Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa

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.Peer reviewe

Investigating the Bivalve Tree of Life -- an exemplar-based approach combining molecular and novel morphological characters.

To re-evaluate the relationships of the major bivalve lineages, we amassed detailed morpho-anatomical, ultrastructural and molecular sequence data for a targeted selection of exemplar bivalves spanning the phylogenetic diversity of the class. We included molecular data for 103 bivalve species (up to five markers) and also analysed a subset of taxa with four additional nuclear protein-encoding genes. Novel as well as historically employed morphological characters were explored, and we systematically disassembled widely used descriptors such as gill and stomach ‘types’. Phylogenetic analyses, conducted using parsimony direct optimisation and probabilistic methods on static alignments (maximum likelihood and Bayesian inference) of the molecular data, both alone and in combination with morphological characters, offer a robust test of bivalve relationships. A calibrated phylogeny also provided insights into the tempo of bivalve evolution. Finally, an analysis of the informativeness of morphological characters showed that sperm ultrastructure characters are among the best morphological features to diagnose bivalve clades, followed by characters of the shell, including its microstructure. Our study found support for monophyly of most broadly recognised higher bivalve taxa, although support was not uniform for Protobranchia. However, monophyly of the bivalves with protobranchiate gills was the best-supported hypothesis with incremental morphological and/or molecular sequence data. Autobranchia, Pteriomorphia, Heteroconchia, Palaeoheterodonta, Archiheterodonta, Euheterodonta, Anomalodesmata and Imparidentia new clade ( = Euheterodonta excluding Anomalodesmata) were recovered across analyses, irrespective of data treatment or analytical framework. Another clade supported by our analyses but not formally recognised in the literature includes Palaeoheterodonta and Archiheterodonta, which emerged under multiple analytical conditions. The origin and diversification of each of these major clades is Cambrian or Ordovician, except for Archiheterodonta, which diverged from Palaeoheterodonta during the Cambrian, but diversified during the Mesozoic. Although the radiation of some lineages was shifted towards the Palaeozoic (Pteriomorphia, Anomalodesmata), or presented a gap between origin and diversification (Archiheterodonta, Unionida), Imparidentia showed steady diversification through the Palaeozoic and Mesozoic. Finally, a classification system with six major monophyletic lineages is proposed to comprise modern Bivalvia: Protobranchia, Pteriomorphia, Palaeoheterodonta, Archiheterodonta, Anomalodesmata and Imparidentia

How Many Sipunculan Species Are Hiding in Our Oceans?

Sipuncula, long considered a separate phylum, are now commonly included in the Annelida based on phylogenomic analyses. The sipunculan body consists of an unsegmented trunk and a retractable introvert, usually with a set of tentacles at its anterior end. Unlike other annelids, they have no chaetae, but the introvert is often adorned with proteinaceous hooks that can be important taxonomic characters. Other external taxonomic characters include the tentacles (number, shape and arrangement), body papillae and, in some cases, hardened shields, as well as length ratios. Many species require dissection for correct identification to reveal internal characteristics, such as introvert retractor muscles, nephridia and contractile vessels. Here we summarize the state of the current knowledge of species diversity in sipunculans. We emphasize molecular studies, conducted over the past two decades, that have revealed multiple complexes of cryptic or pseudocryptic species. It has become obvious that diversity is significantly higher than the current taxonomic scheme accounts for, but formal species descriptions are lagging behind. Although the major branches in the sipunculan phylogeny have become increasingly consolidated, the internal relationships within most branches are still in flux

Are There True Cosmopolitan Sipunculan Worms? A Genetic Variation Study Within Phascolosoma perlucens (Sipuncula, Phascolosomatidae)

Phascolosoma perlucens is one of the most common intertidal sipunculan species and has been considered a circumtropical cosmopolitan taxon due to the presence of a long-lived larva. To verify whether P. perlucens is a true cosmopolitan species or a complex of cryptic forms, we examined the population structure and demographics of 56 putative P. perlucens individuals from 13 localities throughout the tropics. Analysis of two mitochondrial markers, cytochrome c oxidase subunit I and 16S rRNA, suggests high levels of genetic differentiation between distantly located populations of P. perlucens. At least four different lineages identified morphologically as P. perlucens were distinguished. These lineages are likewise supported by phylogenetic analysis of the two mitochondrial markers and by the haplotype network analysis. Our results suggest that P. perlucens is a case of overconservative taxonomy, rejecting the alleged cosmopolitanism of P. perlucens. However, cryptic speciation also exists in some areas, including a possible case of geminate species across the Isthmus of Panama.Organismic and Evolutionary Biolog

On the amphi-Atlantic Siphonaria pectinata (Linnaeus, 1758) (Gastropoda: Heterobranchia: Siphonariidae): invader from the east or endemic?

Organismic and Evolutionary Biolog

Sipunculans and Echiurans of Isla del Coco (Cocos Island), Costa Rica

Vargas, Rita, Kawauchi, Gisele Y. (2010): Sipunculans and Echiurans of Isla del Coco (Cocos Island), Costa Rica. Zootaxa 2557: 60-68, DOI: 10.5281/zenodo.19693

Sipunculan phylogeny based on six genes, with a new classification and the descriptions of two new families

The internal phylogeny of Sipuncula has proven elusive, with the monophyly of multiple traditional groups in question. Repeated attempts to infer sipunculan relationships have attained discordant results, possibly owing to fragmentary molecular sequence data sets. We reassessed the phylogeny of Sipuncula using a six-gene data set and with larger target amplicons of certain loci. We additionally dated the molecular phylogeny employing recently discovered fossil taxa to constrain node ages. Our multilocus data set recovers six major clades of Sipuncula across multiple analytical treatments. Some groups considered suspect in previous studies are vindicated (e.g. Aspidosiphonidae), but most traditional sipunculan families were recovered as para- or polyphyletic groups, especially Sipunculidae, whose members appear in three distinct clades. To redress the dissonance between the current classification and the phylogeny of Sipuncula, we provide a new classification of the group, wherein (i) we erect two new families, Siphonosomatidae fam. nov. and Antillesomatidae fam. nov.; (ii) Phascolionidae and Themistidae are synonymized with Golfingiidae, new synonymies (iii) Phascolopsis is transferred to Golfingiidae, new familial assignment; and (iv) Lithacrosiphon is synonymized with Aspidosiphon, new synonymy. We observe that the origins of all families recognized are ancient, dating at least to the Mesozoic.Organismic and Evolutionary Biolog

Running WILD: the case for exploring mixed parameter sets in sensitivity analysis

The robustness of clades to parameter variation may be a desirable quality or even a goal in phylogenetic analyses. Sensitivity analyses used to assess clade stability have invoked the incongruence length difference (ILD or $_WILD$) metric, a measure of congruence among datasets, to compare a series of most-parsimonious results from re-running analyses under different analytical conditions. It is also common practice to select a single “optimal” parameter set that minimizes $_WILD$ across all parameter sets. However, the divergent molecular evolution of ribosomal genes and protein-encoding genes—specifically the bias against transversion events in coding genes of conserved function—suggests that deployment of multiple parameter sets could outperform the use of a single parameter set applied to all molecules. We explored congruence in five published datasets by including mixed parameter sets in our sensitivity analysis. In four cases, mixed parameter sets outperformed the previously reported, single optimal parameter set. Conversely, multiple parameter sets did not outperform a single optimal parameter set in a case in which actual strong topological conflict exists between data partitions. Exploration of mixed parameter sets may prove useful when combining ribosomal and protein-encoding genes, due to the relatively higher frequency of single- and double-base pair indel events in the former, and the relatively lower frequency of transversions in the latter.Organismic and Evolutionary Biolog