Loss of Conserved Noncoding Elements Likely Shaped the Evolution of Regressed Phenotypes in Cavefish.

ABSTRACT: 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 throug

SUBMITTER: Lal M 

PROVIDER: S-EPMC12662050 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature