{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,23]],"date-time":"2025-12-23T07:34:37Z","timestamp":1766475277126,"version":"3.48.0"},"reference-count":55,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2025,11,12]],"date-time":"2025-11-12T00:00:00Z","timestamp":1762905600000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Department of Biotechnology, India","award":["BT\/PR40149\/BTIS\/137\/36\/2022"],"award-info":[{"award-number":["BT\/PR40149\/BTIS\/137\/36\/2022"]}]},{"name":"Department of Biotechnology, India","award":["BT\/PR40198\/BTIS\/137\/56\/2023"],"award-info":[{"award-number":["BT\/PR40198\/BTIS\/137\/56\/2023"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,11,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The Mexican cavefish, Astyanax mexicanus, is a captivating model for probing cave adaptations, showcasing pronounced divergence in traits like vision, brain morphology, behavior, pigmentation, metabolism, and hypoxia tolerance compared to its surface-dwelling counterpart. However, only a small number of protein-coding variants have been found in cave-morphs, leaving the vast phenotypic gap between the two morphs largely unexplained. We aligned the genomes of five closely related teleosts and identified 46,914 conserved noncoding elements, of which 473 were specifically lost in cave-morphs. These conserved noncoding elements, confirmed in Zebrafish, displayed activating histone modifications, possessed binding sites of neuronal transcription factors, and interacted with cognate genes through chromatin loops. Genes crucial for eye and nervous system development were located adjacent to conserved noncoding elements lost in cave morphs. Notably, the flanking genes were gradually downregulated during embryonic development of cave-morphs, contrasting with surface morphs. These insights underscore how dampened developmental pathways, stemming from the loss of distal regulatory elements, may have contributed to the evolutionary regression of phenotypes in cave morphs.<\/jats:p>","DOI":"10.1093\/gbe\/evaf211","type":"journal-article","created":{"date-parts":[[2025,11,8]],"date-time":"2025-11-08T12:53:47Z","timestamp":1762606427000},"source":"Crossref","is-referenced-by-count":0,"title":["Loss of Conserved Noncoding Elements Likely Shaped the Evolution of Regressed Phenotypes in Cavefish"],"prefix":"10.1093","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-7067-9171","authenticated-orcid":false,"given":"Mohan","family":"Lal","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)\u2014Mohali , Knowledge city, Sector 81, SAS Nagar, Manauli PO 140306 ,","place":["India"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-1130-4084","authenticated-orcid":false,"given":"Jui","family":"Bhattacharya","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)\u2014Mohali , Knowledge city, Sector 81, SAS Nagar, Manauli PO 140306 ,","place":["India"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7632-6339","authenticated-orcid":false,"given":"Kuljeet Singh","family":"Sandhu","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)\u2014Mohali , Knowledge city, Sector 81, SAS Nagar, Manauli PO 140306 ,","place":["India"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2025,11,11]]},"reference":[{"key":"2025122302315435600_evaf211-B1","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1002\/cne.21488","article-title":"Developmental mechanisms for retinal degeneration in the blind cavefish Astyanax mexicanus","volume":"505","author":"Alunni","year":"2007","journal-title":"J Comp Neurol."},{"key":"2025122302315435600_evaf211-B2","doi-asserted-by":"publisher","first-page":"2922","DOI":"10.1007\/s12035-017-0554-y","article-title":"Lhx9 is required for the development of retinal nitric oxide-synthesizing amacrine cell subtype","volume":"55","author":"Balasubramanian","year":"2018","journal-title":"Mol Neurobiol."},{"key":"2025122302315435600_evaf211-B3","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1002\/dneu.22053","article-title":"Protocadherin-17 function in Zebrafish retinal development","volume":"73","author":"Chen","year":"2013","journal-title":"Dev Neurobiol."},{"key":"2025122302315435600_evaf211-B4","doi-asserted-by":"publisher","DOI":"10.1093\/oso\/9780198820765.001.0001","volume-title":"The biology of caves and other subterranean habitats, Biology of habitats series","author":"Culver","year":"2019"},{"key":"2025122302315435600_evaf211-B5","doi-asserted-by":"publisher","first-page":"341","DOI":"10.1016\/j.cell.2016.08.071","article-title":"Mutations in human accelerated regions disrupt cognition and social behavior","volume":"167","author":"Doan","year":"2016","journal-title":"Cell"},{"key":"2025122302315435600_evaf211-B6","doi-asserted-by":"publisher","first-page":"446","DOI":"10.1093\/oxfordjournals.molbev.a004100","article-title":"Evidence for multiple genetic forms with similar eyeless phenotypes in the blind cavefish, Astyanax mexicanus","volume":"19","author":"Dowling","year":"2002","journal-title":"Mol Biol Evol."},{"issue":"12","key":"2025122302315435600_evaf211-B7","doi-asserted-by":"publisher","first-page":"e2013136118","DOI":"10.1073\/pnas.2013136118","article-title":"Meis homeobox genes control progenitor competence in the retina","volume":"118","author":"Dupacova","year":"2021","journal-title":"Proc. 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