title: Temporally isolated lineages of pink salmon reveal unique signatures of selection on distinct pools of standing genetic variation.
abstract: A species' genetic diversity bears the marks of evolutionary processes that have occurred throughout its history. However, robust detection of selection in wild populations is difficult and often impeded by lack of replicate tests. Here, we investigate selection in pink salmon (Oncorhynchus gorbuscha) using genome scans coupled with inference from a haploid-assisted linkage map. Pink salmon have a strict 2-year semelparous life history which has resulted in temporally isolated (allochronic) lineages that remain sympatric through sharing of spawning habitats in alternate years. The lineages differ in a range of adaptive traits, suggesting different genetic backgrounds. We used genotyping by sequencing of haploids to generate a high-density linkage map with 7035 loci and screened an existing panel of 8036 loci for signatures of selection. The linkage map enabled identification of novel genomic regions displaying signatures of parallel selection shared between lineages. Furthermore, 24 loci demonstrated divergent selection and differences in genetic diversity between lineages, suggesting that adaptation in the 2 lineages has arisen from different pools of standing genetic variation. Findings have implications for understanding asynchronous population abundances as well as predicting future ecosystem impacts from lineage-specific responses to climate change.
authors.affiliation: From the School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA 98195 (Limborg, Waples, Seeb, Seeb); and the National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600 Silkeborg, Denmark (Limborg). moli@uw.edu.
authors.forename: Morten T
authors.initials: MT
authors.lastname: Limborg
authors.affiliation: From the School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA 98195 (Limborg, Waples, Seeb, Seeb); and the National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600 Silkeborg, Denmark (Limborg).
authors.forename: Ryan K
authors.initials: RK
authors.lastname: Waples
authors.affiliation: From the School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA 98195 (Limborg, Waples, Seeb, Seeb); and the National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600 Silkeborg, Denmark (Limborg).
authors.forename: James E
authors.initials: JE
authors.lastname: Seeb
authors.affiliation: From the School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA 98195 (Limborg, Waples, Seeb, Seeb); and the National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600 Silkeborg, Denmark (Limborg).
authors.forename: Lisa W
authors.initials: LW
authors.lastname: Seeb
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D000818:Animals; D002874:Chromosome Mapping; D057231:Climate Change; D005260:Female; D008040:Genetic Linkage; D056426:Genetic Loci; D014644:Genetic Variation; D005828:Genetics, Population; D005838:Genotype; D006238:Haploidy; D008297:Male; D012474:Salmon / Q000235:genetics*
keywords: climate change; haploid; life history; linkage mapping; parallel evolution