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However, the role of miRNAs in mediating adaptation to diverse environments in natural study systems remains largely unexplored. Here, we characterized miRNAs and their expression in <jats:italic>Poecilia mexicana<\/jats:italic>, a species of small fish that inhabits both normal streams and extreme environments in the form of springs rich in toxic hydrogen sulphide (H<jats:sub>2<\/jats:sub>S). We found that <jats:italic>P.\u00a0mexicana<\/jats:italic> has a similar number of miRNA genes as other teleosts. In addition, we identified a large population of mature miRNAs that were differentially expressed between locally adapted populations in contrasting habitats, indicating that miRNAs may contribute to <jats:italic>P.\u00a0mexicana<\/jats:italic> adaptation to sulphidic environments. In silico identification of differentially expressed miRNA\u2010mRNA pairs revealed, in the sulphidic environment, the downregulation of miRNAs predicted to target mRNAs involved in sulphide detoxification and cellular homeostasis, which are pathways essential for life in H<jats:sub>2<\/jats:sub>S\u2010rich springs. In addition, we found that predicted targets of upregulated miRNAs act in the mitochondria (16.6% of predicted annotated targets), which is the main site of H<jats:sub>2<\/jats:sub>S toxicity and detoxification, possibly modulating mitochondrial function. Together, the differential regulation of miRNAs between these natural populations suggests that miRNAs may be involved in H<jats:sub>2<\/jats:sub>S adaptation by promoting functions needed for survival and reducing functions affected by H<jats:sub>2<\/jats:sub>S. This study lays the groundwork for further research to directly demonstrate the role of miRNAs in adaptation to H<jats:sub>2<\/jats:sub>S. Overall, this study provides a critical stepping\u2010stone towards a comprehensive understanding of the regulatory mechanisms underlying the adaptive variation in gene expression in a natural system.<\/jats:p>","DOI":"10.1111\/jeb.13727","type":"journal-article","created":{"date-parts":[[2020,10,30]],"date-time":"2020-10-30T02:27:16Z","timestamp":1604024836000},"page":"977-988","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":29,"title":["microRNA expression variation as a potential molecular mechanism contributing to adaptation to hydrogen sulphide"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7731-605X","authenticated-orcid":false,"given":"Joanna L.","family":"Kelley","sequence":"first","affiliation":[{"name":"School of Biological Sciences Washington State University  Pullman WA USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5126-8785","authenticated-orcid":false,"given":"Thomas","family":"Desvignes","sequence":"additional","affiliation":[{"name":"Institute of Neuroscience University of Oregon  Eugene OR USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6388-3873","authenticated-orcid":false,"given":"Kerry L.","family":"McGowan","sequence":"additional","affiliation":[{"name":"School of Biological Sciences Washington State University  Pullman WA USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3867-1902","authenticated-orcid":false,"given":"Marcos","family":"Perez","sequence":"additional","affiliation":[{"name":"School of Molecular Biosciences Washington State University  Pullman WA USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8025-5569","authenticated-orcid":false,"given":"Lenin Arias","family":"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":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6100-2470","authenticated-orcid":false,"given":"Anthony P.","family":"Brown","sequence":"additional","affiliation":[{"name":"School of Biological Sciences Washington State University  Pullman WA USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4662-1932","authenticated-orcid":false,"given":"Zach","family":"Culumber","sequence":"additional","affiliation":[{"name":"Biological Sciences Department University of Alabama in Huntsville  Huntsville AL USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0326-0890","authenticated-orcid":false,"given":"Michael","family":"Tobler","sequence":"additional","affiliation":[{"name":"Division of Biology Kansas State University  Manhattan KS USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,11,28]]},"reference":[{"key":"e_1_2_8_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ympev.2012.12.012"},{"key":"e_1_2_8_3_1","volume-title":"FastQC: A quality control tool for high throughput sequence data","author":"Andrews S.","year":"2010"},{"key":"e_1_2_8_4_1","first-page":"161","article-title":"The role of microRNAs in human diseases","volume":"2","author":"Ardekani A. 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