{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T21:46:35Z","timestamp":1792100795867,"version":"4.4.0"},"reference-count":129,"publisher":"Wiley","issue":"15","license":[{"start":{"date-parts":[[2023,5,16]],"date-time":"2023-05-16T00:00:00Z","timestamp":1684195200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Molecular Ecology"],"published-print":{"date-parts":[[2025,8]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>A main goal of evolutionary biology is to understand the genetic basis of adaptive evolution. Although the genes that underlie some adaptive phenotypes are now known, the molecular pathways and regulatory mechanisms mediating the phenotypic effects of those genes often remain a black box. Unveiling this black box is necessary to fully understand the genetic basis of adaptive phenotypes, and to understand why particular genes might be used during phenotypic evolution. Here, we investigated which genes and regulatory mechanisms are mediating the phenotypic effects of the <jats:italic>Eda<\/jats:italic> haplotype, a locus responsible for the loss of lateral plates and changes in the sensory lateral line of freshwater threespine stickleback (<jats:italic>Gasterosteus aculeatus<\/jats:italic>) populations. Using a combination of RNAseq and a cross design that isolated the <jats:italic>Eda<\/jats:italic> haplotype on a fixed genomic background, we found that the <jats:italic>Eda<\/jats:italic> haplotype affects both gene expression and alternative splicing of genes related to bone development, neuronal development and immunity. These include genes in conserved pathways, like the BMP, netrin and bradykinin signalling pathways, known to play a role in these biological processes. Furthermore, we found that differentially expressed and differentially spliced genes had different levels of connectivity and expression, suggesting that these factors might influence which regulatory mechanisms are used during phenotypic evolution. Taken together, these results provide a better understanding of the mechanisms mediating the effects of an important adaptive locus in stickleback and suggest that alternative splicing could be an important regulatory mechanism mediating adaptive phenotypes.<\/jats:p>","DOI":"10.1111\/mec.16989","type":"journal-article","created":{"date-parts":[[2023,5,16]],"date-time":"2023-05-16T23:15:11Z","timestamp":1684278911000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Molecular mechanisms of <i>Eda<\/i>\u2010mediated adaptation to freshwater in threespine stickleback"],"prefix":"10.1111","volume":"34","author":[{"given":"Carlos E.","family":"Rodr\u00edguez\u2010Ram\u00edrez","sequence":"first","affiliation":[{"name":"Division of Evolutionary Ecology, Institute of Ecology and Evolution University of Bern  Bern Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melanie","family":"Hiltbrunner","sequence":"additional","affiliation":[{"name":"Division of Evolutionary Ecology, Institute of Ecology and Evolution University of Bern  Bern Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Verena","family":"Saladin","sequence":"additional","affiliation":[{"name":"Division of Evolutionary Ecology, Institute of Ecology and Evolution University of Bern  Bern Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephanie","family":"Walker","sequence":"additional","affiliation":[{"name":"Division of Evolutionary Ecology, Institute of Ecology and Evolution University of Bern  Bern Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Araxi","family":"Urrutia","sequence":"additional","affiliation":[{"name":"Department of Biology and Biochemistry, and Milner Centre for Evolution University of Bath  Bath UK"},{"name":"Institute of Ecology UNAM  Mexico City Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7731-8944","authenticated-orcid":false,"given":"Catherine L.","family":"Peichel","sequence":"additional","affiliation":[{"name":"Division of Evolutionary Ecology, Institute of Ecology and Evolution University of Bern  Bern Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2023,5,16]]},"reference":[{"key":"e_1_2_11_2_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1098095"},{"key":"e_1_2_11_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2020.05.051"},{"key":"e_1_2_11_4_1","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.37001"},{"key":"e_1_2_11_5_1","doi-asserted-by":"publisher","DOI":"10.1002\/evl3.175"},{"key":"e_1_2_11_6_1","doi-asserted-by":"publisher","DOI":"10.1111\/evo.14044"},{"key":"e_1_2_11_7_1","doi-asserted-by":"publisher","DOI":"10.1182\/blood\u20102017\u201003\u2010768507"},{"key":"e_1_2_11_8_1","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.173.6.3653"},{"key":"e_1_2_11_9_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1159978"},{"issue":"4","key":"e_1_2_11_10_1","first-page":"377","article-title":"Contemporary evolution, allelic recycling, and adaptive radiation of the threespine stickleback","volume":"15","author":"Bell M. 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