{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T15:44:15Z","timestamp":1792683855946,"version":"4.5.0"},"reference-count":78,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Eawag"},{"DOI":"10.13039\/501100003338","name":"Swiss Federal Office for the Environment","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003338","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Alpenrhein-Bodensee-Hochrhein"},{"DOI":"10.13039\/501100008530","name":"European Regional Development Fund","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>When populations experience heterogeneous environments, multifarious divergent selection may lead to ecological speciation or even adaptive radiation. The underlying genetic architecture of adaptation can be simple or complex and is relevant for predicting evolutionary responses. Whitefish have radiated across Swiss perialpine lakes, and within the radiation, more than 30 species have been taxonomically described. Across Swiss lake systems, several phenotypically similar species (ie ecomorphs) have evolved independently and utilize distinct environmental niches. Profundal species, adapted to spawn in depths below 60\u2005m, have repeatedly evolved in Lakes Thun, Constance, Lucerne, Zug, and Walen. We here analyzed whole-genome resequencing data of all three to six whitefish species of four of these lakes (Thun, Constance, Lucerne, and Walen) to identify genomic signals of parallel profundal adaptation. The results indicate that a small but spread-out fraction of the genome shows signals of parallel differentiation across all four studied lakes, with pairwise tests revealing more genomic regions with evidence of parallel evolution between profundal species when both were pelagic. Consistent with previous work investigating parallel divergence between two different Alpine whitefish ecomorphs, these results suggest a polygenic basis of adaptation, including genotypic redundancy, which makes repeated evolution more likely but results in little repeatability of its genetic basis.<\/jats:p>","DOI":"10.1093\/gbe\/evag242","type":"journal-article","created":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T12:02:19Z","timestamp":1790769739000},"source":"Crossref","is-referenced-by-count":0,"title":["The Genomic Basis of Adaptation to Profundal Habitats Across the Swiss Alpine Whitefish Radiation"],"prefix":"10.1093","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5779-2817","authenticated-orcid":false,"given":"David","family":"Frei","sequence":"first","affiliation":[{"name":"Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology , Kastanienbaum ,","place":["Switzerland"]},{"name":"Division of Aquatic Ecology, Institute of Ecology and Evolution, University of Bern , Bern ,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6598-1434","authenticated-orcid":false,"given":"Ole","family":"Seehausen","sequence":"additional","affiliation":[{"name":"Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology , Kastanienbaum ,","place":["Switzerland"]},{"name":"Division of Aquatic Ecology, Institute of Ecology and Evolution, University of Bern , Bern ,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8078-1788","authenticated-orcid":false,"given":"Philine G D","family":"Feulner","sequence":"additional","affiliation":[{"name":"Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology , Kastanienbaum ,","place":["Switzerland"]},{"name":"Division of Aquatic Ecology, Institute of Ecology and Evolution, University of Bern , Bern ,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,10,1]]},"reference":[{"key":"2026102211162193100_evag242-B1","doi-asserted-by":"publisher","first-page":"1600","DOI":"10.1093\/bioinformatics\/btl140","article-title":"Improved scoring of functional groups from gene expression data by decorrelating GO graph structure","volume":"22","author":"Alexa","year":"2006","journal-title":"Bioinformatics"},{"key":"2026102211162193100_evag242-B2","doi-asserted-by":"publisher","first-page":"769","DOI":"10.1038\/s41576-020-0250-z","article-title":"Polygenic adaptation: a unifying framework to understand positive selection","volume":"21","author":"Barghi","year":"2020","journal-title":"Nat Rev Genet"},{"key":"2026102211162193100_evag242-B3","doi-asserted-by":"publisher","first-page":"4773","DOI":"10.1111\/mec.13795","article-title":"Investigating genomic and phenotypic parallelism between piscivorous and planktivorous lake trout (Salvelinus namaycush) ecotypes by means of RADseq and morphometrics analyses","volume":"25","author":"Bernatchez","year":"2016","journal-title":"Mol Ecol"},{"key":"2026102211162193100_evag242-B4","doi-asserted-by":"publisher","first-page":"1514","DOI":"10.1101\/gr.154831.113","article-title":"Estimating and interpreting FST: the impact of rare variants","volume":"23","author":"Bhatia","year":"2013","journal-title":"Genome Res"},{"key":"2026102211162193100_evag242-B5","doi-asserted-by":"publisher","first-page":"2061","DOI":"10.1111\/mec.12241","article-title":"Pervasive selection or is it\u2026? 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