Improved phylogenetic resolution within Siphonophora (Cnidaria) with implications for trait evolution

Siphonophores are a diverse group of hydrozoans (Cnidaria) that are found at most depths of the ocean - from the surface, like the familiar Portuguese man of war, to the deep sea. They play important roles in ocean ecosystems, and are among the most abundant gelatinous predators. A previous phylogenetic study based on two ribosomal RNA genes provided insight into the internal relationships between major siphonophore groups. There was, however, little support for many deep relationships within the clade Codonophora. Here, we present a new siphonophore phylogeny based on new transcriptome data from 29 siphonophore species analyzed in combination with 14 publicly available genomic and transcriptomic datasets. We use this new phylogeny to reconstruct several traits that are central to siphonophore biology, including sexual system (monoecy vs. dioecy), gain and loss of zooid types, life history traits, and habitat. The phylogenetic relationships in this study are largely consistent with the previous phylogeny, but we find strong support for new clades within Codonophora that were previously unresolved. These results have important implications for trait evolution within Siphonophora, including favoring the hypothesis that monoecy arose at least twice

The role of networks to overcome large-scale challenges in tomography : the non-clinical tomography users research network

Our ability to visualize and quantify the internal structures of objects via computed tomography (CT) has fundamentally transformed science. As tomographic tools have become more broadly accessible, researchers across diverse disciplines have embraced the ability to investigate the 3D structure-function relationships of an enormous array of items. Whether studying organismal biology, animal models for human health, iterative manufacturing techniques, experimental medical devices, engineering structures, geological and planetary samples, prehistoric artifacts, or fossilized organisms, computed tomography has led to extensive methodological and basic sciences advances and is now a core element in science, technology, engineering, and mathematics (STEM) research and outreach toolkits. Tomorrow's scientific progress is built upon today's innovations. In our data-rich world, this requires access not only to publications but also to supporting data. Reliance on proprietary technologies, combined with the varied objectives of diverse research groups, has resulted in a fragmented tomography-imaging landscape, one that is functional at the individual lab level yet lacks the standardization needed to support efficient and equitable exchange and reuse of data. Developing standards and pipelines for the creation of new and future data, which can also be applied to existing datasets is a challenge that becomes increasingly difficult as the amount and diversity of legacy data grows. Global networks of CT users have proved an effective approach to addressing this kind of multifaceted challenge across a range of fields. Here we describe ongoing efforts to address barriers to recently proposed FAIR (Findability, Accessibility, Interoperability, Reuse) and open science principles by assembling interested parties from research and education communities, industry, publishers, and data repositories to approach these issues jointly in a focused, efficient, and practical way. By outlining the benefits of networks, generally, and drawing on examples from efforts by the Non-Clinical Tomography Users Research Network (NoCTURN), specifically, we illustrate how standardization of data and metadata for reuse can foster interdisciplinary collaborations and create new opportunities for future-looking, large-scale data initiatives

Resolving the evolutionary relationships of molluscs with phylogenomic tools

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.Organismic and Evolutionary Biolog

Data from: Resolving the evolutionary relationships of molluscs with phylogenomic tools

Molluscs (snails, octopuses, clams, and relatives) have great body plan disparity, and among 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 morphological evolution within the group. These include whether the shell-less vermiform aplacophoran molluscs diverged prior to the origin of the shelled molluscs (Conchifera), or secondarily lost their shell. Monoplacophora were not included in molecular studies until recently , when it was proposed that they constitute a clade with chitons named Serialia, 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 be shell-less but with a typical molluscan radula and serially repeated gills. In order to better resolve the relationships among molluscs we generated transcriptome data for 15 molluscs 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 1185 gene regions using multiple models and methods. Our results support a clade Aculifera, containing the three molluscan groups with spicules but without true shells, as well as the monophyly of Conchifera—the shelled molluscs. Monoplacophora are not the sister group to other Conchifera, but constitute the sister group to the highly modified cephalopods. Strong support is found for a clade comprised of 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 in mollusc evolution, development and anatomy

Extraordinary eyes reveal hidden diversity within the holopelagic genus Paraphronima (Amphipoda: Hyperiidea)

Highlights: • The holopelagic amphipod Paraphronima is shown to contain hidden genetic diversity. • Diversity appears biogeographically restricted to regional scales. • A new species is described using a morpho-molecular approach. • Compound eye characters are shown to be useful in distinguishing species. • The inclusion of compound eyes is recommended in taxonomic studies of Hyperiidea. Holopelagic animals were long assumed to have widespread geographic distributions due to the failure to recognize hydrographic species' barriers in the open ocean. As molecular genetic tools are more commonly used to study the ocean's inhabitants, diversity is found to be substantially higher than when inferred from morphological taxonomies alone. Here, we investigate the morphological and genetic diversity of hyperiid amphipods within the genus Paraphronima, currently comprising two supposedly cosmopolitan species. By combining phylogenetic analyses and four species delimitation methods (GMYC, mPTP, bPTP, ABGD), we reveal substantial species-level genetic variation. Instead of two species inhabiting multiple ocean basins, the biogeography of Paraphronima species appears to be limited to more regional scales. Moreover, there is morphological evidence to corroborate the observed genetic diversity. By using an integrative morpho-molecular approach, a third species from the Gulf of California, Paraphronima robisoni sp. nov., is described. Interestingly, the morphological characters that best distinguish the species within the genus are characters of the compound eyes, which have rarely been used for taxonomy despite being the most obvious and varied features of hyperiids. Our results warrant further investigation of presumably cosmopolitan holopelagic amphipods, while we recommend the inclusion of eye morphology in future taxonomic studies

Data from: Phylogenomic analyses of deep gastropod relationships reject Orthogastropoda

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

Description, redescription and revision of sixteen putatively closely related species of Echinoderes (Kinorhyncha: Cyclorhagida), with the proposition of a new species group – the Echinoderes dujardinii group

Thirteen species of Echinoderes with nearly identical spine/tube patterns, and apparently similar tergal extensions were re-examined and compared. Based on this, redescriptions and/or emended species diagnoses are provided for Echinoderes aureus, E. dujardinii, E. gerardi, E. imperforatus, E. pacificus, E. pilosus, E. sensibilis, E. sublicarum and E. worthingi, and new details about cuticular structures are added for E. kozloffi and E. gizoensis. The new information derived from the redescriptions, and the subsequent comparative studies revealed that: 1) the holotype of Echinoderes lanceolatus is identical with the types of Echinoderes aureus, and E. lanceolatus is thus a junior synonym of E. aureus; other potentially synonymous species that should be addressed further in the future include: E. dujardinii + E. gerardi; E. imperforatus + E. sensibilis, and E. pacificus + E. sublicarum; 2) the paratypes of E. lanceolatus represented a different yet undescribed species, here described as E. songae Sørensen & Chang sp. nov.; 3) a comparison with literature information about E. ehlersi showed that the species is so insufficiently described that a redescription of topotype material is required before the species should be considered for taxonomic comparison; 4) specimens from the Andaman Islands, India, that previously have been reported as Echinoderes cf. ehlersi represent two different undescribed species, of which one is described as E. chandrasekharai Sørensen & Chatterjee sp. nov. and the other is left undescribed due to the limited material available; 5) out of a total of fifteen addressed species, it is proposed that eleven represent a putatively monophyletic group that is named the Echinoderes dujardinii group. The group includes following species: E. dujardinii, E. ehlersi, E. gerardi, E. imperforatus, E. kozloffi, E. sensibilis, E. pacificus, E. sublicarum, E. songae Sørensen & Chang sp. nov., E. chandrasekharai Sørensen & Chatterjee sp. nov., and Echinoderes sp. from the Andaman Islands, and is supported by a similar spine/tube pattern (except for variation regarding the presence of lateral accessory tubes on segment 8); generally short middorsal spines, especially on segments 4 to 6; glandular cell outlets type 1 always present in middorsal positions on segments 1 to 3, and in subdorsal positions on segments 4 to 9; glandular cell outlets type 2 always present in laterodorsal or midlateral positions on segment 8, and sometimes in same positions on segment 9 but never at any other segments or positions; female papillae always present on sternal plates of segments 7 and 8, and occasionally also on segment 6; tergal extensions well-spaced, triangular, gradually tapered cones, and pectinate fringes of sternal extensions are differentiated into seta-like tufts. The comparisons furthermore showed potential taxonomic significance of two echinoderid character traits that previously have been slightly neglected as diagnostic traits, namely the presence and appearance of female papillae, and the dorsal pattern of glandular cell outlets type 1. Female papillae may occur on the sternal plates of segments 6 to 8, but the positions may differ from ventrolateral to ventromedial, and the morphology of the intracuticular substructure also differ at species level. Information about position and morphology of female papillae proved helpful for species recognition, but it might also provide information of phylogenetic importance. Analyses of glandular cell outlet type 1 patterns on the dorsal sides of segments 1 to 9 in species of Echinoderidae, revealed several apparently unique or rare patterns, but also three distinct patterns that applied to larger groups of species. One pattern is the one present in all species of the E. dujardinii group, whereas the other two common patterns included 1) middorsal outlets on segments 1 to 3, and paradorsal outlets on segments 4 to 9 (found in 27 species), and 2) middorsal outlets on segments 1 to 3, 5 and 7, and paradorsal outlets on segments 4, 6 and 8 to 9 (found in 27 species)

Spiralian phylogeny informs the evolution of microscopic lineages

SummaryDespite rapid advances in the study of metazoan evolutionary history [1], phylogenomic analyses have so far neglected a number of microscopic lineages that possess a unique combination of characters and are thus informative for our understanding of morphological evolution. Chief among these lineages are the recently described animal groups Micrognathozoa and Loricifera, as well as the two interstitial “Problematica” Diurodrilus and Lobatocerebrum [2]. These genera show a certain resemblance to Annelida in their cuticle and gut [3, 4]; however, both lack primary annelid characters such as segmentation and chaetae [5]. Moreover, they show unique features such as an inverted body-wall musculature or a novel pharyngeal organ. This and their ciliated epidermis have led some to propose relationships with other microscopic spiralians, namely Platyhelminthes, Gastrotricha, and in the case of Diurodrilus, with Micrognathozoa [6, 7]—lineages that are grouped by some analyses into “Platyzoa,” a clade whose status remains uncertain [1, 8–11]. Here, we assess the interrelationships among the meiofaunal and macrofaunal members of Spiralia using 402 orthologs mined from genome and transcriptome assemblies of 90 taxa. Lobatocerebrum and Diurodrilus are found to be deeply nested members of Annelida, and unequivocal support is found for Micrognathozoa as the sister group of Rotifera. Analyses using site-heterogeneous substitution models further recover a lophophorate clade and position Loricifera + Priapulida as sister group to the remaining Ecdysozoa. Finally, with several meiofaunal lineages branching off early in the diversification of Spiralia, the emerging concept of a microscopic, acoelomate, direct-developing ancestor of Spiralia is reviewed

Assembled data generated for study

This archive contains the transcriptome sequences generated for this study

Phylogenetic matrices and trees

Contained within this archive are the phylogenetic matrices and trees generated for this study. NOTE: Please use revised_phylo.tar.gz, an updated version of the data file that was added on 2012-11-15