Publications

2017
Kvist, S., A. Oceguera-Figueroa, M. Tessler, J. Jiménez-Armenta, R.M. Freeman, G. Giribet, and M.E. Siddall. 2017. “When predator becomes prey: investigating the salivary transcriptome of the shark-feeding leech Pontobdella macrothela (Hirudinea: Piscicolidae).” Zoological Journal of the Linnean Society 179 (4): 725–737. Publisher's VersionAbstract
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.
2016
Wheeler, W.C., and G. Giribet. 2016. “Molecular data in systematics: a promise fulfilled, a future beckoning.” The Future of Phylogenetic Systematics: The Legacy of Willi Hennig, 13: 229-343. Cambridge University Press, 13, 229-343.
Costa, C.S., and G. Giribet. 2016. “Taxonomic Notes on Mesoperipatus tholloni (Onychophora: Peripatidae), an Elusive Velvet Worm from Gabon.” Breviora 552: 1-10. Publisher's VersionAbstract
The velvet worm Mesoperipatus tholloni (Bouvier, 1898) is among the least understood of the velvet worms, the only species in the genus Mesoperipatus Evans, 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 São Paulo (MZUSP). We also provide the first scanning electron micrographs of this species.
Lemer, S., D.J. Combosch, F. Sotto, G. Giribet, D. Dumale, and V. Soliman. 2016. “The family Pinnidae (Bivalvia) in the Philippine archipelago: observations on its distribution and phylogeography.” The Nautilus 130 (4): 137–145. Publisher's VersionAbstract

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. 

Sundberg, P., S.C.S. Andrade, T. Bartolomaeus, P. Beckers, J. von Döhren, D. Krämer, R. Gibson, et al. 2016. “The future of nemertean taxonomy (phylum Nemertea) — a proposal.” Zoologica Scripta 45 (6): 579–582. Publisher's Version
Selden, P.A., J. A. Dunlop, G. Giribet, W. Zhang, and D. Ren. 2016. “The oldest armoured harvestman (Arachnida: Opiliones: Laniatores), from Upper Cretaceous Myanmar amber.” Cretaceous Research 65: 206-212. Publisher's VersionAbstract
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. 44–49 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.
Giribet, G. 2016. “Zoology: At Last an Exit for Ctenophores.” Current Biology 26 (20): R918-R920. Publisher's Version
Giribet, G., S.L. Boyer, C.M. Baker, R. Fernández, Sharma. PP, BL de Bivort, S. R. Daniels, M. S. Harvey, and C.E. Griswold. 2016. “A molecular phylogeny of the temperate Gondwanan family Pettalidae (Arachnida, Opiliones, Cyphophthalmi) and the limits of taxonomic sampling.” Zoological Journal of the Linnean Society 178 (3): 523–545. Publisher's VersionAbstract
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 & Sørensen, 1904,syn. nov. The following new combinations are proposed: Parapurcellia transvaalica (Lawrence, 1963comb. nov.Purcellia argasiformis (Lawrence, 1931comb. nov.
Giribet, G. 2016. “Genomics and the animal tree of life: conflicts and future prospects.” Zoologica Scripta 45 (S1): 14–21. Publisher's VersionAbstract
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.
Carbayo, F., T.M. Francoy, and G. Giribet. 2016. “Non-destructive imaging to describe a new species of Obama land planarian (Platyhelminthes, Tricladida).” Zoologica Scripta 45 (5): 566–578. Publisher's VersionAbstract
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 – difficult to interpret – 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 μCT-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 μCT data and virtual histological sections were deposited in an open repository (GigaDB) and are freely available. This work leads us to conclude that μCT 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.
Garwood, R. J., G.D. Edgecombe, S. Charbonnier, D. Chabard, D. Sotty, and G. Giribet. 2016. “Carboniferous Onychophora from Montceau-les-Mines, France, and onychophoran terrestrialization.” Invertebrate Biology 135 (3): 179–190. Publisher's VersionAbstract
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 Lagerstätte, 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.
Giribet, G., G. Hormiga, and G.D. Edgecombe. 2016. “The meaning of categorical ranks in evolutionary biology.” Organisms Diversity & Evolution 16 (3): 427–430. Publisher's VersionAbstract
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.
Lozano-Fernandez, J., R. Carton, A.R. Tanner, M.N. Puttick, M. Blaxter, J. Vinther, J. Olesen, G. Giribet, G.D. Edgecombe, and D. Pisani. 2016. “A molecular palaeobiological exploration of arthropod terrestrialization.” Philosophical Transactions of the Royal Society B 371: 20150133. Publisher's VersionAbstract
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.
Giribet, G. 2016. “Zoology: Invertebrates that Parasitize Invertebrates.” Current Biology 26 (13): R537-R539. Publisher's Version
Couto, D.R., P. Bouchet, Y.I. Kantor, L.R.L. Simone, and G. Giribet. 2016. “A multilocus molecular phylogeny of Fasciolariidae (Neogastropoda: Buccinoidea).” Molecular Phylogenetics and Evolution 99: 309–322. Publisher's VersionAbstract
The neogastropod family Fasciolariidae Gray, 1853 – 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 Mörch, 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.
Gonzalez, V. L., S. Lemer, R. Bieler, and G. Giribet. 2016. “Cementing mussels to oysters in the pteriomorphian tree: a phylogenomic approach.” Proceedings of the Royal Society B 283: 20160857. Publisher's VersionAbstract
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.
Dunlop, J. A., P.A. Selden, and G. Giribet. 2016. “Penis morphology in a Burmese amber harvestman.” The Science of Nature 103 (11): 1-5. Publisher's VersionAbstract
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.
Harvey, M. S., J.A. Huey, M.J. Hillyer, E. McIntyre, and G. Giribet. 2016. “The first troglobitic species of Gymnobisiidae (Pseudoscorpiones : Neobisioidea), from Table Mountain (Western Cape Province, South Africa) and its phylogenetic position.” Invertebrate Systematics 30 (1): 75-85. Publisher's VersionAbstract
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 – described as Gymnobisium inukshuk Harvey & Giribet, sp. nov. – 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.
Combosch, D.J., and G. Giribet. 2016. “Clarifying phylogenetic relationships and the evolutionary history of the bivalve order Arcida (Mollusca: Bivalvia: Pteriomorphia).” Molecular Phylogenetics and Evolution 94: 298-312. Publisher's VersionAbstract
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.
Fernandez, R., G.D. Edgecombe, and G. Giribet. 2016. “Exploring Phylogenetic Relationships within Myriapoda and the Effects of Matrix Composition and Occupancy on Phylogenomic Reconstruction.” Systematic Biology 65 (5): 871–889. Publisher's VersionAbstract

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.

Pages