| With an estimated 8,000-20,000 species, bivalves represent the second largest living class of molluscs (Bieler et al. 2013). Revived interest in molluscan phylogeny has resulted in a torrent of molecular sequence data from phylogenetic, mitogenomic, and phylogenomic studies. Despite recent progress, basal relationships of the class Bivalvia remain contentious, owing to conflicting hypotheses often between morphology and molecules.;In Chapter 1, the utility of four nuclear protein-encoding genes---ATP synthase beta, elongation factor-1alpha, myosin heavy chain type II, and RNA polymerase II---- were evaluated for their adequacy in resolving the basal relationships within Bivalvia. Marked insensitivity of the basal tree topology to dataset manipulation was indicative of signal robustness in these four genes, but resolution was missing in some key areas. Subsequently, a phylogenomic study using transcriptomic data was designed to re-evaluate the bivalve Tree of Life.;In Chapter 2, I provide the first phylogenomic analysis of Bivalvia in an attempt to resolve deep divergences within this group. All six major lineages of bivalves (Archiheterodonta, Anomalodesmata, Inaequidonta, Palaeoheterodonta, Protobranchia, and Pteriomorphia) were sampled resulting in 31 newly sequenced Illumina-based bivalve transcriptomes. This constitutes the most comprehensive phylogenomic dataset to date for inferring deep relationships within Bivalvia. Subsequent analyses obtained robust resolution of major bivalve lineages, largely corroborating classical taxonomic relationships based mostly on paleontological and morphological data.;In Chapter 3, a multi-locus phylogeny of archiheterodont bivalves was constructed to resolve relationships among constituent families; the relationships and internal phylogeny of Archiheterodonta remain poorly understood. By virtue of the contentious placement within Bivalvia and lack of internal phylogenic work, Archiheterodonta (including Astartidae, Carditidae, Crassatellidae, and Condylocardiidae) remain an enigmatic clade of phylogenetic interest. Here I investigate relationships within Archiheterodonta using molecular information from six genes (28S rRNA, 18S rRNA, histone H3, cytochrome c oxidase subunit I, internal transcribed spacer 2, and cytochrome b), including the first molecular sequence information for Condylocardiidae.;Lastly, in Chapter 4, I investigated the potential cryptic speciation within a complex of carditid bivalves from the Gulf of California (Archiheterodonta, Carditidae). Carditamera bajaensis, new species, is described from semi-infaunal specimens collected in the intertidal zone in the Gulf of California, Baja California Sur, Mexico. This species, overlapping in distribution with the congeneric C. affinis, yet subsequently found to be genetically distinct, was differentiated initially due to life mode and shell morphology. |
