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.
Highlights
Bivalvia is among the most diverse molluscan classes, totalling almost 10 000 described extant species inhabiting various aquatic environments, spanning freshwater, brackish and marine, as well as ranging from the shallow continental shelve to the deep sea, including hydrothermal vents and hydrocarbon seeps
Bivalves adopt a multitude of different life modes, from detritivory to filter feeding, with extreme cases of photo- and chemosymbiosis to carnivory [2,3,4,5]
Bivalves are being increasingly used to study the spread of cancer in natural environments, as a model of contagious tumours [10], and to assess gene expression of cancer-related genes [11]. Because of their filter feeding habits, they hold a major function in coastal ecosystems and reef ecology [12,13]
Summary
Bivalvia is among the most diverse molluscan classes, totalling almost 10 000 described extant species (see [1]) inhabiting various aquatic environments, spanning freshwater, brackish and marine, as well as ranging from the shallow continental shelve to the deep sea, including hydrothermal vents and hydrocarbon seeps. Two initial data matrices following occupancy thresholds [34] were generated for phylogenetic analyses, using a custom Python script: the first one, Matrix 1, targeting a minimum gene occupancy of 50%, was constructed by selecting the OMA orthogroups present in 55 or more taxa (resulting in 312 orthogroups). To explore the complex topology of the Imparidentia subclade, a second orthology assignment run was performed using OMA 2.0, with taxa from the Imparidentia clade only (52 taxa) and six outgroups (see electronic supplementary material, table S1 for details) The objective of this approach was to design matrices optimized for Imparidentia rather than subsamples of the original dataset (as done in [36]). Concatenated matrices were compiled using a threshold of per cent gene occupancy Both Matrix 1 and Matrix 2 contained data for all the taxa included in the study, though each taxon varied in gene representation (electronic supplementary material, figure S1).
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