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

Abstract

Background: 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.

Results: 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 substitution rates in 3' and 5' UTRs to be significantly lower than Ks substitution rates implying negative selection in these regions.

Conclusions: We 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.

Fig. 1

Plot of (Ka) nonsynonymous vs. (Ks) synonymous substitutions. Blue diamonds indicate values with a Ks < 0.1, whereas red triangles indicate Ks values greater than 0.1 but less than 0.5. The black line suggests neutrality, values above the line are subject to positive selection and values below are subject to purifying selection

Fig. 2

ML tree generated for ZPAX and ZPB genes found within S. goodei and S. saxicola with 1000 bootstrap replicates. Additional teleost species were used to construct this phylogeny, and bootstrap values greater than 70 are displayed

Fig. 3

ML tree generated for ZPC genes found within S. goodei and S. saxicola with 1000 bootstrap replicates. Additional teleost species were used to construct this phylogeny, and bootstrap values greater than 70 are displayed

Fig. 4

Comparison of UTR divergence with alignment length and Ks divergence. Blue diamonds indicate ortholog pairs with a Ks > 0.1, whereas red triangles indicate Ks values that are greater than 0.1 and less than 0.5

Fig. 5

Frequency of ortholog pairs with synonymous substitution estimates. The black dotted line indicates the traditional cut off line and the red dotted line indicates our new threshold cut-off