Population genomics of premature termination codons in cavefish with substantial trait loss

Molecular Biology and Evolution, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 21, 2025

Abstract Loss-of-function alleles are a pertinent source of genetic variation with the potential to contribute adaptation. Cave-adapted organisms exhibit striking loss ancestral traits such as eyes and pigment, suggesting that loss-of-function may play an outsized role in these systems. Here, we leverage 141 whole genome sequences evaluate evolutionary history adaptive single nucleotide premature termination codons (PTCs) Mexican tetra. We find cave populations contain significantly more PTCs at high frequency than surface populations. also occur frequently genes inherent relaxed constraint relative rest genome. Using SLiM simulate PTC evolution cavefish population, show smaller population size increased drift is sufficient account for observed increase without positive selection. CRISPR-Cas9, mutation one genes, pde6c, produces phenotypes tetra mimic cave-derived traits. Finally, identify small subset candidate populations, within selective sweeps, beneficial reduced energy expenditure, handful be adaptive. Overall, our work provides rare characterization across wild finds they have important phenotypes, contributing growing body literature showing through subterranean organisms.

Language: Английский

Therx3gene contributes to the evolution of eye loss in the cavefishAstyanax mexicanus

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 15, 2024

Abstract Uncovering mechanisms by which sensory systems evolve is critical for understanding how organisms adapt to a novel environment. Astyanax mexicanus species of fish with populations surface that inhabit rivers and streams cavefish have adapted life within caves. Cavefish evolved system changes relative their counterparts, providing an opportunity investigate underlying evolution. Here, we report the role gene retinal homeobox 3 ( rx3 ) in eye We generated putative loss-of-function mutations using CRISPR-Cas9 determine this development species. These mutant fail develop eyes, demonstrating required development. Further, exhibit altered behaviors wild-type fish, suggesting loss eyes impacts sensory-dependent behaviors. Finally, cave-surface hybrid inherit allele from siblings allele, cis-regulatory variation at locus contributes size evolution cavefish. Together, these findings demonstrate that, as other species, A. . Moreover, they suggest plays reduction cavefish, shedding light on genetic response extreme environmental changes.

Language: Английский