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We identify a small genomic region in salmon that governs complex life history variation and has diversified across four WGDs to fine-tune trait expression. Within this region, three large-effect loci on three chromosomes modulate migration timing across four species - a critical trait optimizing fitness by synchronizing reproduction and environmental conditions. Life history and genome resequencing data support intraspecific evolution of polymorphisms related to early- and late-reproducing phenotypes. We demonstrate that the repeated evolution of loci underlying reproductive timing carries the signature of WGD-facilitated adaptive evolution. This adaptation is driven by the subsequent subfunctionalization of genes within the highly conserved HPG axis, which regulates vertebrate reproduction.<\/jats:p>","DOI":"10.1101\/2024.03.30.587279","type":"posted-content","created":{"date-parts":[[2024,4,1]],"date-time":"2024-04-01T21:20:11Z","timestamp":1712006411000},"source":"Crossref","is-referenced-by-count":6,"title":["Large-effect loci in a duplicated genomic region modulate reproductive phenology in salmon"],"prefix":"10.64898","author":[{"given":"Patrick D.","family":"Barry","sequence":"first","affiliation":[{"name":"National Oceanic and Atmospheric Administration; Juneau, AK, 99801, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natasha","family":"Howe","sequence":"additional","affiliation":[{"name":"Pacific States Marine Fisheries Commission; Seattle, WA, 98115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gregory L.","family":"Owens","sequence":"additional","affiliation":[{"name":"University of Victoria, Department of Biology; Victoria, BC V8P 5C2, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Diana S.","family":"Baetscher","sequence":"additional","affiliation":[{"name":"National Oceanic and Atmospheric Administration; Juneau, AK, 99801, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katie","family":"D\u2019Amelio","sequence":"additional","affiliation":[{"name":"National Oceanic and Atmospheric Administration; Juneau, AK, 99801, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scott","family":"Vulstek","sequence":"additional","affiliation":[{"name":"National Oceanic and Atmospheric Administration; Juneau, AK, 99801, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joshua","family":"Russell","sequence":"additional","affiliation":[{"name":"National Oceanic and Atmospheric Administration; Juneau, AK, 99801, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elizabeth","family":"Lee","sequence":"additional","affiliation":[{"name":"Alaska Department of Fish and Game; Anchorage, AK, 99518, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew","family":"Barclay","sequence":"additional","affiliation":[{"name":"Alaska Department of Fish and Game; Anchorage, AK, 99518, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anthony J.","family":"Gharrett","sequence":"additional","affiliation":[{"name":"University of Alaska Fairbanks, College of Fisheries and Ocean Sciences; Juneau, AK, 99801, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David A.","family":"Tallmon","sequence":"additional","affiliation":[{"name":"University of Alaska Southeast, Biology and Marine Biology Program; Juneau, AK, 99801, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wesley A.","family":"Larson","sequence":"additional","affiliation":[{"name":"National Oceanic and Atmospheric Administration; Juneau, AK, 99801, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026080311101132000_2024.03.30.587279v3.1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msj083"},{"key":"2026080311101132000_2024.03.30.587279v3.2","doi-asserted-by":"publisher","DOI":"10.1038\/nrg2600"},{"key":"2026080311101132000_2024.03.30.587279v3.3","doi-asserted-by":"publisher","DOI":"10.1093\/plcell\/koac076"},{"key":"2026080311101132000_2024.03.30.587279v3.4","doi-asserted-by":"publisher","DOI":"10.1126\/science.1075472"},{"key":"2026080311101132000_2024.03.30.587279v3.5","doi-asserted-by":"publisher","DOI":"10.1126\/science.1126121"},{"key":"2026080311101132000_2024.03.30.587279v3.6","doi-asserted-by":"crossref","unstructured":"D. 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