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Parallel selection on ecologically relevant gene functions in the transcriptomes of highly diversifying salmonids
Kevin Schneider1, Colin E Adams1,2, Kathryn R Elmer3
1Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
BMC Genomics
|December 25, 2019
Summary
Salmonid fish diversification is linked to specific gene evolution patterns. Relaxed, intensified, and diversifying selection on gene orthogroups highlight key genes involved in ecological adaptation.
Area of Science:
- Evolutionary biology
- Genomics
- Ecology
Background:
- Salmonid fishes exhibit remarkable adaptive variation in ecology and life history.
- Certain salmonid species, like charr and whitefish, show rapid parallel diversification within lakes.
- Understanding the genetic basis of these predictable diversifications is crucial.
Purpose of the Study:
- To identify genes and gene categories under selection during salmonid diversification.
- To compare selection patterns in rapidly diversifying salmonids versus less dynamic lineages.
Main Methods:
- Analysis of 2702 orthogroups across two charr, two whitefish species, five other salmonid lineages, and one outgroup.
- Comparative genomic analysis to detect relaxed, intensified, and diversifying selection.
Main Results:
- More orthogroups showed relaxed selection (122) than intensified selection (78).
- Relaxed selection was enriched in amino acid metabolism and transcriptional regulation; intensified selection in signaling and actin/lipid metabolism.
- Diversifying selection (92 orthogroups) was enriched in signal transduction, transport, and metabolism, often involving transcriptional regulation and development.
Conclusions:
- The study identified specific genomic targets associated with different selection types in salmonids.
- Relaxed, intensified, and diversifying selection impact ecologically relevant genes in charr and whitefish.
- These selected genes are proposed to play a role in the replicated ecological diversifications observed in these salmonid lineages.
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