A combined approach toward resolving the phylogeny of Mollusca
Type of Degreedissertation
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With estimates of up to 200,000 extant species, Mollusca is second in number of species only to Arthropoda. Moreover, with species as different as meiofaunal worms and giant squid, Mollusca is one of the most morphologically variable metazoan phyla. This extreme disparity in morphology among the major lineages (i.e., classes) has prompted numerous conflicting phylogenetic hypotheses which have been widely debated. Likewise, relationships within some major molluscan lineages (e.g., Gastropoda and Aplacophora) and which other phylum or phyla constitute the sister taxon of Mollusca have also been long-standing questions. In order to address these questions, in my Ph.D. dissertation research, I have employed high-throughput DNA sequencing technologies and bioinformatic tools in a phylogenomic approach. Chapter 1 provides an introduction to Mollusca and outlines the objectives of my dissertation research. Chapter 2 corresponds to a publication in the journal Nature where my collaborators and I sought to address the relationships among the major lineages of Mollusca using a phylogenomic approach. I lead the development of a novel bioinformatic pipeline and analyzed data from 308 nuclear protein-coding genes from 42 diverse molluscs plus outgroups. My collaborators and I recovered, for the first time, a well-supported phylogeny for Mollusca. Our results strongly supported the Aculifera hypothesis placing chitons in a clade with a monophyletic Aplacophora (worm-like molluscs). This clade was placed sister to Conchifera, more familiar shelled molluscs such as gastropods, bivalves, and cephalopods. Within Conchifera, we found strong support for a sister taxon relationship between Gastropoda and Bivalvia, a group not previously hypothesized by morphologists. In light of these results, we conducted ancestral character state reconstruction which indicated that aculiferans have retained several molluscan plesiomorphies and that advanced cephalization and shells may have had multiple origins within Mollusca. Pulmonates, with more than 30,000 described species, represent the largest radiation of molluscs. Studies based on mitochondrial genomes versus datasets dominated by nuclear ribosomal RNA genes drew conflicting conclusions about pulmonate monophyly, and support for a sister group has been lacking, hindering our understanding of this major animal radiation. Chapter 3 presents an attempt to resolve evolutionary relationships at the base of the pulmonate radiation through phylogenomic analysis of 102 nuclear protein-coding genes from 19 gastropods. We recovered Opisthobranchia (sea slugs) paraphyletic with respect to Panpulmonata, a clade in which Sacoglossa (an opisthobranch group that feeds algae) was sister to Pulmonata. Siphonarioidea (intertidal, limpet-like snails) was recovered as the basal pulmonate lineage. Siphonarioideans, which share a similar gill structure with the putatively plesiomorphic shelled sacoglossans but lack the contractile pneumostome of pulmonates, likely descended from an evolutionary intermediate that facilitated the gastropod radiation into non-marine habitats. These results have important implications for understanding the series of evolutionary events that facilitated the pulmonate radiation into non-marine habitats. Because Aculifera is the sister taxon of all other molluscs, understanding the phylogeny of this group is critical to understanding early molluscan evolution. In particular, a well-resolved phylogeny for Aplacophora would provide polarity for the evolution of key morphological characters such as the radula. Accordingly, my collaborators and I employed a phylogenomic approach to resolve the evolutionary relationships of Aplacophora. Ancestral character state reconstruction was utilized to improve understanding of the evolution of key molluscan characters. For this chapter, I also collaborated with Dr. Christiane Todt to describe four new species of solenogasters from histological, SEM, and LM data (Appendix 1). For my last dissertation data chapter, my collaborators and I sought to identify the sister taxon of Mollusca and improve understanding of the phylogeny of Lophotrochozoa as a whole. To this end, my collaborators and I sequenced cDNA libraries from 34 diverse lophotrochozoans using the Illumina HiSeq platform. Phylogenetic analyses of this dataset indicate that a clade including annelids, brachiopods, and phoronids constitutes the sister taxon of Mollusca. Entoprocta, which has been hypothesized to be the molluscan sister taxon based on morphological characters, was instead placed sister to Ectoprocta with strong support.