Gonadal transcriptomics elucidate patterns of adaptive evolution within marine rockfishes (Sebastes)

BMC Genomics
Joseph HerasAndres Aguilar

Abstract

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. 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. We 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 substitut...Continue Reading

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Datasets Mentioned

BETA
JZ693907-JZ704944
SRR1212396

Methods Mentioned

BETA
454 sequencing
454 sequencer

Software Mentioned

tblastx
PhyML
blast
extract
mira
pal2nal
_ calculator
blast2go
Ensembl
Perl scripts

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