Gonadal transcriptomics elucidate patterns of adaptive evolution within marine rockfishes (Sebastes).
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.
Department of Ecology and Evolutionary Biology, University of California Irvine, 321 Steinhaus Hall, Irvine, CA, 92697, USA. herasj@uci.edu.
Joseph
J
Heras
School of Natural Sciences and Graduate Group in Quantitative and Systems Biology, University of California Merced, 5200 N Lake Rd, Merced, CA, 95344, USA. kmcclntck@gmail.com.
Kelly
K
McClintock
European Molecular Biology Laboratory, Meyerhofstr 1, 69117, Heidelberg, Germany. sunagawa@embl.de.
Shinichi
S
Sunagawa
Department of Biological Sciences, California State University Los Angeles, 5151 State University Dr, Los Angeles, CA, 90032, USA. aaguil67@calstatela.edu.
Andres
A
Aguilar
D000222:Adaptation, Physiological / Q000235:genetics*; D000818:Animals; D059001:Aquatic Organisms / Q000235:genetics*; D005075:Biological Evolution; D014644:Genetic Variation; D006066:Gonads / Q000378:metabolism*; D016013:Likelihood Functions; D058977:Molecular Sequence Annotation; D010473:Perciformes / Q000235:genetics*; D010802:Phylogeny; D012641:Selection, Genetic; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000235:genetics*; D020506:Untranslated Regions / Q000235:genetics
D020506:Untranslated Regions