Genomic approaches to identify chromosomal regions responding to divergent selection in multiple Sebastes species (subgenus: Sebastosomus)

The role of selection during speciation is a key component towards fully diverged species, yet the processes and time required for genomic divergence to evolve new species remains an active area of research in evolution. A population genomics approach provides a promising means to understanding evolutionary processes influencing genomic divergence. To determine the effects selection has on the genome, I used Sebastes as a model system due to its rapid adaptive radiation in the North Pacific Ocean. Species in Sebastes inhabit a wide range of environments providing a unique system to study a range of divergence from local adaptation between populations to incipient speciation. I identified genomic regions diverging due to local adaptation and candidate genomic regions involved in the incipient speciation of a lineage within the subgenus Sebastosomus. I developed 67 microsatellites from expressed sequence tagged (EST) libraries from three different Sebastes species to identify gene function responding to selection. I then implemented a low-density genome scan on a species pair (S. flavidus & S. melanops) and identified outlier loci with two outlier detection methods. The two species are distributed sympatrically but differ in pelagic larval duration (PLD). S. flavidus has a three to four month PLD had a higher number of identified candidate outlier loci while S. melanops which has a four to six month PLD had significantly fewer suggesting that gene flow may reduce local adaptation. I identified two outliers in S. flavidus associated with oceanic variables influencing genetic structure while none were found in S. melanops. Finally, I assembled a restriction site associated (RAD) library and sequenced using the Illumina Hiseq technology from two divergent S. mystinus morphotypes. I sampled 21,318 single nucleotide polymorphic (SNP) loci across six populations from Oregon to San Francisco. Population structure analyses identified two morphotypes previously described as genetically distinct groups and highlighted a population maintaining signatures of hybridization. I identified 209 SNP loci diverging between morphotypes providing an initial set of genomic regions diverging due to speciation. My dissertation highlights the importance of integrating novel genomic techniques to address fundamental evolutionary questions that seek to identify genomic responses to selection