Molecular Evolution in Embiotocid Surfperches
Here, in embiotocid surfperches I have investigated diverse evolutionary processes on different genomic scales using advances in massively parallel DNA sequencing technologies. First I reconstructed phylogenetic relationships among all genera and 21 out of 23 embiotocid species using restriction-site associated DNA sequence (RADseq) markers. In Embiotocidae I found that RADseq supermatrices that retained 91% of orthologous markers across sampled species, which corresponded to 523 loci, yielded trees with the highest support values. The resulting phylogenetic hypotheses support a scenario where embiotocids first diverged into clades associated with sandy and reef habitats during the middle Miocene (13–18 million years ago) with subsequent invasions of novel habitats in the reef associated clade, and northern range expansion in the Northwest Pacific. In all cases, radiations occurred within specific habitats, a pattern consistent with niche partitioning. For my second chapter I characterized the complete mitochondrial genome of the black surfperch, Embiotoca jacksoni. The genome contains 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and the non-coding control region (Dloop), the gene order of which is identical to that observed in most vertebrates. I then compared the protein-coding mitochondrial DNA gene sequences of E. jacksoni with two other embiotocid surfperches with available complete mitochondrial genomes, Cymatogaster aggregata and Ditrema temminckii. Across all mitochondrial protein-coding genes in surfperches the weighted average substitution rate was 2.079% per million years and average dN/dS ratios for each protein-coding gene ranged from 0.016 in CytB to 0.608 in ND3. Substitution rates and dN/dS ratios were relatively high for ATP8 compared to other protein-coding genes. Although most protein-coding genes showed signals of purifying selection, I found evidence for positive selection in ND3 in E. jacksoni. Finally for chapter three I performed exploratory genome scans for selection in four species of Embiotocid surfperches between populations in Monterey Bay, California, USA and Punta Banda, Baja California, Mexico again using RADseq markers. These localities are on opposite sides of a well-known biogeographic break and experience significantly different sea surface temperatures (SST) as well heterogeneous species assemblages. Using a FST outlier approach, I detected strong signals of intraspecific balancing and divergent selection as well as clear evidence for interspecific parallel selection with some loci aligning to known proteins. These results suggest that California surfperches represent an ideal system for investigating different forms of selection in a natural marine environment.