examination of historical material from the original collections lodged at the MCZ and the Museu de Zoologia, Universidade de S{\~a}o Paulo (MZUSP). We also provide the first scanning electron micrographs of this species.}, url = {http://www.bioone.org/doi/abs/10.3099/MCZ30.1}, author = {Costa, C.S. and Giribet, G.} } @article {1065116, title = {The family Pinnidae (Bivalvia) in the Philippine archipelago: observations on its distribution and phylogeography}, journal = {The Nautilus}, volume = {130}, year = {2016}, pages = {137{\textendash}145}, abstract = {

The Philippine archipelago, located in the northern apex of the Coral Triangle, is known for its high diversity and endemism, both caused by a complex physical setting modelled by the long tectonic history of the archipelago and by the more recent Pleistocene sea-level fluctuations. In order to assess the influ- ences of the complex Philippines geography on benthic marine species, we conducted phylogenetic and phylogeographic analyses on 71 specimens (out 112 originally collected) of ten species of Pinnidae, sequencing two mitochondrial and two nuclear markers. Our results suggest that the Philippines is a diversity hotspot for pinnids, with all sampling sites hosting three or more species, but with marked differences in species composition in each site, indicating that most pinnids have a patchy distribution. Our data also suggest that most species exhibit high levels of genetic connectivity even over large geo- graphical distances. As previouly suggested, our data also sup- port the idea that the nominal taxon Pinna atropurpurea includes at least 2 cryptic species in the Philippines.\ 

}, url = {https://www.researchgate.net/profile/Sarah_Lemer/publication/311487777_The_family_Pinnidae_Bivalvia_in_the_Philippine_archipelago_observations_on_its_distribution_and_phylogeography/links/5848aa9908aeda696825e93d.pdf}, author = {Lemer, S. and Combosch, D.J. and Sotto, F. and Giribet, G. and Dumale, D. and Soliman, V.} } @article {1065096, title = {The future of nemertean taxonomy (phylum Nemertea) {\textemdash} a proposal}, journal = {Zoologica Scripta}, volume = {45}, year = {2016}, pages = {579{\textendash}582}, url = {http://onlinelibrary.wiley.com/doi/10.1111/zsc.12182/full}, author = {Sundberg, P. and Andrade, S.C.S. and Bartolomaeus, T. and Beckers, P. and von D{\"o}hren, J. and Kr{\"a}mer, D. and Gibson, R. and Giribet, G. and Herrera-Bachiller, A. and J. Junoy and Kajihara, H. and S. Kvist and K{\r a}nneby, T. and Sun, S.C. and Thiel, M. and Turbeville, J. M. and Strand, M.} } @article {1065086, title = {The oldest armoured harvestman (Arachnida: Opiliones: Laniatores), from Upper Cretaceous Myanmar amber}, journal = {Cretaceous Research}, volume = {65}, year = {2016}, pages = {206-212}, abstract = {The oldest laniatorean harvestman,\ Petrobunoides sharmai\ gen. et sp. nov. (Opiliones: Laniatores) is described, from the Upper Cretaceous (lowermost Cenomanian) amber of Myanmar. This is the first fossil Laniatores recovered from Southeast Asia, which is placed in the extant family Epedanidae. It is also the first fossil known within the superfamily Epedanoidea; a relatively derived clade of Laniatores restricted to Southeast Asia today. At ca. 99\ Ma, this new amber inclusion is substantially older than the previous oldest record of a member of Laniatores from Baltic amber (ca. 44{\textendash}49\ Ma); however, given the Palaeozoic age of Laniatores implied by molecular data, the new record from Burmese amber is probably still too young for constraining or calibrating the date of cladogenesis for total group Laniatores. Nevertheless, it provides a much better constraint for Epedanoidea, adding the first useful laniatorean fossil to provide an internal calibration point for a clade of Grassatores.}, url = {http://www.sciencedirect.com/science/article/pii/S0195667116300945}, author = {Selden, P.A. and Dunlop, J. A. and Giribet, G. and Zhang, W. and Ren, D.} } @article {1065081, title = {Zoology: At Last an Exit for Ctenophores}, journal = {Current Biology}, volume = {26}, year = {2016}, pages = {R918-R920}, url = {http://www.sciencedirect.com/science/article/pii/S0960982216309800}, author = {Giribet, G.} } @article {1065076, title = {A molecular phylogeny of the temperate Gondwanan family Pettalidae (Arachnida, Opiliones, Cyphophthalmi) and the limits of taxonomic sampling}, journal = {Zoological Journal of the Linnean Society}, volume = {178}, year = {2016}, pages = {523{\textendash}545}, abstract = {We evaluate the phylogenetic and biogeographical relationships of the members of the family Pettalidae (Opiliones, Cyphophthalmi), a textbook example of an ancient temperate Gondwanan taxon, by means of DNA sequence data from four markers. Taxon sampling is optimized to cover more than 70\% of the described species in the family, with 117 ingroup specimens included in the analyses. The data were submitted to diverse analytical treatments, including static and dynamic homology, untrimmed and trimmed alignments, and a variety of optimality criteria including parsimony and maximum-likelihood (traditional search and Bayesian). All analyses found strong support for the monophyly of the family Pettalidae and of all its genera, with the exception of\ Speleosiro, which is nested within\ Purcellia. However, the relationships among genera are poorly resolved, with the exceptions of a first split between the South African genus\ Parapurcellia\ and the remaining species, and, less supported, a possible relationship between\ Chileogovea\ and the other South African genus\ Purcellia. The diversification of most genera is Mesozoic, and of the three New Zealand genera, two show evidence of constant diversification through time, contradicting scenarios of total submersion of New Zealand during the Oligocene drowning episode. The genera\ Karripurcellia\ from Western Australia and\ Neopurcellia\ from the Australian plate of New Zealand show a pattern typical of relicts, with ancient origin, depauperate extant diversity and recent diversification. The following taxonomic actions are taken:\ MilipurcelliaKaraman, 2012\ is synonymized with\ Karripurcellia\ Giribet, 2003\ syn. nov.;\ SpeleosiroLawrence, 1931\ is synonymised with\ PurcelliaHansen \& S{\o}rensen, 1904,syn. nov.\ The following new combinations are proposed:\ Parapurcellia transvaalica\ (Lawrence, 1963)\ comb. nov.;\ Purcellia argasiformis\ (Lawrence, 1931)\ comb. nov.}, url = {https://academic.oup.com/zoolinnean/article/178/3/523/2667465/A-molecular-phylogeny-of-the-temperate-Gondwanan}, author = {Giribet, G. and S.L. Boyer and Baker, C.M. and Fern{\'a}ndez, R. and Sharma. PP and de Bivort, BL and Daniels, S. R. and Harvey, M. S. and Griswold, C.E.} } @article {1065071, title = {Genomics and the animal tree of life: conflicts and future prospects}, journal = {Zoologica Scripta}, volume = {45}, year = {2016}, pages = {14{\textendash}21}, abstract = {Providing consistent resolution for the animal tree of life is a major goal of animal systematists and a desire of every zoologist. Towards this goal, many major nodes have been successfully resolved. However, some major controversies and poorly resolved deep nodes still remain. Here, I discuss some of these controversies (e.g. whether Ctenophora or Porifera is sister group to all other animals), clarify others (e.g. the position of Xenacoelomorpha) and identify major clades that still require resolution. But most importantly, a discussion about the possible conflict in some of these nodes and the relation to the nature of phylogenomic data are provided by exploring the meaning of total support in phylogenomic analyses, highlighting cases in which a data set can provide total support for contradictory nodes. Finally, our efforts should focus on generating genomic data for key candidate taxa, such as the large disparity of undescribed placozoans, which may in the end add to the current data quantity, the quality of data needed to resolve the base of the animal tree.}, url = {http://onlinelibrary.wiley.com/doi/10.1111/zsc.12215/full}, author = {Giribet, G.} } @article {1065066, title = {Non-destructive imaging to describe a new species of Obama land planarian (Platyhelminthes, Tricladida)}, journal = {Zoologica Scripta}, volume = {45}, year = {2016}, pages = {566{\textendash}578}, abstract = {The land planarians in the genus\ Obama\ include the largest species of the Neotropical Geoplaninae. Morphological discrimination of\ Obama\ species can be difficult, as many species are morphologically similar and some present asymmetric {\textendash} difficult to interpret {\textendash} copulatory organs. New techniques are thus welcomed to provide faster species description and identification. Here, we study several specimens of\ Obama\ by means of mainly 2D and 3D\ Î¼CT-based images obtained through X-ray microcomputed tomography (μCT) of a paratype, and, complementarily, histological sections of the holotype and a second paratype, which were digitized into virtual slides. Comparison of these images with traditional histological sections and descriptions of the known species of the genus allows us to conclude that our specimens constitute a new species, which we describe here. We further evaluate the phylogenetic placement of the new species using gene fragments from the mitochondrial cytochrome\ c\ oxidase subunit I and the nuclear elongation factor-1α. Raw and derivative\ Î¼CT data and virtual histological sections were deposited in an open repository (GigaDB) and are freely available. This work leads us to conclude that\ Î¼CT constitutes a relatively fast, inexpensive non-destructive method that produces results comparable to those of traditional histology, and is thus amenable for describing flatworm species.}, url = {http://onlinelibrary.wiley.com/doi/10.1111/zsc.12175/full}, author = {Carbayo, F. and Francoy, T.M. and Giribet, G.} } @article {1065061, title = {Carboniferous Onychophora from Montceau-les-Mines, France, and onychophoran terrestrialization}, journal = {Invertebrate Biology}, volume = {135}, year = {2016}, pages = {179{\textendash}190}, abstract = {The geological age of the onychophoran crown-group, and when the group came onto land, have been sources of debate. Although stem-group Onychophora have been identified from as early as the Cambrian, the sparse record of terrestrial taxa from before the Cretaceous is subject to contradictory interpretations. A Late Carboniferous species from the Mazon Creek biota of the USA,\ Helenodora inopinata, originally interpreted as a crown-group onychophoran, has recently been allied to early Cambrian stem-group taxa. Here we describe a fossil species from the Late Carboniferous Montceau-les-Mines Lagerst{\"a}tte, France, informally referred to as an onychophoran for more than 30\ years. The onychophoran affinities of\ Antennipatus montceauensis\ gen. nov., sp. nov. are indicated by the form of the trunk plicae and the shape and spacing of their papillae, details of antennal annuli, and the presence of putative slime papillae. The poor preservation of several key systematic characters for extant Onychophora, however, prohibits the precise placement of the Carboniferous fossil in the stem or crown of the two extant families, or the onychophoran stem-group as a whole. Nevertheless,\ A. montceauensis\ is the most compelling candidate to date for a terrestrial Paleozoic onychophoran.}, url = {http://onlinelibrary.wiley.com/doi/10.1111/ivb.12130/full}, author = {Garwood, R. J. and G.D. Edgecombe and Charbonnier, S. and Chabard, D. and Sotty, D. and Giribet, G.} } @article {1065056, title = {The meaning of categorical ranks in evolutionary biology}, journal = {Organisms Diversity \& Evolution}, volume = {16}, year = {2016}, pages = {427{\textendash}430}, abstract = {Despite having been utilized for over 250\ years, Linnaean ranks are periodically dismissed by some systematists and evolutionary biologists. Here, we discuss recent criticisms and point out that they are often the result of a misunderstanding of both the meaning and the intent of such ranks. Although arbitrary in some cases, ranks contain meaningful taxonomic information, facilitate communication, and serve as proxies for a fully resolved and correctly dated tree of life. Ranks favor communication and evolutionary comparisons, but they do not make assumptions about equal age or diversity for any two taxa with the same Linnaean category.}, url = {https://link.springer.com/article/10.1007/s13127-016-0263-9}, author = {Giribet, G. and Hormiga, G. and G.D. Edgecombe} } @article {1065046, title = {A molecular palaeobiological exploration of arthropod terrestrialization}, journal = {Philosophical Transactions of the Royal Society B}, volume = {371}, year = {2016}, pages = {20150133}, abstract = {Understanding animal terrestrialization, the process through which animals colonized the land, is crucial to clarify extant biodiversity and biological adaptation. Arthropoda (insects, spiders, centipedes and their allies) represent the largest majority of terrestrial biodiversity. Here we implemented a molecular palaeobiological approach, merging molecular and fossil evidence, to elucidate the deepest history of the terrestrial arthropods. We focused on the three independent, Palaeozoic arthropod terrestrialization events (those of Myriapoda, Hexapoda and Arachnida) and showed that a marine route to the colonization of land is the most likely scenario. Molecular clock analyses confirmed an origin for the three terrestrial lineages bracketed between the Cambrian and the Silurian. While molecular divergence times for Arachnida are consistent with the fossil record, Myriapoda are inferred to have colonized land earlier, substantially predating trace or body fossil evidence. An estimated origin of myriapods by the Early Cambrian precedes the appearance of embryophytes and perhaps even terrestrial fungi, raising the possibility that terrestrialization had independent origins in crown-group myriapod lineages, consistent with morphological arguments for convergence in tracheal systems.}, url = {http://rstb.royalsocietypublishing.org/content/371/1699/20150133}, author = {Lozano-Fernandez, J. and Carton, R. and Tanner, A.R. and Puttick, M.N. and Blaxter, M. and Vinther, J. and Olesen, J. and Giribet, G. and G.D. Edgecombe and Pisani, D.} } @article {1065041, title = {Zoology: Invertebrates that Parasitize Invertebrates}, journal = {Current Biology}, volume = {26}, year = {2016}, pages = {R537-R539}, url = {http://www.sciencedirect.com/science/article/pii/S0960982216305358}, author = {Giribet, G.} } @article {1065036, title = {A multilocus molecular phylogeny of Fasciolariidae (Neogastropoda: Buccinoidea)}, journal = {Molecular Phylogenetics and Evolution}, volume = {99}, year = {2016}, pages = {309{\textendash}322}, abstract = {The neogastropod family Fasciolariidae Gray, 1853 {\textendash} tulips, horse-conchs, spindles, etc., comprises important representatives of tropical and subtropical molluscan assemblages, with over 500 species in the subfamilies Fasciolariinae Gray, 1853, Fusininae Wrigley, 1927 and Peristerniinae Tryon, 1880. Fasciolariids have had a rather complicated taxonomical history, with several genus names for a long time used as waste baskets to group many unrelated species; based on shell characters, recent taxonomic revisions have, however, began to set some order in its taxonomy. The present work is the first molecular approach to the phylogeny of Fasciolariidae based on a multigene dataset, which provides support for fasciolariids, an old group with a fossil record dating back to the Cretaceous. Molecular markers used were the mitochondrial genes 16S rRNA and cytochrome\ c\ oxidase subunit I, and the nuclear genes 18S rRNA, 28S rRNA and histone H3, sequenced for up to 116 ingroup taxa and 17 outgroups. Phylogenetic analyses revealed monophyly of\ Dolicholatirus\ Bellardi, 1884 and\ Teralatirus\ Coomans, 1965, however it was not possible to discern if the group is the sister clade to the remaining fasciolariids; the latter, on the other hand, proved monophyletic and contained highly supported groups. A first split grouped fusinines and\ Pseudolatirus\ Bellardi, 1884; a second split grouped the peristerniine genera\ Peristernia\ M{\"o}rch, 1852 and\ FusolatirusKuroda and Habe, 1971, while the last group comprised fasciolariines and the remaining peristerniines. None of these clades correspond to the present-day accepted circumscription of the three recognized subfamilies.}, url = {http://www.sciencedirect.com/science/article/pii/S1055790316300173}, author = {Couto, D.R. and Bouchet, P. and Kantor, Y.I. and Simone, L.R.L. and Giribet, G.} } @article {1065026, title = {Cementing mussels to oysters in the pteriomorphian tree: a phylogenomic approach}, journal = {Proceedings of the Royal Society B}, volume = {283}, year = {2016}, pages = {20160857}, abstract = {Mussels (Mytilida) are a group of bivalves with ancient origins and some of the most important commercial shellfish worldwide. Mytilida consists of approximately 400 species found in various littoral and deep-sea environments, and are part of the higher clade Pteriomorphia, but their exact position within the group has been unstable. The multiple adaptive radiations that occurred within Pteriomorphia have rendered phylogenetic classifications difficult and uncertainty remains regarding the relationships among most families. To address this phylogenetic uncertainty, novel transcriptomic data were generated to include all five orders of Pteriomorphia. Our results, derived from complex analyses of large datasets from 41 transcriptomes and evaluating possible pitfalls affecting phylogenetic reconstruction (matrix occupancy, heterogeneity, evolutionary rates, evolutionary models), consistently recover a well-supported phylogeny of Pteriomorphia, with the only exception of the most complete but smallest data matrix (Matrix 3: 51 genes, 90\% gene occupancy). Maximum-likelihood and Bayesian mixture model analyses retrieve strong support for: (i) the monophyly of Pteriomorphia, (ii) Mytilida as a sister group to Ostreida, and (iii) Arcida as sister group to all other pteriomorphians. The basal position of Arcida is congruent with its shell microstructure (solely composed of aragonitic crystals), whereas Mytilida and Ostreida display a combination of a calcitic outer layer with an aragonitic inner layer composed of nacre tablets, the latter being secondarily lost in Ostreoidea.}, url = {http://rspb.royalsocietypublishing.org/content/283/1833/20160857}, author = {Gonzalez, V. L. and Lemer, S. and Bieler, R. and Giribet, G.} } @article {1065021, title = {Penis morphology in a Burmese amber harvestman}, journal = {The Science of Nature}, volume = {103}, year = {2016}, pages = {1-5}, abstract = {A unique specimen of the fossil harvestman\ Halitherses grimaldii\ Giribet and Dunlop,\ 2005(Arachnida: Opiliones) from the Cretaceous (ca. 99\ Ma) Burmese amber of Myanmar reveals a fully extended penis. This is the first record of a male copulatory organ of this nature preserved in amber and is of special importance due to the age of the deposit. The penis has a slender, distally flattened truncus, a spatulate heart-shaped glans and a short distal stylus, twisted at the tip. In living harvestmen, the penis yields crucial characters for their systematics. Male genital morphology in\ H. grimaldii\ appears to be unique among the wider Dyspnoi clade to which this fossil belongs. The large eyes in the fossil differ markedly from other members of the subfamily Ortholasmatinae to which\ H. grimaldii\ was originally referred. Based on recent data, it has been argued that large eyes may be plesiomorphic for Palpatores (i.e. the suborders Eupnoi and Dyspnoi), potentially rendering this character plesiomorphic for the fossil too. Thus, the unique structure of the penis seen here, and the probable lack of diaphanous teeth, present in all other extant non-acropsopilionid Dyspnoi, suggest that\ H. grimaldii\ represents a new, extinct family of large-eyed dyspnoid harvestmen, Halithersidae fam. nov.; a higher taxon in amber diagnosed here on both somatic and genital characters.}, url = {https://link.springer.com/article/10.1007/s00114-016-1337-4}, author = {Dunlop, J. A. and Selden, P.A. and Giribet, G.} } @article {1065006, title = {The first troglobitic species of Gymnobisiidae (Pseudoscorpiones\ :\ Neobisioidea), from Table Mountain (Western Cape Province, South Africa) and its phylogenetic position}, journal = {Invertebrate Systematics}, volume = {30}, year = {2016}, pages = {75-85}, abstract = {Fully troglobitic pseudoscorpions are rare in the Afrotropical Region, and we explored the identity and phylogenetic relationships of specimens of a highly modified troglobite of the family Gymnobisiidae in the dark zone of the Wynberg Cave system, on Table Mountain, South Africa. This large pseudoscorpion {\textendash} described as\ Gymnobisium inukshuk\ Harvey \& Giribet, sp. nov. {\textendash} lacks eyes and has extremely long appendages, and has been found together with other troglobitic fauna endemic only to this cave system. Phylogenetic analyses using the nuclear ribosomal genes\ 18S rRNAand\ 28S rRNA\ and the mitochondrial protein-encoding gene\ cytochrome\ c\ oxidase subunit Iunambiguously place the new species with other surface\ Gymnobisium\ from South Africa. This placement receives strong support and is stable to analytical treatments, including static and dynamic homology, parsimony and maximum likelihood, and data removal for ambiguously aligned sites. This species is the first troglobitic species of the family and one of the most highly modified pseudoscorpions from the Afrotropical Region.}, url = {http://www.publish.csiro.au/is/Fulltext/IS15044}, author = {Harvey, M. S. and Huey, J.A. and Hillyer, M.J. and E. McIntyre and Giribet, G.} } @article {1064996, title = {Clarifying phylogenetic relationships and the evolutionary history of the bivalve order Arcida (Mollusca: Bivalvia: Pteriomorphia)}, journal = {Molecular Phylogenetics and Evolution}, volume = {94}, year = {2016}, pages = {298-312}, abstract = {The systematics of the bivalve order Arcida constitutes an unresolved conundrum in bivalve systematics. The current definition of Arcida encompasses two superfamilies: Limopsoidea, which includes the recent families Philobryidae and Limopsidae, and Arcoidea, which encompasses the families Arcidae, Cucullaeidae, Noetiidae, Glycymerididae and Parallelodontidae. This classification, however, is controversial particularly with respect to the position and taxonomic status of Glycymerididae. Previous molecular phylogenies were limited either by the use of only a single molecular marker or by including only a few limopsoid and glycymeridid taxa. The challenging nature of Arcida taxonomy and the controversial results of some of the previous studies, prompted us to use a broad range of taxa (55 species), three nuclear markers (18S rRNA, 28S rRNA and histone H3) and a wide range of algorithmic approaches. This broad but stringent approach led to a number of results that differ significantly from previous studies. We provide the first molecular evidence that supports the separation of Arcoidea from Limopsoidea, although the exact position of Glycymerididae remains unresolved, and the monophyly of Limopsoidea is algorithm-dependent. In addition, we present the first time-calibrated evolutionary tree of Arcida relationships, indicating a significant increase in the diversification of arcidan lineages at the beginning of the Cretaceous, around 140\ Ma. The monophyly of Arcida, which has been supported previously, was confirmed in all our analyses. Although relationships among families remain somehow unresolved we found support for the monophyly of most arcidan families, at least under some analytical conditions (i.e., Glycymerididae, Noetiidae, Philobryidae, and Limopsidae). However, Arcidae, and particularly Arcinae, remain a major source of inconsistency in the current system of Arcida classification and are in dire need of taxonomic revision.}, url = {http://www.sciencedirect.com/science/article/pii/S1055790315002821?via\%3Dihub}, author = {Combosch, D.J. and Giribet, G.} } @article {743651, title = {Exploring Phylogenetic Relationships within Myriapoda and the Effects of Matrix Composition and Occupancy on Phylogenomic Reconstruction}, journal = {Systematic Biology}, volume = {65}, year = {2016}, pages = {871{\textendash}889}, abstract = {

Myriapods, including the diverse and familiar centipedes and millipedes, are one of the dominant terrestrial arthropod groups. Although molecular evidence has shown that Myriapoda is monophyletic, its internal phylogeny remains contentious and understudied, especially when compared to those of Chelicerata and Hexapoda. Until now, efforts have focused on taxon sampling (e.g., by including a handful of genes from many species) or on maximizing matrix size (e.g., by including hundreds or thousands of genes in just a few species), but a phylogeny maximizing sampling at both levels remains elusive. In this study, we analyzed 40 Illumina transcriptomes representing 3 of the 4 myriapod classes (Diplopoda, Chilopoda, and Symphyla); 25 transcriptomes were newly sequenced to maximize representation at the ordinal level in Diplopoda and at the family level in Chilopoda. Ten supermatrices were constructed to explore the effect of several potential phylogenetic biases (e.g., rate of evolution, heterotachy) at 3 levels of gene occupancy per taxon (50\%, 75\%, and 90\%). Analyses based on maximum likelihood and Bayesian mixture models retrieved monophyly of each myriapod class, and resulted in 2 alternative phylogenetic positions for Symphyla, as sister group to Diplopoda + Chilopoda, or closer to Diplopoda, the latter hypothesis having been traditionally supported by morphology. Within centipedes, all orders were well supported, but 2 deep nodes remained in conflict in the different analyses despite dense taxon sampling at the family level. Relationships among centipede orders in all analyses conducted with the most complete matrix (90\% occupancy) are at odds not only with the sparser but more gene-rich supermatrices (75\% and 50\% supermatrices) and with the matrices optimizing phylogenetic informativeness or most conserved genes, but also with previous hypotheses based on morphology, development, or other molecular data sets. Our results indicate that a high percentage of ribosomal proteins in the most complete matrices, in conjunction with distance from the root, can act in concert to compromise the estimated relationships within the ingroup. We discuss the implications of these findings in the context of the ever more prevalent quest for completeness in phylogenomic studies.

}, url = {http://biorxiv.org/content/early/2015/11/09/030973}, author = {Fernandez, R. and G.D. Edgecombe and Giribet, G.} } @article {743626, title = {How many species of Siphonaria pectinata (Gastropoda: Heterobranchia) are there?}, journal = {Journal of Molluscan Studies}, volume = {82}, year = {2016}, pages = {137{\textendash}143}, abstract = {

Siphonaria pectinata (Linnaeus, 1758) has been considered a widespread species with Amphiatlantic distribution or a case of cryptic taxonomy where sibling species exist. We undertook molecular evaluation of 66 specimens from across its putative distribution range. We examined up to three molecular markers (mitochondrial cytochrome c oxidase subunit I and 16S rRNA, and nuclear internal transcribed spacer-2) of putative S. pectinata, including populations from the Mediterranean Sea, eastern Atlantic (Spain, Canary Islands, Cape Verde Islands, Cameroon and Gabon) and western Atlantic (Florida and Mexico), covering most of the natural range of the species. While little information could be derived from the shell morphology, molecular data clearly distinguished three lineages with no apparent connectivity. These lineages correspond to what we interpret as three species, two suspected from prior work: S. pectinata, restricted to the eastern Atlantic and Mediterranean and S. naufragum Stearns, 1872 in Florida and the Gulf of Mexico. A third species has been identified for the Cape Verde Archipelago, for which we use the available name S. placentula Menke, 1853.

}, url = {http://mollus.oxfordjournals.org/content/early/2015/09/03/mollus.eyv038.abstract}, author = {Giribet, G. and Kawauchi, G. Y.} } @article {743631, title = {New Animal Phylogeny: Future challenges for animal phylogeny in the age of phylogenomics}, journal = {Organisms Diversity \& Evoution}, volume = {16}, year = {2016}, pages = {419{\textendash}426}, abstract = {

The science of phylogenetics, and specially the subfield of molecular systematics, has grown exponentially not only in the amount of publications and general interest, but also especially in the amount of genetic data available. Modern phylogenomic analyses use large genomic and transcriptomic resources, yet a comprehensive molecular phylogeny of animals, including the newest types of data for all phyla, remains elusive. Future challenges need to address important issues with taxon sampling{\textemdash}especially for rare and small animals{\textemdash}orthology assignment, algorithmic developments, and data storage and to figure out better ways to integrate information from genomes and morphology in order to place fossils more precisely in the animal tree of life. Such precise placement will also aid in providing more accurate dates to major evolutionary events during the evolution of our closest kingdom.

}, url = {http://link.springer.com/article/10.1007\%2Fs13127-015-0236-4}, author = {Giribet, G.} } @article {743601, title = {Phylogeography of the harvestman Metasiro (Arthropoda, Arachnida, Opiliones) reveals a potential solution to the Pangean paradox.}, journal = {Organisms Diversity \& Evoution}, volume = {16}, year = {2016}, pages = {167{\textendash}184}, abstract = {

At both global and local scales, mite harvestmen (Opiliones, Cyphophthalmi) have been shown to have achieved their current global distribution strictly through vicariance. However, the implicit low dispersal capability of this group does not explain how they expand their ranges and come to occupy enormous landmasses prior to rifting. To investigate at the population level the limited vagility that characterizes the suborder generally, and how its dispersal capacity determines diversification dynamics, range expansion, and historical biogeography, we examined as a test case the phylogeography of the genus\ Metasiro. This genus consists of three widely separated, morphologically cryptic species that inhabit the Southeastern United States. Distances between sampling sites spanned a range of geographic scales, from 4\ m to over 500\ km. Population structure was inferred from fragments of six loci (three mitochondrial, three nuclear) amplified from 221 specimens. We tested for population structure and gene flow, constructed a dated phylogeny of the genus, and developed a program for estimating the effective population size with confidence intervals. Individuals of\ Metasiro americanus\ demonstrate remarkable population structure at scales of less than 25\ m, but populations vary in their haplotypic diversity, and some exhibit evidence of historical gene flow. The estimated timing of cladogenesis within the genus accords closely with the geological history of the North American coastline, and the three species are at the endpoints of large watersheds. This suggests that mite harvestman lineages expand their ranges by hydrochory, providing for the first time a plausible mechanism whereby these animals dispersed across Pangea despite their low vagility in stable environments.

}, url = {http://link.springer.com/article/10.1007\%2Fs13127-015-0233-7}, author = {Clouse, R.M. and Sharma, P. P. and J.C. Stuart and L.R. Davis and Giribet, G. and S.L. Boyer and W.C. Wheeler} } @article {747596, title = {Articulating "archiannelids": Phylogenomics and annelid relationships, with emphasis on meiofaunal taxa.}, journal = {Molecular Biology and Evolution }, volume = {32}, year = {2015}, note = {

doi: 10.1093/molbev/msv157

}, pages = {2860-2875}, author = {Andrade, SCS. and Novo, M. and Kawauchi, G. Y. and Worsaae, K. and F Pleijei and Giribet, G. and Rouse, G. W.} } @article {747676, title = {Comparative phylogeography and population genetic structure of three widespread mollusc species in the Mediterranean and near Atlantic}, journal = {Marine Ecology}, volume = {36}, year = {2015}, pages = {96-103}, author = {Fernandez, R. and Lemer, S. and E. McIntyre and Giribet, G.} } @article {747621, title = {Cyphophthalmus solentiensis sp. nov. (Cyphophthalmi, Sironidae) a new endogean mite harvestman species from Croatia, with an application of confocal laser microscopy to illustrate genitalia in Opiliones.}, journal = {Breviora}, volume = {543}, year = {2015}, pages = {1-15}, author = {Dreszer, TB. and T. Radja and Giribet, G.} } @article {747686, title = {Morphology should not be forgotten in the era of genomics-a phylogenetic perspective}, journal = {Zoologischer Anzeriger}, volume = {256}, year = {2015}, pages = {96-103}, author = {Giribet, G.} } @article {747736, title = {Phylogeny of Nemertea with special interest in the placement of diversity from Far East Russia and northeast Asia.}, journal = {Hydrobiologia}, volume = {760}, year = {2015}, note = {

doi:10.1007/s10750-015-2310-5

}, pages = {105-119}, author = {S. Kvist and AV. Chernyshev and Giribet, G.} } @article {747701, title = {Polyphyly of Caddoidea, reinstatement of the family Acropsopilionidae in Dyspnoi, and a revised classification system of Palpatores (Arachnida, Opiliones)}, journal = {Cladistics}, volume = {31}, year = {2015}, pages = {277-290}, author = {Groh, S and Giribet, G.} } @article {747721, title = {Redescription of Micrura dellechiajei (Hubrecht, 1879) (Nemertea, Pilidiophora, Lineidae), a rare Mediterranean species.}, journal = {Journal of the Marine Biological Association of the U.K.}, volume = {95}, year = {2015}, note = {

doi: 10.1017/S002531541500090

}, pages = {1091-1100}, author = {Herrera-Bachiller, A and S. Kvist and Giribet, G. and J. Junoy} } @article {747646, title = {Species limits and phylogeography of Newportia (Scolopendromorpha) and implications for widespread morphospecies.}, journal = {ZooKeys}, volume = {510}, year = {2015}, pages = {65-77}, author = {Edgecombe, GD. and V. Vahtera and Giribet, G. and P. Kaunisto} } @article {747741, title = {Spiralian phylogeny informs the evolution of microscopic lineages}, journal = {Current Biology}, volume = {25}, year = {2015}, note = {

doi: 10.1016/j.cub.2015.06.068

}, pages = {2000-2006}, author = {Laumer, C. E. and N. Bekkouche and A, Kerbl and F. Goetz and RC. Neves and MV. Sorensen and RM. Kristensen and Hejnol, A. and CW. Dunn and Giribet, G.} } @article {747746, title = {Unearthing the historical biogeography of Mediterranean earthworms (Annelida: Hormogastridae)}, journal = {Journal of Biogeogrpahy}, volume = {42}, year = {2015}, pages = {751-762}, author = {Novo, M. and Fernandez, R. and D. Fernandez Marchan and D. Trigo and DJ. Diaz Cosin and Giribet, G.} } @article {747656, title = {Unnoticed in the tropics: phylogenomic resolution of the poorly known arachnid order Ricinulei (Arachnida)}, journal = {Royal Society Open Science}, volume = {2}, year = {2015}, pages = {150065}, author = {Fernandez, R. and Giribet, G.} } @article {640616, title = {Evolutionary biology of harvestmen (arachnida, opiliones)}, journal = {Annu Rev Entomol}, volume = {60}, year = {2015}, note = {

Giribet, GonzaloSharma, Prashant PengResearch Support, Non-U.S. Gov{\textquoteright}t2014/10/24 06:00Annu Rev Entomol. 2015 Jan 7;60:157-75. doi: 10.1146/annurev-ento-010814-021028. Epub 2014 Oct 9.

}, month = {Jan 7}, pages = {157-75}, abstract = {

Opiliones are one of the largest arachnid orders, with more than 6,500 species in 50 families. Many of these families have been erected or reorganized in the last few years since the publication of The Biology of Opiliones. Recent years have also seen an explosion in phylogenetic work on Opiliones, as well as in studies using Opiliones as test cases to address biogeographic and evolutionary questions more broadly. Accelerated activity in the study of Opiliones evolution has been facilitated by the discovery of several key fossils, including the oldest known Opiliones fossil, which represents a new, extinct suborder. Study of the group{\textquoteright}s biology has also benefited from rapid accrual of genomic resources, particularly with respect to transcriptomes and functional genetic tools. The rapid emergence and utility of Phalangium opilio as a model for evolutionary developmental biology of arthropods serve as demonstrative evidence of a new area of study in Opiliones biology, made possible through transcriptomic data.

}, keywords = {biogeography, daddy long-legs, evo-devo, Paleontology, Phylogeny}, isbn = {1545-4487 (Electronic)0066-4170 (Linking)}, author = {Giribet, G. and Sharma, P. P.} } @article {640651, title = {Nuclear genomic signals of the {\textquoteright}microturbellarian{\textquoteright} roots of platyhelminth evolutionary innovation}, journal = {Elife}, volume = {4}, year = {2015}, note = {

Laumer, Christopher EHejnol, AndreasGiribet, GonzaloengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.England2015/03/13 06:00Elife. 2015 Mar 12;4. doi: 10.7554/eLife.05503.

}, abstract = {

Flatworms number among the most diverse invertebrate phyla and represent the most biomedically significant branch of the major bilaterian clade Spiralia, but to date, deep evolutionary relationships within this group have been studied using only a single locus (the rRNA operon), leaving the origins of many key clades unclear. In this study, using a survey of genomes and transcriptomes representing all free-living flatworm orders, we provide resolution of platyhelminth interrelationships based on hundreds of nuclear protein-coding genes, exploring phylogenetic signal through concatenation as well as recently developed consensus approaches. These analyses robustly support a modern hypothesis of flatworm phylogeny, one which emphasizes the primacy of the often-overlooked {\textquoteright}microturbellarian{\textquoteright} groups in understanding the major evolutionary transitions within Platyhelminthes: perhaps most notably, we propose a novel scenario for the interrelationships between free-living and vertebrate-parasitic flatworms, providing new opportunities to shed light on the origins and biological consequences of parasitism in these iconic invertebrates.

}, keywords = {evolutionary biology, Genomics, parasitism, Phylogeny, Platyhelminthes, RNA-seq}, isbn = {2050-084X (Electronic)2050-084X (Linking)}, author = {Laumer, C. E. and Hejnol, A. and Giribet, G.} } @article {640636, title = {A phylogenetic backbone for Bivalvia: an RNA-seq approach}, journal = {Proc Biol Sci}, volume = {282}, number = {1801}, year = {2015}, note = {

Gonzalez, Vanessa LAndrade, Sonia C SBieler, RudigerCollins, Timothy MDunn, Casey WMikkelsen, Paula MTaylor, John DGiribet, GonzaloengResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.England2015/01/16 06:00Proc Biol Sci. 2015 Feb 22;282(1801):20142332. doi: 10.1098/rspb.2014.2332.

}, month = {Feb 22}, pages = {20142332}, abstract = {

Bivalves are an ancient and ubiquitous group of aquatic invertebrates with an estimated 10 000-20 000 living species. They are economically significant as a human food source, and ecologically important given their biomass and effects on communities. Their phylogenetic relationships have been studied for decades, and their unparalleled fossil record extends from the Cambrian to the Recent. Nevertheless, a robustly supported phylogeny of the deepest nodes, needed to fully exploit the bivalves as a model for testing macroevolutionary theories, is lacking. Here, we present the first phylogenomic approach for this important group of molluscs, including novel transcriptomic data for 31 bivalves obtained through an RNA-seq approach, and analyse these data with published genomes and transcriptomes of other bivalves plus outgroups. Our results provide a well-resolved, robust phylogenetic backbone for Bivalvia with all major lineages delineated, addressing long-standing questions about the monophyly of Protobranchia and Heterodonta, and resolving the position of particular groups such as Palaeoheterodonta, Archiheterodonta and Anomalodesmata. This now fully resolved backbone demonstrates that genomic approaches using hundreds of genes are feasible for resolving phylogenetic questions in bivalves and other animals.

}, keywords = {bivalves, Mollusca, phylogenetics, phylogenomics}, isbn = {1471-2954 (Electronic)0962-8452 (Linking)}, author = {Gonzalez, V. L. and Andrade, S. C. and Bieler, R. and Collins, T. M. and Dunn, C. W. and Mikkelsen, P. M. and Taylor, J. D. and Giribet, G.} } @article {640761, title = {A Proposal for the Evolution of Cathepsin and Silicatein in Sponges}, journal = {J Mol Evol }, volume = {80}, number = {5-6}, year = {2015}, note = {

Riesgo, AnaMaldonado, ManuelLopez-Legentil, SusannaGiribet, GonzaloengGermany2015/05/20 06:00J Mol Evol. 2015 Jun;80(5-6):278-91. doi: 10.1007/s00239-015-9682-z. Epub 2015 May 19.

}, month = {Jun}, pages = {278-91}, abstract = {

Cathepsins are enzymes capable of degrading proteins intracellularly. They occur ubiquitously in opisthokonts, but their potential to provide insight across the evolutionary transition from protists to metazoans remains poorly investigated. Here, we explore the evolution of cathepsins using comparative analyses of transcriptomic datasets, focusing on both, protists (closely related to metazoans), and early divergent animals (i.e., sponges). We retrieved DNA sequences of nine cathepsin types (B, C, D, F, H, L, O, Z, and silicatein) in the surveyed taxa. In choanoflagellates, only five types (B, C, L, O, Z) were identified, all of them being also found in sponges, indicating that while all cathepsins present in protists were conserved across metazoan lineages, cathepsins F and H (and probably D) are metazoan acquisitions. The phylogeny of cysteine protease cathepsins (excluding cathepsin D) revealed two major lineages: lineage B (cathepsins B and C) and lineage L (cathepsins F, H, L, O, Z). In the latter lineage, a mutation at the active site of cathepsin L gave rise to silicatein, an enzyme exclusively known to date from siliceous sponges and involved in the production of their silica spicules. However, we found that several sponges with siliceous spicules did not express silicatein genes and that, in contrast, several aspiculate sponges did contain silicatein genes. Our results suggest that the ability to silicify may have evolved independently within sponges, some of them losing this capacity secondarily. We also show that most phylogenies based on cathepsin and silicatein genes (except for that of cathepsin O) failed to recover the major lineages of sponges.

}, isbn = {1432-1432 (Electronic)0022-2844 (Linking)}, author = {Riesgo, A. and Maldonado, M. and Lopez-Legentil, S. and Giribet, G.} } @article {640661, title = {Re-evaluating the phylogeny of Sipuncula through transcriptomics}, journal = {Mol Phylogenet Evol}, volume = {83}, year = {2015}, note = {

Lemer, SarahKawauchi, Gisele YAndrade, Sonia C SGonzalez, Vanessa LBoyle, Michael JGiribet, GonzaloengResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2014/12/03 06:00Mol Phylogenet Evol. 2015 Feb;83:174-83. doi: 10.1016/j.ympev.2014.10.019. Epub 2014 Oct 30.

}, month = {Feb}, pages = {174-83}, abstract = {

Sipunculans (also known as peanut worms) are an ancient group of exclusively marine worms with a global distribution and a fossil record that dates back to the Early Cambrian. The systematics of sipunculans, now considered a distinct subclade of Annelida, has been studied for decades using morphological and molecular characters, and has reached the limits of Sanger-based approaches. Here, we reevaluate their family-level phylogeny by comparative transcriptomic analysis of eight species representing all known families within Sipuncula. Two data matrices with alternative gene occupancy levels (large matrix with 675 genes and 62\% missing data; reduced matrix with 141 genes and 23\% missing data) were analysed using concatenation and gene-tree methods, yielding congruent results and resolving each internal node with maximum support. We thus corroborate prior phylogenetic work based on molecular data, resolve outstanding issues with respect to the familial relationships of Aspidosiphonidae, Antillesomatidae and Phascolosomatidae, and highlight the next area of focus for sipunculan systematics.

}, keywords = {*Phylogeny, *Transcriptome, Animals, Annelida, Gene Library, Likelihood Functions, Models, Genetic, Peanut worms, phylogenomics, Polychaeta/*classification, Sequence Analysis, DNA, Systematics}, isbn = {1095-9513 (Electronic)1055-7903 (Linking)}, author = {Lemer, S. and Kawauchi, G. Y. and Andrade, S. C. and Gonzalez, V. L. and Boyle, M. J. and Giribet, G.} } @article {747836, title = {On Aculifera: A review of hypotnesis in tribute to Christopher Schander}, journal = {Journal of Natural History}, volume = {48}, year = {2014}, pages = {2739-2749}, author = {Giribet, G.} } @article {747756, title = {Animal phylogeny and its evolutionary implications}, journal = {Annual Review of Ecology, Evolution and Systematics}, volume = {28}, year = {2014}, pages = {371-395}, author = {Dunn, C. W. and Giribet, G. and Edgecombe, GD. and Hejnol, A.} } @article {747921, title = {Prosogynopora riseri gen. et spec. nov., a phylogenetically problematic lithophoran proseriate (Platyhelminthes : Rhabditophora) with inverted genital pores from the New England coast}, journal = {Invertebrate Systematics}, volume = {75}, year = {2014}, pages = {11-23}, author = {Laumer, C. E. and Giribet, G. and M. Curini-Galletti} } @article {747901, title = {Sipunculus nudus Linnaeus, 1766 (Sipuncula): cosmopolitan or a group of pseudo-cryptic species? An integrated molecular and morphological approach}, journal = {Marine Ecology}, volume = {35}, year = {2014}, pages = {478-491}, author = {Kawauchi, G. Y. and Giribet, G.} } @article {747876, title = {The first phylogenetic analysis of Palpigradi (Arachnida)-the most enigmatic arthropod order}, journal = {Invertebrate Systematics}, volume = {28}, year = {2014}, note = {

the

}, pages = {350-360}, author = {Giribet, G. and E. McIntyre and E. Christian and L. Espinasa and RL. Ferreira and OF. Francke and MS. Harvey and M. Isaia and Kovac and L. McCutchen and MFVR Souza and M. Zagmajster} } @article {747861, title = {On four poorly known harvestmen from New Zealand (Arachnida, Opiliones: Cyphophthalmi, Eupnoi, Dyspnoi, Laniatores)}, journal = {New Zealand Journal of Zoology}, volume = {41}, year = {2014}, pages = {223-233}, author = {Giribet, G. and Fernandez, R. and SL. Boyer} } @article {747931, title = {The Global Invertebrate Genomics Alliance (GIGA): Developing community resources to study diverse invertebrate genomes}, journal = {Journal of Heredity}, volume = {105}, year = {2014}, pages = {1-18}, author = {Lopez, JV and Bracken-Grissom, H. and AG. Collins and Collins, T. and Crandall, K. and Distel, D. and Dunn, C. and Giribet, G. and Haddock, S. and Knowlton, N. and Martindale, M. and Mn. Medina and Messing, C. and SJ. O{\textquoteright}Brien and Paulay, G. and Putnam, N. and Ravasi, T. and GW. Rouse and JF. Ryan and Schulze, A. and Worheide, G. and Adamska, M. and Bailly, X. and Breinholt, J. and WE. Browne and MC. Diaz and Evans, N. and J-F. Flot and Fogarty, N. and Johnston, M. and Kamel, B. and AY. Kawahara and Laberge, T. and Lavrov, D. and Michonneau, F. and LL. Moroz and Oakley, T. and K. Osbourne and SA. Pomponi and Rhodes, A. and M. Rodriquez-Lanetty and SR. Santos and Satoh, N. and RW. Thacker and YVd. Peer and CR. Voolstra and DM. Welch and Winston, J. and Zhou, X.} } @article {747916, title = {Inclusive taxon sampling suggests a single, stepwise origin of ectolecithality in Platyhelminthes}, journal = {Biological Journal of the Linnean Society}, volume = {111}, year = {2014}, pages = {570-588}, author = {Laumer, C. E. and Giribet, G.} } @article {747936, title = {Inferring the ancestral sexuality and reproductive condition in sponges}, journal = {Zoologica Scripta}, volume = {43}, year = {2014}, note = {

Inferr

}, pages = {101-117}, author = {Riesgo, A. and Novo, M. and PP. Sharma and M. Peterson and Maldonado, M. and Giribet, G.} } @article {747751, title = {Investigating the Bivalve Tree of Life - an exemplar-based approach combining molecular and novel morphological characters}, journal = {Invertebrate Systematics}, volume = {28}, year = {2014}, pages = {32-115}, author = {Bieler, R. and PM. Mikkelsen and TM. Collins and EA. Glover and VL. Gonzalez and DL. Graf and EM. Harper and JM. Healy and GY. Kawauchi and PP. Sharma and S. Staubach and EE. Strong and JD. Taylor and I. Temkin and JD. Zardus and S. Clark and A. Guzman and E. McIntyre and P. Sharp and Giribet, G.} } @article {747786, title = {Linking genetic diversity and morphological disparity: biodiversity assessment of a highly unexplored family of harvestmen (Arachnida : Opiliones : Neopilionidae) in New Zealand}, journal = {Invertebrate Systematics}, volume = {28}, year = {2014}, note = {

doi: 10.1071/IS14029

}, pages = {590-604}, author = {Fernandez, R. and S. Velez and Giribet, G.} } @article {747941, title = {A molecular phylogenetic approach to the New Zealand species of Enantiobuninae (Opiliones : Eupnoi : Neopilionidae)}, journal = {Invertebrate Systematics}, volume = {28}, year = {2014}, note = {

doi: 10.1071/IS14030

}, pages = {565-589}, author = {Velez, S. and Fernandez, R. and Giribet, G.} } @article {747891, title = {A multilocus phylogeny of archiheterodont bivalves (Mollusca, Bivalvia, Archiheterodonta)}, journal = {Zoologica Scripta}, volume = {44}, year = {2014}, pages = {41-58}, author = {Gonzalez, V. L. and Giribet, G.} } @article {747911, title = {New insights into the phylogeny, systematics and DNA barcoding of Nemertea}, journal = {Invertebrate Systematics}, volume = {28}, year = {2014}, pages = {287-308}, author = {Kvist, S. and CE. Laumer and J. Junoy and Giribet, G.} } @article {747926, title = {Occurrence of a bivalve-inhabiting marine hydrozoan (Hydrozoa: Hydroidolina: Leptothecata) in the amber pen-shell Pinna carnea GMELIN, 1971 (Bivalvia: Pteriomorphia: Pinnidae) from Bocas del Toro}, journal = {Journal of Molluscan Studies}, volume = {80}, year = {2014}, note = {

doi: 10.1093/mollus/eyu059

}, pages = {464-468}, author = {Lemer, S. and Giribet, G.} } @article {747871, title = {On the occurrence of Tuleariocaris neglecta Chace, 1969 (Decapoda, Palaemonidae, Pontoniinae) in Echinometra lucunter (Linnaeus, 1758) (Echinodermata, Echinoidea, Echinometridae) in the Archipelago of Bocas del Toro, Panama}, journal = {Crustaceana}, volume = {87}, year = {2014}, pages = {634-638}, author = {Giribet, G. and Lemer, S.} } @article {747766, title = {Phylogeography and species delimitation in the New Zealand endemic, genetically hypervariable harvestman species, Aoraki denticulate (Arachnida, Opiliones, Cyphophthalmi)}, journal = {Invertebrate Systematics}, volume = {28}, year = {2014}, pages = {401-414}, author = {Fernandez, R. and Giribet, G.} } @article {747906, title = {Pyrosequencing of the salivary transcriptome of Haeadipsa interrupta (Annelida: Clitellata: Haemadipsidae) reveals a wide array of anticoagulants and provides insights into the evolution of anticoagulation capabilities in leeches}, journal = {Invertebrate Biology}, volume = {13}, year = {2014}, pages = {74-98}, author = {Kvist, S. and MR. Brugler and TG. Goh and Giribet, G. and ME. Siddall} } @article {747796, title = {Walk it off: Predictive power of appendicular characters toward inference of higher-level relationships in Laniatores (Arachnida: Opiliones)}, journal = {Cladistics}, volume = {30}, year = {2014}, pages = {120-138}, author = {Gainett, G and PP. Sharma and R. Pinto-da-Rocha and Giribet, G. and RH. Willemart} } @article {640756, title = {The analysis of eight transcriptomes from all poriferan classes reveals surprising genetic complexity in sponges}, journal = {Mol Biol Evol}, volume = {31}, number = {5}, year = {2014}, note = {

Riesgo, AnaFarrar, NathanWindsor, Pamela JGiribet, GonzaloLeys, Sally PengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2014/02/06 06:00Mol Biol Evol. 2014 May;31(5):1102-20. doi: 10.1093/molbev/msu057. Epub 2014 Feb 4.

}, month = {May}, pages = {1102-20}, abstract = {

Sponges (Porifera) are among the earliest evolving metazoans. Their filter-feeding body plan based on choanocyte chambers organized into a complex aquiferous system is so unique among metazoans that it either reflects an early divergence from other animals prior to the evolution of features such as muscles and nerves, or that sponges lost these characters. Analyses of the Amphimedon and Oscarella genomes support this view of uniqueness-many key metazoan genes are absent in these sponges-but whether this is generally true of other sponges remains unknown. We studied the transcriptomes of eight sponge species in four classes (Hexactinellida, Demospongiae, Homoscleromorpha, and Calcarea) specifically seeking genes and pathways considered to be involved in animal complexity. For reference, we also sought these genes in transcriptomes and genomes of three unicellular opisthokonts, two sponges (A. queenslandica and O. carmela), and two bilaterian taxa. Our analyses showed that all sponge classes share an unexpectedly large complement of genes with other metazoans. Interestingly, hexactinellid, calcareous, and homoscleromorph sponges share more genes with bilaterians than with nonbilaterian metazoans. We were surprised to find representatives of most molecules involved in cell-cell communication, signaling, complex epithelia, immune recognition, and germ-lineage/sex, with only a few, but potentially key, absences. A noteworthy finding was that some important genes were absent from all demosponges (transcriptomes and the Amphimedon genome), which might reflect divergence from main-stem lineages including hexactinellids, calcareous sponges, and homoscleromorphs. Our results suggest that genetic complexity arose early in evolution as shown by the presence of these genes in most of the animal lineages, which suggests sponges either possess cryptic physiological and morphological complexity and/or have lost ancestral cell types or physiological processes.

}, keywords = {*Evolution, Molecular, adhesion, Animals, Cell Adhesion/genetics, coordination, epithelia, Genetic Speciation, genome, Immunity, Innate/genetics, innate immunity, Phylogeny, Porifera/*classification/*genetics/physiology, Reproduction/genetics, RNAseq, sex-determination, Signal Transduction/genetics, signaling, Synaptic Transmission/genetics, Transcriptome}, isbn = {1537-1719 (Electronic)0737-4038 (Linking)}, author = {Riesgo, A. and Farrar, N. and Windsor, P. J. and Giribet, G. and Leys, S. P.} } @article {640666, title = {A dataset comprising four micro-computed tomography scans of freshly fixed and museum earthworm specimens}, journal = {Gigascience}, volume = {3}, year = {2014}, note = {

Lenihan, JenniferKvist, SebastianFernandez, RosaGiribet, GonzaloZiegler, AlexanderengEngland2014/05/20 06:00Gigascience. 2014 May 16;3:6. doi: 10.1186/2047-217X-3-6. eCollection 2014.

}, pages = {6}, abstract = {

BACKGROUND: ALTHOUGH MOLECULAR TOOLS ARE INCREASINGLY EMPLOYED TO DECIPHER INVERTEBRATE SYSTEMATICS, EARTHWORM (ANNELIDA: Clitellata: {\textquoteright}Oligochaeta{\textquoteright}) taxonomy is still largely based on conventional dissection, resulting in data that are mostly unsuitable for dissemination through online databases. In order to evaluate if micro-computed tomography (muCT) in combination with soft tissue staining techniques could be used to expand the existing set of tools available for studying internal and external structures of earthworms, muCT scans of freshly fixed and museum specimens were gathered. FINDINGS: Scout images revealed full penetration of tissues by the staining agent. The attained isotropic voxel resolutions permit identification of internal and external structures conventionally used in earthworm taxonomy. The muCT projection and reconstruction images have been deposited in the online data repository GigaDB and are publicly available for download. CONCLUSIONS: The dataset presented here shows that earthworms constitute suitable candidates for muCT scanning in combination with soft tissue staining. Not only are the data comparable to results derived from traditional dissection techniques, but due to their digital nature the data also permit computer-based interactive exploration of earthworm morphology and anatomy. The approach pursued here can be applied to freshly fixed as well as museum specimens, which is of particular importance when considering the use of rare or valuable material. Finally, a number of aspects related to the deposition of digital morphological data are briefly discussed.

}, keywords = {anatomy, Aporrectodea, Imaging, Lumbricidae, MicroCT, Morphology, muCT, Repository, Taxonomy}, isbn = {2047-217X (Electronic)2047-217X (Linking)}, author = {Lenihan, J. and S. Kvist and Fernandez, R. and Giribet, G. and Ziegler, A.} } @article {640471, title = {Evaluating topological conflict in centipede phylogeny using transcriptomic data sets}, journal = {Mol Biol Evol}, volume = {31}, number = {6}, year = {2014}, note = {

Fernandez, RosaLaumer, Christopher EVahtera, VarpuLibro, SilviaKaluziak, StefanSharma, Prashant PPerez-Porro, Alicia REdgecombe, Gregory DGiribet, GonzaloengResearch Support, Non-U.S. Gov{\textquoteright}t2014/03/29 06:00Mol Biol Evol. 2014 Jun;31(6):1500-13. doi: 10.1093/molbev/msu108. Epub 2014 Mar 26.

}, month = {Jun}, pages = {1500-13}, abstract = {

Relationships between the five extant orders of centipedes have been considered solved based on morphology. Phylogenies based on samples of up to a few dozen genes have largely been congruent with the morphological tree apart from an alternative placement of one order, the relictual Craterostigmomorpha, consisting of two species in Tasmania and New Zealand. To address this incongruence, novel transcriptomic data were generated to sample all five orders of centipedes and also used as a test case for studying gene-tree incongruence. Maximum likelihood and Bayesian mixture model analyses of a data set composed of 1,934 orthologs with 45\% missing data, as well as the 389 orthologs in the least saturated, stationary quartile, retrieve strong support for a sister-group relationship between Craterostigmomorpha and all other pleurostigmophoran centipedes, of which the latter group is newly named Amalpighiata. The Amalpighiata hypothesis, which shows little gene-tree incongruence and is robust to the influence of among-taxon compositional heterogeneity, implies convergent evolution in several morphological and behavioral characters traditionally used in centipede phylogenetics, such as maternal brood care, but accords with patterns of first appearances in the fossil record.

}, keywords = {*Phylogeny, Animals, Arthropods/*classification/*genetics, Bayes Theorem, Chilopoda, Evolution, Molecular, Genomics/*methods, High-Throughput Nucleotide Sequencing, Illumina, incongruence, Likelihood Functions, molecular dating, Myriapoda, next-generation sequencing, phylogenomics, Transcriptome}, isbn = {1537-1719 (Electronic)0737-4038 (Linking)}, author = {Fernandez, R. and Laumer, C. E. and V. Vahtera and Libro, S. and Kaluziak, S. and Sharma, P. P. and Perez-Porro, A. R. and G.D. Edgecombe and Giribet, G.} } @article {640656, title = {First molecular phylogeny of the circumtropical bivalve family Pinnidae (Mollusca, Bivalvia): evidence for high levels of cryptic species diversity}, journal = {Mol Phylogenet Evol}, volume = {75}, year = {2014}, note = {

Lemer, SarahBuge, BarbaraBemis, AmandaGiribet, GonzaloengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2014/02/27 06:00Mol Phylogenet Evol. 2014 Jun;75:11-23. doi: 10.1016/j.ympev.2014.02.008. Epub 2014 Feb 22.

}, month = {Jun}, pages = {11-23}, abstract = {

The family Pinnidae Leach, 1819, includes approximately 50 species of large subtidal and coastal marine bivalves. These commercially important species occur in tropical and temperate waters around the world and are most frequently found in seagrass meadows. The taxonomy of the family has been revised a number of times since the early 20th Century, the most recent revision recognizing 55 species distributed in three genera: Pinna, Atrina and Streptopinna, the latter being monotypic. However, to date no phylogenetic analysis of the family has been conducted using morphological or molecular data. The present study analyzed 306 pinnid specimens from around the world, comprising the three described genera and ca. 25 morphospecies. We sequenced the mitochondrial genes 16S rRNA and cytochrome c oxidase subunit I, and the nuclear ribosomal genes 18S rRNA and 28S rRNA. Phylogenetic analysis of the data revealed monophyly of the genus Atrina but also that the genus Streptopinna is nested within Pinna. Based on the strong support for this relationship we propose a new status for Streptopinna Martens, 1880 and treat it as a subgenus (status nov.) of Pinna Linnaeus, 1758. The phylogeny and the species delimitation analyses suggest the presence of cryptic species in many morphospecies displaying a wide Indo-Pacific distribution, including Pinna muricata, Atrina assimilis, A. exusta and P. (Streptopinna) saccata but also in the Atlantic species A. rigida. Altogether our results highlight the challenges associated with morphological identifications in Pinnidae due to the presence of both phenotypic plasticity and morphological stasis and reveal that many pinnid species are not as widely distributed as previously thought.

}, keywords = {*Phylogeny, Animals, Bayes Theorem, biogeography, Bivalvia/*classification/genetics, diversification, DNA, Mitochondrial/genetics, Electron Transport Complex IV/genetics, Evolution, Molecular, Likelihood Functions, Models, Genetic, Morphological stasis, Penshell, Phenotypic plasticity, Pteriomorphia, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 18S/genetics, RNA, Ribosomal, 28S/genetics, Sequence Analysis, DNA}, isbn = {1095-9513 (Electronic)1055-7903 (Linking)}, author = {Lemer, S. and Buge, B. and Bemis, A. and Giribet, G.} } @article {640791, title = {The Global Invertebrate Genomics Alliance (GIGA): developing community resources to study diverse invertebrate genomes}, journal = {J Hered}, volume = {105}, number = {1}, year = {2014}, note = {

Bracken-Grissom, HeatherCollins, Allen GCollins, TimothyCrandall, KeithDistel, DanielDunn, CaseyGiribet, GonzaloHaddock, StevenKnowlton, NancyMartindale, MarkMedina, MonicaMessing, CharlesO{\textquoteright}Brien, Stephen JPaulay, GustavPutnam, NicolasRavasi, TimothyRouse, Greg WRyan, Joseph FSchulze, AnjaWorheide, GertAdamska, MajaBailly, XavierBreinholt, JesseBrowne, William EDiaz, M ChristinaEvans, NathanielFlot, Jean-FrancoisFogarty, NicoleJohnston, MatthewKamel, BishoyKawahara, Akito YLaberge, TammyLavrov, DennisMichonneau, FrancoisMoroz, Leonid LOakley, ToddOsborne, KarenPomponi, Shirley ARhodes, AdelaideSantos, Scott RSatoh, NoriThacker, Robert WVan de Peer, YvesVoolstra, Christian RWelch, David MarkWinston, JudithZhou, XinengR01 MH097062/MH/NIMH NIH HHS/Research Support, Non-U.S. Gov{\textquoteright}t2013/12/18 06:00J Hered. 2014 Jan-Feb;105(1):1-18. doi: 10.1093/jhered/est084.

}, month = {Jan-Feb}, pages = {1-18}, abstract = {

Over 95\% of all metazoan (animal) species comprise the "invertebrates," but very few genomes from these organisms have been sequenced. We have, therefore, formed a "Global Invertebrate Genomics Alliance" (GIGA). Our intent is to build a collaborative network of diverse scientists to tackle major challenges (e.g., species selection, sample collection and storage, sequence assembly, annotation, analytical tools) associated with genome/transcriptome sequencing across a large taxonomic spectrum. We aim to promote standards that will facilitate comparative approaches to invertebrate genomics and collaborations across the international scientific community. Candidate study taxa include species from Porifera, Ctenophora, Cnidaria, Placozoa, Mollusca, Arthropoda, Echinodermata, Annelida, Bryozoa, and Platyhelminthes, among others. GIGA will target 7000 noninsect/nonnematode species, with an emphasis on marine taxa because of the unrivaled phyletic diversity in the oceans. Priorities for selecting invertebrates for sequencing will include, but are not restricted to, their phylogenetic placement; relevance to organismal, ecological, and conservation research; and their importance to fisheries and human health. We highlight benefits of sequencing both whole genomes (DNA) and transcriptomes and also suggest policies for genomic-level data access and sharing based on transparency and inclusiveness. The GIGA Web site (http://giga.nova.edu) has been launched to facilitate this collaborative venture.

}, keywords = {*Genome, Animals, Biodiversity, Biological Evolution, comparative genomics, consortium, Evolution, Genomics/*methods, Giga, Invertebrates, Invertebrates/*classification/*genetics, metazoa, Organizations, Phylogeny}, isbn = {1465-7333 (Electronic)0022-1503 (Linking)}, author = {Bracken-Grissom, H. and Collins, A. G. and Collins, T. and Crandall, K. and Distel, D. and Dunn, C. and Giribet, G. and Haddock, S. and Knowlton, N. and Martindale, M. and Medina, M. and Messing, C. and O{\textquoteright}Brien, S. J. and Paulay, G. and Putnam, N. and Ravasi, T. and Rouse, G. W. and Ryan, J. F. and Schulze, A. and Worheide, G. and Adamska, M. and Bailly, X. and Breinholt, J. and Browne, W. E. and Diaz, M. C. and Evans, N. and Flot, J. F. and Fogarty, N. and Johnston, M. and Kamel, B. and Kawahara, A. Y. and Laberge, T. and Lavrov, D. and Michonneau, F. and Moroz, L. L. and Oakley, T. and Osborne, K. and Pomponi, S. A. and Rhodes, A. and Santos, S. R. and Satoh, N. and Thacker, R. W. and Van de Peer, Y. and Voolstra, C. R. and Welch, D. M. and Winston, J. and Zhou, X.} } @article {640701, title = {A living fossil tale of Pangaean biogeography}, journal = {Proc Biol Sci}, volume = {281}, number = {1775}, year = {2014}, note = {

Murienne, JeromeDaniels, Savel RBuckley, Thomas RMayer, GeorgGiribet, GonzaloengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.England2013/11/29 06:00Proc Biol Sci. 2013 Nov 27;281(1775):20132648. doi: 10.1098/rspb.2013.2648. Print 2014 Jan 22.

}, month = {Jan 22}, pages = {20132648}, abstract = {

The current distributions of widespread groups of terrestrial animals and plants are supposedly the result of a mixture of either vicariance owing to continental split or more recent trans-oceanic dispersal. For organisms exhibiting a vicariant biogeographic pattern-achieving their current distribution by riding on the plates of former supercontinents-this view is largely inspired by the belief that Pangaea lacked geographical or ecological barriers, or that extinctions and dispersal would have erased any biogeographic signal since the early Mesozoic. We here present a time-calibrated molecular phylogeny of Onychophora (velvet worms), an ancient and exclusively terrestrial panarthropod group distributed throughout former Pangaean landmasses. Our data not only demonstrate that trans-oceanic dispersal does not need be invoked to explain contemporary distributions, but also reveal that the early diversification of the group pre-dates the break-up of Pangaea, maintaining regionalization even in landmasses that have remained contiguous throughout the history of the group. These results corroborate a growing body of evidence from palaeontology, palaeogeography and palaeoclimatic modelling depicting ancient biogeographic regionalization over the continuous landmass of Pangaea.

}, keywords = {*Geography, *Phylogeography, Animals, biogeography, Invertebrates/anatomy \& histology/*genetics, molecular dating, Onychophora, Phylogeny, Sequence Analysis, DNA, velvet worms}, isbn = {1471-2954 (Electronic)0962-8452 (Linking)}, author = {Murienne, J. and Daniels, S. R. and Buckley, T. R. and Mayer, G. and Giribet, G.} } @article {640481, title = {A Paleozoic stem group to mite harvestmen revealed through integration of phylogenetics and development}, journal = {Curr Biol}, volume = {24}, number = {9}, year = {2014}, note = {

Garwood, Russell JSharma, Prashant PDunlop, Jason AGiribet, GonzaloengResearch Support, Non-U.S. Gov{\textquoteright}tEngland2014/04/15 06:00Curr Biol. 2014 May 5;24(9):1017-23. doi: 10.1016/j.cub.2014.03.039. Epub 2014 Apr 10.

}, month = {May 5}, pages = {1017-23}, abstract = {

Successfully placing fossils in phylogenies is integral to understanding the tree of life. Crown-group Paleozoic members of the arachnid order Opiliones are indicative of ancient origins and one of the earliest arthropod terrestrialization events [1, 2]. Opiliones epitomize morphological stasis, and all known fossils have been placed within the four extant suborders [3-5]. Here we report a Carboniferous harvestman species, Hastocularis argusgen. nov., sp. nov., reconstructed with microtomography (microCT). Phylogenetic analysis recovers this species, and the Devonian Eophalangium sheari, as members of an extinct harvestman clade. We establish the suborder Tetrophthalmi subordo nov., which bore four eyes, to accommodate H. argus and E. sheari, the latter previously considered to be a phalangid [6-9]. Furthermore, embryonic gene expression in the extant species Phalangium opilio demonstrates vestiges of lateral eye tubercles. These lateral eyes are lost in all crown-group Phalangida, but are observed in both our fossil and outgroup chelicerate orders. These data independently corroborate the diagnosis of two eye pairs in the fossil and demonstrate retention of eyes of separate evolutionary origins in modern harvestmen [10-12]. The discovery of Tetrophthalmi alters molecular divergence time estimates, supporting Carboniferous rather than Devonian diversification for extant suborders and directly impacting inferences of terrestrialization history and biogeography. Multidisciplinary approaches integrating fossil and neontological data increase confidence in phylogenies and elucidate evolutionary history.

}, keywords = {*Biological Evolution, Animals, Evolution, Molecular, Eye/anatomy \& histology, Fossils/*anatomy \& histology, Gene Expression Regulation, Developmental, Mites/*anatomy \& histology/*classification, Molecular Sequence Data, Phylogeny}, isbn = {1879-0445 (Electronic)0960-9822 (Linking)}, author = {Garwood, R. J. and Sharma, P. P. and Dunlop, J. A. and Giribet, G.} } @article {640886, title = {Phylogenomic analyses of deep gastropod relationships reject Orthogastropoda}, journal = {Proc Biol Sci}, volume = {281}, number = {1794}, year = {2014}, note = {

Zapata, FelipeWilson, Nerida GHowison, MarkAndrade, Sonia C SJorger, Katharina MSchrodl, MichaelGoetz, Freya EGiribet, GonzaloDunn, Casey WengP30RR031153/RR/NCRR NIH HHS/Research Support, N.I.H., ExtramuralResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.England2014/09/19 06:00Proc Biol Sci. 2014 Nov 7;281(1794):20141739. doi: 10.1098/rspb.2014.1739.

}, month = {Nov 7}, pages = {20141739}, abstract = {

Gastropods are a highly diverse clade of molluscs that includes many familiar animals, such as limpets, snails, slugs and sea slugs. It is one of the most abundant groups of animals in the sea and the only molluscan lineage that has successfully colonized land. Yet the relationships among and within its constituent clades have remained in flux for over a century of morphological, anatomical and molecular study. Here, we re-evaluate gastropod phylogenetic relationships by collecting new transcriptome data for 40 species and analysing them in combination with publicly available genomes and transcriptomes. Our datasets include all five main gastropod clades: Patellogastropoda, Vetigastropoda, Neritimorpha, Caenogastropoda and Heterobranchia. We use two different methods to assign orthology, subsample each of these matrices into three increasingly dense subsets, and analyse all six of these supermatrices with two different models of molecular evolution. All 12 analyses yield the same unrooted network connecting the five major gastropod lineages. This reduces deep gastropod phylogeny to three alternative rooting hypotheses. These results reject the prevalent hypothesis of gastropod phylogeny, Orthogastropoda. Our dated tree is congruent with a possible end-Permian recovery of some gastropod clades, namely Caenogastropoda and some Heterobranchia subclades.

}, keywords = {*Evolution, Molecular, *Phylogeny, Animals, Gastropoda, Gastropoda/*classification/*genetics, Genome/*genetics, Heterobranchia, Mollusca, phylogenomics, Sequence Analysis, RNA, Transcriptome/*genetics}, isbn = {1471-2954 (Electronic)0962-8452 (Linking)}, author = {Zapata, F. and Wilson, N. G. and Howison, M. and Andrade, S. C. and Jorger, K. M. and Schrodl, M. and Goetz, F. E. and Giribet, G. and Dunn, C. W.} } @article {640461, title = {Phylogenomic analysis of spiders reveals nonmonophyly of orb weavers}, journal = {Curr Biol}, volume = {24}, number = {15}, year = {2014}, note = {

Fernandez, RosaHormiga, GustavoGiribet, GonzaloengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.England2014/07/22 06:00Curr Biol. 2014 Aug 4;24(15):1772-7. doi: 10.1016/j.cub.2014.06.035. Epub 2014 Jul 17.

}, month = {Aug 4}, pages = {1772-7}, abstract = {

Spiders constitute one of the most successful clades of terrestrial predators. Their extraordinary diversity, paralleled only by some insects and mites, is often attributed to the use of silk, and, in one of the largest lineages, to stereotyped behaviors for building foraging webs of remarkable biomechanical properties. However, our understanding of higher-level spider relationships is poor and is largely based on morphology. Prior molecular efforts have focused on a handful of genes but have provided little resolution to key questions such as the origin of the orb weavers. We apply a next-generation sequencing approach to resolve spider phylogeny, examining the relationships among its major lineages. We further explore possible pitfalls in phylogenomic reconstruction, including missing data, unequal rates of evolution, and others. Analyses of multiple data sets all agree on the basic structure of the spider tree and all reject the long-accepted monophyly of Orbiculariae, by placing the cribellate orb weavers (Deinopoidea) with other groups and not with the ecribellate orb weavers (Araneoidea). These results imply independent origins for the two types of orb webs (cribellate and ecribellate) or a much more ancestral origin of the orb web with subsequent loss in the so-called RTA clade. Either alternative demands a major reevaluation of our current understanding of the spider evolutionary chronicle.

}, keywords = {*Phylogeny, Animals, Arthropod Proteins/*genetics, Biological Evolution, Molecular Sequence Data, Predatory Behavior, Sequence Analysis, DNA, Spiders/*classification/*genetics/physiology}, isbn = {1879-0445 (Electronic)0960-9822 (Linking)}, author = {Fernandez, R. and Hormiga, G. and Giribet, G.} } @article {640816, title = {Phylogenomic interrogation of arachnida reveals systemic conflicts in phylogenetic signal}, journal = {Mol Biol Evol}, volume = {31}, number = {11}, year = {2014}, note = {

Sharma, Prashant PKaluziak, Stefan TPerez-Porro, Alicia RGonzalez, Vanessa LHormiga, GustavoWheeler, Ward CGiribet, GonzaloengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, P.H.S.2014/08/12 06:00Mol Biol Evol. 2014 Nov;31(11):2963-84. doi: 10.1093/molbev/msu235. Epub 2014 Aug 8.

}, month = {Nov}, pages = {2963-84}, abstract = {

Chelicerata represents one of the oldest groups of arthropods, with a fossil record extending to the Cambrian, and is sister group to the remaining extant arthropods, the mandibulates. Attempts to resolve the internal phylogeny of chelicerates have achieved little consensus, due to marked discord in both morphological and molecular hypotheses of chelicerate phylogeny. The monophyly of Arachnida, the terrestrial chelicerates, is generally accepted, but has garnered little support from molecular data, which have been limited either in breadth of taxonomic sampling or in depth of sequencing. To address the internal phylogeny of this group, we employed a phylogenomic approach, generating transcriptomic data for 17 species in combination with existing data, including two complete genomes. We analyzed multiple data sets containing up to 1,235,912 sites across 3,644 loci, using alternative approaches to optimization of matrix composition. Here, we show that phylogenetic signal for the monophyly of Arachnida is restricted to the 500 slowest-evolving genes in the data set. Accelerated evolutionary rates in Acariformes, Pseudoscorpiones, and Parasitiformes potentially engender long-branch attraction artifacts, yielding nonmonophyly of Arachnida with increasing support upon incrementing the number of concatenated genes. Mutually exclusive hypotheses are supported by locus groups of variable evolutionary rate, revealing significant conflicts in phylogenetic signal. Analyses of gene-tree discordance indicate marked incongruence in relationships among chelicerate orders, whereas derived relationships are demonstrably robust. Consistently recovered and supported relationships include the monophyly of Chelicerata, Euchelicerata, Tetrapulmonata, and all orders represented by multiple terminals. Relationships supported by subsets of slow-evolving genes include Ricinulei + Solifugae; a clade comprised of Ricinulei, Opiliones, and Solifugae; and a clade comprised of Tetrapulmonata, Scorpiones, and Pseudoscorpiones. We demonstrate that outgroup selection without regard for branch length distribution exacerbates long-branch attraction artifacts and does not mitigate gene-tree discordance, regardless of high gene representation for outgroups that are model organisms. Arachnopulmonata (new name) is proposed for the clade comprising Scorpiones + Tetrapulmonata (previously named Pulmonata).

}, keywords = {*DNA Barcoding, Taxonomic, *Genome, *Phylogeny, *Transcriptome, ancient rapid radiation, Animals, Arachnida/*classification/genetics, arachnids, Arthropoda, Bayes Theorem, concatenation, Evolution, Molecular, Fossils, Genetic Speciation, High-Throughput Nucleotide Sequencing, orthology prediction, topological conflict, transcriptomics}, isbn = {1537-1719 (Electronic)0737-4038 (Linking)}, author = {Sharma, P. P. and Kaluziak, S. T. and Perez-Porro, A. R. and Gonzalez, V. L. and Hormiga, G. and W.C. Wheeler and Giribet, G.} } @article {640806, title = {A revised dated phylogeny of the arachnid order Opiliones}, journal = {Front Genet}, volume = {5}, year = {2014}, note = {

Sharma, Prashant PGiribet, GonzaloengSwitzerland2014/08/15 06:00Front Genet. 2014 Jul 28;5:255. doi: 10.3389/fgene.2014.00255. eCollection 2014.

}, pages = {255}, abstract = {

Dating the Opiliones tree of life has become an important enterprise for this group of arthropods, due to their ancient origins and important biogeographic implications. To incorporate both methodological innovations in molecular dating as well as new systematic discoveries of harvestman diversity, we conducted total evidence dating on a data set uniting morphological and/or molecular sequence data for 47 Opiliones species, including all four well-known Palaeozoic fossils, to test the placement of both fossils and newly discovered lineages in a single analysis. Furthermore, we investigated node dating with a phylogenomic data set of 24,202 amino acid sites for 14 species of Opiliones, sampling all extant suborders. In this way, we approached molecular dating of basal harvestman phylogeny using different data sets and approaches to assess congruence of divergence time estimates. In spite of the markedly different composition of data sets, our results show congruence across all analyses for age estimates of basal nodes that are well constrained with respect to fossil calibrations (e.g., Opiliones, Palpatores). By contrast, derived nodes that lack fossil calibrations (e.g., the suborders Cyphophthalmi, and Laniatores) have large uncertainty intervals in diversification times, particularly in the total evidence dating analysis, reflecting the dearth of calibration points and undersampling of derived lineages. Total evidence dating consistently produced older median ages than node dating for ingroup nodes, due to the nested placement of multiple Palaeozoic fossils. Our analyses support basal diversification of Opiliones in the Ordovician-Devonian period, corroborating the inferred ancient origins of this arthropod order, and underscore the importance of diversity discovery-both paleontological and neontological-in evolutionary inference.

}, keywords = {arachnids, Arthropods, molecular dating, node dating, phylogenomics, total evidence dating}, isbn = {1664-8021 (Electronic)1664-8021 (Linking)}, author = {Sharma, P. P. and Giribet, G.} } @article {640466, title = {Sine systemate chaos? A versatile tool for earthworm taxonomy: non-destructive imaging of freshly fixed and museum specimens using micro-computed tomography}, journal = {PLoS One}, volume = {9}, number = {5}, year = {2014}, note = {

Fernandez, RosaKvist, SebastianLenihan, JenniferGiribet, GonzaloZiegler, AlexanderengResearch Support, Non-U.S. Gov{\textquoteright}t2014/05/20 06:00PLoS One. 2014 May 16;9(5):e96617. doi: 10.1371/journal.pone.0096617. eCollection 2014.

}, pages = {e96617}, abstract = {

In spite of the high relevance of lumbricid earthworms ({\textquoteright}Oligochaeta{\textquoteright}: Lumbricidae) for soil structure and functioning, the taxonomy of this group of terrestrial invertebrates remains in a quasi-chaotic state. Earthworm taxonomy traditionally relies on the interpretation of external and internal morphological characters, but the acquisition of these data is often hampered by tedious dissections or restricted access to valuable and rare museum specimens. The present state of affairs, in conjunction with the difficulty of establishing primary homologies for multiple morphological features, has led to an almost unrivaled instability in the taxonomy and systematics of certain earthworm groups, including Lumbricidae. As a potential remedy, we apply for the first time a non-destructive imaging technique to lumbricids and explore the future application of this approach to earthworm taxonomy. High-resolution micro-computed tomography (muCT) scanning of freshly fixed and museum specimens was carried out using two cosmopolitan species, Aporrectodea caliginosa and A. trapezoides. By combining two-dimensional and three-dimensional dataset visualization techniques, we demonstrate that the morphological features commonly used in earthworm taxonomy can now be analyzed without the need for dissection, whether freshly fixed or museum specimens collected more than 60 years ago are studied. Our analyses show that muCT in combination with soft tissue staining can be successfully applied to lumbricid earthworms. An extension of the approach to other families is poised to strengthen earthworm taxonomy by providing a versatile tool to resolve the taxonomic chaos currently present in this ecologically important, but taxonomically neglected group of terrestrial invertebrates.

}, keywords = {Animals, Classification/*methods, Imaging, Three-Dimensional/methods, Museums, Oligochaeta/*anatomy \& histology/*classification, Species Specificity, Specimen Handling/methods, Staining and Labeling/methods, X-Ray Microtomography/*methods}, isbn = {1932-6203 (Electronic)1932-6203 (Linking)}, author = {Fernandez, R. and S. Kvist and Lenihan, J. and Giribet, G. and Ziegler, A.} } @article {640381, title = {A transcriptomic approach to ribbon worm systematics (nemertea): resolving the pilidiophora problem}, journal = {Mol Biol Evol}, volume = {31}, number = {12}, year = {2014}, note = {

Andrade, Sonia C SMontenegro, HoracioStrand, MalinSchwartz, Megan LKajihara, HiroshiNorenburg, Jon LTurbeville, James MSundberg, PerGiribet, GonzaloengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2014/08/30 06:00Mol Biol Evol. 2014 Dec;31(12):3206-15. doi: 10.1093/molbev/msu253. Epub 2014 Aug 27.

}, month = {Dec}, pages = {3206-15}, abstract = {

Resolving the deep relationships of ancient animal lineages has proven difficult using standard Sanger-sequencing approaches with a handful of markers. We thus reassess the relatively well-studied phylogeny of the phylum Nemertea (ribbon worms)-for which the targeted gene approaches had resolved many clades but had left key phylogenetic gaps-by using a phylogenomic approach using Illumina-based de novo assembled transcriptomes and automatic orthology prediction methods. The analysis of a concatenated data set of 2,779 genes (411,138 amino acids) with about 78\% gene occupancy and a reduced version with 95\% gene occupancy, under evolutionary models accounting or not for site-specific amino acid replacement patterns results in a well-supported phylogeny that recovers all major accepted nemertean clades with the monophyly of Heteronemertea, Hoplonemertea, Monostilifera, being well supported. Significantly, all the ambiguous patterns inferred from Sanger-based approaches were resolved, namely the monophyly of Palaeonemertea and Pilidiophora. By testing for possible conflict in the analyzed supermatrix, we observed that concatenation was the best solution, and the results of the analyses should settle prior debates on nemertean phylogeny. The study highlights the importance, feasibility, and completeness of Illumina-based phylogenomic data matrices.

}, keywords = {concatenation, Illumina, Neonemertea, Palaeonemertea, Phylogeny, Pilidiophora, supermatrix}, isbn = {1537-1719 (Electronic)0737-4038 (Linking)}, author = {Andrade, S. C. and Montenegro, H. and Strand, M. and Schwartz, M. L. and Kajihara, H. and Norenburg, J. L. and Turbeville, J. M. and Sundberg, P. and Giribet, G.} } @article {748101, title = {Bivalvia-A discussion of known unknowns}, journal = {American Malacological Bulletin }, volume = {31}, year = {2013}, pages = {123-133}, author = {Bieler, R. and Mikkelsen. PM and Giribet. G} } @article {748111, title = {Book Review: Animal Evolution: Interrelationships of the Living Phyla. 3rd ed.}, journal = {Integrative and Comparative Biology}, volume = {53}, year = {2013}, pages = {532-534}, author = {Giribet, G.} } @article {748126, title = {Congruence between molecular phylogeny and cuticular design in Echiniscoidea (Tardigrada, Heterotardigrada)}, journal = {Zoological Journal of the Linnean Society}, volume = {169}, year = {2013}, pages = {713-736}, author = {N. Guil and Jorgensen. A and Giribet. G and Kristensen. RM} } @article {748136, title = {Corrigendum: Resolving the evolutionary relationships of molluscs with phylogenomic tools}, journal = {Nature}, volume = {493}, year = {2013}, pages = {708}, author = {SA. Smith and Wilson. NG and Goetz. FE and Feehery. C and Andrade. SCS and Rouse. GW and Giribet. G and Dunn. CW} } @article {748131, title = {Description of the male, larva and nymphal stages of Crypocellus iaci (Arachnida, Ricinulei), with an overview of tarsal sensilla and other integumental structures}, journal = {Zootaxa}, volume = {3709}, year = {2013}, pages = {149-161}, author = {L. Salvatierra and Tourinho. AL and Giribet. G} } @article {748141, title = {On the identity of two Antarctic brooding nemerteans: redescription of Antarctonemertes valida (Burger, 1893) and description of a new species in the genus Antarctonemertes Friedrich, 1995 (Nemertea, Hoplonemertea)}, journal = {Polar Biology}, volume = {36}, year = {2013}, pages = {1415-1430}, author = {S. Taboada and Junoy. J and Andrade. SCS and Giribet. G and Cristobo. J and Avila. C} } @article {748106, title = {Opiliones fosiles. Los aracnidos actuales de origen mas remoto}, journal = {Fundamental!}, volume = {23}, year = {2013}, pages = {1-58}, author = {RJ. Garwood and Dunlop. JA and Giribet. G and Sutton. MD} } @article {748151, title = {Phylogenetics}, journal = {Invertebrate Systematics}, volume = {27}, year = {2013}, pages = {578-602}, author = {V. Vahtera and Edgecombe. GD and Giribet. G} } @article {748096, title = {A revision of selected clades of Neotropical mite harvestmen (Arachnida, Opiliones, Cyphophthalmi, Neogoveidae) with the description of eight new species}, journal = {Bulletin of the Museum of Comparative Zoology }, volume = {161}, year = {2013}, pages = {1-44}, author = {LR. Benavides and Giribet. G} } @article {748116, title = {On Speleosiro argasiformis-a troglobitic Cyphopthalmi (Arachnida: Opiliones: Pettalidae) from Table Mountain, South Africa}, journal = {The Journal of Arachnology}, volume = {41}, year = {2013}, pages = {416-419}, author = {Giribet, G. and de Bivort. BL and Hitchcock. A and Swart. P} } @article {748121, title = {Stable phylogenetic patterns in scuigeromorph centipedes (Myriapoda : Chilopda : Scutigeromorpha): dating the diversification of an ancient lineage of terrestrial arthropods}, journal = {Invertebrate Systematics}, volume = {27}, year = {2013}, pages = {485-501}, author = {Giribet, G. and Edgecombe. GD} } @article {640831, title = {Distal-less and dachshund pattern both plesiomorphic and apomorphic structures in chelicerates: RNA interference in the harvestman Phalangium opilio (Opiliones)}, journal = {Evol Dev}, volume = {15}, number = {4}, year = {2013}, note = {

Sharma, Prashant PSchwager, Evelyn EGiribet, GonzaloJockusch, Elizabeth LExtavour, Cassandra GengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2013/07/03 06:00Evol Dev. 2013 Jul-Aug;15(4):228-42. doi: 10.1111/ede.12029. Epub 2013 May 14.

}, month = {Jul-Aug}, pages = {228-42}, abstract = {

The discovery of genetic mechanisms that can transform a morphological structure from a plesiomorphic (=primitive) state to an apomorphic (=derived) one is a cardinal objective of evolutionary developmental biology. However, this objective is often impeded for many lineages of interest by limitations in taxonomic sampling, genomic resources, or functional genetic methods. In order to investigate the evolution of appendage morphology within Chelicerata, the putative sister group of the remaining arthropods, we developed an RNA interference (RNAi) protocol for the harvestman Phalangium opilio. We silenced the leg gap genes Distal-less (Dll) and dachshund (dac) in the harvestman via zygotic injections of double-stranded RNA (dsRNA), and used in situ hybridization to confirm RNAi efficacy. Consistent with the conserved roles of these genes in patterning the proximo-distal axis of arthropod appendages, we observed that embryos injected with Dll dsRNA lacked distal parts of appendages and appendage-like structures, such as the labrum, the chelicerae, the pedipalps, and the walking legs, whereas embryos injected with dac dsRNA lacked the medial podomeres femur and patella in the pedipalps and walking legs. In addition, we detected a role for these genes in patterning structures that do not occur in well-established chelicerate models (spiders and mites). Dll RNAi additionally results in loss of the preoral chamber, which is formed from pedipalpal and leg coxapophyses, and the ocularium, a dorsal outgrowth bearing the eyes. In one case, we observed that an embryo injected with dac dsRNA lacked the proximal segment of the chelicera, a plesiomorphic podomere that expresses dac in wild-type embryos. This may support the hypothesis that loss of the cheliceral dac domain underlies the transition to the two-segmented chelicera of derived arachnids.

}, keywords = {*Gene Expression Regulation, Developmental, *RNA Interference, Animals, Cloning, Molecular, Evolution, Molecular, Genetic Markers, Homeodomain Proteins/genetics/*physiology, In Situ Hybridization, Phenotype, Phylogeny, RNA, Double-Stranded/genetics, Spiders/*genetics, Transcription Factors/genetics/*physiology}, isbn = {1525-142X (Electronic)1520-541X (Linking)}, author = {Sharma, P. P. and Schwager, E. E. and Giribet, G. and Jockusch, E. L. and Extavour, C. G.} } @article {640431, title = {Elongation factor-1alpha, a putative single-copy nuclear gene, has divergent sets of paralogs in an arachnid}, journal = {Mol Phylogenet Evol}, volume = {68}, number = {3}, year = {2013}, note = {

Clouse, Ronald MSharma, Prashant PGiribet, GonzaloWheeler, Ward CengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2013/05/15 06:00Mol Phylogenet Evol. 2013 Sep;68(3):471-81. doi: 10.1016/j.ympev.2013.04.025. Epub 2013 May 10.

}, month = {Sep}, pages = {471-81}, abstract = {

Identification of paralogy in candidate nuclear loci is an important prerequisite in phylogenetics and statistical phylogeography, but one that is often overlooked. One marker commonly assumed to be a single-copy gene and claimed to harbor great utility for inferring recent divergences is elongation factor-1alpha (EF-1alpha). To test this hypothesis, we systematically cloned EF-1alpha in three disjunct populations of the harvestman Metasiro americanus. Here we show that EF-1alpha has a large number of paralogs in this species. The paralogs do not evolve in a concerted manner, and the paralogs diverged prior to the population divergence. Moreover, the paralogs of M. americanus are not comparable to the highly divergent EF-1alpha paralogs found in bees and spiders, which are easily recognized and separated through the use of specific primers. We demonstrate statistically that our detection of paralogs cannot be attributed to amplification error. The presence of EF-1alpha paralogs in M. americanus prevents its use in statistical phylogeography, and the presence of out-paralogs argues against its use in phylogenetic inference among recently diverged clades. These data contradict the common assumption that EF-1alpha is for most or all taxa a single-copy gene, or that it has a small number of paralogs that are homogenized through gene conversion, unequal crossing over, or other processes.

}, keywords = {*Gene Dosage, *Gene Duplication, Animals, Arachnida/*genetics, Cloning, Molecular, Evolution, Molecular, Gene Conversion, Genetic Variation, Molecular Sequence Data, Peptide Elongation Factor 1/*genetics, Phylogeny, Sequence Analysis, DNA}, isbn = {1095-9513 (Electronic)1055-7903 (Linking)}, author = {Clouse, R.M. and Sharma, P. P. and Giribet, G. and W.C. Wheeler} } @article {640696, title = {Forest refugia in Western and Central Africa as {\textquoteright}museums{\textquoteright} of Mesozoic biodiversity}, journal = {Biol Lett}, volume = {9}, number = {1}, year = {2013}, note = {

Murienne, JeromeBenavides, Ligia RPrendini, LorenzoHormiga, GustavoGiribet, GonzaloengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.England2012/11/30 06:00Biol Lett. 2013 Feb 23;9(1):20120932. doi: 10.1098/rsbl.2012.0932.

}, month = {Feb 23}, pages = {20120932}, abstract = {

The refugial speciation model, or {\textquoteright}species pump{\textquoteright}, is widely accepted in the context of tropical biogeography and has been advocated as an explanation for present species distributions in tropical Western and Central Africa. In order to test this hypothesis, a phylogeny of the cryptic arachnid order Ricinulei, based on four nuclear and mitochondrial DNA markers, was inferred. This ancient clade of litter-dwelling arthropods, endemic to the primary forests of Western and Central Africa and the Neotropics, might provide insights into the mode and tempo of evolution in Africa. Twenty-six African ricinuleid specimens were sampled from eight countries spanning the distribution of Ricinulei on the continent, and analysed together with Neotropical samples plus other arachnid outgroups. The phylogenetic and molecular dating results suggest that Ricinulei diversified in association with the fragmentation of Gondwana. The early diversification of Ricinoides in Western and Central Africa around 88 (+/-33) Ma fits old palaeogeographical events better than recent climatic fluctuations. Unlike most recent molecular studies, these results agree with fossil evidence, suggesting that refugia may have acted as {\textquoteright}museums{\textquoteright} conserving ancient diversity rather than as engines generating diversity during successive episodes of climatic fluctuation in Africa.

}, keywords = {*Biological Evolution, *Ecosystem, Africa, Central, Africa, Western, Animals, Arachnida/*genetics, Biodiversity, Molecular Sequence Data, Phylogeny, Sequence Analysis, DNA, Sequence Homology}, isbn = {1744-957X (Electronic)1744-9561 (Linking)}, author = {Murienne, J. and Benavides, L. R. and Prendini, L. and Hormiga, G. and Giribet, G.} } @article {640836, title = {Into the deep: a phylogenetic approach to the bivalve subclass Protobranchia}, journal = {Mol Phylogenet Evol}, volume = {69}, number = {1}, year = {2013}, note = {

Sharma, Prashant PZardus, John DBoyle, Elizabeth EGonzalez, Vanessa LJennings, Robert MMcIntyre, ErinWheeler, Ward CEtter, Ron JGiribet, GonzaloengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2013/06/08 06:00Mol Phylogenet Evol. 2013 Oct;69(1):188-204. doi: 10.1016/j.ympev.2013.05.018. Epub 2013 Jun 4.

}, month = {Oct}, pages = {188-204}, abstract = {

A molecular phylogeny of Protobranchia, the subclass of bivalve mollusks sister to the remaining Bivalvia, has long proven elusive, because many constituent lineages are deep-sea endemics, which creates methodological challenges for collecting and preserving genetic material. We obtained 74 representatives of all 12 extant protobranch families and investigated the internal phylogeny of this group using sequence data from five molecular loci (16S rRNA, 18S rRNA, 28S rRNA, cytochrome c oxidase subunit I, and histone H3). Model-based and dynamic homology parsimony approaches to phylogenetic reconstruction unanimously supported four major clades of Protobranchia, irrespective of treatment of hypervariable regions in the nuclear ribosomal genes 18S rRNA and 28S rRNA. These four clades correspond to the superfamilies Nuculoidea (excluding Sareptidae), Nuculanoidea (including Sareptidae), Solemyoidea, and Manzanelloidea. Salient aspects of the phylogeny include (1) support for the placement of the family Sareptidae with Nuculanoidea; (2) the non-monophyly of the order Solemyida (Solemyidae+Nucinellidae); (3) and the non-monophyly of most nuculoid and nuculanoid genera and families. In light of this first family-level phylogeny of Protobranchia, we present a revised classification of the group. Estimation of divergence times in concert with analyses of diversification rates demonstrate the signature of the end-Permian mass extinction in the phylogeny of extant protobranchs.

}, keywords = {*Genetic Speciation, *Phylogeny, Algorithms, Animals, Bivalvia, Bivalvia/*classification/genetics, Electron Transport Complex IV/*classification/genetics, End-Permian, extinction, Extinction, Biological, Genetic Variation, Histones/*classification/genetics, Likelihood Functions, Models, Genetic, molecular phylogeny, Mollusca, Oceans and Seas, Protobranch gill, RNA, Ribosomal/*classification/genetics, Sequence Analysis, DNA, Tree alignment problem}, isbn = {1095-9513 (Electronic)1055-7903 (Linking)}, author = {Sharma, P. P. and Zardus, J. D. and Boyle, E. E. and Gonzalez, V. L. and Jennings, R. M. and E. McIntyre and W.C. Wheeler and Etter, R. J. and Giribet, G.} } @article {640746, title = {A NGS approach to the encrusting Mediterranean sponge Crella elegans (Porifera, Demospongiae, Poecilosclerida): transcriptome sequencing, characterization and overview of the gene expression along three life cycle stages}, journal = {Mol Ecol Resour}, volume = {13}, number = {3}, year = {2013}, note = {

Perez-Porro, A RNavarro-Gomez, DUriz, M JGiribet, GengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.England2013/02/27 06:00Mol Ecol Resour. 2013 May;13(3):494-509. doi: 10.1111/1755-0998.12085. Epub 2013 Feb 26.

}, month = {May}, pages = {494-509}, abstract = {

Sponges can be dominant organisms in many marine and freshwater habitats where they play essential ecological roles. They also represent a key group to address important questions in early metazoan evolution. Recent approaches for improving knowledge on sponge biological and ecological functions as well as on animal evolution have focused on the genetic toolkits involved in ecological responses to environmental changes (biotic and abiotic), development and reproduction. These approaches are possible thanks to newly available, massive sequencing technologies-such as the Illumina platform, which facilitate genome and transcriptome sequencing in a cost-effective manner. Here we present the first NGS (next-generation sequencing) approach to understanding the life cycle of an encrusting marine sponge. For this we sequenced libraries of three different life cycle stages of the Mediterranean sponge Crella elegans and generated de novo transcriptome assemblies. Three assemblies were based on sponge tissue of a particular life cycle stage, including non-reproductive tissue, tissue with sperm cysts and tissue with larvae. The fourth assembly pooled the data from all three stages. By aggregating data from all the different life cycle stages we obtained a higher total number of contigs, contigs with blast hit and annotated contigs than from one stage-based assemblies. In that multi-stage assembly we obtained a larger number of the developmental regulatory genes known for metazoans than in any other assembly. We also advance the differential expression of selected genes in the three life cycle stages to explore the potential of RNA-seq for improving knowledge on functional processes along the sponge life cycle.

}, keywords = {Animals, Base Sequence, Computational Biology, Gene Expression Profiling, Gene Expression Regulation, Developmental/*genetics, High-Throughput Nucleotide Sequencing, Life Cycle Stages/*genetics, Molecular Sequence Annotation, Molecular Sequence Data, Porifera/*genetics/growth \& development, Spectrophotometry, Ultraviolet}, isbn = {1755-0998 (Electronic)1755-098X (Linking)}, author = {Perez-Porro, A. R. and Navarro-Gomez, D. and Uriz, M. J. and Giribet, G.} } @article {640726, title = {Pheromone evolution, reproductive genes, and comparative transcriptomics in mediterranean earthworms (annelida, oligochaeta, hormogastridae)}, journal = {Mol Biol Evol}, volume = {30}, number = {7}, year = {2013}, note = {

Novo, MartaRiesgo, AnaFernandez-Guerra, AntoniGiribet, GonzaloengResearch Support, Non-U.S. Gov{\textquoteright}t2013/04/19 06:00Mol Biol Evol. 2013 Jul;30(7):1614-29. doi: 10.1093/molbev/mst074. Epub 2013 Apr 16.

}, month = {Jul}, pages = {1614-29}, abstract = {

Animals inhabiting cryptic environments are often subjected to morphological stasis due to the lack of obvious agents driving selection, and hence chemical cues may be important drivers of sexual selection and individual recognition. Here, we provide a comparative analysis of de novo-assembled transcriptomes in two Mediterranean earthworm species with the objective to detect pheromone proteins and other reproductive genes that could be involved in cryptic speciation processes, as recently characterized in other earthworm species. cDNA libraries of unspecific tissue of Hormogaster samnitica and three different tissues of H. elisae were sequenced in an Illumina Genome Analyzer II or Hi-Seq. Two pheromones, Attractin and Temptin were detected in all tissue samples and both species. Attractin resulted in a reliable marker for phylogenetic inference. Temptin contained multiple paralogs and was slightly overexpressed in the digestive tissue, suggesting that these pheromones could be released with the casts. Genes involved in sexual determination and fertilization were highly expressed in reproductive tissue. This is thus the first detailed analysis of the molecular machinery of sexual reproduction in earthworms.

}, keywords = {*Evolution, Molecular, Animals, Annelida, Annelida/genetics/physiology, earthworm, Gene Expression Profiling, Gene Library, Oligochaeta/*genetics/physiology, pheromones, Pheromones/*genetics/physiology, Phylogeny, Reproduction/*genetics, reproductive genes, Sequence Alignment, transcriptomes}, isbn = {1537-1719 (Electronic)0737-4038 (Linking)}, author = {Novo, M. and Riesgo, A. and Fernandez-Guerra, A. and Giribet, G.} } @article {748811, title = {A comprehensive molecular phylogeny of tardigrades-adding genes and taxa to a poorly resolved phylum-level phylogeny}, journal = {Cladistics}, volume = {28}, year = {2012}, note = {

doi:10.1111/j.1096-0031.2011.00364.x

}, pages = {21-49}, author = {N. Guil and Giribet. G} } @article {748631, title = {An equisitely preserved harvestman (Arthropoda, Arachnida, Opiliones) from the Middle Jurassic of China}, journal = {Organisms, Diversity and Evolution}, volume = {12}, year = {2012}, note = {

doi:10.1007/s13127-011-0067-x

}, pages = {51-56}, author = {Giribet, G. and Tourinho. AL and Shih. C and Ren. D} } @article {748931, title = {Evolution of blindness in scolopendromorph centipedes (Chilopoda: Scolopendromorpha): insight from an expanded sampling of molecular data}, journal = {Cladistics}, volume = {28}, year = {2012}, note = {

doi: 10.1111/j.1096-0031.2011.00361.x

}, pages = {4-20}, author = {V. Vahtera and Edgecombe. GD and Giribet. G} } @article {748881, title = {Evolution of the chelicerae: a dachshund domain is retained in the deutocerebral appendage of Opiliones (Arthropoda, Chelicerata)}, journal = {Evolution \& Development}, volume = {14}, year = {2012}, note = {

doi: 10.1111/ede.12005

}, pages = {522-533}, author = {PP. Sharma and Schwager. EE and Extavour. CG and Giribet. G} } @article {748626, title = {Evolutionary and biogeographical history of an ancient and global group of arachnids (Arachnida: Opiliones: Cyphophthalmi) with a new taxonomic arrangement}, journal = {Biological Journal of the Linnean Society}, volume = {105}, year = {2012}, pages = {92-130}, author = {Giribet, G. and Sharma. PP and Benavides. LR and Boyer. SL and Clouse. RM and de Bivort. BL and Dimitrov. D and Kawauchi. GY and Murienne. JY and Schwendinger. PJ} } @article {748926, title = {First cytogenetic study of a member of the harvestman family Pettalidae (Opiliones: Cyphophtalmi)}, journal = {Australian Journal of Entomology}, volume = {51}, year = {2012}, note = {

doi: 10.1111/j.1440-6055.2012.00870.x

}, pages = {299-302}, author = {F. Stahalavsky and Boyer. SL and Harvey. MS and Giribet. G} } @article {748831, title = {Forgotten gods: Zalmoxidae of the Philippines and Borneo (Opiliones: Laniatores)}, journal = {Zootaxa}, volume = {3280}, year = {2012}, pages = {29-55}, author = {PP. Sharma and Buenavente. PAC and Clouse. RM and Diesmos. AC and Giribet. G} } @article {748636, title = {A new cryptic species of bivalve from the Gulf of California (Mollusca, Bivalvia, Archiheterodonta, Carditidae)}, journal = {Malacologia}, volume = {55}, year = {2012}, author = {VL. Gonzalez and Giribet. G} } @article {748826, title = {A place for nourishment or a slaughterhouse? Elucidating the role of spermathecae in ther terrestrial annelid Hormogaster elisae (Clitellata: Opisthopora: Hormogastridae)}, journal = {Zoomorphology}, volume = {131}, year = {2012}, note = {

doi:10.1007/s00435-012-0151-6

}, pages = {171-184}, author = {Novo, M. and Riesgo. A and Roldan. C and Giribet. G and Diaz Cosin. DJ} } @article {748641, title = {Population structure and connectivity in the Atlantic scleractinian coral Montastraea cavernosa (Linnaeus, 1767)}, journal = {Marine Ecology}, volume = {33}, year = {2012}, note = {

doi:10.1111/j.1439-0485.2011.00452.x

}, pages = {32-48}, author = {G. Goodbody-Gringley and Woollacott. RM and Giribet. G} } @article {748621, title = {A scolopocryptopid centipede (Chilopoda: Scolopendromorpha) from Mexican amber: synchrotron microtomography and phylogenetic placement using a combined morphological and molecular dataset}, journal = {Zoological Journal of the Linnean Society}, volume = {166}, year = {2012}, pages = {768-786}, author = {Edgecombe, GD. and Vahtera. V and Stock. SR and Kallonen. A and Xioa. X and Rack. A and Giribet. G} } @article {748821, title = {Sipunculan phylogeny based on six genes, with a new classification and the description of two new families}, journal = {Zoologica Scripta}, volume = {41}, year = {2012}, note = {

doi:10.1111/j.1463-6409.2011.00507.x

}, pages = {186-210}, author = {GY. Kawauchi and Sharma. PP and Giribet. G} } @article {748991, title = {Spiracle structure in scolopendromorph centipedes (Chilopoda: Scolopendromorpha) and its contribution to phylogenetics}, journal = {Zoomorphology}, volume = {131}, year = {2012}, note = {

doi: 10.1007/s00435-012-0157-0

}, pages = {225-248}, author = {V. Vahtera and Edgecombe. GD and Giribet. G} } @article {748181, title = {A cladistic reconstruction of the ancestral mite harvestman (Arachnida, Opiliones, Cyphophthalmi): portrait of a Paleozoic detritivore}, journal = {Cladistics}, volume = {28}, year = {2012}, note = {

doi:10.111/j.1096-0031.2012.00407.x

}, pages = {582-597}, author = {D. Dimitrov and Lopardo. L and Giribet. G} } @article {748171, title = {On the Cyphophthalmi (Arachnida, Opiliones) types from the Museo Civico di Storia Naturale "Giacomo Doria"}, journal = {Bulletin of the Museum of Comparative Zoology}, volume = {160(5)}, year = {2012}, pages = {241-257}, author = {RM. Clouse and Giribet. G} } @article {748166, title = {Disentangling ribbon worm relationships: multi-locus analysis supports traditional classification of the phylum Nemertea}, journal = {Cladistics}, volume = {28}, year = {2012}, note = {

doi:10.1111/j.1096-0031.2011.00376

}, pages = {141-159}, author = {Andrade, SCS. and Strand, M. and M. Schwartz and Chen. H and Kajihara. H and von Dohren. J and Sun. S and Junoy. J and Theil. M and Norenburg. JL and Turbeville. JM and Giribet. G and Sundberg. P} } @article {748186, title = {Tangled in a sparse spider web: single origin of orb weavers and their spinning work unraveled by denser taxonomic sampling}, journal = {Proceedings of the Royal Society B}, volume = {279}, year = {2012}, note = {

doi:10.1098/rspb.2011.2011

}, pages = {1341-1350}, author = {D. Dimitrov and Lopardo. L and Giribet. G and Arnedo. MA and Alvarez-Padilla. F and Hormiga. G} } @article {748161, title = {Testing relationships among the vetigastropod taxa: A molecular approach.}, journal = {Journal of Molluscan Studies }, volume = {78}, year = {2012}, note = {

doi:10.1093/mollus/eyr023

}, pages = {12-27}, author = {SW. Aktipis and Giribet. G} } @article {640866, title = {An anatomical description of a miniaturized acorn worm (hemichordata, enteropneusta) with asexual reproduction by paratomy}, journal = {PLoS One}, volume = {7}, number = {11}, year = {2012}, note = {

Worsaae, KatrineSterrer, WolfgangKaul-Strehlow, SabrinaHay-Schmidt, AndersGiribet, GonzaloengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2012/11/13 06:00PLoS One. 2012;7(11):e48529. doi: 10.1371/journal.pone.0048529. Epub 2012 Nov 7.

}, pages = {e48529}, abstract = {

The interstitial environment of marine sandy bottoms is a nutrient-rich, sheltered habitat whilst at the same time also often a turbulent, space-limited, and ecologically challenging environment dominated by meiofauna. The interstitial fauna is one of the most diverse on earth and accommodates miniaturized representatives from many macrofaunal groups as well as several exclusively meiofaunal phyla. The colonization process of this environment, with the restrictions imposed by limited space and low Reynolds numbers, has selected for great morphological and behavioral changes as well as new life history strategies.Here we describe a new enteropneust species inhabiting the interstices among sand grains in shallow tropical waters of the West Atlantic. With a maximum body length of 0.6 mm, it is the first microscopic adult enteropneust known, a group otherwise ranging from 2 cm to 250 cm in adult size. Asexual reproduction by paratomy has been observed in this new species, a reproductive mode not previously reported among enteropneusts. Morphologically, Meioglossus psammophilus gen. et sp. nov. shows closest resemblance to an early juvenile stage of the acorn worm family Harrimaniidae, a result congruent with its phylogenetic placement based on molecular data. Its position, clearly nested within the larger macrofaunal hemichordates, suggests that this represents an extreme case of miniaturization. The evolutionary pathway to this simple or juvenile appearance, as chiefly demonstrated by its small size, dense ciliation, and single pair of gill pores, may be explained by progenesis. The finding of M. psammophilus gen. et sp. nov. underscores the notion that meiofauna may constitute a rich source of undiscovered metazoan diversity, possibly disguised as juveniles of other species.

}, keywords = {Animals, Base Sequence, Body Size/*physiology, Female, Helminths/*anatomy \& histology/classification/*physiology/ultrastructure, Likelihood Functions, Male, Phylogeny, Reproduction, Asexual, RNA, Ribosomal, 18S/genetics}, isbn = {1932-6203 (Electronic)1932-6203 (Linking)}, author = {Worsaae, K. and Sterrer, W. and Kaul-Strehlow, S. and Hay-Schmidt, A. and Giribet, G.} } @article {640721, title = {Appearances can be deceptive: different diversification patterns within a group of Mediterranean earthworms (Oligochaeta, Hormogastridae)}, journal = {Mol Ecol}, volume = {21}, number = {15}, year = {2012}, note = {

Novo, MartaAlmodovar, AnaFernandez, RosaTrigo, DoloresDiaz-Cosin, Dario JGiribet, GonzaloengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.England2012/07/19 06:00Mol Ecol. 2012 Aug;21(15):3776-93. doi: 10.1111/j.1365-294X.2012.05648.x.

}, month = {Aug}, pages = {3776-93}, abstract = {

Many recent studies on invertebrates have shown how morphology not always captures the true diversity of taxa, with cryptic speciation often being discussed in this context. Here, we show how diversification patterns can be very different in two clades of closely related earthworms in the genus Hormogaster stressing the risk of using nonspecific substitution rate values across taxa. On the one hand, the Hormogaster elisae species complex, endemic to the central Iberian Peninsula, shows morphological stasis. On the other hand, a clade of Hormogaster from the NE Iberian Peninsula shows an enormous morphological variability, with 15 described morphospecies. The H. elisae complex, however, evolves faster genetically, and this could be explained by the harsher environmental conditions to which it is confined-as detected in this study, that is, sandier and slightly poorer soils with lower pH values than those of the other species in the family. These extreme conditions could be at the same time limiting morphological evolution and thus be responsible for the observed morphological stasis in this clade. Contrarily, Hormogaster species from the NE Iberian Peninsula, although still inhabiting harsher milieu than other earthworm groups, have had the opportunity to evolve into a greater morphological disparity. An attempt to delimit species within this group following the recently proposed general mixed Yule-coalescent method showed a higher number of entities than expected under the morphospecies concept, most probably due to the low vagility of these animals, which considerably limits gene flow between distant conspecific populations, but also because of the decoupling between morphological and genetic evolution in the H. elisae complex.

}, keywords = {*Environment, *Genetic Speciation, *Genetic Variation, Animals, France, Italy, Molecular Sequence Data, Oligochaeta/anatomy \& histology/*classification/genetics, Phylogeny, Principal Component Analysis, Sequence Analysis, DNA, Soil, Spain}, isbn = {1365-294X (Electronic)0962-1083 (Linking)}, author = {Novo, M. and Almodovar, A. and Fernandez, R. and Trigo, D. and Diaz-Cosin, D. J. and Giribet, G.} } @article {640856, title = {Biogeography in a continental island: population structure of the relict endemic centipede Craterostigmus tasmanianus (Chilopoda, Craterostigmomorpha) in Tasmania using 16S rRNA and COI}, journal = {J Hered}, volume = {103}, number = {1}, year = {2012}, note = {

Velez, SebastianMesibov, RobertGiribet, GonzaloengResearch Support, Non-U.S. Gov{\textquoteright}t2011/11/08 06:00J Hered. 2012 Jan-Feb;103(1):80-91. doi: 10.1093/jhered/esr110. Epub 2011 Nov 3.

}, month = {Jan-Feb}, pages = {80-91}, abstract = {

We used 16S ribosomal RNA (rRNA) and cytochrome c oxidase subunit I (COI) sequence data to investigate the population structure in the centipede Craterostigmus tasmanianus Pocock, 1902 (Chilopoda: Craterostigmomorpha: Craterostigmidae) and to look for possible barriers to gene flow on the island of Tasmania, where C. tasmanianus is a widespread endemic. We first confirmed a molecular diagnostic character in 28S rRNA separating Tasmanian Craterostigmus from its sister species Craterostigmus crabilli (Edgecombe and Giribet 2008) in New Zealand and found no shared polymorphism in this marker for the 2 species. In Tasmania, analysis of molecular variance analysis showed little variation at the 16S rRNA and COI loci within populations (6\% and 13\%, respectively), but substantial variation (56\% and 48\%, respectively) among populations divided geographically into groups. We found no clear evidence of isolation by distance using a Mantel test. Bayesian clustering and gene network analysis both group the C. tasmanianus populations in patterns which are broadly concordant with previously known biogeographical divisions within Tasmania, but we did not find that genetic distance varied in a simple way across cluster boundaries. The coarse-scale geographical sampling on which this study was based should be followed in the future by sampling at a finer spatial scale and to investigate genetic structure within clusters and across cluster boundaries.

}, keywords = {Animals, Arthropods/*genetics, Bayes Theorem, Cluster Analysis, Electron Transport Complex IV/*genetics, Gene Flow, Genetic Variation, Multivariate Analysis, Phylogeny, phylogeography, RNA, Ribosomal, 16S/*genetics, RNA, Ribosomal, 28S/genetics, Sequence Analysis, DNA, Tasmania}, isbn = {1465-7333 (Electronic)0022-1503 (Linking)}, author = {Velez, S. and Mesibov, R. and Giribet, G.} } @article {640751, title = {Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa}, journal = {Front Zool}, volume = {9}, number = {1}, year = {2012}, note = {

Riesgo, AnaAndrade, Sonia C SSharma, Prashant PNovo, MartaPerez-Porro, Alicia RVahtera, VarpuGonzalez, Vanessa LKawauchi, Gisele YGiribet, GonzaloengEngland2012/11/30 06:00Front Zool. 2012 Nov 29;9(1):33. doi: 10.1186/1742-9994-9-33.

}, pages = {33}, abstract = {

INTRODUCTION: Traditionally, genomic or transcriptomic data have been restricted to a few model or emerging model organisms, and to a handful of species of medical and/or environmental importance. Next-generation sequencing techniques have the capability of yielding massive amounts of gene sequence data for virtually any species at a modest cost. Here we provide a comparative analysis of de novo assembled transcriptomic data for ten non-model species of previously understudied animal taxa. RESULTS: cDNA libraries of ten species belonging to five animal phyla (2 Annelida [including Sipuncula], 2 Arthropoda, 2 Mollusca, 2 Nemertea, and 2 Porifera) were sequenced in different batches with an Illumina Genome Analyzer II (read length 100 or 150 bp), rendering between ca. 25 and 52 million reads per species. Read thinning, trimming, and de novo assembly were performed under different parameters to optimize output. Between 67,423 and 207,559 contigs were obtained across the ten species, post-optimization. Of those, 9,069 to 25,681 contigs retrieved blast hits against the NCBI non-redundant database, and approximately 50\% of these were assigned with Gene Ontology terms, covering all major categories, and with similar percentages in all species. Local blasts against our datasets, using selected genes from major signaling pathways and housekeeping genes, revealed high efficiency in gene recovery compared to available genomes of closely related species. Intriguingly, our transcriptomic datasets detected multiple paralogues in all phyla and in nearly all gene pathways, including housekeeping genes that are traditionally used in phylogenetic applications for their purported single-copy nature. CONCLUSIONS: We generated the first study of comparative transcriptomics across multiple animal phyla (comparing two species per phylum in most cases), established the first Illumina-based transcriptomic datasets for sponge, nemertean, and sipunculan species, and generated a tractable catalogue of annotated genes (or gene fragments) and protein families for ten newly sequenced non-model organisms, some of commercial importance (i.e., Octopus vulgaris). These comprehensive sets of genes can be readily used for phylogenetic analysis, gene expression profiling, developmental analysis, and can also be a powerful resource for gene discovery. The characterization of the transcriptomes of such a diverse array of animal species permitted the comparison of sequencing depth, functional annotation, and efficiency of genomic sampling using the same pipelines, which proved to be similar for all considered species. In addition, the datasets revealed their potential as a resource for paralogue detection, a recurrent concern in various aspects of biological inquiry, including phylogenetics, molecular evolution, development, and cellular biochemistry.

}, isbn = {1742-9994 (Electronic)1742-9994 (Linking)}, author = {Riesgo, A. and Andrade, S. C. and Sharma, P. P. and Novo, M. and Perez-Porro, A. R. and Vahtera, V. and Gonzalez, V. L. and Kawauchi, G. Y. and Giribet, G.} } @article {640821, title = {Evolution of the chelicera: a dachshund domain is retained in the deutocerebral appendage of Opiliones (Arthropoda, Chelicerata)}, journal = {Evol Dev}, volume = {14}, number = {6}, year = {2012}, note = {

Sharma, Prashant PSchwager, Evelyn EExtavour, Cassandra GGiribet, GonzaloengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2012/11/09 06:00Evol Dev. 2012 Nov-Dec;14(6):522-33. doi: 10.1111/ede.12005.

}, month = {Nov-Dec}, pages = {522-33}, abstract = {

The proximo-distal axis of the arthropod leg is patterned by mutually antagonistic developmental expression domains of the genes extradenticle, homothorax, dachshund, and Distal-less. In the deutocerebral appendages (the antennae) of insects and crustaceans, the expression domain of dachshund is frequently either absent or, if present, is not required to pattern medial segments. By contrast, the dachshund domain is entirely absent in the deutocerebral appendages of spiders, the chelicerae. It is unknown whether absence of dachshund expression in the spider chelicera is associated with the two-segmented morphology of this appendage, or whether all chelicerates lack the dachshund domain in their chelicerae. We investigated gene expression in the harvestman Phalangium opilio, which bears the plesiomorphic three-segmented chelicera observed in "primitive" chelicerate orders. Consistent with patterns reported in spiders, in the harvestman chelicera homothorax, extradenticle, and Distal-less have broadly overlapping developmental domains, in contrast with mutually exclusive domains in the legs and pedipalps. However, unlike in spiders, the harvestman chelicera bears a distinct expression domain of dachshund in the proximal segment, the podomere that is putatively lost in derived arachnids. These data suggest that a tripartite proximo-distal domain structure is ancestral to all arthropod appendages, including deutocerebral appendages. As a corollary, these data also provide an intriguing putative genetic mechanism for the diversity of arachnid chelicerae: loss of developmental domains along the proximo-distal axis.

}, keywords = {*Gene Expression Regulation, Developmental, Animals, Arachnida/*embryology/*genetics/metabolism, Arthropod Proteins/genetics, DNA, Complementary, Embryo, Nonmammalian/embryology/metabolism, Extremities/embryology, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction, Sequence Alignment, Sequence Analysis, DNA}, isbn = {1525-142X (Electronic)1520-541X (Linking)}, author = {Sharma, P. P. and Schwager, E. E. and Extavour, C. G. and Giribet, G.} } @article {640826, title = {Hox gene expression in the harvestman Phalangium opilio reveals divergent patterning of the chelicerate opisthosoma}, journal = {Evol Dev}, volume = {14}, number = {5}, year = {2012}, note = {

Sharma, Prashant PSchwager, Evelyn EExtavour, Cassandra GGiribet, GonzaloengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2012/09/06 06:00Evol Dev. 2012 Sep-Oct;14(5):450-63. doi: 10.1111/j.1525-142X.2012.00565.x.

}, month = {Sep-Oct}, pages = {450-63}, abstract = {

Among chelicerates, Hox gene expression has only been investigated in representatives of two arachnid orders to date: Acari (mites and ticks) and Araneae (spiders). Limited data are available for the "primitive" arachnid orders, such as Scorpiones (scorpions) and Opiliones (harvestmen). Here, we present the first data on Hox gene expression in the harvestman Phalangium opilio. Ten Hox genes of this species were obtained from a de novo assembled developmental transcriptome using the Illumina GAII platform. All 10 genes are expressed in characteristic Hox-like expression patterns, and the expression of the anterior and central Hox genes is similar to those of other chelicerates. However, intriguingly, the three posteriormost genes-Ultrabithorax, abdominal-A, and Abdominal-B-share an identical anterior expression boundary in the second opisthosomal segment, and their expression domains extend through the opisthosoma to the posterior growth zone. The overlap in expression domains of the posterior Hox genes is correlated with the absence of opisthosomal organs posterior to the tubular tracheae, which occur on the second opisthosomal segment. Together with the staggered profile of posterior Hox genes in spiders, these data suggest the involvement of abdominal-A and Abdominal-B in the evolution of heteronomous patterning of the chelicerate opisthosoma, providing a mechanism that helps explain the morphological diversity of chelicerates.

}, keywords = {*Genes, Homeobox, *Transcriptome, Animals, Arachnida/classification/embryology/*genetics/metabolism, Biological Evolution, Embryo, Nonmammalian/embryology/metabolism, Homeodomain Proteins/genetics/metabolism, Phylogeny}, isbn = {1525-142X (Electronic)1520-541X (Linking)}, author = {Sharma, P. P. and Schwager, E. E. and Extavour, C. G. and Giribet, G.} } @article {640766, title = {Optimization of preservation and storage time of sponge tissues to obtain quality mRNA for next-generation sequencing}, journal = {Mol Ecol Resour}, volume = {12}, number = {2}, year = {2012}, note = {

Riesgo, AnaPerez-Porro, Alicia RCarmona, SusanaLeys, Sally PGiribet, GonzaloengEvaluation StudiesResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.England2011/12/06 06:00Mol Ecol Resour. 2012 Mar;12(2):312-22. doi: 10.1111/j.1755-0998.2011.03097.x. Epub 2011 Dec 4.

}, month = {Mar}, pages = {312-22}, abstract = {

Transcriptome sequencing with next-generation sequencing technologies has the potential for addressing many long-standing questions about the biology of sponges. Transcriptome sequence quality depends on good cDNA libraries, which requires high-quality mRNA. Standard protocols for preserving and isolating mRNA often require optimization for unusual tissue types. Our aim was assessing the efficiency of two preservation modes, (i) flash freezing with liquid nitrogen (LN(2)) and (ii) immersion in RNAlater, for the recovery of high-quality mRNA from sponge tissues. We also tested whether the long-term storage of samples at -80 degrees C affects the quantity and quality of mRNA. We extracted mRNA from nine sponge species and analysed the quantity and quality (A260/230 and A260/280 ratios) of mRNA according to preservation method, storage time, and taxonomy. The quantity and quality of mRNA depended significantly on the preservation method used (LN(2)) outperforming RNAlater), the sponge species, and the interaction between them. When the preservation was analysed in combination with either storage time or species, the quantity and A260/230 ratio were both significantly higher for LN(2)-preserved samples. Interestingly, individual comparisons for each preservation method over time indicated that both methods performed equally efficiently during the first month, but RNAlater lost efficiency in storage times longer than 2 months compared with flash-frozen samples. In summary, we find that for long-term preservation of samples, flash freezing is the preferred method. If LN(2) is not available, RNAlater can be used, but mRNA extraction during the first month of storage is advised.

}, keywords = {Animals, Porifera/chemistry/*genetics, Preservation, Biological/*methods, RNA, Messenger/chemistry/*genetics, Sequence Analysis, DNA, Time Factors}, isbn = {1755-0998 (Electronic)1755-098X (Linking)}, author = {Riesgo, A. and Perez-Porro, A. R. and Carmona, S. and Leys, S. P. and Giribet, G.} } @article {640801, title = {Out of the Neotropics: Late Cretaceous colonization of Australasia by American arthropods}, journal = {Proc Biol Sci}, volume = {279}, number = {1742}, year = {2012}, note = {

Sharma, Prashant PGiribet, GonzaloengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.England2012/05/26 06:00Proc Biol Sci. 2012 Sep 7;279(1742):3501-9. doi: 10.1098/rspb.2012.0675. Epub 2012 May 23.

}, month = {Sep 7}, pages = {3501-9}, abstract = {

The origins of tropical southwest Pacific diversity are traditionally attributed to southeast Asia or Australia. Oceanic and fragment islands are typically colonized by lineages from adjacent continental margins, resulting in attrition of diversity with distance from the mainland. Here, we show that an exceptional tropical family of harvestmen with a trans-Pacific disjunct distribution has its origin in the Neotropics. We found in a multi-locus phylogenetic analysis that the opilionid family Zalmoxidae, which is distributed in tropical forests on both sides of the Pacific, is a monophyletic entity with basal lineages endemic to Amazonia and Mesoamerica. Indo-Pacific Zalmoxidae constitute a nested clade, indicating a single colonization event. Lineages endemic to putative source regions, including Australia and New Guinea, constitute derived groups. Divergence time estimates and probabilistic ancestral area reconstructions support a Neotropical origin of the group, and a Late Cretaceous (ca 82 Ma) colonization of Australasia out of the Fiji Islands and/or Borneo, which are consistent with a transoceanic dispersal event. Our results suggest that the endemic diversity within traditionally defined zoogeographic boundaries might have more complex evolutionary origins than previously envisioned.

}, keywords = {*Evolution, Molecular, Americas, Animals, Arachnida/*genetics, Asia, Southeastern, Australasia, Bayes Theorem, Cell Nucleus/*genetics, Likelihood Functions, Male, Mitochondria/*genetics, Molecular Sequence Data, phylogeography, Sequence Alignment, Sequence Analysis, DNA}, isbn = {1471-2954 (Electronic)0962-8452 (Linking)}, author = {Sharma, P. P. and Giribet, G.} } @article {640811, title = {Phylogenetic analysis of four nuclear protein-encoding genes largely corroborates the traditional classification of Bivalvia (Mollusca)}, journal = {Mol Phylogenet Evol}, volume = {65}, number = {1}, year = {2012}, note = {

Sharma, Prashant PGonzalez, Vanessa LKawauchi, Gisele YAndrade, Sonia C SGuzman, AlejandraCollins, Timothy MGlover, Emily AHarper, Elizabeth MHealy, John MMikkelsen, Paula MTaylor, John DBieler, RudigerGiribet, GonzaloengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2012/06/05 06:00Mol Phylogenet Evol. 2012 Oct;65(1):64-74. doi: 10.1016/j.ympev.2012.05.025. Epub 2012 Jun 1.

}, month = {Oct}, pages = {64-74}, abstract = {

Revived interest in molluscan phylogeny has resulted in a torrent of molecular sequence data from phylogenetic, mitogenomic, and phylogenomic studies. Despite recent progress, basal relationships of the class Bivalvia remain contentious, owing to conflicting morphological and molecular hypotheses. Marked incongruity of phylogenetic signal in datasets heavily represented by nuclear ribosomal genes versus mitochondrial genes has also impeded consensus on the type of molecular data best suited for investigating bivalve relationships. To arbitrate conflicting phylogenetic hypotheses, we evaluated the utility of four nuclear protein-encoding genes-ATP synthase beta, elongation factor-1alpha, myosin heavy chain type II, and RNA polymerase II-for resolving the basal relationships of Bivalvia. We sampled all five major lineages of bivalves (Archiheterodonta, Euheterodonta [including Anomalodesmata], Palaeoheterodonta, Protobranchia, and Pteriomorphia) and inferred relationships using maximum likelihood and Bayesian approaches. To investigate the robustness of the phylogenetic signal embedded in the data, we implemented additional datasets wherein length variability and/or third codon positions were eliminated. Results obtained include (a) the clade (Nuculanida+Opponobranchia), i.e., the traditionally defined Protobranchia; (b) the monophyly of Pteriomorphia; (c) the clade (Archiheterodonta+Palaeoheterodonta); (d) the monophyly of the traditionally defined Euheterodonta (including Anomalodesmata); and (e) the monophyly of Heteroconchia, i.e., (Palaeoheterodonta+Archiheterodonta+Euheterodonta). The stability of the basal tree topology to dataset manipulation is indicative of signal robustness in these four genes. The inferred tree topology corresponds closely to those obtained by datasets dominated by nuclear ribosomal genes (18S rRNA and 28S rRNA), controverting recent taxonomic actions based solely upon mitochondrial gene phylogenies.

}, keywords = {*Phylogeny, Animals, Bayes Theorem, Bivalvia/*genetics, Likelihood Functions, Mitochondrial Proton-Translocating ATPases/genetics, Myosin Heavy Chains/genetics, Nuclear Proteins/*genetics, Peptide Elongation Factor 1/genetics, RNA Polymerase II/genetics}, isbn = {1095-9513 (Electronic)1055-7903 (Linking)}, author = {Sharma, P. P. and Gonzalez, V. L. and Kawauchi, G. Y. and Andrade, S. C. and Guzman, A. and Collins, T. M. and Glover, E. A. and Harper, E. M. and Healy, J. M. and Mikkelsen, P. M. and Taylor, J. D. and Bieler, R. and Giribet, G.} } @article {640586, title = {Reevaluating the arthropod tree of life}, journal = {Annu Rev Entomol}, volume = {57}, year = {2012}, note = {

Giribet, GonzaloEdgecombe, Gregory DengReview2011/09/14 06:00Annu Rev Entomol. 2012;57:167-86. doi: 10.1146/annurev-ento-120710-100659. Epub 2011 Sep 9.

}, pages = {167-86}, abstract = {

Arthropods are the most diverse group of animals and have been so since the Cambrian radiation. They belong to the protostome clade Ecdysozoa, with Onychophora (velvet worms) as their most likely sister group and tardigrades (water bears) the next closest relative. The arthropod tree of life can be interpreted as a five-taxon network, containing Pycnogonida, Euchelicerata, Myriapoda, Crustacea, and Hexapoda, the last two forming the clade Tetraconata or Pancrustacea. The unrooted relationship of Tetraconata to the three other lineages is well established, but of three possible rooting positions the Mandibulata hypothesis receives the most support. Novel approaches to studying anatomy with noninvasive three-dimensional reconstruction techniques, the application of these techniques to new and old fossils, and the so-called next-generation sequencing techniques are at the forefront of understanding arthropod relationships. Cambrian fossils assigned to the arthropod stem group inform on the origin of arthropod characters from a lobopodian ancestry. Monophyly of Pycnogonida, Euchelicerata, Myriapoda, Tetraconata, and Hexapoda is well supported, but the interrelationships of arachnid orders and the details of crustacean paraphyly with respect to Hexapoda remain the major unsolved phylogenetic problems.

}, keywords = {*Biodiversity, *Phylogeny, Animals, Arthropods/*classification/genetics/growth \& development, developmental biology, Models, Animal}, isbn = {1545-4487 (Electronic)0066-4170 (Linking)}, author = {Giribet, G. and Edgecombe, G. D.} } @article {640436, title = {Tangled in a sparse spider web: single origin of orb weavers and their spinning work unravelled by denser taxonomic sampling}, journal = {Proc Biol Sci}, volume = {279}, number = {1732}, year = {2012}, note = {

Dimitrov, DimitarLopardo, LaraGiribet, GonzaloArnedo, Miquel AAlvarez-Padilla, FernandoHormiga, GustavoengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.England2011/11/04 06:00Proc Biol Sci. 2012 Apr 7;279(1732):1341-50. doi: 10.1098/rspb.2011.2011. Epub 2011 Nov 2.

}, month = {Apr 7}, pages = {1341-50}, abstract = {

In order to study the tempo and the mode of spider orb web evolution and diversification, we conducted a phylogenetic analysis using six genetic markers along with a comprehensive taxon sample. The present analyses are the first to recover the monophyly of orb-weaving spiders based solely on DNA sequence data and an extensive taxon sample. We present the first dated orb weaver phylogeny. Our results suggest that orb weavers appeared by the Middle Triassic and underwent a rapid diversification during the end of the Triassic and Early Jurassic. By the second half of the Jurassic, most of the extant orb-weaving families and web designs were already present. The processes that may have given origin to this diversification of lineages and web architectures are discussed. A combination of biotic factors, such as key innovations in web design and silk composition, as well as abiotic environmental changes, may have played important roles in the diversification of orb weavers. Our analyses also show that increased taxon sampling density in both ingroups and outgroups greatly improves phylogenetic accuracy even when extensive data are missing. This effect is particularly important when addition of character data improves gene overlap.

}, keywords = {*Evolution, Molecular, Animals, Fossils, Genetic Markers, Phylogeny, Silk/genetics/physiology, Spiders/classification/*genetics/*physiology}, isbn = {1471-2954 (Electronic)0962-8452 (Linking)}, author = {Dimitrov, D. and Lopardo, L. and Giribet, G. and Arnedo, M. A. and Alvarez-Padilla, F. and Hormiga, G.} } @article {640386, title = {A time-calibrated molecular phylogeny of the precious corals: reconciling discrepancies in the taxonomic classification and insights into their evolutionary history}, journal = {BMC Evol Biol}, volume = {12}, year = {2012}, note = {

Ardila, Nestor EGiribet, GonzaloSanchez, Juan AengResearch Support, Non-U.S. Gov{\textquoteright}tEngland2012/12/20 06:00BMC Evol Biol. 2012 Dec 18;12:246. doi: 10.1186/1471-2148-12-246.

}, pages = {246}, abstract = {

BACKGROUND: Seamount-associated faunas are often considered highly endemic but isolation and diversification processes leading to such endemism have been poorly documented at those depths. Likewise, species delimitation and phylogenetic studies in deep-sea organisms remain scarce, due to the difficulty in obtaining samples, and sometimes controversial. The phylogenetic relationships within the precious coral family Coralliidae remain largely unexplored and the monophyly of its two constituent genera, Corallium Cuvier and Paracorallium Bayer \& Cairns, has not been resolved. As traditionally recognized, the diversity of colonial forms among the various species correlates with the diversity in shape of their supporting axis, but the phylogenetic significance of these characters remains to be tested. We thus used mitochondrial sequence data to evaluate the monophyly of Corallium and Paracorallium and the species boundaries for nearly all named taxa in the family. Species from across the coralliid range, including material from Antarctica, Hawaii, Japan, New Zealand, Taiwan, Tasmania, the eastern Pacific and the western Atlantic were examined. RESULTS: The concatenated analysis of five mitochondrial regions (COI, 16S rRNA, ND2, and ND3-ND6) recovered two major coralliid clades. One clade is composed of two subgroups, the first including Corallium rubrum, the type species of the genus, together with a small group of Paracorallium species (P. japonicum and P. tortuosum) and C. medea (clade I-A); the other subgroup includes a poorly-resolved assemblage of six Corallium species (C. abyssale, C. ducale, C. imperiale, C. laauense, C. niobe, and C. sulcatum; clade I-B). The second major clade is well resolved and includes species of Corallium and Paracorallium (C. elatius, C. kishinouyei, C. konojoi, C. niveum, C. secundum, Corallium sp., Paracorallium nix, Paracorallium thrinax and Paracorallium spp.). A traditional taxonomic study of this clade delineated 11 morphospecies that were congruent with the general mixed Yule-coalescent (GMYC) model. A multilocus species-tree approach also identified the same two well-supported clades, being Clade I-B more recent in the species tree (18.0-15.9 mya) than in the gene tree (35.2-15.9 mya). In contrast, the diversification times for Clade II were more ancient in the species tree (136.4-41.7 mya) than in the gene tree (66.3-16.9 mya). CONCLUSIONS: Our results provide no support for the taxonomic status of the two currently recognized genera in the family Coralliidae. Given that Paracorallium species were all nested within Corallium, we recognize the coralliid genus Corallium, which includes the type species of the family, and thus consider Paracorallium a junior synonym of Corallium. We propose the use of the genus Hemicorallium Gray for clade I-B (species with long rod sclerites, cylindrical autozooids and smooth axis). Species delimitation in clade I-B remains unclear and the molecular resolution for Coralliidae species is inconsistent in the two main clades. Some species have wide distributions, recent diversification times and low mtDNA divergence whereas other species exhibit narrower allopatric distributions, older diversification times and greater levels of mtDNA resolution.

}, keywords = {*Evolution, Molecular, *Genetic Variation, *Phylogeny, Animals, Anthozoa/anatomy \& histology/classification/*genetics, DNA, Intergenic/genetics, DNA, Mitochondrial/chemistry/genetics, Electron Transport Complex I/genetics, Electron Transport Complex IV/genetics, Hawaii, Japan, Molecular Sequence Data, New Zealand, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Taiwan, Tasmania, Time Factors}, isbn = {1471-2148 (Electronic)1471-2148 (Linking)}, author = {Ardila, N. E. and Giribet, G. and Sanchez, J. A.} } @article {749156, title = {On the amphi-Atlantic Siphonaria pectinata (Linnaeus, 1758) (Gastropoda: Heterobranchia: Siphonariidae): invader from the East or endemic?}, journal = {Journal of Molluscan Studies}, volume = {77}, year = {2011}, pages = {196-201}, author = {GY. Kawauchi and Giribet. G} } @article {749036, title = {Another step towards understanding the slit-limpets (Fissurellidae, Fissurelloidea, Vetigastropoda, Gastropoda): a combined five-gene molecular phylogeny}, journal = {Zoologica Scripta}, volume = {40}, year = {2011}, note = {

doi: 10.1111/j.1463-6409.2010.00468.x

}, pages = {238-259}, author = {SH. Aktipis and Boehm. E and Giribet. G} } @article {749191, title = {Application of magnetic resonance imaging in zoology}, journal = {Zoomorphoology}, volume = {130}, year = {2011}, note = {

doi: 10.1007/s00435-011-0138-8

}, pages = {227-254}, author = {Ziegler, A. and Kunth. M and Mueller. S and Bock. C and Pohmann. R and Schroder. L and Faber. C and Giribet. G} } @article {749166, title = {Comparative phylogeography of the centipedes Cryptops pictus and C. niuensis in New Caledonia, Fiji, and Vanuatu}, journal = {Organisms Diversity \& Evolution}, volume = {11}, year = {2011}, note = {

doi: 10.1007/s13127-011-0041-7

}, pages = {61-74}, author = {Murienne, J. and Edgecombe. GD and Giribet. G} } @article {749151, title = {Shearogovea, a new genus of Cyphiphthalmi (Arachnida, Opiliones) of uncertain position from Oaxacan caves, Mexico}, journal = {Breviora}, volume = {528}, year = {2011}, pages = {1-7}, author = {Giribet, G.} } @article {749171, title = {The evolutionary and biogeographic history of the armoured harvestmen - Laniatores phylogeny based on ten molecular markers, with the description of two new families of Opiliones (Arachnida)}, journal = {Invertebrate Systematics}, volume = {25}, year = {2011}, pages = {538-549}, author = {PP. Sharma and Giribet. G} } @article {749121, title = {Higher-level metazoan relationships: recent progress and remaining questions}, journal = {Organisms, Diversity \& Evolution }, volume = {11}, year = {2011}, note = {

doi:10.1007/s13127-011-0044-4

}, pages = {151-172}, author = {Edgecombe, GD. and Giribet. G and Dunn. CW and Hejnol. A and Kristensen. RM and Neves. RC and Rouse. GW and Worsaae. K and Sorensen. MV} } @article {749046, title = {Letter to the Editor: Phylogenetic signal in morphometric data}, journal = {Cladistics}, volume = {27}, year = {2011}, note = {

doi: 10.1111/j.1096-0031.2010.00346.x

}, pages = {337-340}, author = {RM. Clouse and de Bivort. BL and Giribet. G} } @article {749161, title = {Morphology to the rescue: Molecular data and the signal of morphological characters in combined phylogenetic analyses-a case study from mysmenid spiders (Aranaea, Mysmenudae), with comments on the evolution of web architecture}, journal = {Cladistics}, volume = {27}, year = {2011}, note = {

doi: 10.1111/j.1096-0031.2010.00332.x

}, pages = {287-330}, author = {L. Lopardo and Giribet. G and Hormiga. G} } @article {749181, title = {A new family of Laniatores (Arachnida : Opiliones) from the Afrotropics}, journal = {Invertebrate Systematics}, volume = {25}, year = {2011}, pages = {143-154}, author = {PP. Sharma and Prieto. CE and Giribet. G} } @article {749101, title = {An old lineage of Cyphophthalmi (Opiliones) discovered on Mondanao highlights the need for biogeographical research in the Phillipines}, journal = {The Journal of Arachnology}, volume = {39}, year = {2011}, pages = {147-153}, author = {RM. Clouse and General. DM and Diesmos. AC and Giribet. G} } @article {749186, title = {Running WLD: The case for exploring mixed parameter sets in sensitivity analysis}, journal = {Cladistics}, volume = {27}, year = {2011}, note = {

doi: 10.1111/j.1096-0031.2010.00345.x

}, pages = {538-549}, author = {PP. Sharma and Vahtera. V and Kawauchi. GY and Giribet. G} } @article {749176, title = {The Zalmoxidae (Arachnida: Opiliones: Laniatores) of the Paleotropics: a catalogue of Southeast Asian and Indo-Pacific species}, journal = {Zootaxa}, volume = {2972}, year = {2011}, pages = {37-58}, author = {PP. Sharma and Kury. AB and Giribet. G} } @article {640476, title = {Anatomically modern Carboniferous harvestmen demonstrate early cladogenesis and stasis in Opiliones}, journal = {Nat Commun}, volume = {2}, year = {2011}, note = {

Garwood, Russell JDunlop, Jason AGiribet, GonzaloSutton, Mark DengResearch Support, Non-U.S. Gov{\textquoteright}tEngland2011/08/25 06:00Nat Commun. 2011 Aug 23;2:444. doi: 10.1038/ncomms1458.

}, pages = {444}, abstract = {

Harvestmen, the third most-diverse arachnid order, are an ancient group found on all continental landmasses, except Antarctica. However, a terrestrial mode of life and leathery, poorly mineralized exoskeleton makes preservation unlikely, and their fossil record is limited. The few Palaeozoic species discovered to date appear surprisingly modern, but are too poorly preserved to allow unequivocal taxonomic placement. Here, we use high-resolution X-ray micro-tomography to describe two new harvestmen from the Carboniferous ( approximately 305 Myr) of France. The resulting computer models allow the first phylogenetic analysis of any Palaeozoic Opiliones, explicitly resolving both specimens as members of different extant lineages, and providing corroboration for molecular estimates of an early Palaeozoic radiation within the order. Furthermore, remarkable similarities between these fossils and extant harvestmen implies extensive morphological stasis in the order. Compared with other arachnids--and terrestrial arthropods generally--harvestmen are amongst the first groups to evolve fully modern body plans.

}, keywords = {*Genetic Speciation, Animals, Arachnida/anatomy \& histology/*classification/*genetics, Biological Evolution, Fossils, Phylogeny}, isbn = {2041-1723 (Electronic)2041-1723 (Linking)}, author = {Garwood, R. J. and Dunlop, J. A. and Giribet, G. and Sutton, M. D.} } @article {640841, title = {Resolving the evolutionary relationships of molluscs with phylogenomic tools}, journal = {Nature}, volume = {480}, number = {7377}, year = {2011}, note = {

Smith, Stephen AWilson, Nerida GGoetz, Freya EFeehery, CaitlinAndrade, Sonia C SRouse, Greg WGiribet, GonzaloDunn, Casey WengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.England2011/10/28 06:00Nature. 2011 Oct 26;480(7377):364-7. doi: 10.1038/nature10526.

}, month = {Dec 15}, pages = {364-7}, abstract = {

Molluscs (snails, octopuses, clams and their relatives) have a great disparity of body plans and, among the animals, only arthropods surpass them in species number. This diversity has made Mollusca one of the best-studied groups of animals, yet their evolutionary relationships remain poorly resolved. Open questions have important implications for the origin of Mollusca and for morphological evolution within the group. These questions include whether the shell-less, vermiform aplacophoran molluscs diverged before the origin of the shelled molluscs (Conchifera) or lost their shells secondarily. Monoplacophorans were not included in molecular studies until recently, when it was proposed that they constitute a clade named Serialia together with Polyplacophora (chitons), reflecting the serial repetition of body organs in both groups. Attempts to understand the early evolution of molluscs become even more complex when considering the large diversity of Cambrian fossils. These can have multiple dorsal shell plates and sclerites or can be shell-less but with a typical molluscan radula and serially repeated gills. To better resolve the relationships among molluscs, we generated transcriptome data for 15 species that, in combination with existing data, represent for the first time all major molluscan groups. We analysed multiple data sets containing up to 216,402 sites and 1,185 gene regions using multiple models and methods. Our results support the clade Aculifera, containing the three molluscan groups with spicules but without true shells, and they support the monophyly of Conchifera. Monoplacophora is not the sister group to other Conchifera but to Cephalopoda. Strong support is found for a clade that comprises Scaphopoda (tusk shells), Gastropoda and Bivalvia, with most analyses placing Scaphopoda and Gastropoda as sister groups. This well-resolved tree will constitute a framework for further studies of mollusc evolution, development and anatomy.

}, keywords = {*Phylogeny, Animals, Bivalvia/classification/genetics, Cephalopoda/classification/genetics, Gastropoda/classification/genetics, Gene Expression Profiling, Likelihood Functions, Models, Biological, Mollusca/*classification/*genetics, Species Specificity, Transcriptome/*genetics}, isbn = {1476-4687 (Electronic)0028-0836 (Linking)}, author = {Smith, S. A. and Wilson, N. G. and Goetz, F. E. and Feehery, C. and Andrade, S. C. and Rouse, G. W. and Giribet, G. and Dunn, C. W.} } @article {640716, title = {Understanding the biogeography of a group of earthworms in the Mediterranean basin--the phylogenetic puzzle of Hormogastridae (Clitellata: Oligochaeta)}, journal = {Mol Phylogenet Evol}, volume = {61}, number = {1}, year = {2011}, note = {

Novo, MartaAlmodovar, AnaFernandez, RosaGiribet, GonzaloDiaz Cosin, Dario JengResearch Support, Non-U.S. Gov{\textquoteright}t2011/06/21 06:00Mol Phylogenet Evol. 2011 Oct;61(1):125-35. doi: 10.1016/j.ympev.2011.05.018. Epub 2011 Jun 13.

}, month = {Oct}, pages = {125-35}, abstract = {

Traditional earthworm taxonomy is hindered due to their anatomical simplicity and the plasticity of the characteristics often used for diagnosing species. Making phylogenetic inferences based on these characters is more than difficult. In this study we use molecular tools to unravel the phylogeny of the clitellate family Hormogastridae. The family includes species of large to mid-sized earthworms distributed almost exclusively in the western Mediterranean region where they play an important ecological role. We analyzed individuals from 46 locations spanning the Iberian Peninsula to Corsica and Sardinia, representing the four described genera in the family and 20 species. Molecular markers include mitochondrial regions of the cytochrome c oxidase subunit I gene (COI), 16S rRNA and tRNAs for Leu, Ala, and Ser, two nuclear ribosomal genes (nearly complete 18S rRNA and a fragment of 28S rRNA) and two nuclear protein-encoding genes (histones H3 and H4). Analyses of the data using different approaches corroborates monophyly of Hormogastridae, but the genus Hormogaster is paraphyletic and Hormogaster pretiosa appears polyphyletic, stressing the need for taxonomic revisionary work in the family. The genus Vignysa could represent an early offshoot in the family, although the relationships with other genera are uncertain. The genus Hemigastrodrilus is related to the Hormogaster elisae complex and both are found in the Atlantic drainage of the Iberian Peninsula and France. From a biogeographic perspective Corsica and Sardinia include members of two separate hormogastrid lineages. The species located in Corsica and Northern Sardinia are related to Vignysa, whereas Hormogaster pretiosa pretiosa, from Southern Sardinia, is closely related to the Hormogaster species from the NE Iberian Peninsula. A molecular dating of the tree using the separation of the Sardinian microplate as a calibration point (at 33 MY) and assuming a model of vicariance indicates that the diversification of Hormogastridae may be ancient, ranging from 97 to 67 Ma.

}, keywords = {*Phylogeny, Animals, Base Sequence, Biological Evolution, Biological Markers, DNA, Mitochondrial/genetics, Electron Transport Complex IV/genetics, Evolution, Molecular, Genetic Speciation, Genetic Variation, Geography, Histones/genetics, Mediterranean Sea, Mitochondria/genetics, Molecular Sequence Data, Oligochaeta/*classification/*genetics, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 18S/genetics, RNA, Ribosomal, 28S/genetics, RNA, Transfer, Ala/genetics, RNA, Transfer, Leu/genetics, RNA, Transfer, Ser/genetics, Sequence Alignment, Sequence Analysis, DNA}, isbn = {1095-9513 (Electronic)1055-7903 (Linking)}, author = {Novo, M. and Almodovar, A. and Fernandez, R. and Giribet, G. and Diaz Cosin, D. J.} } @article {749331, title = {Are there true cosmopolitan sipunculan worms? A genetic variation study within Phascolosoma perlucens (Sipuncula, Phascolosomatidae)}, journal = {Marine Biology}, volume = {157}, year = {2010}, pages = {1417-1431}, author = {GY. Kawauchi and Giribet. G} } @article {749271, title = {Brooding in Mecistocephalus togensis (Geophilomorpha: Placodesmata) and the evolution of parental care in centipedes (Chilopoda)}, journal = {International Journal of Myriapodology}, volume = {3}, year = {2010}, pages = {139-144}, author = {Edgecombe, GD. and Bonato. L and Giribet. G} } @article {749246, title = {Canga renatae, a new genus and species of Cyphophthalmi from Brazilian Amazon caves (Opiliones: Neogoveidae)}, journal = {Zootaxa}, volume = {2508}, year = {2010}, pages = {45-55}, author = {MB. DaSilva and Pinto-da-Rocha. R and Giribet. G} } @article {749356, title = {Evolution in the deep sea: a combined analysis of the earliest diverging living chitons (Mollusca : Polyplacophora : Lepidopleurida)}, journal = {Invertebrate Systematics}, volume = {24}, year = {2010}, pages = {560-572}, author = {J. Sigwart and Schwabe. E and Saito. H and Samadi. S and Giribet. G} } @article {749351, title = {Explosive evolution of an ancient group of Cyphophthalmi (Arachnida: Opiliones) in the Balkan Peninsula}, journal = {Journal of Biogeography}, volume = {37}, year = {2010}, note = {

doi: 10.1111/j.1365-2699.2009.02180.x

}, pages = {90-102}, author = {Murienne, J. and Karaman. I and Giribet. G} } @article {749301, title = {The genus Siro Latreille, 1976 (Opiliones, Cyphophthalmi, Sironidae), in North America with a phylogenetic analysis based on molecular data and the description of four new species}, journal = {Bulletin of the Museum of Comparative Zoology}, volume = {160}, year = {2010}, pages = {1-33}, author = {Giribet, G. and Shear. WA} } @article {749321, title = {Limited gene flow in the brooding coral Favia fragum (Esper, 1797)}, journal = {Marine Biology}, volume = {157}, year = {2010}, pages = {2591-2602}, author = {G. Goodbody-Gringley and Vollmer. SV and Woollacott. RM and Giribet. G} } @article {749361, title = {The linguistic problem of morphology: Structure versus homology and the standardization of morphological data}, journal = {Cladistics}, volume = {26}, year = {2010}, pages = {301-325}, author = {L. Vogt and Bartolomaeus. T and Giribet. G} } @article {749296, title = {{\textquoteright}Moa{\textquoteright}s Ark{\textquoteright} or {\textquoteright}Goodbye Gondwana{\textquoteright}: Is the origin of New Zealand{\textquoteright}s terrestrial invertebrate fauna ancient, recent, or both?}, journal = {Invertebrate Systematics}, volume = {24}, year = {2010}, pages = {1-8}, author = {Giribet, G. and Boyer. SL} } @article {749256, title = {A morphometrics-based phylogeny of the temperate Gondwanan mite harvestmen (Opiliones: Cyphophthalmi, Pettalidae)}, journal = {Journal of Zoological Systematics and Evolutionary Research}, volume = {48}, year = {2010}, pages = {294-309}, author = {B. de Bivort and Clouse. RM and Giribet. G} } @article {749316, title = {A multilocus approach to harvestman (Arachinda: Opiliones) phylogeny with emphasis on biogeography and the systematics of Laniatores}, journal = {Cladistics}, volume = {26}, year = {2010}, note = {

doi: 10.111/j.1096-031.2009.00296.x

}, pages = {408-437}, author = {Giribet. G and Vogt. L and Perez Gonzalez. A and Sharma. P and Kury. AB} } @article {749281, title = {A new dimension in combining data? The use of morphology and phylogenomic data in metazoan systematics}, journal = {Acta Zoologica (Stockholm)}, volume = {91}, year = {2010}, pages = {11-19}, author = {Giribet, G.} } @article {749326, title = {Phylogenetic placement of a new hoplonemertean species commensal of ascidians}, journal = {Invertebrate Systematics}, volume = {24}, year = {2010}, note = {

Phy

}, pages = {616-629}, author = {J. Junoy and Andrade. SCS and Giribet. G} } @article {749201, title = {A phylogeny of Vetigastropoda and other "archaeogastropods": re-organizing old gastropod clades}, journal = {Invertebrate Biology}, volume = {129}, year = {2010}, note = {

doi:10.111/j.1744-7410.2010.00198.x

}, pages = {220-240}, author = {SW. Aktipis and Giribet. G} } @article {749236, title = {Report of a cohesive gelatinous egg mass produced by a tropical marine bivalve}, journal = {Invertebrate Biology}, volume = {129}, year = {2010}, pages = {165-171}, author = {R. Collin and Giribet. G} } @article {749211, title = {Resolving the phylogenetic position of enigmatic New Guinea and Seychelles Scutigeromorpha (Chilopoda): a molecular and morphological assessment of Ballonemini}, journal = {Invertebrate Systematics}, volume = {24}, year = {2010}, pages = {539-559}, author = {AD. Butler and Edgecombe. GD and Ball. AD and Giribet. G} } @article {749366, title = {A scanning electron microscopic survey of the cuticle in Cyphophthalmi (Arachnida, Opiliones) with the description of novel sensory and glandular structures}, journal = {Zoomorphology}, volume = {129}, year = {2010}, pages = {175-183}, author = {RH. Willemart and Giribet. G} } @article {749261, title = {A systematic revision of the South African Pettalidae (Arachnida : Opiliones : Cyphophthalmi) based on a combined analysis of discrete and continuous morphological characters with the description of seven new species}, journal = {Invertebrate Systematics}, volume = {24}, year = {2010}, pages = {371-406}, author = {B. de Bivort and Giribet. G} } @article {749221, title = {When Thailand was an island - the phylogeny and biogeography of mite harvestmen (Opiliones, Cyphophthalmi, Stylocellidae) in Southeast Asia}, journal = {Journal of Biogeography}, volume = {37}, year = {2010}, note = {

doi: 10.1111/j.1365-2699.2010.02274.x

}, pages = {1114-1130}, author = {Clouse. RM and Giribet. G} } @article {640861, title = {Assessing the molluscan hypothesis Serialia (Monoplacophora+Polyplacophora) using novel molecular data}, journal = {Mol Phylogenet Evol}, volume = {54}, number = {1}, year = {2010}, note = {

Wilson, Nerida GRouse, Greg WGiribet, GonzaloengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2009/08/04 09:00Mol Phylogenet Evol. 2010 Jan;54(1):187-93. doi: 10.1016/j.ympev.2009.07.028. Epub 2009 Jul 30.

}, month = {Jan}, pages = {187-93}, abstract = {

A consensus on molluscan relationships has yet to be achieved, largely because of conflicting morphological and molecular hypotheses. Monoplacophora show marked seriality of ctenidia, atria, muscles and nephridia and this has been interpreted as plesiomorphic for Mollusca, reflecting a segmented ancestry. More recently this seriality, also partly seen in Polyplacophora, has been seen as a derived condition. Analysis of the first published monoplacophoran DNA sequence from Laevilipilina antarctica Waren \& Hain, 1992 [Giribet, G., Okusu, A., Lindgren, A.R., Huff, S., Schrodl, M., Nishiguchi, M.K., 2006. Evidence for a clade composed of molluscs with serially repeated structures: Monoplacophorans are related to chitons. Proc. Natl. Acad. Sci. USA 103, 7723-7728. 10.1073/pnas.0602578103], showed Monoplacophora inside Polyplacophora. These taxa were then grouped under the name Serialia, reflecting the hypothesis that their seriality is a synapomorphy. Subsequent examination revealed that part of the L. antarctica published sequence was the result of contamination with Polyplacophora (Giribet, Supplementary Material S1). We collected and sequenced another monoplacophoran, Laevipilina hyalina McLean, 1979, resulting in the first multi-gene dataset representing all molluscan classes. Our analyses did not show unambiguous support for Serialia. Model-based approaches strongly supported Serialia as a clade, however, parsimony analyses under dynamic and static homology did not resolve the position of Monoplacophora. Although our study provides support for Serialia and none for Conchifera, it appears that further resolution of molluscan relationships will require large increases of data.

}, keywords = {*Evolution, Molecular, *Phylogeny, Animals, Cell Nucleus/genetics, DNA, Mitochondrial/genetics, Models, Genetic, Mollusca/*classification/genetics, Sequence Alignment, Sequence Analysis, DNA}, isbn = {1095-9513 (Electronic)1055-7903 (Linking)}, author = {Wilson, N. G. and Rouse, G. W. and Giribet, G.} } @article {640706, title = {Including secondary structure, fossils and molecular dating in the centipede tree of life}, journal = {Mol Phylogenet Evol}, volume = {57}, number = {1}, year = {2010}, note = {

Murienne, JeromeEdgecombe, Gregory DGiribet, GonzaloengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2010/07/06 06:00Mol Phylogenet Evol. 2010 Oct;57(1):301-13. doi: 10.1016/j.ympev.2010.06.022. Epub 2010 Jun 30.

}, month = {Oct}, pages = {301-13}, abstract = {

A well-corroborated morphological scheme of interrelationships for centipedes, once broadly accepted, has been in conflict with molecular data with respect to deep branching events. Expanded taxonomic coverage compared to previous analyses adds longer fragments for 28S rRNA and a structural alignment as part of a sample of four genes (two nuclear ribosomal and two mitochondrial) for 111 extant species; these sequence data are combined with morphology under parsimony and maximum likelihood, exploring both traditional multiple sequence alignment and direct optimization approaches. Novel automated procedures to incorporate secondary structure information are also explored. The molecular data in combination yield trees that are highly congruent with morphology as regards the monophyly of all centipede orders as well as the major groups within each of the large orders. Regardless of the optimality criterion or alignment strategy, the Tasmanian/New Zealand Craterostigmomorpha is resolved in a different position by the molecular data than by morphology. Addition of morphology overturns the placement of Craterostigmomorpha in favour of the traditional morphological resolution and eliminates the need to posit major character reversals with respect to developmental mode and maternal care. Calibration of the tree with Palaeozoic and Mesozoic fossils for a relaxed clock analysis corroborates the palaeontological signal that divergences between centipede orders date to the Silurian and earliest Devonian, and familial divergences are likewise almost wholly Palaeozoic.

}, keywords = {*Evolution, Molecular, *Fossils, Animals, Arthropods/anatomy \& histology/classification/*genetics, Likelihood Functions, Nucleic Acid Conformation, Phylogeny, Sequence Alignment, Sequence Analysis, DNA}, isbn = {1095-9513 (Electronic)1055-7903 (Linking)}, author = {Murienne, J. and G.D. Edgecombe and Giribet, G.} } @article {749456, title = {The chemical defenses of a stylocellid (Arachnida, Opiliones, Stylocellidae) from Sulawesi with comparisons to other Cyphophthalmi}, journal = {Arachnol}, volume = {37}, year = {2009}, pages = {147-150}, author = {T. H. Jones and Shear. WA and Giribet. G} } @article {749491, title = {The family Troglosironidae (Opiliones: Cyphophthalmi) of New Caledonia}, journal = {Zoologia Neocaledonica. Biodiversity Studies in New Caledonia}, volume = {7}, year = {2009}, pages = {83-123}, author = {PP. Sharma and Giribet. G} } @article {749451, title = {Further use of molecular data in studying biogeographic patterns within the centipede genus Craterostigmus: the case for a monophyletic New Zealand species}, journal = {Soil Organisms}, volume = {81}, year = {2009}, pages = {557-563}, author = {Giribet, G. and Guzman Cuellar. A and Edgecombe. GD} } @article {749471, title = {The Iberian Peninsula: ancient history of a hot spot of mite harvestmen (Arachnida: Opiliones: Cyphophthalmi: Sironidae) diversity.}, journal = {Zool. J. Linnean Soc.}, volume = {156}, year = {2009}, pages = {785-800}, author = {Murienne, J. and Giribet. G} } @article {749441, title = {Living in the dark - species delimitation based on combined molecular and morphological evidence in the nicoletiid genus Texoreddellia Wygodzinsky, 1973 (Hexapoda: Zygentoma: Nicoletiidae) in Texas and Mexico}, journal = {Texas Memorial Musuem Speleological Monographs}, volume = {7}, year = {2009}, pages = {87-110}, author = {L. Espinasa and Giribet. G} } @article {749406, title = {A phylogenetic analysis for the South-east Asian mite harvestman family Stylocellidae (Opiliones : Cyphophthalmi) - a combined anaylsis using morphometric and molecular data}, journal = {Invertebrate Systematics}, volume = {23}, year = {2009}, pages = {515-529}, author = {RM. Clouse and de Bivort. BL and Giribet. G} } @article {749386, title = {Phylogenetic relationships of the spider family Tetragnathidae (Araneae, Araneoidea) based on morphological and DNA sequence data.}, journal = {Cladistics}, volume = {25}, year = {2009}, pages = {109-146}, author = {F. Alvarez-Padilla and Dimitrov. D and Giribet. G and Hormiga. G} } @article {749421, title = {Phylogenetics of scutigeromorph centipedes (Myriapoda: Chilopoda) with implications for species delimitation and historical biogeography of the Austrlaian and New Caledonian faunas}, journal = {Cladistics}, volume = {25}, year = {2009}, pages = {406-427}, author = {Edgecombe, GD. and Giribet. G} } @article {749381, title = {Ultrastructure of spermatozoa of different species of Neogoveidae, Sironidae, and Stylocellidae (Cyphophthalmi: Opiliones)}, journal = {Contributions to Natural History - Scientific papers from the Natural History Museum Bern}, volume = {12}, year = {2009}, pages = {53-69}, author = {Alberti, G. and Giribet. G and Gutjahr. M} } @article {749396, title = {Welcome back New Zealand: Regional biogeography and Gondwanan origin of three endemic genera of mite harvestmen (Arachnida, Opiliones, Cyphophthalmi)}, journal = {J. Biogegr.}, volume = {36}, year = {2009}, pages = {1084-1099}, author = {SL. Boyer and Giribet. G} } @article {747886, title = {On the endemic Sri Lankan genus Pettalus (Opiliones, Cyphophthalmi, Pettalidae) with the description of a new species and a discussion on the magnitude of its diversity.}, journal = {Journal of Arachnology}, volume = {37}, year = {2009}, pages = {60-67}, author = {Sharma, P. and Karunarathna, I. and Giribet, G.} } @article {747881, title = {Field collection of Laevipilina hyalina McLean, 1979 from southern California, the most accessible living monoplacophoran.}, journal = {Journal of Molluscan Studies}, volume = {75}, year = {2009}, pages = {195-197}, author = {Wilson, N. G. and D Huang and MC Goldstein and H Cha and Giribet, G. and Rouse, G. W.} } @article {747896, title = {A relict in New Caledonia: Phylogenetic relationships of the family Troglosironidae (Opiliones: Cyphophthalmi)}, journal = {Cladistics}, volume = {25}, year = {2009}, pages = {279-294}, author = {Sharma, P. and Giribet, G.} } @article {640646, title = {Assessing the root of bilaterian animals with scalable phylogenomic methods}, journal = {Proc Biol Sci}, volume = {276}, number = {1677}, year = {2009}, note = {

Hejnol, AndreasObst, MatthiasStamatakis, AlexandrosOtt, MichaelRouse, Greg WEdgecombe, Gregory DMartinez, PedroBaguna, JaumeBailly, XavierJondelius, UlfWiens, MatthiasMuller, Werner E GSeaver, ElaineWheeler, Ward CMartindale, Mark QGiribet, GonzaloDunn, Casey WengResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.England2009/09/18 06:00Proc Biol Sci. 2009 Dec 22;276(1677):4261-70. doi: 10.1098/rspb.2009.0896. Epub 2009 Sep 16.

}, month = {Dec 22}, pages = {4261-70}, abstract = {

A clear picture of animal relationships is a prerequisite to understand how the morphological and ecological diversity of animals evolved over time. Among others, the placement of the acoelomorph flatworms, Acoela and Nemertodermatida, has fundamental implications for the origin and evolution of various animal organ systems. Their position, however, has been inconsistent in phylogenetic studies using one or several genes. Furthermore, Acoela has been among the least stable taxa in recent animal phylogenomic analyses, which simultaneously examine many genes from many species, while Nemertodermatida has not been sampled in any phylogenomic study. New sequence data are presented here from organisms targeted for their instability or lack of representation in prior analyses, and are analysed in combination with other publicly available data. We also designed new automated explicit methods for identifying and selecting common genes across different species, and developed highly optimized supercomputing tools to reconstruct relationships from gene sequences. The results of the work corroborate several recently established findings about animal relationships and provide new support for the placement of other groups. These new data and methods strongly uphold previous suggestions that Acoelomorpha is sister clade to all other bilaterian animals, find diminishing evidence for the placement of the enigmatic Xenoturbella within Deuterostomia, and place Cycliophora with Entoprocta and Ectoprocta. The work highlights the implications that these arrangements have for metazoan evolution and permits a clearer picture of ancestral morphologies and life histories in the deep past.

}, keywords = {*Biological Evolution, *Phylogeny, Amino Acid Sequence, Animals, Base Sequence, Computational Biology, Likelihood Functions, Models, Genetic, Molecular Sequence Data, Sequence Analysis, DNA, Sequence Homology, Turbellaria/*classification/*genetics}, isbn = {1471-2954 (Electronic)0962-8452 (Linking)}, author = {Hejnol, A. and Obst, M. and Stamatakis, A. and Ott, M. and Rouse, G. W. and G.D. Edgecombe and Martinez, P. and Baguna, J. and Bailly, X. and Jondelius, U. and Wiens, M. and Muller, W. E. and Seaver, E. and W.C. Wheeler and M.Q. Martindale and Giribet, G. and Dunn, C. W.} } @article {640641, title = {Fine scale population structure in the Echiniscus blumi-canadensis series (Heterotardigrada, Tardigrada) in an Iberian mountain range-When morphology fails to explain genetic structure}, journal = {Mol Phylogenet Evol}, volume = {51}, number = {3}, year = {2009}, note = {

Guil, NoemiGiribet, GonzaloengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2009/03/07 09:00Mol Phylogenet Evol. 2009 Jun;51(3):606-13. doi: 10.1016/j.ympev.2009.02.019. Epub 2009 Mar 3.

}, month = {Jun}, pages = {606-13}, keywords = {*Genetics, Population, *Phylogeny, Animals, DNA, Mitochondrial/genetics, Evolution, Molecular, Genetic Variation, Geography, Haplotypes, Invertebrates/anatomy \& histology/classification/*genetics, Sequence Analysis, DNA, Spain, Species Specificity}, isbn = {1095-9513 (Electronic)1055-7903 (Linking)}, author = {N. Guil and Giribet, G.} } @article {640796, title = {Sandokanid phylogeny based on eight molecular markers--the evolution of a southeast Asian endemic family of Laniatores (Arachnida, Opiliones)}, journal = {Mol Phylogenet Evol}, volume = {52}, number = {2}, year = {2009}, note = {

Sharma, PrashantGiribet, GonzaloengResearch Support, Non-U.S. Gov{\textquoteright}t2009/03/28 09:00Mol Phylogenet Evol. 2009 Aug;52(2):432-47. doi: 10.1016/j.ympev.2009.03.013. Epub 2009 Mar 24.

}, month = {Aug}, pages = {432-47}, abstract = {

Little is known about the familial and generic level phylogeny of Laniatores, the most diverse suborder of Opiliones. We investigated the internal phylogeny of the family Sandokanidae (formerly Oncopodidae), the putative sister group of the other families of the highly diverse infraorder Grassatores (Opiliones: Laniatores), on the basis of sequence data from eight molecular loci: 18S rRNA, 28S rRNA, 12S rRNA, 16S rRNA, cytochrome c oxidase subunit I (COI), histones H3, H4, and U2 snRNA. Exemplars of all recognized sandokanid genera, as well as a putative new genus from Thailand, were included. Data analyses were based on a direct optimization approach using parsimony, as well as maximum likelihood and Bayesian approaches on static alignments. The results obtained include the monophyly of Sandokanidae and its stability under a variety of parameter sets and methods. The internal phylogeny is relatively robust to parameter choice and demonstrates the monophyly of nearly all described genera, corroborating previous morphological observations. However, conflict among data sets exists with respect to the monophyly of the largest genus Gnomulus. Morphological character evolution, particularly of characters used to define genera, such as tarsal count and male genitalia, is reexamined and the performance of the eight molecular markers in phylogenetic estimation is evaluated.

}, keywords = {*Evolution, Molecular, *Phylogeny, Animals, Arachnida/anatomy \& histology/classification/*genetics, Bayes Theorem, Cell Nucleus/genetics, DNA, Mitochondrial/genetics, Genetic Markers, Histones/genetics, Likelihood Functions, RNA, Ribosomal/genetics, Sequence Analysis, DNA}, isbn = {1095-9513 (Electronic)1055-7903 (Linking)}, author = {Sharma, P. and Giribet, G.} } @article {640546, title = {On velvet worms and caterpillars: science, fiction, or science fiction?}, journal = {Proc Natl Acad Sci U S A}, volume = {106}, number = {47}, year = {2009}, note = {

Giribet, GonzaloengCommentLetter2009/11/03 06:00Proc Natl Acad Sci U S A. 2009 Nov 24;106(47):E131; author reply E132. doi: 10.1073/pnas.0910279106. Epub 2009 Oct 30.

}, month = {Nov 24}, pages = {E131; author reply E132}, keywords = {*Biological Evolution, *Insects/genetics/growth \& development, *Nucleic Acid Hybridization, *Phylogeny, Animals, Fossils, Peer Review, Research, Science}, isbn = {1091-6490 (Electronic)0027-8424 (Linking)}, author = {Giribet, G.} } @article {747866, title = {Exploring the molecular diversity of terrestrial nemerteans (Hoplonemertea, Monostilifera, Acteonemertidae) in a continental landmass.}, journal = {Zoologica Scripta}, volume = {37}, year = {2008}, pages = {235-243}, author = {Mateos, E and Giribet, G.} } @article {747856, title = {On the identity of Pettalus cimiciformis and P. brevicauda (Opiliones, Pettalidae) from Sri Lanka.}, journal = {Journal of Arachnology}, volume = {36}, year = {2008}, pages = {199-201}, author = {Giribet, G.} } @article {747851, title = {A New Zeland species of the trans-Tasman centipede order Craterostigmomorpha (Arthropoda: Chilopoda) corroborated by molecular evidence.}, journal = {Invertrabrate Systematics}, volume = {22}, year = {2008}, pages = {1-15}, author = {Edgecombe, G. D. and Giribet, G.} } @article {747846, title = {Two markers and one history: phylogeography of the edible common sea urchin Paracentrotus lividus in the Lusitanian region}, journal = {Marine Biology}, volume = {154}, year = {2008}, pages = {137-151}, author = {Calderon, I. and Giribet, G. and Turon, X.} } @article {747841, title = {On the ultrastructure and identity of the eyes of Cyphophthalmi based on a study of Stylocellus sp. (Opiliones, Stylocellidae).}, journal = {Journal of Arachnology}, volume = {36}, year = {2008}, pages = {379-387}, author = {Alberti, G. and E Lipke and Giribet, G.} } @article {640541, title = {Assembling the lophotrochozoan (=spiralian) tree of life}, journal = {Philos Trans R Soc Lond B Biol Sci}, volume = {363}, number = {1496}, year = {2008}, note = {

Giribet, GonzaloengResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.ReviewEngland2008/01/15 09:00Philos Trans R Soc Lond B Biol Sci. 2008 Apr 27;363(1496):1513-22. doi: 10.1098/rstb.2007.2241.

}, month = {Apr 27}, pages = {1513-22}, abstract = {

The advent of numerical methods for analysing phylogenetic relationships, along with the study of morphology and molecular data, has driven our understanding of animal relationships for the past three decades. Within the protostome branch of the animal tree of life, these data have sufficed to establish its two main side branches, the moulting Ecdysozoa and the non-moulting Lophotrochozoa. In this review, I explore our current knowledge of protostome relationships and discuss progress and future perspectives and strategies to increase resolution within the main lophotrochozoan clades. Novel approaches to coding morphological characters are needed by scoring real observations on species selected as terminals. Still, methodological issues, for example, how to deal with inapplicable characters or the coding of absences, may require novel algorithmic developments. Taxon sampling is another key issue, as phyla should include enough species so as to represent their span of anatomical disparity. On the molecular side, phylogenomics is playing an increasingly important role in elucidating animal relationships, but genomic sampling is still fairly limited within the lophotrochozoan protostomes, for which only three phyla are represented in currently available phylogenies. Future work should therefore concentrate on generating novel morphological observations and on producing genomic data for the lophotrochozoan side of the animal tree of life.

}, keywords = {*Biological Evolution, *Phylogeny, Animals, Evolution, Molecular, Invertebrates/anatomy \& histology/*classification/*genetics, Models, Biological}, isbn = {0962-8436 (Print)0962-8436 (Linking)}, author = {Giribet, G.} } @article {640441, title = {Broad phylogenomic sampling improves resolution of the animal tree of life}, journal = {Nature}, volume = {452}, number = {7188}, year = {2008}, note = {

Dunn, Casey WHejnol, AndreasMatus, David QPang, KevinBrowne, William ESmith, Stephen ASeaver, ElaineRouse, Greg WObst, MatthiasEdgecombe, Gregory DSorensen, Martin VHaddock, Steven H DSchmidt-Rhaesa, AndreasOkusu, AkikoKristensen, Reinhardt MobjergWheeler, Ward CMartindale, Mark QGiribet, GonzaloengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.England2008/03/07 09:00Nature. 2008 Apr 10;452(7188):745-9. doi: 10.1038/nature06614. Epub 2008 Mar 5.

}, month = {Apr 10}, pages = {745-9}, abstract = {

Long-held ideas regarding the evolutionary relationships among animals have recently been upended by sometimes controversial hypotheses based largely on insights from molecular data. These new hypotheses include a clade of moulting animals (Ecdysozoa) and the close relationship of the lophophorates to molluscs and annelids (Lophotrochozoa). Many relationships remain disputed, including those that are required to polarize key features of character evolution, and support for deep nodes is often low. Phylogenomic approaches, which use data from many genes, have shown promise for resolving deep animal relationships, but are hindered by a lack of data from many important groups. Here we report a total of 39.9 Mb of expressed sequence tags from 29 animals belonging to 21 phyla, including 11 phyla previously lacking genomic or expressed-sequence-tag data. Analysed in combination with existing sequences, our data reinforce several previously identified clades that split deeply in the animal tree (including Protostomia, Ecdysozoa and Lophotrochozoa), unambiguously resolve multiple long-standing issues for which there was strong conflicting support in earlier studies with less data (such as velvet worms rather than tardigrades as the sister group of arthropods), and provide molecular support for the monophyly of molluscs, a group long recognized by morphologists. In addition, we find strong support for several new hypotheses. These include a clade that unites annelids (including sipunculans and echiurans) with nemerteans, phoronids and brachiopods, molluscs as sister to that assemblage, and the placement of ctenophores as the earliest diverging extant multicellular animals. A single origin of spiral cleavage (with subsequent losses) is inferred from well-supported nodes. Many relationships between a stable subset of taxa find strong support, and a diminishing number of lineages remain recalcitrant to placement on the tree.

}, keywords = {*Phylogeny, Animals, Bayes Theorem, Classification/*methods, Computational Biology, Databases, Genetic, Evolution, Molecular, Expressed Sequence Tags, Gene Library, Humans, Markov Chains, Reproducibility of Results, Sample Size, Sensitivity and Specificity}, isbn = {1476-4687 (Electronic)0028-0836 (Linking)}, author = {Dunn, C. W. and Hejnol, A. and Matus, D. Q. and Pang, K. and Browne, W. E. and Smith, S. A. and Seaver, E. and Rouse, G. W. and Obst, M. and G.D. Edgecombe and Sorensen, M. V. and Haddock, S. H. and Schmidt-Rhaesa, A. and Okusu, A. and Kristensen, R. M. and W.C. Wheeler and M.Q. Martindale and Giribet, G.} } @article {640711, title = {First molecular phylogeny of the major clades of Pseudoscorpiones (Arthropoda: Chelicerata)}, journal = {Mol Phylogenet Evol}, volume = {49}, number = {1}, year = {2008}, note = {

Murienne, JeromeHarvey, Mark SGiribet, GonzaloengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2008/07/08 09:00Mol Phylogenet Evol. 2008 Oct;49(1):170-84. doi: 10.1016/j.ympev.2008.06.002. Epub 2008 Jun 17.

}, month = {Oct}, pages = {170-84}, abstract = {

The phylogenetic relationships of the major lineages of the arachnid order Pseudoscorpiones are investigated for the first time using molecular sequence data from two nuclear ribosomal genes and one mitochondrial protein-encoding gene. The data were analyzed using a dynamic homology approach with the new program POY v.4 under parsimony as the optimality criterion. The data show monophyly of Pseudoscorpiones as well as many of its superfamilies (Feaelloidea, Chthonioidea, Cheiridioidea and Sternophoroidea), but not for Neobisiodea or Garypoidea. Cheliferoidea was not monophyletic either due to the position of Neochelanops, which grouped with some garypoids. In all the analyses, Feaelloidea constituted the sister group to all other pseudoscorpions; Chthonioidea is the sister group to the remaining families, which constitute the group Iocheirata sensu Harvey--a clade including pseudoscorpions with venom glands within the pedipalpal fingers. This phylogenetic pattern suggests that venom glands evolved just once within this order of arachnids.

}, keywords = {*Phylogeny, Algorithms, Animals, Arachnida/*classification/*genetics, DNA, Mitochondrial/genetics, DNA, Ribosomal/genetics, Electron Transport Complex IV/genetics, Evolution, Molecular, Genes, Mitochondrial, Genes, rRNA, Mitochondria/genetics, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 18S/genetics, Sequence Analysis, DNA}, isbn = {1095-9513 (Electronic)1055-7903 (Linking)}, author = {Murienne, J. and Harvey, M. S. and Giribet, G.} } @article {747811, title = {Across Lydekker{\textquoteright}s Line -- first report of mite harvestmen (Opiliones: Cyphophthalmi: Stylocellidae) from New Guinea.}, journal = {Invertrabrate Systematics}, volume = {21}, year = {2007}, pages = {207-227}, author = {Clouse, R. M. and Giribet, G.} } @article {747791, title = {Biogeography of the world: a case study from cyphophthalmid Opiliones, a globally distributed group of arachnids.}, journal = {Journal of Biogeography}, volume = {34}, year = {2007}, pages = {2070-2085}, author = {Boyer, S. L. and Clouse, R. M. and Benavides, L. R. and Sharma, P. and Schwendinger, PJ and Karunarathna, I. and Giribet, G.} } @article {747826, title = {The case for sensitivity: a response to Grant and Kluge.}, journal = {Cladistics}, volume = {23}, year = {2007}, pages = {297-296}, author = {Giribet, G. and Wheeler, W.C.} } @article {747771, title = {Cryptic speciation in the recently discovered American cycliophoran Symbion americanus; genetic structure and population expansion}, journal = {Marine Biology}, volume = {151}, year = {2007}, pages = {2183-2193}, author = {Baker, J. M. and Funch, P. and Giribet, G.} } @article {747781, title = {An illustrated catalogue to the South American species of the cyphophthalmid family Neogoveidae (Arthropoda, Opiliones, Cyphophthalmi) with a report on 37 new species.}, journal = {Zootaxa}, volume = {1509}, year = {2007}, pages = {1-15}, author = {Benavides, L. R. and Giribet, G.} } @inbook {747831, title = {A modern look at the Animal Tree of Life.}, booktitle = {Linnaeus Tercentenary: Progress in Invertebrate Taxonomy}, year = {2007}, note = {

Zhang, Z.-Q., WA Shear (eds)

}, pages = {61-79}, publisher = {Magnolia Press}, organization = {Magnolia Press}, address = {Auckland}, author = {Giribet, G. and Dunn, C. W. and Edgecombe, G. D. and Rouse, G. W.} } @article {747776, title = {A molecular phylogenetic approach to the phylum Cycliophora provides further evidence for cryptic speciation in Symbion americanus.}, journal = {Zoologica Scripta}, volume = {36}, year = {2007}, pages = {353-359}, author = {Baker, J. M. and Giribet, G.} } @article {747821, title = {A new genus and species of Cyphophthalmi (Arachnida: Opiliones) from the north-eastern states of India.}, journal = {Zoological Journal of the Linnean Society}, volume = {151}, year = {2007}, pages = {663-670}, author = {Giribet, G. and Sharma, P. P. and DB Bastawade} } @article {747801, title = {A new model Gondwanan taxon: systematics and biogeography of the harvestman family Pettalidae (Arachnida, Opiliones, Cyphophthalmi), with a taxonomic revision of genera from Australia and New Zealand.}, journal = {Cladistics}, volume = {23}, year = {2007}, pages = {337-361}, author = {Boyer, S. L. and Giribet, G.} } @article {747816, title = {Phylogeny of the American silverfish Cubacubaninae (Hexapoda: Zygentoma: Nicoletiidae): a combined approach using morphology and five molecular loci.}, journal = {Cladistics}, volume = {23}, year = {2007}, pages = {22-40}, author = {Espinasa, L and C Flick and Giribet, G.} } @article {640416, title = {Deep genetic divergences in Aoraki denticulata (Arachnida, Opiliones, Cyphophthalmi): a widespread {\textquoteright}mite harvestman{\textquoteright} defies DNA taxonomy}, journal = {Mol Ecol}, volume = {16}, number = {23}, year = {2007}, note = {

Boyer, Sarah LBaker, Jessica MGiribet, GonzaloengResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.England2007/10/20 09:00Mol Ecol. 2007 Dec;16(23):4999-5016. Epub 2007 Oct 16.

}, month = {Dec}, pages = {4999-5016}, abstract = {

Aoraki denticulata (Arachnida, Opiliones, Cyphophthalmi, Pettalidae), a widespread {\textquoteright}mite harvestman{\textquoteright} endemic to the South Island of New Zealand, is found in leaf littler habitats throughout Nelson and Marlborough, and as far south as Arthur{\textquoteright}s Pass. We investigated the phylogeography and demographic history of A. denticulata in the first genetic population-level study within Opiliones. A total of 119 individuals from 17 localities were sequenced for 785 bp of the gene cytochrome c oxidase subunit I; 102 of these individuals were from the Aoraki subspecies A. denticulata denticulata and the remaining 17 were from the subspecies A. denticulata major. An extraordinarily high degree of genetic diversity was discovered in A. denticulata denticulata, with average uncorrected p-distances between populations as high as 19.2\%. AMOVA, average numbers of pairwise differences, and pairwise F(ST) values demonstrated a significant amount of genetic diversity both within and between populations of this subspecies. Phylogenetic analysis of the data set revealed many well-supported groups within A. denticulata denticulata, generally corresponding to clusters of specimens from single populations with short internal branches, but separated by long branches from individuals from other populations. No haplotypes were shared between populations of the widespread small subspecies, A. denticulata denticulata. These results indicate a subspecies within which very little genetic exchange occurs between populations, a result consistent with the idea that Cyphophthalmi are poor dispersers. The highly structured populations and deep genetic divergences observed in A. denticulata denticulata may indicate the presence of cryptic species. However, we find a highly conserved morphology across sampling localities and large genetic divergences within populations from certain localities, equivalent to those typically found between populations from different localities. Past geological events may have contributed to the deep genetic divergences observed between sampling localities; additionally, the high divergence within populations of A. denticulata denticulata suggests that the rate of COI evolution may be accelerated in this taxon. In contrast, the larger subspecies A. denticulata major shows much less differentiation between and within sampling localities, suggesting that it may disperse more easily than its smaller counterpart. The fact that the remarkable genetic divergences within populations of A. denticulata denticulata from certain localities are equivalent to divergences between localities poses a challenge to the rapidly spreading practice of DNA taxonomy.

}, keywords = {*Genetic Variation, Animals, Arachnida/classification/genetics/ultrastructure, Arthropods/classification/*genetics/ultrastructure, DNA, Mitochondrial/chemistry/*genetics, Geography, Microscopy, Electron, Scanning, Molecular Sequence Data, New Zealand, Phylogeny, Sequence Analysis, DNA}, isbn = {0962-1083 (Print)0962-1083 (Linking)}, author = {S.L. Boyer and Baker, J. M. and Giribet, G.} } @article {640536, title = {Efficient tree searches with available algorithms}, journal = {Evol Bioinform Online}, volume = {3}, year = {2007}, note = {

Giribet, GonzaloengNew Zealand2007/01/01 00:00Evol Bioinform Online. 2007 Nov 12;3:341-56.

}, pages = {341-56}, abstract = {

Phylogenetic methods based on optimality criteria are highly desirable for their logic properties, but time-consuming when compared to other methods of tree construction. Traditionally, researchers have been limited to exploring tree space by using multiple replicates of Wagner addition followed by typical hill climbing algorithms such as SPR or/and TBR branch swapping but these methods have been shown to be insufficient for "large" data sets (or even for small data sets with a complex tree space). Here, I review different algorithms and search strategies used for phylogenetic analysis with the aim of clarifying certain aspects of this important part of the phylogenetic inference exercise. The techniques discussed here apply to both major families of methods based on optimality criteria-parsimony and maximum likelihood-and allow the thorough analysis of complex data sets with hundreds to thousands of terminal taxa. A new technique, called pre-processed searches is proposed for reusing phylogenetic results obtained in previous analyses, to increase the applicability of the previously proposed jumpstarting phylogenetics method. This article is aimed to serve as an educational and algorithmic reference to biologists interested in phylogenetic analysis.

}, isbn = {1176-9343 (Electronic)1176-9343 (Linking)}, author = {Giribet, G.} } @article {640456, title = {Evolutionary biology of centipedes (Myriapoda: Chilopoda)}, journal = {Annu Rev Entomol}, volume = {52}, year = {2007}, note = {

Edgecombe, Gregory DGiribet, GonzaloengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.Review2006/07/29 09:00Annu Rev Entomol. 2007;52:151-70.

}, pages = {151-70}, abstract = {

New insights into the anatomy, systematics, and biogeography of centipedes have put these predatory terrestrial arthropods at the forefront of evolutionary studies. Centipedes have also played a pivotal role in understanding high-level arthropod relationships. Their deep evolutionary history, with a fossil record spanning 420 million years, explains their current worldwide distribution. Recent analyses of combined morphological and molecular data provide a stable phylogeny that underpins evolutionary interpretations of their biology. The centipede trunk, with its first pair of legs modified into a venom-delivering organ followed by 15 to 191 leg pairs, is a focus of arthropod segmentation studies. Gene expression studies and phylogenetics shed light on key questions in evolutionary developmental biology concerning the often group-specific fixed number of trunk segments, how some centipedes add segments after hatching whereas others hatch with the complete segment count, the addition of segments through evolution, and the invariably odd number of leg-bearing trunk segments.

}, keywords = {*Arthropods/classification, *Biological Evolution, Animals, Fossils, Geography, Predatory Behavior}, isbn = {0066-4170 (Print)0066-4170 (Linking)}, author = {G.D. Edgecombe and Giribet, G.} } @article {640786, title = {Phylogeny of sipunculan worms: A combined analysis of four gene regions and morphology}, journal = {Mol Phylogenet Evol}, volume = {42}, number = {1}, year = {2007}, note = {

Schulze, AnjaCutler, Edward BGiribet, GonzaloengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2006/08/22 09:00Mol Phylogenet Evol. 2007 Jan;42(1):171-92. Epub 2006 Jul 5.

}, month = {Jan}, pages = {171-92}, abstract = {

The intra-phyletic relationships of sipunculan worms were analyzed based on DNA sequence data from four gene regions and 58 morphological characters. Initially we analyzed the data under direct optimization using parsimony as optimality criterion. An implied alignment resulting from the direct optimization analysis was subsequently utilized to perform a Bayesian analysis with mixed models for the different data partitions. For this we applied a doublet model for the stem regions of the 18S rRNA. Both analyses support monophyly of Sipuncula and most of the same clades within the phylum. The analyses differ with respect to the relationships among the major groups but whereas the deep nodes in the direct optimization analysis generally show low jackknife support, they are supported by 100\% posterior probability in the Bayesian analysis. Direct optimization has been useful for handling sequences of unequal length and generating conservative phylogenetic hypotheses whereas the Bayesian analysis under mixed models provided high resolution in the basal nodes of the tree.

}, keywords = {*Phylogeny, Animals, Electron Transport Complex IV/genetics, Histones/genetics, Invertebrates/anatomy \& histology/classification/*genetics, Molecular Sequence Data, RNA, Ribosomal, 18S/genetics, RNA, Ribosomal, 28S/genetics, Sequence Analysis, DNA, Species Specificity}, isbn = {1055-7903 (Print)1055-7903 (Linking)}, author = {Schulze, A. and Cutler, E. B. and Giribet, G.} } @article {747691, title = {A century later -- a total evidence re-evaluation of the phylogeny of scutigeromorph centipedes (Myriapoda: Chiloposa).}, journal = {Invertrabrate Systematics}, volume = {20}, year = {2006}, pages = {503-525}, author = {Edgecombe, G. D. and Giribet, G.} } @article {747706, title = {Confirmation of the type locality and the distributional range of Suzukielus sauteri (Opiliones, Cyphophthalmi) in Japan.}, journal = {Acta Arachnologica}, volume = {55}, year = {2006}, pages = {87-90}, author = {Giribet, G. and N Tsurusaki and Boyer, S. L.} } @article {747726, title = {Gnathostomulid phylogeny inferred from a combined approach of four molecular loci and morphology.}, journal = {Cladistics}, volume = {22}, year = {2006}, pages = {32-58}, author = {Sorensen, M. V. and Sterrer, W. and Giribet, G.} } @article {747696, title = {The importance of looking at small-scale patterns when inferring Gondwanan biogeography: a case study of the centipede Paralamyctes (Chilopoda, Lithobiomorpha, Henicopidae)}, journal = {Biological Journal of the Linnean Society}, volume = {89}, year = {2006}, pages = {65-78}, author = {Giribet, G. and Edgecombe, G. D.} } @article {747716, title = {A new Pettalus species (Opiliones, Cyphophthalmi, Pettalidae) from Sri Lanka with a discussion on the evolution of eyes in Cyphophthalmi.}, journal = {Journal of Arachnology}, volume = {34}, year = {2006}, pages = {331-341}, author = {Sharma, P. and Giribet, G.} } @article {747711, title = {A new species of Cyphophthalmi (Arachnida, Opiliones, Sironidae) from Eastern Slovenia.}, journal = {Zootaxa}, volume = {1330}, year = {2006}, pages = {27-42}, author = {Novak, T and Giribet, G.} } @article {640581, title = {Conflict between datasets and phylogeny of centipedes: an analysis based on seven genes and morphology}, journal = {Proc Biol Sci}, volume = {273}, number = {1586}, year = {2006}, note = {

Giribet, GonzaloEdgecombe, Gregory DengResearch Support, Non-U.S. Gov{\textquoteright}tEngland2006/03/16 09:00Proc Biol Sci. 2006 Mar 7;273(1586):531-8.

}, month = {Mar 7}, pages = {531-8}, abstract = {

Although the phylogeny of centipedes has found ample agreement based on morphology, recent analyses incorporating molecular data show major conflict at resolving the deepest nodes in the centipede tree. While some genes support the classical (morphological) hypothesis, others suggest an alternative tree in which the relictual order Craterostigmomorpha, restricted to Tasmania and New Zealand, is resolved as the sister group to all other centipedes. We combined all available data including seven genes (totalling more than 8 kb of genetic information) and 153 morphological characters for 24 centipedes, and conducted a sensitivity analysis to evaluate where the conflict resides. Our data showed that the classical hypothesis is obtained primarily when nuclear ribosomal genes exert dominance in the character data matrix (at high gap costs), while the alternative tree is obtained when protein-encoding genes account for most of the cladogram length (at low gap costs). In this particular case, the addition of genetic data does not produce a more stable hypothesis for deep centipede relationships than when analysing certain genes independently, but the overall conflict in the data can be clearly detected via a sensitivity analysis, and support and stability of shallow nodes increase as data are added.

}, keywords = {Animals, Arthropods/anatomy \& histology/*genetics, Base Sequence, DNA/chemistry/genetics, Electron Transport Complex IV/chemistry/genetics, Molecular Sequence Data, Peptide Elongation Factor 1/chemistry/genetics, Peptide Elongation Factor 2/chemistry/genetics, Phylogeny, RNA Polymerase II/chemistry/genetics, RNA, Ribosomal, 16S/chemistry/genetics, RNA, Ribosomal, 18S/chemistry/genetics, RNA, Ribosomal, 28S/chemistry/genetics, Sequence Analysis, DNA}, isbn = {0962-8452 (Print)0962-8452 (Linking)}, author = {Giribet, G. and G.D. Edgecombe} } @article {640601, title = {Evidence for a clade composed of molluscs with serially repeated structures: monoplacophorans are related to chitons}, journal = {Proc Natl Acad Sci U S A}, volume = {103}, number = {20}, year = {2006}, note = {

Giribet, GonzaloOkusu, AkikoLindgren, Annie RHuff, Stephanie WSchrodl, MichaelNishiguchi, Michele KengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2006/05/06 09:00Proc Natl Acad Sci U S A. 2006 May 16;103(20):7723-8. Epub 2006 May 4.

}, month = {May 16}, pages = {7723-8}, abstract = {

Monoplacophorans are among the rarest members of the phylum Mollusca. Previously only known from fossils since the Cambrian, the first living monoplacophoran was discovered during the famous second Galathea deep-sea expedition. The anatomy of these molluscs shocked the zoological community for presenting serially repeated gills, nephridia, and eight sets of dorsoventral pedal retractor muscles. Seriality of organs in supposedly independent molluscan lineages, i.e., in chitons and the deep-sea living fossil monoplacophorans, was assumed to be a relic of ancestral molluscan segmentation and was commonly accepted to support a direct relationship with annelids. We were able to obtain one specimen of a monoplacophoran Antarctic deep-sea species for molecular study. The first molecular data on monoplacophorans, analyzed together with the largest data set of molluscs ever assembled, clearly illustrate that monoplacophorans and chitons form a clade. This "Serialia" concept may revolutionize molluscan systematics and may have important implications for metazoan evolution as it allows for new interpretations for primitive segmentation in molluscs.

}, keywords = {*Biological Evolution, *Fossils, Animals, Base Sequence, Molecular Sequence Data, Mollusca/*anatomy \& histology/*classification/genetics, Phylogeny, Polyplacophora/*anatomy \& histology/*classification/genetics, Sequence Alignment}, isbn = {0027-8424 (Print)0027-8424 (Linking)}, author = {Giribet, G. and Okusu, A. and Lindgren, A. R. and Huff, S. W. and Schrodl, M. and Nishiguchi, M. K.} } @article {640741, title = {First molecular data on the phylum Loricifera: an investigation into the phylogeny of ecdysozoa with emphasis on the positions of Loricifera and Priapulida}, journal = {Zoolog Sci}, volume = {23}, number = {11}, year = {2006}, note = {

Park, Joong-KiRho, Hyun SooKristensen, Reinhardt MobjergKim, WonGiribet, GonzaloengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.Japan2006/12/27 09:00Zoolog Sci. 2006 Nov;23(11):943-54.

}, month = {Nov}, pages = {943-54}, abstract = {

Recent progress in molecular techniques has generated a wealth of information for phylogenetic analysis. Among metazoans all but a single phylum have been incorporated into some sort of molecular analysis. However, the minute and rare species of the phylum Loricifera have remained elusive to molecular systematists. Here we report the first molecular sequence data (nearly complete 18S rRNA) for a member of the phylum Loricifera, Pliciloricus sp. from Korea. The new sequence data were analyzed together with 52 other ecdysozoan sequences, with all other phyla represented by three or more sequences. The data set was analyzed using parsimony as an optimality criterion under direct optimization as well as using a Bayesian approach. The parsimony analysis was also accompanied by a sensitivity analysis. The results of both analyses are largely congruent, finding monophyly of each ecdysozoan phylum, except for Priapulida, in which the coelomate Meiopriapulus is separate from a clade of pseudocoelomate priapulids. The data also suggest a relationship of the pseudocoelomate priapulids to kinorhynchs, and a relationship of nematodes to tardigrades. The Bayesian analysis placed the arthropods as the sister group to a clade that includes tardigrades and nematodes. However, these results were shown to be parameter dependent in the sensitivity analysis. The position of Loricifera was extremely unstable to parameter variation, and support for a relationship of loriciferans to any particular ecdysozoan phylum was not found in the data.

}, keywords = {*Phylogeny, Animals, DNA, Protozoan/genetics, Eukaryota/*classification/*genetics}, isbn = {0289-0003 (Print)0289-0003 (Linking)}, author = {Park, J. K. and Rho, H. S. and Kristensen, R. M. and Kim, W. and Giribet, G.} } @article {640671, title = {Further use of nearly complete 28S and 18S rRNA genes to classify Ecdysozoa: 37 more arthropods and a kinorhynch}, journal = {Mol Phylogenet Evol}, volume = {40}, number = {3}, year = {2006}, note = {

Mallatt, JonGiribet, GonzaloengComparative Study2006/06/20 09:00Mol Phylogenet Evol. 2006 Sep;40(3):772-94. Epub 2006 May 5.

}, month = {Sep}, pages = {772-94}, abstract = {

This work expands on a study from 2004 by Mallatt, Garey, and Shultz [Mallatt, J.M., Garey, J.R., Shultz, J.W., 2004. Ecdysozoan phylogeny and Bayesian inference: first use of nearly complete 28S and 18S rRNA gene sequences to classify the arthropods and their kin. Mol. Phylogenet. Evol. 31, 178-191] that evaluated the phylogenetic relationships in Ecdysozoa (molting animals), especially arthropods. Here, the number of rRNA gene-sequences was effectively doubled for each major group of arthropods, and sequences from the phylum Kinorhyncha (mud dragons) were also included, bringing the number of ecdysozoan taxa to over 80. The methods emphasized maximum likelihood, Bayesian inference and statistical testing with parametric bootstrapping, but also included parsimony and minimum evolution. Prominent findings from our combined analysis of both genes are as follows. The fundamental subdivisions of Hexapoda (insects and relatives) are Insecta and Entognatha, with the latter consisting of collembolans (springtails) and a clade of proturans plus diplurans. Our rRNA-gene data provide the strongest evidence to date that the sister group of Hexapoda is Branchiopoda (fairy shrimps, tadpole shrimps, etc.), not Malacostraca. The large, Pancrustacea clade (hexapods within a paraphyletic Crustacea) divided into a few basic subclades: hexapods plus branchiopods; cirripedes (barnacles) plus malacostracans (lobsters, crabs, true shrimps, isopods, etc.); and the basally located clades of (a) ostracods (seed shrimps) and (b) branchiurans (fish lice) plus the bizarre pentastomids (tongue worms). These findings about Pancrustacea agree with a recent study by Regier, Shultz, and Kambic that used entirely different genes [Regier, J.C., Shultz, J.W., Kambic, R.E., 2005a. Pancrustacean phylogeny: hexapods are terrestrial crustaceans and maxillopods are not monophyletic. Proc. R. Soc. B 272, 395-401]. In Malacostraca, the stomatopod (mantis shrimp) was not at the base of the eumalacostracans, as is widely claimed, but grouped instead with an euphausiacean (krill). Within centipedes, Craterostigmus was the sister to all other pleurostigmophorans, contrary to the consensus view. Our trees also united myriapods (millipedes and centipedes) with chelicerates (horseshoe crabs, spiders, scorpions, and relatives) and united pycnogonids (sea spiders) with chelicerates, but with much less support than in the previous rRNA-gene study. Finally, kinorhynchs joined priapulans (penis worms) at the base of Ecdysozoa.

}, keywords = {Animals, Arthropods/*classification/*genetics, Bayes Theorem, Helminths/*classification/*genetics, Phylogeny, RNA, Ribosomal, 18S/analysis/*genetics, RNA, Ribosomal, 28S/analysis/*genetics}, isbn = {1055-7903 (Print)1055-7903 (Linking)}, author = {Mallatt, J. and Giribet, G.} } @article {640846, title = {A modern approach to rotiferan phylogeny: combining morphological and molecular data}, journal = {Mol Phylogenet Evol}, volume = {40}, number = {2}, year = {2006}, note = {

Sorensen, Martin VGiribet, GonzaloengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2006/05/13 09:00Mol Phylogenet Evol. 2006 Aug;40(2):585-608. Epub 2006 Apr 6.

}, month = {Aug}, pages = {585-608}, abstract = {

The phylogeny of selected members of the phylum Rotifera is examined based on analyses under parsimony direct optimization and Bayesian inference of phylogeny. Species of the higher metazoan lineages Acanthocephala, Micrognathozoa, Cycliophora, and potential outgroups are included to test rotiferan monophyly. The data include 74 morphological characters combined with DNA sequence data from four molecular loci, including the nuclear 18S rRNA, 28S rRNA, histone H3, and the mitochondrial cytochrome c oxidase subunit I. The combined molecular and total evidence analyses support the inclusion of Acanthocephala as a rotiferan ingroup, but do not support the inclusion of Micrognathozoa and Cycliophora. Within Rotifera, the monophyletic Monogononta is sister group to a clade consisting of Acanthocephala, Seisonidea, and Bdelloidea-for which we propose the name Hemirotifera. We also formally propose the inclusion of Acanthocephala within Rotifera, but maintaining the name Rotifera for the new expanded phylum. Within Monogononta, Gnesiotrocha and Ploima are also supported by the data. The relationships within Ploima remain unstable to parameter variation or to the method of phylogeny reconstruction and poorly supported, and the analyses showed that monophyly was questionable for the families Dicranophoridae, Notommatidae, and Brachionidae, and for the genus Proales. Otherwise, monophyly was generally supported for the represented ploimid families and genera.

}, keywords = {*Phylogeny, Animals, Base Sequence, Microscopy, Electron, Scanning, Molecular Sequence Data, Rotifera/*anatomy \& histology/*genetics/ultrastructure}, isbn = {1055-7903 (Print)1055-7903 (Linking)}, author = {Sorensen, M. V. and Giribet, G.} } @article {747601, title = {Generating implied alignments under direct optimization using POY.}, journal = {Cladistics}, volume = {21}, year = {2005}, pages = {396-402}, author = {Giribet, G.} } @article {747671, title = {A new Troglosiro species (Opiliones, Cyphophthalmi, Troglosironidae) from New Caledonia. }, journal = {Zootaxa}, volume = {1053}, year = {2005}, pages = {47-60}, author = {Sharma, P. and Giribet, G.} } @article {747681, title = {Phylogenetic position of the meiofaunal family Nerillidae (Annelida: Polychaeta) analyzed by direct optimization of combined molecular and morphological datasets.}, journal = {Zoologica Scripta}, volume = {34}, year = {2005}, pages = {313-328}, author = {Worsaae, K. and A Nygren and Rouse, G. W. and Giribet, G. and J Persson and Sundberg, P. and F Pleijel} } @article {747631, title = {Reconstructing the phylogeny of the Sipuncula. }, journal = {Hydrobiologia}, volume = {535/536}, year = {2005}, pages = {277-296}, author = {Schulze, A. and Cutler, E. B. and Giribet, G.} } @article {747666, title = {The systematics of the south-east Asian genus Fangensis Ramble (Opiliones: Cyphophthalmi: Stylocellidae)}, journal = {Invertrabrate Systematics}, volume = {19}, year = {2005}, pages = {297-323}, author = {Schwendinger, PJ and Giribet, G.} } @article {640576, title = {First identifiable Mesozoic harvestman (Opiliones: Dyspnoi) from Cretaceous Burmese amber}, journal = {Proc Biol Sci}, volume = {272}, number = {1567}, year = {2005}, note = {

Giribet, GonzaloDunlop, Jason AengComparative StudyEngland2005/07/19 09:00Proc Biol Sci. 2005 May 22;272(1567):1007-13.

}, month = {May 22}, pages = {1007-13}, abstract = {

Two inclusions in a piece of Upper Cretaceous (Albian) Burmese amber from Myanmar are described as a harvestman (Arachnida: Opiliones), Halitherses grimaldii new genus and species. The first Mesozoic harvestman to be named can be referred to the suborder Dyspnoi for the following reasons: prosoma divided into two regions, the posterior formed by the fusion of the meso- and metapeltidium; palp lacking a terminal claw, with clavate setae, and tarsus considerably shorter than the tibia. The bilobed, anteriorly projecting ocular tubercle is reminiscent of that of ortholasmatine nemastomatids. The status of other Mesozoic fossils referred to Opiliones is briefly reviewed.

}, keywords = {*Amber, *Fossils, *Phylogeny, Animals, Arachnida/*anatomy \& histology/classification, Myanmar, Species Specificity}, isbn = {0962-8452 (Print)0962-8452 (Linking)}, author = {Giribet, G. and Dunlop, J. A.} } @article {640421, title = {The genus Cyphophthalmus (Arachnida, Opiliones, Cyphophthalmi) in Europe: a phylogenetic approach to Balkan Peninsula biogeography}, journal = {Mol Phylogenet Evol}, volume = {36}, number = {3}, year = {2005}, note = {

Boyer, Sarah LKaraman, IvoGiribet, GonzaloengResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2005/07/02 09:00Mol Phylogenet Evol. 2005 Sep;36(3):554-67.

}, month = {Sep}, pages = {554-67}, abstract = {

In this study, we present phylogenetic data to characterize the relationships among sironids centered in the Balkan region, and use these results to discuss biogeographical aspects of sironid evolution. Analysis of ca. 4.5 kb of sequence data from three nuclear and two mitochondrial genes reveals monophyly of a Balkan clade for which we resurrect the name Cyphophthalmus, considered a junior synonym of Siro for over a century. This clade diversified into several groups, and at least three of them--the duricorius group, the serbicus group, and the minutus group--are well corroborated by the data as monophyletic lineages. The members of the different groups, mostly living in troglobitic environments, have diversified in overlapping geographic regions, with evidence of an eastern origin for the group. Our data also suggest that mitochondrial and nuclear genes are all contributing towards the final resolution of the combined analysis of the data.

}, keywords = {*Geography, *Phylogeny, Animals, Arthropods/*classification/*genetics, DNA, Mitochondrial/genetics, Europe, Eastern, Nuclear Proteins/genetics, Ribosomal Proteins/genetics}, isbn = {1055-7903 (Print)1055-7903 (Linking)}, author = {S.L. Boyer and Karaman, I. and Giribet, G.} } @article {640731, title = {Hidden diversity and host specificity in cycliophorans: a phylogeographic analysis along the North Atlantic and Mediterranean Sea}, journal = {Mol Ecol}, volume = {14}, number = {14}, year = {2005}, note = {

Obst, MatthiasFunch, PeterGiribet, GonzaloengComparative StudyResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.England2005/11/30 09:00Mol Ecol. 2005 Dec;14(14):4427-40.

}, month = {Dec}, pages = {4427-40}, abstract = {

In order to elucidate the evolutionary history and the population structure of the members of the phylum Cycliophora, which live commensally on three species of lobsters, we studied sequence variation in the mitochondrial gene cyctochrome c oxidase subunit I. Overall 242 sequences from 16 locations on both coasts of the North Atlantic, including the North Sea and the Mediterranean, were analysed, revealing 28 haplotypes, with a maximum sequence divergence of 16.6\%. Total genetic diversity was high (h = 0.8322, pi = 0.0898), as it was for the commensals on Homarus americanus (17 haplotypes, h = 0.7506, pi = 0.0504). However, it was low for commensals on Nephrops norvegicus (6 haplotypes, h = 0.3899, pi = 0.0035), and intermediate for cycliophorans on Homarus gammarus (5 haplotypes, h = 0.3020, pi = 0.0140). Although two of the host lobsters co-inhabit the coastal waters of Europe, a strong genetic structure (78.45\% of the observed genetic variation) was detected among populations on all host species, indicating the existence of a reproductively isolated species on each lobster. In addition, genetic structure over long distances exists among populations on each host species. Such patterns can be explained by the limited dispersal ability of the cycliophoran chordoid larva. Demographic and phylogenetic analyses suggest old and possibly cryptic populations present on H. americanus and H. gammarus, while the latter may have experienced recent bottlenecks, perhaps during Pleistocene glaciations. Populations on N. norvegicus appear to be of recent origin.

}, keywords = {*Genetic Variation, *Genetics, Population, *Phylogeny, Animals, Atlantic Ocean, Base Sequence, DNA Primers, DNA, Mitochondrial/genetics, Haplotypes/genetics, Invertebrates/*genetics, Likelihood Functions, Mediterranean Sea, Models, Genetic, Molecular Sequence Data, Nephropidae/*parasitology, Sequence Analysis, DNA, Species Specificity}, isbn = {0962-1083 (Print)0962-1083 (Linking)}, author = {Obst, M. and Funch, P. and Giribet, G.} } @article {640676, title = {Neuroanatomy of sea spiders implies an appendicular origin of the protocerebral segment}, journal = {Nature}, volume = {437}, number = {7062}, year = {2005}, note = {

Maxmen, AmyBrowne, William EMartindale, Mark QGiribet, GonzaloengResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.England2005/10/21 09:00Nature. 2005 Oct 20;437(7062):1144-8.

}, month = {Oct 20}, pages = {1144-8}, abstract = {

Independent specialization of arthropod body segments has led to more than a century of debate on the homology of morphologically diverse segments, each defined by a lateral appendage and a ganglion of the central nervous system. The plesiomorphic composition of the arthropod head remains enigmatic because variation in segments and corresponding appendages is extreme. Within extant arthropod classes (Chelicerata, Myriapoda, Crustacea and Hexapoda--including the insects), correspondences between the appendage-bearing second (deutocerebral) and third (tritocerebral) cephalic neuromeres have been recently resolved on the basis of immunohistochemistry and Hox gene expression patterns. However, no appendage targets the first ganglion, the protocerebrum, and the corresponding segmental identity of this anterior region remains unclear. Reconstructions of stem-group arthropods indicate that the anteriormost region originally might have borne an ocular apparatus and a frontal appendage innervated by the protocerebrum. However, no study of the central nervous system in extant arthropods has been able to corroborate this idea directly, although recent analyses of cephalic gene expression patterns in insects suggest a segmental status for the protocerebral region. Here we investigate the developmental neuroanatomy of a putative basal arthropod, the pycnogonid sea spider, with immunohistochemical techniques. We show that the first pair of appendages, the chelifores, are innervated at an anterior position on the protocerebrum. This is the first true appendage shown to be innervated by the protocerebrum, and thus pycnogonid chelifores are not positionally homologous to appendages of extant arthropods but might, in fact, be homologous to the {\textquoteright}great appendages{\textquoteright} of certain Cambrian stem-group arthropods.

}, keywords = {*Biological Evolution, *Models, Biological, Aging, Animals, Arthropods/*anatomy \& histology/embryology/growth \& development/physiology, Brain/*anatomy \& histology/cytology/embryology/*growth \& development, Development, Extremities/anatomy \& histology/embryology/growth \& development/physiology, Fossils, Ganglia, Invertebrate/anatomy \& histology/cytology/embryology/growth \&, Gene Expression Regulation, Developmental, Genes, Homeobox/genetics, Immunohistochemistry, Larva/anatomy \& histology/growth \& development, Male, Neuroanatomy, Phylogeny, Tubulin/analysis}, isbn = {1476-4687 (Electronic)0028-0836 (Linking)}, author = {Maxmen, A. and Browne, W. E. and M.Q. Martindale and Giribet, G.} } @article {747606, title = {Adding mitochondrial sequence data (16S rRNA and cytochrome c oxidase subunit I) to the phylogeny of centipedes (Myriapoda, Chilopoda): an analysis of morphology and four molecular loci. }, journal = {Journal of Zoological Systematics and Evolutionary Research}, volume = {42}, year = {2004}, pages = {89.134}, author = {Edgecombe, G. D. and Giribet, G.} } @article {747626, title = {Is Ellipura monophyletic? A combined analysis of basal hexapod relationships with emphasis on the origin of insects.}, journal = {Orignism Diversity Evolution}, volume = {4}, year = {2004}, pages = {319-340}, author = {Giribet, G. and G.D. Edgecombe and JM Carpenter and CA D{\textquoteright}Haese and Wheeler, W.C.} } @article {747636, title = {Investigations into the phylogenetic position of Micrognathozoa using four molecular loci.}, journal = {Cladistics}, volume = {20}, year = {2004}, pages = {1-13}, author = {Giribet, G. and Sorensen, M. V. and Funch, P. and Kristensen, R. M. and Sterrer, W.} } @article {747641, title = {Investigations into the phylogenetic relationships of the threatened freshwater pearl-mussels (Bivalvia, Unionoidea, Margaritiferidae) based on molecular data: implications for their taxonomy and biogeography.}, journal = {Journal of Molluscan Studies}, volume = {70}, year = {2004}, pages = {379-388}, author = {Huff, S. W. and D Campbell and DL Gustafson and C Lydeard and CR Altaba and Giribet, G.} } @article {747616, title = {Molecular phylogeny of Australasian anopsobiine centipedes (Chilopoda: Lithobiomorpha).}, journal = {Invertrabrate Systematics}, volume = {18}, year = {2004}, pages = {235-249}, author = {Edgecombe, G. D. and Giribet, G.} } @article {747581, title = {A new genus of cyphophthalmid from the Iberian Peninsula with a phylogenetic analysis of the Sironidae (Arachnida: Opiliones: Cyphophthalmi) and a SEM database of external morphology.}, journal = {Invertrabrate Systematics}, volume = {18}, year = {2004}, pages = {7-52}, author = {de Bivort, BL and Giribet, G.} } @article {747586, title = {Phylogeographic history of the sponge Crambe crambe (Porifera, Poecilosclerida): range expansion and recent invasion of Macaronesian Islands from the Mediterranean Sea.}, journal = {Molecular Ecology}, volume = {13}, year = {2004}, pages = {109-122}, author = {Duran, S. and Giribet, G. and Turon, X.} } @article {747661, title = {A remarkable new cave-dwelling Stylocellus (Opiliones, Cyphophthalmi) from Peninsular Malaysia, with a discussion on taxonomic characters in the family Stylocellidae.}, journal = {Journal of Natural History}, volume = {38}, year = {2004}, pages = {1421-1435}, author = {Schwendinger, PJ and Giribet, G. and H Steiner} } @article {747651, title = {The systematics of the south-east Asian genus Fangensis Rambla (Opiliones: Cyphophthalmi: Stylocellidae).}, journal = {Invertrabrate Systematics}, volume = {19}, year = {2004}, pages = {297-323}, author = {Schwendinger, PJ and Giribet, G.} } @article {640451, title = {Genetic diversity and population structure of the commercially harvested sea urchin Paracentrotus lividus (Echinodermata, Echinoidea)}, journal = {Mol Ecol}, volume = {13}, number = {11}, year = {2004}, note = {

Duran, SandraPalacin, CruzBecerro, Mikel ATuron, XavierGiribet, GonzaloengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.England2004/10/19 09:00Mol Ecol. 2004 Nov;13(11):3317-28.

}, month = {Nov}, pages = {3317-28}, abstract = {

The population structure of the edible Atlanto-Mediterranean sea urchin Paracentrotus lividus is described by analysing sequence variation in a fragment of the mitochondrial gene cytochrome c oxidase subunit I in 127 individuals from 12 localities across south-west Europe. The study revealed high levels of genetic diversity but low levels of genetic structure, suggesting a large degree of gene flow between populations and panmixis within each, the Mediterranean and Atlantic basins. However, we found significant genetic differentiation between the two basins probably due to restricted gene flow across the geographical boundary imposed by the area of the Strait of Gibraltar. Populations of P. lividus appeared to have experienced a recent demographic expansion in the late Pleistocene. We provide new evidence on the population structure of this commercial species, predicting a healthy stock of this sea urchin on the Mediterranean and Atlantic coasts.

}, keywords = {*Genetic Variation, Animals, Atlantic Ocean, DNA, Mitochondrial/analysis, Electron Transport Complex IV/classification/genetics, Haplotypes, Mediterranean Sea, Molecular Sequence Data, Paracentrotus/*genetics, Phylogeny, Protein Subunits/classification/genetics}, isbn = {0962-1083 (Print)0962-1083 (Linking)}, author = {Duran, S. and C. Palacin and Becerro, M. A. and X. Turon and Giribet, G.} } @article {747576, title = {Adiciones a la fauna malacologica del litoral del Garraf (NE de la Peninsula Iberica).}, journal = {Iberus}, volume = {21}, year = {2003}, pages = {177-189}, author = {A Penas and Giribet, G.} } @article {747546, title = {Karripurcellia, a new pettalid genus (Arachnida: Opiliones: Cyphophthalmi) from Western Australia, with a cladistic analysis of the family Pettalidae}, journal = {Invertrabrate Systematics}, volume = {17}, year = {2003}, pages = {387-406}, author = {Giribet, G.} } @article {747521, title = {The first fossil cyphophthalmid (Arachnida: Opiliones), from Bitterfeld amber, Germany}, journal = {Journal of Arachnology}, volume = {31}, year = {2003}, pages = {371-378}, author = {Dunlop, J. A. and Giribet, G.} } @article {747556, title = {New 18S rRNA sequences from enomenioid aplacophorans and the possible origin of persistent exogenous contamination.}, journal = {Journal of Molluscan Studies}, volume = {69}, year = {2003}, pages = {385-387}, author = {Okusu, A. and Giribet, G.} } @article {747566, title = {A new Afrotropical Ogovea (Opiliones, Cyphophthalmi) from Cameroon, with a discussion on the taxonomic characters in the family Ogoveidae.}, journal = {Zootaxa}, volume = {329}, year = {2003}, pages = {1-18}, author = {Giribet, G. and CE Prieto} } @article {747541, title = {A new blind Lamyctes (Chilopoda: Lithobiomorpha) from Tasmania with an analysis of molecular sequence data for the Lamyctes-Henicops Group.}, journal = {Zootaxa}, volume = {152}, year = {2003}, pages = {1-23}, author = {Edgecombe, G. D. and Giribet, G.} } @article {747516, title = {A new Rakaia species (Opiliones, Cyphophthalmi, Pettalidae) from Otaga, New Zealand.}, journal = {Zootaxa}, volume = {133}, year = {2003}, pages = {1-14}, author = {S.L. Boyer and Giribet, G.} } @article {747531, title = {Relationships of Henicopidae (Chilopoda: Lithobiomorpha): New molecular data, classification and biogeography.}, journal = {African Invertebrates}, volume = {44}, year = {2003}, pages = {13-38}, author = {Edgecombe, G. D. and Giribet, G.} } @article {747571, title = {Towards a phylogeny of chitons (Mollusca, Polyplacophora) based on combined analysis of five molecular loci.}, journal = {Organisms Diversity \& Evoution}, volume = {3}, year = {2003}, pages = {281-302}, author = {Okusu, A. and E Schwabe and DJ Eernisse and Giribet, G.} } @article {640681, title = {Evolutionary relationships within the protostome phylum Sipuncula: a molecular analysis of ribosomal genes and histone H3 sequence data}, journal = {Mol Phylogenet Evol}, volume = {27}, number = {3}, year = {2003}, note = {

Maxmen, Amy BKing, Burnett FCutler, Edward BGiribet, GonzaloengComparative Study2003/05/14 05:00Mol Phylogenet Evol. 2003 Jun;27(3):489-503.

}, month = {Jun}, pages = {489-503}, abstract = {

The phylogenetic relationships of the members of the phylum Sipuncula are investigated by means of DNA sequence data from three nuclear markers, two ribosomal genes (18S rRNA and the D3 expansion fragment of 28S rRNA), and one protein-coding gene, histone H3. Phylogenetic analysis via direct optimization of DNA sequence data using parsimony as optimality criterion is executed for 12 combinations of parameter sets accounting for different indel costs and transversion/transition cost ratios in a sensitivity analysis framework. Alternative outgroup analyses are also performed to test whether they affected rooting of the sipunculan topology. Nodal support is measured by parsimony jackknifing and Bremer support values. Results from the different partitions are highly congruent, and the combined analysis for the parameter set that minimizes overall incongruence supports monophyly of Sipuncula, but nonmonophyly of several higher taxa recognized for the phylum. Mostly responsible for this is the split of the family Sipunculidae in three main lineages, with the genus Sipunculus being the sister group to the remaining sipunculans, the genus Phascolopsis nesting within the Golfingiiformes, and the genus Siphonosoma being associated to the Phascolosomatidea. Other interesting results are the position of Phascolion within Golfingiidae and the position of Antillesoma within Aspidosiphonidae. These results are not affected by the loci selected or by the outgroup chosen. The position of Apionsoma is discussed, although more data would be needed to better ascertain its phylogenetic affinities. Monophyly of the genera with multiple representatives (Themiste, Aspidosiphon, and Phascolosoma) is well supported, but not the monophyly of the genera Nephasoma or Golfingia. Interesting phylogeographic questions arise from analysis of multiple representatives of a few species.

}, keywords = {*Phylogeny, Animals, Base Sequence, Genes, rRNA/*genetics, Histones/*genetics, Invertebrates/*classification/genetics, Molecular Sequence Data}, isbn = {1055-7903 (Print)1055-7903 (Linking)}, author = {Maxmen, A. B. and King, B. F. and Cutler, E. B. and Giribet, G.} } @article {640526, title = {Molecules, development and fossils in the study of metazoan evolution; Articulata versus Ecdysozoa revisited}, journal = {Zoology (Jena)}, volume = {106}, number = {4}, year = {2003}, note = {

Giribet, GonzaloengGermany2005/12/15 09:00Zoology (Jena). 2003;106(4):303-26.

}, pages = {303-26}, abstract = {

Two conflicting hypotheses of protostome relationships, Articulata and Ecdysozoa, are reviewed by evaluating the evidence in favor and against each one of them. Understanding early embryonic development and segmentation in non-arthropod non-annelid protostomes seems crucial to the debate. New ways of coding metazoan matrices, avoiding ground-patterns and higher taxa, and incorporating fossil evidence seems the best way to avoid circular debates. Molecular data served as the catalyzer for the Ecdysozoa hypothesis, although morphological support had been implicitly suggested. Most molecular analyses published so far have shown some support for Ecdysozoa, whereas none has ever supported Articulata. Here, new analyses of up to four nuclear loci, including 18S rRNA, myosin heavy chain II, histone H3 and elongation factor 1-alpha are conducted to test the molecular support for Ecdysozoa, and, at least under some parameter sets, most data sets show a clade formed by the molting animals. In contrast, support for Articulata is not found under any analytical conditions.

}, isbn = {0944-2006 (Print)0944-2006 (Linking)}, author = {Giribet, G.} } @article {640531, title = {Stability in phylogenetic formulations and its relationship to nodal support}, journal = {Syst Biol}, volume = {52}, number = {4}, year = {2003}, note = {

Giribet, GonzaloengComparative StudyEngland2003/07/15 05:00Syst Biol. 2003 Aug;52(4):554-64.

}, month = {Aug}, pages = {554-64}, keywords = {*Phylogeny, Animals, Arthropods/classification, Data Interpretation, Statistical, Models, Genetic, Mollusca/classification, Research Design, Sequence Alignment}, isbn = {1063-5157 (Print)1063-5157 (Linking)}, author = {Giribet, G.} } @article {747496, title = {On bivalve phylogeny: a high-level analysis of the Bivalvia (Mollusca) based on combined morphology and DNA sequence data.}, journal = {Invertebrate Biology}, volume = {121}, year = {2002}, pages = {271-324}, author = {Giribet, G. and Wheeler, W.C.} } @article {747481, title = {A cladistic analysis of the cyphophthalmid genera (Opiliones, Cyphophthalmi).}, journal = {Journal of Archnology}, volume = {30}, year = {2002}, pages = {110-128}, author = {Giribet, G. and Boyer, S. L.} } @article {747476, title = {Stylocellus ramblae, a new stylocellid (Opiliones, Cyphophthalmi) from Singapore, with a discussion of the family Stylocellidae.}, journal = {Journal of Archnology}, volume = {30}, year = {2002}, pages = {1-9}, author = {Giribet, G.} } @article {747466, title = {Phylogeny of Henicopidae (Chilopoda: Lithobiomorpha): A combined analysis of morphology and five molecular loci.}, journal = {Systematic Entomology}, volume = {27}, year = {2002}, pages = {31-64}, author = {Edgecombe, G. D. and Giribet, G. and Wheeler, W.C.} } @article {640516, title = {Current advances in the phylogenetic reconstruction of metazoan evolution. A new paradigm for the Cambrian explosion?}, journal = {Mol Phylogenet Evol}, volume = {24}, number = {3}, year = {2002}, note = {

Giribet, GonzaloengReview2002/09/11 10:00Mol Phylogenet Evol. 2002 Sep;24(3):345-57.

}, month = {Sep}, pages = {345-57}, abstract = {

The study of metazoan evolution has fascinated biologists for centuries, and it will certainly keep doing so. Recent interest on the origin of metazoan body plans, early metazoan evolution, genetic mechanisms generating disparity and diversity, molecular clock information, paleontology, and biogeochemistry is contributing to a better understanding of the current phyletic diversity. Unfortunately, the pattern of the metazoan tree of life still shows some important gaps in knowledge. It is the aim of this article to review some of the most important issues related to the inference of the metazoan tree, and point towards possible ways of solving certain obscure aspects in the history of animal evolution. A new hypothesis of the metazoan diversification during the Cambrian explosion is proposed by synthesizing ideas from phylogenetics, molecular evolution, paleontology, and developmental biology.

}, keywords = {*Biological Evolution, Animals, Invertebrates/classification/*genetics, Phylogeny, RNA, Ribosomal}, isbn = {1055-7903 (Print)1055-7903 (Linking)}, author = {Giribet, G.} } @article {640631, title = {DNA multiple sequence alignments}, journal = {EXS}, number = {92}, year = {2002}, note = {

Giribet, GonzaloWheeler, Ward CMuona, JyrkiengSwitzerland2002/04/02 10:00EXS. 2002;(92):107-14.

}, pages = {107-14}, abstract = {

In this chapter we examine the procedure of multiple sequence alignment. We first examine the heuristic procedures commonly used in multiple sequence alignment. Next we examine sources of ambiguity involved in the alignment procedure. We suggest that several alignment parameters be employed to examine alignment sensitivity. We end by presenting an experiment with humans showing the ambiguity involved in manual alignment.

}, keywords = {*Sequence Analysis, DNA, *Sequence Homology, Nucleic Acid, Humans, Sequence Alignment/*methods}, isbn = {1023-294X (Print)1023-294X (Linking)}, author = {Giribet, G. and W.C. Wheeler and Muona, J.} } @article {640596, title = {Phylogeny and systematic position of Opiliones: a combined analysis of chelicerate relationships using morphological and molecular data}, journal = {Cladistics}, volume = {18}, number = {1}, year = {2002}, note = {

Giribet, GonzaloEdgecombe, Gregory DWheeler, Ward CBabbitt, CourtneyengResearch Support, Non-U.S. Gov{\textquoteright}t2003/10/14 05:00Cladistics. 2002 Feb;18(1):5-70.

}, month = {Feb}, pages = {5-70}, abstract = {

The ordinal level phylogeny of the Arachnida and the suprafamilial level phylogeny of the Opiliones were studied on the basis of a combined analysis of 253 morphological characters, the complete sequence of the 18S rRNA gene, and the D3 region of the 28S rRNA gene. Molecular data were collected for 63 terminal taxa. Morphological data were collected for 35 exemplar taxa of Opiliones, but groundplans were applied to some of the remaining chelicerate groups. Six extinct terminals, including Paleozoic scorpions, are scored for morphological characters. The data were analyzed using strict parsimony for the morphological data matrix and via direct optimization for the molecular and combined data matrices. A sensitivity analysis of 15 parameter sets was undertaken, and character congruence was used as the optimality criterion to choose among competing hypotheses. The results obtained are unstable for the high-level chelicerate relationships (except for Tetrapulmonata, Pedipalpi, and Camarostomata), and the sister group of the Opiliones is not clearly established, although the monophyly of Dromopoda is supported under many parameter sets. However, the internal phylogeny of the Opiliones is robust to parameter choice and allows the discarding of previous hypotheses of opilionid phylogeny such as the "Cyphopalpatores" or "Palpatores." The topology obtained is congruent with the previous hypothesis of "Palpatores" paraphyly as follows: (Cyphophthalmi (Eupnoi (Dyspnoi + Laniatores))). Resolution within the Eupnoi, Dyspnoi, and Laniatores (the latter two united as Dyspnolaniatores nov.) is also stable to the superfamily level, permitting a new classification system for the Opiliones.

}, keywords = {*Phylogeny, Animals, Arachnida/anatomy \& histology/*classification/*genetics, Biological Evolution, DNA, Ribosomal, Female, Fossils, Genes, rRNA, Male, Molecular Sequence Data, NASA Discipline Evolutionary Biology, Non-NASA Center, RNA, Ribosomal, 18S/*genetics, RNA, Ribosomal, 28S/*genetics, Sequence Homology, Nucleic Acid}, isbn = {0748-3007 (Print)0748-3007 (Linking)}, author = {Giribet, G. and G.D. Edgecombe and W.C. Wheeler and Babbitt, C.} } @article {640566, title = {{\textquoteright}Pluralism{\textquoteright} and the aims of phylogenetic research}, journal = {EXS}, number = {92}, year = {2002}, note = {

Giribet, GonzaloDeSalle, RobWheeler, Ward CengSwitzerland2002/04/02 10:00EXS. 2002;(92):141-6.

}, pages = {141-6}, abstract = {

In science, and particularly in the field of phylogenetic systematics, investigators may choose among different methods to analyze their data. These methods include neighbor-joining (or other genetic distance approaches), maximum-likelihood, and cladistic parsimony, among others. These distinct methods of analysis differ considerably in how they process information from the observed data. However, many published molecular analyses utilize trees generated under more than one of these methods, which we will call a {\textquoteright}pluralistic{\textquoteright} approach. Here, we explore the statistical, philosophical and operational aspects of the pluralistic approach. We suggest that the pluralistic approach is misguided from all three perspectives and we propose an alternative, logically consistent, strategy as an aim of phylogenetic research.

}, keywords = {*Phylogeny, Animals}, isbn = {1023-294X (Print)1023-294X (Linking)}, author = {Giribet, G. and DeSalle, R. and W.C. Wheeler} } @article {640521, title = {Relationships among metazoan phyla as inferred from 18S rRNA sequence data: a methodological approach}, journal = {EXS}, number = {92}, year = {2002}, note = {

Giribet, GonzaloengSwitzerland2002/04/02 10:00EXS. 2002;(92):85-101.

}, pages = {85-101}, abstract = {

The relationships among the phyla of Metazoa have been investigated by several authors. Different genes have been applied to this problem, but only the ribosomal gene 18S rRNA has been investigated for enough phyla so as to attempt an answer to the question of how the current living forms are related to each other (only one phylum, the Loricifera, is missing). In this chapter, I propose an alternative way to analyze the data obtained from ribosomal genes, or other non-coding genes that show sequence length variation.

}, keywords = {*Phylogeny, Animals, Base Sequence, RNA, Ribosomal, 18S/*genetics, Sequence Analysis, DNA}, isbn = {1023-294X (Print)1023-294X (Linking)}, author = {Giribet, G.} } @article {747461, title = {Some unusual small-subunit ribosomal RNA sequences of metazoans.}, journal = {American Museum Novitates}, volume = {3337}, year = {2001}, pages = {1-14}, author = {Giribet, G. and Wheeler, W.C.} } @article {640591, title = {Arthropod phylogeny based on eight molecular loci and morphology}, journal = {Nature}, volume = {413}, number = {6852}, year = {2001}, note = {

Giribet, GEdgecombe, G DWheeler, W CengResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.England2001/09/15 10:00Nature. 2001 Sep 13;413(6852):157-61.

}, month = {Sep 13}, pages = {157-61}, abstract = {

The interrelationships of major clades within the Arthropoda remain one of the most contentious issues in systematics, which has traditionally been the domain of morphologists. A growing body of DNA sequences and other types of molecular data has revitalized study of arthropod phylogeny and has inspired new considerations of character evolution. Novel hypotheses such as a crustacean-hexapod affinity were based on analyses of single or few genes and limited taxon sampling, but have received recent support from mitochondrial gene order, and eye and brain ultrastructure and neurogenesis. Here we assess relationships within Arthropoda based on a synthesis of all well sampled molecular loci together with a comprehensive data set of morphological, developmental, ultrastructural and gene-order characters. The molecular data include sequences of three nuclear ribosomal genes, three nuclear protein-coding genes, and two mitochondrial genes (one protein coding, one ribosomal). We devised new optimization procedures and constructed a parallel computer cluster with 256 central processing units to analyse molecular data on a scale not previously possible. The optimal {\textquoteright}total evidence{\textquoteright} cladogram supports the crustacean-hexapod clade, recognizes pycnogonids as sister to other euarthropods, and indicates monophyly of Myriapoda and Mandibulata.

}, keywords = {Animals, Arthropods/anatomy \& histology/*classification/genetics, Genes, Insect, Molecular Sequence Data, NASA Discipline Evolutionary Biology, Non-NASA Center, Phylogeny, Ribosomes/genetics}, isbn = {0028-0836 (Print)0028-0836 (Linking)}, author = {Giribet, G. and G.D. Edgecombe and W.C. Wheeler} } @article {640511, title = {Exploring the behavior of POY, a program for direct optimization of molecular data}, journal = {Cladistics}, volume = {17}, number = {1 Pt 2}, year = {2001}, note = {

Giribet, GengComparative StudyResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2002/09/21 10:00Cladistics. 2001 Mar;17(1 Pt 2):S60-70.

}, month = {Mar}, pages = {S60-70}, abstract = {

The performance of the computer program for phylogenetic analysis, POY, and its two implemented methods, "optimization alignment" and "fixed-states optimization," are explored for four data sets. Four gap costs are analyzed for every partition; some of the partitions (the 18S rRNA) are treated as a single fragment or in increasing fragments of 3, 10, and 30. Comparisons within and among methods are undertaken according to gap cost, number of fragments in which the sequences are divided, tree length, character congruence, topological congruence, primary homology statements, and computation time.

}, keywords = {*Phylogeny, *Sequence Homology, Nucleic Acid, *Software, Animals, Invertebrates, Mollusca, RNA, Ribosomal, 18S/*analysis/genetics, RNA, Ribosomal, 28S/*analysis/genetics, spiders}, isbn = {0748-3007 (Print)0748-3007 (Linking)}, author = {Giribet, G.} } @article {747441, title = {Catalogue of the Cyphophthalmi of the World (Arachnida, Opiliones)}, journal = {Revista Iberica de Aracnologia}, volume = {2}, year = {2000}, pages = {49-76}, author = {Giribet, G.} } @article {747446, title = {A review of arthropod phylogeny: new data based on ribosomal DNA sequences and direct character optimization.}, journal = {Cladistics}, volume = {16}, year = {2000}, pages = {204-231}, author = {Giribet, G. and Ribera, C.} } @article {640571, title = {Triploblastic relationships with emphasis on the acoelomates and the position of Gnathostomulida, Cycliophora, Plathelminthes, and Chaetognatha: a combined approach of 18S rDNA sequences and morphology}, journal = {Syst Biol}, volume = {49}, number = {3}, year = {2000}, note = {

Giribet, GDistel, D LPolz, MSterrer, WWheeler, W CengResearch Support, Non-U.S. Gov{\textquoteright}tEngland2002/07/16 10:00Syst Biol. 2000 Sep;49(3):539-62.

}, month = {Sep}, pages = {539-62}, abstract = {

Triploblastic relationships were examined in the light of molecular and morphological evidence. Representatives for all triploblastic "phyla" (except Loricifera) were represented by both sources of phylogenetic data. The 18S ribosomal (rDNA) sequence data for 145 terminal taxa and 276 morphological characters coded for 36 supraspecific taxa were combined in a total evidence regime to determine the most consistent picture of triploblastic relationships for these data. Only triploblastic taxa are used to avoid rooting with distant outgroups, which seems to happen because of the extreme distance that separates diploblastic from triploblastic taxa according to the 18S rDNA data. Multiple phylogenetic analyses performed with variable analysis parameters yield largely inconsistent results for certain groups such as Chaetognatha, Acoela, and Nemertodermatida. A normalized incongruence length metric is used to assay the relative merit of the multiple analyses. The combined analysis having the least character incongruence yields the following scheme of relationships of four main clades: (1) Deuterostomia [((Echinodermata + Enteropneusta) (Cephalochordata (Urochordata + Vertebrata)))]; (2) Ecdysozoa [(((Priapulida + Kinorhyncha) (Nematoda + Nematomorpha)) ((Onychophora + Tardigrada) Arthropoda))]; (3) Trochozoa [((Phoronida + Brachiopoda) (Entoprocta (Nemertea (Sipuncula (Mollusca (Pogonophora (Echiura + Annelida)))))))]; and (4) Platyzoa [((Gnathostomulida (Cycliophora + Syndermata)) (Gastrotricha + Plathelminthes))]. Chaetognatha, Nemertodermatida, and Bryozoa cannot be assigned to any one of these four groups. For the first time, a data analysis recognizes a clade of acoelomates, the Platyzoa (sensu Cavalier-Smith, Biol. Rev. 73:203-266, 1998). Other relationships that corroborate some morphological analyses are the existence of a clade that groups Gnathostomulida + Syndermata (= Gnathifera), which is expanded to include the enigmatic phylum Cycliophora, as sister group to Syndermata.

}, keywords = {*Phylogeny, Animals, DNA, Ribosomal/*genetics, Gnathostoma/classification/*genetics, Invertebrates/classification/*genetics, Platyhelminths/classification/*genetics, RNA, Ribosomal, 18S/*genetics}, isbn = {1063-5157 (Print)1063-5157 (Linking)}, author = {Giribet, G. and Distel, D. L. and Polz, M. and Sterrer, W. and W.C. Wheeler} } @article {747401, title = {From morphology and karyology to molecules. New methods for taxonomical identification of asexual populations of freshwater planarians. A tribute to Professor Mario Benazzi.}, journal = {Italian Journal of Zoology}, volume = {66}, year = {1999}, pages = {207-214}, author = {Baguna, J. and Carranza, S. and M Pala and Ribera, C. and Giribet, G. and Arnedo, M. A. and M Ribas and Riutort, M.} } @article {747431, title = {On gaps.}, journal = {Molecular Phylogenetics and Evolution}, volume = {13}, year = {1999}, pages = {132-143}, author = {Giribet, G. and Wheeler, W.C.} } @article {747426, title = {Phylogeny of the arachnid order Opiliones (Arthropoda) inferred from a combined approach of complete 18S and partial 28S ribosomal DNA sequences and morphology.}, journal = {Molecular Phylogenetics and Evolution}, volume = {11}, year = {1999}, pages = {296-307}, author = {Giribet, G. and Rambla, M. and Carranza, S. and Baguna, J. and Riutort, M. and Ribera, C.} } @article {747416, title = {Revision of the genus Goodallia (Bivalvia: Astartidae) with the description of two new species.}, journal = {Journal of Molluscan Studies}, volume = {65}, year = {1999}, pages = {251-265}, author = {Giribet, G. and A Penas} } @article {640626, title = {On gaps}, journal = {Mol Phylogenet Evol}, volume = {13}, number = {1}, year = {1999}, note = {

Giribet, GWheeler, W CengComparative StudyResearch Support, Non-U.S. Gov{\textquoteright}t1999/10/06Mol Phylogenet Evol. 1999 Oct;13(1):132-43.

}, month = {Oct}, pages = {132-43}, abstract = {

Gaps result from the alignment of sequences of unequal length during primary homology assessment. Viewed as character states originating from particular biological events (mutation), gaps contain historical information suitable for phylogenetic analysis. The effect of gaps as a source of phylogenetic data is explored via sensitivity analysis and character congruence among different data partitions. Example data sets are provided to show that gaps contain important phylogenetic information not recovered by those methods that omit gaps in their calculations. However, gap cost schemes are arbitrary (although they must be explicit) and thus data exploration is a necessity of molecular analyses, while character congruence is necessary as an external criterion for hypothesis decision.

}, keywords = {*Phylogeny, Animals, Arachnida/classification/genetics, Base Sequence, DNA, Ribosomal/genetics, DNA/genetics, Likelihood Functions, Nucleic Acid Conformation, RNA/chemistry/genetics, Sequence Alignment, Sequence Homology, Nucleic Acid}, isbn = {1055-7903 (Print)1055-7903 (Linking)}, author = {Giribet, G. and Wheeler, W.C.} } @article {640561, title = {Internal phylogeny of the Chilopoda (Myriapoda, Arthropoda) using complete 18S rDNA and partial 28S rDNA sequences}, journal = {Philos Trans R Soc Lond B Biol Sci}, volume = {354}, number = {1380}, year = {1999}, note = {

Giribet, GCarranza, SRiutort, MBaguna, JRibera, CengResearch Support, Non-U.S. Gov{\textquoteright}tENGLAND1999/03/24Philos Trans R Soc Lond B Biol Sci. 1999 Jan 29;354(1380):215-22.

}, month = {Jan 29}, pages = {215-22}, abstract = {

The internal phylogeny of the {\textquoteright}myriapod{\textquoteright} class Chilopoda is evaluated for 12 species belonging to the five extant centipede orders, using 18S rDNA complete gene sequence and 28S rDNA partial gene sequence data. Equally and differentially weighted parsimony, neighbour-joining and maximum-likelihood were used for phylogenetic reconstruction, and bootstrapping and branch support analyses were performed to evaluate tree topology stability. The results show that the Chilopoda constitute a monophyletic group that is divided into two lines, Notostigmophora (= Scutigeromorpha) and Pleurostigmophora, as found in previous morphological analyses. The Notostigmophora are markedly modified for their epigenic mode of life. The first offshoot of the Pleurostigmophora are the Lithobiomorpha, followed by the Craterostigmomorpha and by the Epimorpha s. str. (= Scolopendromorpha + Geophilomorpha), although strong support for the monophyly of the Epimorpha s. lat. (= Craterostigmomorpha + Epimorpha s. str.) is only found in the differentially weighted parsimony analysis.

}, keywords = {*Phylogeny, Animals, Arthropods/*physiology, Biological Evolution, DNA, Ribosomal/*genetics, Molecular Sequence Data}, isbn = {0962-8436 (Print)0962-8436 (Linking)}, author = {Giribet, G. and Carranza, S. and Riutort, M. and Baguna, J. and Ribera, C.} } @article {640606, title = {Phylogeny of the arachnid order Opiliones (Arthropoda) inferred from a combined approach of complete 18S and partial 28S ribosomal DNA sequences and morphology}, journal = {Mol Phylogenet Evol}, volume = {11}, number = {2}, year = {1999}, note = {

Giribet, GRambla, MCarranza, SBaguna, JRiutort, MRibera, CengResearch Support, Non-U.S. Gov{\textquoteright}t1999/04/07Mol Phylogenet Evol. 1999 Mar;11(2):296-307.

}, month = {Mar}, pages = {296-307}, abstract = {

The phylogenetic relationships among the main evolutionary lines of the arachnid order Opiliones were investigated by means of molecular (complete 18S rDNA and the D3 region of the 28S rDNA genes) and morphological data sets. Equally and differentially weighted parsimony analyses of independent and combined data sets provide evidence for the monophyly of the Opiliones. In all the analyses, the internal relationships of the group coincide in the monophyly of the following main groups: Cyphophthalmi, Eupnoi Palpatores, Dyspnoi Palpatores, and Laniatores. The Cyphophthalmi are monophyletic and sister to a clade that includes all the remaining opilionid taxa (=Phalangida). Within the Phalangida the most supported hypothesis suggests that Palpatores are paraphyletic, as follows: (Eupnoi (Dyspnoi + Laniatores)), but the alternative hypothesis (Laniatores (Eupnoi + Dyspnoi)) is more parsimonious in some molecular data analyses. Relationships within the four main clades are also addressed. Evolution of some morphological characters is discussed, and plesiomorphic states of these characters are evaluated using molecular data outgroup polarization. Finally, Martens{\textquoteright} hypothesis of opilionid evolution is assessed in relation to our results.

}, keywords = {*Phylogeny, Animals, Arachnida/anatomy \& histology/*classification/*genetics, DNA, Ribosomal/*genetics, Models, Biological, Molecular Sequence Data, Sequence Analysis, DNA}, isbn = {1055-7903 (Print)1055-7903 (Linking)}, author = {Giribet, G. and Rambla, M. and Carranza, S. and Baguna, J. and Riutort, M. and Ribera, C.} } @article {640621, title = {The position of arthropods in the animal kingdom: Ecdysozoa, islands, trees, and the "Parsimony ratchet"}, journal = {Mol Phylogenet Evol}, volume = {13}, number = {3}, year = {1999}, note = {

Giribet, GWheeler, W CengCommentResearch Support, Non-U.S. Gov{\textquoteright}t2000/01/06 09:00Mol Phylogenet Evol. 1999 Dec;13(3):619-23.

}, month = {Dec}, pages = {619-23}, keywords = {*Models, Biological, *Phylogeny, Animals, Arthropods/classification/*physiology, Biology/*methods, DNA, Ribosomal/genetics, Invertebrates/classification/physiology}, isbn = {1055-7903 (Print)1055-7903 (Linking)}, author = {Giribet, G. and W.C. Wheeler} } @article {640551, title = {What can 18S rDNA do for bivalve phylogeny?}, journal = {J Mol Evol}, volume = {48}, number = {3}, year = {1999}, note = {

Giribet, GCarranza, Seng2000/01/08J Mol Evol. 1999 Mar;48(3):256-61.

}, month = {Mar}, pages = {256-61}, keywords = {*DNA, Ribosomal, Animals, Data Interpretation, Statistical, Mollusca/*classification/genetics, Phylogeny, RNA, Ribosomal, 18S/*genetics, Sequence Alignment}, isbn = {0022-2844 (Print)0022-2844 (Linking)}, author = {Giribet, G. and Carranza, S.} } @article {747386, title = {Low densities of sea urchins influence the structure of algal assemblages in the western Mediterranean.}, journal = {Journal of Sea Research}, volume = {39}, year = {1998}, pages = {281-290}, author = {C. Palacin and Giribet, G. and S Carner and L Dantart and Turon, X.} } @article {747366, title = {{\textquoteright}Molluscs as evolving constructions{\textquoteright} and phylogenetic deconstructivism.}, journal = {Iberus}, volume = {16}, year = {1998}, pages = {123-128}, author = {Giribet, G.} } @article {747371, title = {A new Epilepton species (Bivalvia, Montacutidae) from the western Mediterranean.}, journal = {Iberus}, volume = {16}, year = {1998}, pages = {117-121}, author = {Giribet, G. and A. Penas} } @article {747391, title = {Stock evaluation of three littoral echinoid species on the Catalan coast (nrth-western Mediterranean)}, journal = {P.S.Z.N.: Marine Ecology}, volume = {19}, year = {1998}, pages = {163-177}, author = {C. Palacin and Turon, X. and M Ballesteros and Giribet, G. and Lopez, S.} } @article {747376, title = {Terrestrial planarians (Platyhelminthes, Tricladida, Terricola) from the Iberian Peninsula: first records on the family Rhynchodemidae with the description of a new Microplana species.}, journal = {Contributions to Zoology}, volume = {67}, year = {1998}, pages = {267-276} } @article {640611, title = {The position of arthropods in the animal kingdom: a search for a reliable outgroup for internal arthropod phylogeny}, journal = {Mol Phylogenet Evol}, volume = {9}, number = {3}, year = {1998}, note = {

Giribet, GRibera, CengResearch Support, Non-U.S. Gov{\textquoteright}t1998/07/21 02:14Mol Phylogenet Evol. 1998 Jun;9(3):481-8.

}, month = {Jun}, pages = {481-8}, abstract = {

Morphological evidence for the phylogeny of the animal kingdom has been discussed by numerous authors. DNA sequencing and phylogenetic methods for analyzing these data are alternative approaches to animal phylogeny, but the phenomenon of long branch attraction and poor taxonomic sampling have caused misinterpretations of metazoan relationships. Here we report a cladistic approach to metazoan evolution including 133 18S rDNA sequences of 31 animal phyla. Despite the difficulties associated with analyzing large data sets, our data suggest that the Bilateria and Protostomia are monophyletic. The internal phylogeny of the protostomes is divided into two main clades. One clade includes the classical protostome worms (annelids, sipunculans, echiurans, pogonophorans, and vestimentiferans), mollusks, nemerteans, "lophophorates," platyhelminths, rotiferans, and acanthocephalans, although the internal resolution of the clade is very low. The second clade includes arthropods and other molting animals: tardigrades, onychophorans, nematodes, nematomorphans, kinorhynchs, and priapulans. The arthropods and related phyla lack a ciliated larvae, lack a multiciliate (locomotory) epithelium, and share many features, notably, a reduced coelomic cavity and the presence of a cuticle which molts. The use of these outgroups within the molting clade to root arthropod phylogenies is recommended instead of using annelids or other spiralians. The data are quite conclusive in those phyla with a good taxonomic sampling (i.e., platyhelminths and arthropods).

}, keywords = {*Evolution, Molecular, *Phylogeny, Animals, Arthropods/*classification/*genetics/physiology, DNA, Ribosomal/chemistry/*genetics, Molecular Sequence Data, Molting, RNA, Ribosomal, 18S/*genetics}, isbn = {1055-7903 (Print)1055-7903 (Linking)}, author = {Giribet, G. and Ribera, C.} } @article {747356, title = {Malacological marine fauna from Garraf coast (NE Iberian Peninsula)}, journal = {Iberus}, volume = {15}, year = {1997}, pages = {41-93}, author = {Giribet, G. and A. Penas} } @article {747361, title = {Patch recolonization through migration by the sea urchin Paracentrotus lividus (Lamarck) in communities with high algal cover and low sea urchin densities.}, journal = {Cahiers de Biologie Marine}, volume = {38}, year = {1997}, pages = {267-271}, author = {C. Palacin and Giribet, G. and X. Turon} } @article {640426, title = {Evidence that two types of 18S rDNA coexist in the genome of Dugesia (Schmidtea) mediterranea (Platyhelminthes, Turbellaria, Tricladida)}, journal = {Mol Biol Evol}, volume = {13}, number = {6}, year = {1996}, note = {

Carranza, SGiribet, GRibera, CBagunaRiutort, MengComparative StudyResearch Support, Non-U.S. Gov{\textquoteright}t1996/07/01Mol Biol Evol. 1996 Jul;13(6):824-32.

}, month = {Jul}, pages = {824-32}, abstract = {

Sequences of 18S ribosomal DNA (rDNA) are increasingly being used to infer phylogenetic relationships among living taxa. Although the 18S rDNA belongs to a multigene family, all its copies are kept homogeneous by concerted evolution (Dover 1982; Hillis and Dixon 1991). To date, there is only one well-characterized exception to this rule, the protozoan Plasmodium (Gunderson et al. 1987; Waters, Syin, and McCutchan 1989; Qari et al. 1994). Here we report the 1st case of 18S rDNA polymorphism within a metazoan species. Two types (I and II) of 18S rDNA have been found and sequenced in the platyhelminth Dugesia (Schmidtea) mediterranea (Turbellaria, Seriata, Tricladida). Southern blot analysis suggested that both types of rDNA are present in the genome of this flatworm. This was confirmed through sequence comparisons and phylogenetic analysis using the neighbor-joining method and bootstrap test. Although secondary structure analysis suggests that both types are functional, only type I seems to be transcribed to RNA, as demonstrated by Northern blot analysis. The finding of different types of 18S rDNAs in a single genome stresses the need for analyzing a large number of clones whenever 18S sequences obtained by PCR amplification and cloning are being used in phylogenetic reconstruction.

}, keywords = {*Genes, Helminth, Animals, Base Sequence, DNA, Ribosomal/*genetics, Gene Expression Regulation, Molecular Sequence Data, Phylogeny, Plasmodium/genetics, RNA, Ribosomal, 18S/classification/*genetics, Sequence Alignment, Sequence Homology, Nucleic Acid, Species Specificity, Turbellaria/*genetics}, isbn = {0737-4038 (Print)0737-4038 (Linking)}, author = {Carranza, S. and Giribet, G. and Ribera, C. and Baguna, and Riutort, M.} } @article {640556, title = {First molecular evidence for the existence of a Tardigrada + Arthropoda clade}, journal = {Mol Biol Evol}, volume = {13}, number = {1}, year = {1996}, note = {

Giribet, GCarranza, SBaguna, JRiutort, MRibera, CengResearch Support, Non-U.S. Gov{\textquoteright}t1996/01/01Mol Biol Evol. 1996 Jan;13(1):76-84.

}, month = {Jan}, pages = {76-84}, abstract = {

The complete 18S rDNA gene sequence of Macrobiotus group hufelandi (Tardigrada) was obtained and aligned with 18S rDNA and rRNA gene sequences of 24 metazoans (mainly protostomes). Discrete character (maximum-parsimony) and distance (neighbor-joining) methods were used to infer their phylogeny. The evolution of bootstrap proportions with sequence length (pattern of resolved nodes, PRN) was studied to test the resolution of the nodes in neighbor-joining trees. The results show that arthropods are monophyletic. Tardigrades represent the sister group of arthropods (in parsimony analyses) or they are related with crustaceans (distance analysis and PRN). Arthropoda are divided into two main evolutionary lines, the Hexapoda + Crustacea line (weakly supported), and the Myriapoda + Chelicerata line. The Hexapoda + Crustacea line includes Pentastomida, but the internal resolution is far from clear. The Insecta (Ectognatha) are monophyletic, but no evidence for the monophyly of Hexapoda is found. The Chelicerata are a monophyletic group and the Myriapoda cluster close to Arachnida. Overall, the results obtained represent the first molecular evidence for a Tardigrada + Arthropoda clade. In addition, the congruence between molecular phylogenies of the Arthropoda from other authors and this obtained here indicates the need to review those obtained solely on morphological characters.

}, keywords = {*Phylogeny, Animals, Arthropods/*genetics, Base Sequence, Evolution, Molecular, Molecular Sequence Data, Sequence Analysis}, isbn = {0737-4038 (Print)0737-4038 (Linking)}, author = {Giribet, G. and Carranza, S. and Baguna, J. and Riutort, M. and Ribera, C.} } @article {747351, title = {Growth and population structure of Paracentrotus lividus (Echinodermata: Echinoidea) in two contrasting habitats. }, journal = {Marine Ecology Progress Series}, volume = {122}, year = {1995}, pages = {193-204}, author = {Turon, X. and Giribet, G. and S. Lopez and C. Palacin} } @article {747346, title = {Dos neuvas localidades para un nemertino de agua dulce del genero Prostoma Duges, 1828 (Hoplonemertini: Tetrastemmatidae) en la Penisula Iberica}, journal = {Graellsia}, volume = {50}, year = {1994}, pages = {170-172}, author = {Giribet de Sebastian, G and S Carranza Gil Dolz del Castellar} }