The molecular processes that govern speciation are not completely understood, especially within marine ecosystems. Insight on the topic of speciation can be provided by focusing on adaptive radiations, because of the rapid amount of lineages that have arisen within a short natural historical time frame. Rockfishes (genus: Sebastes) are known as a system for adaptive radiations within marine systems and have been considered an ancient species flock. This dissertation concentrates on marine rockfishes from the subgenus (Pteropodus) and closely related congeners to make inferences about speciation and adaptation within marine systems. Brain, kidney, testes, ovaries, and spleen tissues were selected from multiple rockfish species to extract total RNA in order to sequence the transcriptome with the use of Sanger and next generation sequencing techniques. These tissues types are intended to give us a broad spectrum of the rockfish transcriptome and were utilized to identify genes subject to positive selection. Pair-wise and multiple species comparisons were conducted to identify orthologous sequence pairs between/among species and estimated nonsynonymous (Ka) and synonymous (Ks) substitutions.
In the first study, a comparative analysis of Expressed Sequence Tags (ESTs) from Sebastes caurinus and S. rastrelliger was conducted to identify candidate genes under positive selection within the subgenus Pteropodus. Genes with elevated Ka/Ks values belonged to the following functional categories: immune function, metabolism, longevity, and reproductive behavior, indicating that adaptive divergence at immunological, physiological, and reproductive loci may be important in the diversification of this group of fishes. In the second study, ESTs from S. goodei and S. saxicola, a pair of related congeners to Pteropodus, were utilized for identifying positive selection with the use of testes and ovary tissue types. Gonadal tissues were selected from these two species to elucidate patterns of adaptation and speciation because of their recognition to contribute to reproductive barriers between species. Sequence divergence was estimated within the untranslated regions (UTRs) between these two species and was compared with the rate of divergence within coding regions of these genes to gain a clear depiction of neutral substitutional mutation rates. Orthologous gene pairs between the two species were identified and tested for positive selection. In addition, a candidate gene approach from the zona pellucida (ZP) family was selected to determine whether these genes are under positive selection. In the third study of this dissertation, a multi-transcriptomic comparison was conducted, in which three Pteropodus species were analyzed with the addition of S. rastrelliger and S. caurinus datasets to identify a pattern of positive selection within this subgenus. Brain tissue was used to gain the most diverse set of transcripts from the rockfish genome. Genes under positive selection belonged to a variety of gene functions that included sensory perception, growth, and metabolism. In addition we identified 10 sequences under positive selection that were part of the phosphatidylinositol signaling system pathway, although genes under positive selection had a broad range of gene functions and genes identified under positive selection across all five Pteropodus species were not identified in the first study.
These collections of studies are intended to further advance the field of evolutionary biology by providing support of which functional genes are important for adaptation and speciation. Currently, there is no rockfish genome available, in which by sequencing the transcriptome this provides a foundation for future genomic projects to gain a better understanding about the genus. This dissertation was developed to determine whether traditional gene categories, which are known to be under positive selection such as immune function, reproduction, and apoptosis, also play an important role in marine speciation. With transcriptomic data from multiple species within Sebastes, we obtained a suite of candidate genes under positive selection, which can be used to assess whether these genes are responsible for the radiation and how adaptation and speciation occurred across the entire genus of Sebastes.