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To better understand how organisms evolve these complex phenotypic changes, the repeatability and predictability of evolution, and possible constraints on adapting to an extreme environment, it is important to understand how adaptive variation has evolved. Poeciliid fishes represent a particularly fruitful study system for investigations of adaptation to extreme environments due to their repeated colonization of toxic hydrogen sulfide\u2013rich springs across multiple species within the clade. Previous investigations have highlighted changes in the physiology and gene expression in specific species that are thought to facilitate adaptation to hydrogen sulfide\u2013rich springs. However, the presence of adaptive nucleotide variation in coding and regulatory regions and the degree to which convergent evolution has shaped the genomic regions underpinning sulfide tolerance across taxa are unknown. By sampling across seven independent lineages in which nonsulfidic lineages have colonized and adapted to sulfide springs, we reveal signatures of shared evolutionary rate shifts across the genome. We found evidence of genes, promoters, and putative enhancer regions associated with both increased and decreased convergent evolutionary rate shifts in hydrogen sulfide\u2013adapted lineages. Our analysis highlights convergent evolutionary rate shifts in sulfidic lineages associated with the modulation of endogenous hydrogen sulfide production and hydrogen sulfide detoxification. We also found that regions with shifted evolutionary rates in sulfide spring fishes more often exhibited convergent shifts in either the coding region or the regulatory sequence of a given gene, rather than both.<\/jats:p>","DOI":"10.1093\/gbe\/evae087","type":"journal-article","created":{"date-parts":[[2024,5,24]],"date-time":"2024-05-24T21:35:02Z","timestamp":1716586502000},"source":"Crossref","is-referenced-by-count":8,"title":["Evolutionary Rate Shifts in Coding and Regulatory Regions Underpin Repeated Adaptation to Sulfidic Streams in Poeciliid Fishes"],"prefix":"10.1093","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5569-8061","authenticated-orcid":false,"given":"Rishi","family":"De-Kayne","sequence":"first","affiliation":[{"name":"Department of Ecology and Evolutionary Biology, University of California Santa Cruz , Santa Cruz, CA 95060 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Blair W","family":"Perry","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, Washington State University , Pullman, WA 99164 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kerry L","family":"McGowan","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, Washington State University , Pullman, WA 99164 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jake","family":"Landers","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, Washington State University , Pullman, WA 99164 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lenin","family":"Arias-Rodriguez","sequence":"additional","affiliation":[{"name":"Divisi\u00f3n Acad\u00e9mica de Ciencias Biol\u00f3gicas, Universidad Ju\u00e1rez Aut\u00f3noma de Tabasco (UJAT) , Villahermosa , M\u00e9xico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ryan","family":"Greenway","sequence":"additional","affiliation":[{"name":"Division of Biology, Kansas State University , Manhattan, KS 66506, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carlos M","family":"Rodr\u00edguez Pe\u00f1a","sequence":"additional","affiliation":[{"name":"Instituto de Investigaciones Bot\u00e1nicas y Zool\u00f3gicas, Universidad Aut\u00f3noma de Santo Domingo , Santo Domingo 10105 , Dominican Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Tobler","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Missouri\u2013St. Louis , St. Louis, MO 63131 , USA"},{"name":"Whitney R. Harris World Ecology Center, University of Missouri\u2013St. Louis , St. Louis, MO 63121 , USA"},{"name":"WildCare Institute, Saint Louis Zoo , St. Louis, MO 63110 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7731-605X","authenticated-orcid":false,"given":"Joanna L","family":"Kelley","sequence":"additional","affiliation":[{"name":"Department of Ecology and Evolutionary Biology, University of California Santa Cruz , Santa Cruz, CA 95060 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,5,24]]},"reference":[{"issue":"4","key":"2024053114303433800_evae087-B1","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1038\/nrg3891","article-title":"The role of regulatory variation in complex traits and disease","volume":"16","author":"Albert","year":"2015","journal-title":"Nat Rev Genet"},{"issue":"3","key":"2024053114303433800_evae087-B2","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J Mol Biol"},{"issue":"10","key":"2024053114303433800_evae087-B3","doi-asserted-by":"crossref","first-page":"3211","DOI":"10.1111\/pce.14143","article-title":"Convergent evolution of gene regulatory networks underlying plant adaptations to dry environments","volume":"44","author":"Artur","year":"2021","journal-title":"Plant Cell Environ"},{"issue":"4","key":"2024053114303433800_evae087-B4","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1139\/gen-2017-0051","article-title":"Molecular evolution and expression of oxygen transport genes in livebearing fishes (Poeciliidae) from hydrogen sulfide rich springs","volume":"61","author":"Barts","year":"2018","journal-title":"Genome"},{"issue":"1","key":"2024053114303433800_evae087-B5","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1111\/j.1742-4658.2007.06184.x","article-title":"Human retinol dehydrogenase 13 (RDH13) is a mitochondrial short-chain dehydrogenase\/reductase with a retinaldehyde reductase activity","volume":"275","author":"Belyaeva","year":"2008","journal-title":"FEBS J"},{"issue":"1777","key":"2024053114303433800_evae087-B6","doi-asserted-by":"crossref","first-page":"20180240","DOI":"10.1098\/rstb.2018.0240","article-title":"Local ancestry analysis reveals genomic convergence in extremophile fishes","volume":"374","author":"Brown","year":"2019","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"issue":"1749","key":"2024053114303433800_evae087-B7","first-page":"5039","article-title":"The probability of genetic parallelism and convergence in natural populations","volume":"279","author":"Conte","year":"2012","journal-title":"Proc Biol Sci"},{"key":"2024053114303433800_evae087-B22","unstructured":"Dainat J. \u00a0AGAT: Another Gff Analysis Toolkit to handle annotations in any GTF\/GFF format (v0.8.0). 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