Abstract
BackgroundThe genetic mechanisms of speciation and adaptation in the marine environment are not well understood. The rockfish genus Sebastes provides a unique model system for studying adaptive evolution because of the extensive diversity found within this group, which includes morphology, ecology, and a broad range of life spans. Examples of adaptive radiations within marine ecosystems are considered an anomaly due to the absence of geographical barriers and the presence of gene flow. Using marine rockfishes, we identified signatures of natural selection from transcriptomes developed from gonadal tissue of two rockfish species (Sebastes goodei and S. saxicola). We predicted orthologous transcript pairs, and estimated their distributions of nonsynonymous (Ka) and synonymous (Ks) substitution rates.ResultsWe identified 144 genes out of 1079 orthologous pairs under positive selection, of which 11 are functionally annotated to reproduction based on gene ontologies (GOs). One orthologous pair of the zona pellucida gene family, which is known for its role in the selection of sperm by oocytes, out of ten was identified to be evolving under positive selection. In addition to our results in the protein coding-regions of transcripts, we found substitution rates in 3’ and 5’ UTRs to be significantly lower than Ks substitution rates implying negative selection in these regions.ConclusionsWe were able to identify a series of candidate genes that are useful for the assessment of the critical genes that diverged and are responsible for the radiation within this genus. Genes associated with longevity hold potential for understanding the molecular mechanisms that have contributed to the radiation within this genus.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1870-0) contains supplementary material, which is available to authorized users.
Highlights
The genetic mechanisms of speciation and adaptation in the marine environment are not well understood
The rockfish genus Sebastes provides a unique model system for studying adaptive evolution because of the extensive diversity found within this group, which includes variation in morphology, ecology, and a broad range of life spans [10, 12]
This study identifies genes under positive selection between the gonadal transcritomes of two distantly related rockfish species (S. goodei and S. saxicola). 1079 orthologous gene pairs were identified between the two species and of these we found 144 genes under positive selection
Summary
The genetic mechanisms of speciation and adaptation in the marine environment are not well understood. The rockfish genus Sebastes provides a unique model system for studying adaptive evolution because of the extensive diversity found within this group, which includes morphology, ecology, and a broad range of life spans. The rockfish genus Sebastes provides a unique model system for studying adaptive evolution because of the extensive diversity found within this group, which includes variation in morphology, ecology, and a broad range of life spans [10, 12]. This rapid radiation is supported by multiple studies which demonstrate the diversification of this group from a phylogenetic context [13,14,15]. Complex courtship displays and internal fertilization are found within rockfishes, making assortative mating likely [10, 16] and can help us understand how sexual selection is operating within this group
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