UC Riverside

Cetaceans are remarkable among mammals for their numerous adaptations to an aquatic existence, yet many aspects of their phylogeny and molecular evolution remain unresolved. Olfactory receptor (OR) subgenomes of eight cetacean species from four families were sequenced and a multigene tree constructed. Phylogenetic analyses of OR pseudogenes using both gene-tree reconciliation and supermatrix methods yielded resolved, consistently-supported relationships among members of four delphinid subfamilies. Novel DNA sequence data for six nuclear loci and three mitochondrial genes provided an independent test of OR trees. Nucleotide substitutions and indels in OR pseudogenes showed a very low degree of homoplasy in comparison to mitochondrial DNA and, on average, provided more variation than single-copy nuclear DNA. I also merged 37 new sequences from RAG1 and PRM1 with most published molecular data for Cetacea and generated a supermatrix consisting of 42,335 characters. The great majority of these data have never been combined. Model-based analyses of the supermatrix produced a consistent phylogenetic hypothesis for 87 cetacean species. Bayesian analyses corroborated odontocete monophyly, stabilized basal odontocete relationships, and completely resolved branching events within Mysticeti and Delphinidae. The brain development gene microcephalin (MCPH1) was sequenced in 38 cetacean species. Alignments of these data and a published complete sequence from the common bottlenose dolphin with primate MCPH1 were utilized in phylogenetic analyses and to reconstruct patterns of selection intensity using site, branch, and clade models of molecular evolution. I found evidence for positive selection on the lineage leading to Tursiops and a parallel trend of adaptive molecular evolution in hominid primates. However, the strongest signal of positive selection was identified in the hypervariable exon 8 region of MCPH1 from baleen whales. Finally, I combined existing and newly generated sequences from four mitochondrial (mt) genes and 20 nuclear (nu) genes to reconstruct a well supported phylogenetic hypothesis for Delphinidae. This study compared multiple concatenated methods with Bayesian concordance analysis (BCA). Despite finding discordance between mtDNA and individual nuDNA loci, the concatenated matrix recovered a completely resolved and robustly supported phylogeny that was also broadly congruent with BCA trees.