Resolving the evolutionary relationships of molluscs with phylogenomic tools

Abstract

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.

Re-evaluating the phylogeny of Sipuncula through transcriptomics

“…However, we recommend adding more species per family in future studies in order to fully resolve internal relationships, especially within Golfingiidae. In the present case, increasing the amount of data from a few selected genes to hundreds of coding genes has enabled us to confirm previous molecular studies and resolve the last remaining controversies among sipunculan family relationships, supporting phylogenomics as an effective tool for resolving not only sipunculans, but also complex relationships within other spiralian clades, as shown by several recent studies (e.g., Smith et al, 2011;Kocot et al, 2011;Weigert et al, 2014).…”

“…The systematic community has necessarily progressed from candidate genes through EST-based methods to 454 and Illumina-based transcriptome and genome datasets to resolve major relationships among the animal phyla (e.g., Dunn et al, 2008;Hejnol et al, 2009;Nosenko et al, 2013;Ryan et al, 2013;Moroz et al, 2014). Long outstanding issues have been resolved for within-phylum relationships among arthropods, molluscs, and annelids, to mention just some of the largest animal phyla (e.g., Meusemann et al, 2010;Kocot et al, 2011;Smith et al, 2011;Struck et al, 2011;von Reumont et al, 2012;Andrade et al, 2014;Weigert et al, 2014). A third wave now focuses on resolving lower-level phylogenetic questions, relying almost entirely on Illumina-based technology (e.g., Johnson et al, 2013; Kocot et al, 2013;Wheat and Wahlberg, 2013;Dell'Ampio et al, 2014;Fernández et al, 2014aFernández et al, , 2014b.…”

Flashback and foreshadowing—a review of the taxon Opisthobranchia

“…In fact, the topology by Medina et al (2011) contradicted by all phylogenomic and other approaches that include nuclear rather than mitochondrial genes. In contrast, topologies recovered by recent phylogenomic studies (Kocot et al 2011(Kocot et al , 2013Smith et al 2011) and a study based on housekeeping genes (Vinther et al 2011) all are compatible with the backbone topology of the tree presented by Schrödl et al (2011a).…”

Cell Proliferation Pattern and Twist Expression in an Aplacophoran Mollusk Argue Against Segmented Ancestry of Mollusca

“…Together with the fact that recent studies suggest a sister‐group relationship of aplacophorans and polyplacophorans (Kocot et al., 2011; Smith et al., 2011, 2013; Vinther et al., 2012), this places them in the focus of attention when it comes to the question of a potentially segmented ancestry of mollusks. Thus, we investigated cell proliferation patterns and the expression of the mesodermal marker gene twist during larval development in two species of solenogasters, Wirenia argentea Odhner, 1921 and Gymnomenia pellucida Odhner, 1921.…”