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.
Laumer, C.E.,, Fernández, R., Lemer, S., Combosch, D. J., Kocot, K., Andrade, S. C. S., Sterrer, W., M.V. Sørensen, and G. Giribet. 2019. “
Revisiting metazoan phylogeny with genomic sampling of all phyla.” Proceedings of the Royal Society B: Biological Sciences 286: 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.
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.
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.
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 “fresh” specimens preserved in >95% ethanol and stored at −80°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%–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.
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—Caenogastropoda, Heterobranchia, Neritimorpha, Patellogastropoda and Vetigastropoda—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.
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 ‘? Gen. enigmaticus’. 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.; ‘? Gen. enigmaticus Martens, 1969’ is an invalid name according to the ICZN; the corresponding taxon is redescribed and formally named as Neogovea enigmatica Martens, sp. nov.
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—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.