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By integrating ATAC\u2010seq chromatin profiles with population genomic outlier scans and RNA\u2010seq gene expression data, we characterize the functional impact of regulatory elements and identify candidate loci where selection signatures coincide with tissue\u2010specific chromatin and transcriptional shifts. We mapped genome\u2010wide chromatin accessibility in three tissues (eye, liver and spleen) of wild European perch (\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>Perca fluviatilis<\/jats:italic>\n                    <\/jats:styled-content>\n                    ) inhabiting contrasting humic\u2010 (dark\u2010water) and clear\u2010water lakes. We identified over 76,000 accessible chromatin regions spanning 36.1\u2009Mb of the genome, which were enriched for gene functions related to vision, metabolism and immune response. Chromatin landscapes were strongly tissue\u2010specific, while only a subset of regions (0.32%,\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u2009161) showed differential accessibility between environments, suggesting that the regulatory architecture is dominated by tissue identity rather than environmental context. Integrating population genomic outlier scans with chromatin profiles revealed significant enrichment of adaptive SNPs within common open chromatin regions (1.5\u2010fold) and transcription start sites (1.7\u2010fold), directly implicating cis\u2010regulatory elements as frequent targets of natural selection. This study demonstrates that humic adaptation in perch targets specific regulatory regions readily identified by the ATAC\u2010seq approach, highlighting the value of functional chromatin maps in evolutionary genomics. Together, our results provide one of the first genome\u2010wide regulatory maps for a wild vertebrate and establish a functional framework for connecting natural selection to regulatory mechanisms in the wild.\n                  <\/jats:p>","DOI":"10.1111\/mec.70550","type":"journal-article","created":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T04:56:57Z","timestamp":1790053017000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Chromatin Accessibility Reveals Adaptive Regulatory Variation in a Keystone Freshwater Fish"],"prefix":"10.1111","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-5944-2125","authenticated-orcid":false,"given":"Konrad","family":"Taube","sequence":"first","affiliation":[{"name":"Estonian University of Life Sciences  Tartu 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