Evidence of genome-wide relaxed selection on mildly deleterious mutations in an ancient subterranean catfish
Abstract
About 100 subterranean catfish species have been described, resulting from repeated colonization of cave environments by multiple surface lineages. Most cave-dwelling species are found in the Americas, in particular in South America, but a few species also live in Central and North America. Despite the availability of high-quality genome assemblies for two cave species, the Mexican blind catfish Prietella phreatophila and the Colombian blind catfish Trichomycterus rosablanca, genomic approaches to investigate genetic changes associated with subterranean life or to estimate cave colonization times remain largely unexplored. To fill this gap, we additionally sequenced the genomes of four blind and depigmented subterranean catfishes from Peru (three Trichomycterus and one Astroblepus), as well as the genomes of four close surface relatives. We first extracted a large set of light-related genes, such as phototransduction and crystallin genes, and found contrasting decays of these sequences in different cave species, from 1% of pseudogenes in T. rosablanca to 48% in P. phreatophila. Two independent molecular dating methods gave congruent ages, indicating that these catfishes colonized subterranean habitats at different times, ranging from Early Pliocene to Late Pleistocene, supporting the hypothesis that surface catfishes repeatedly and rapidly adapted to subterranean habitats. The oldest cave species, P. phreatophila, appears to have been thriving in the dark for over 3.5 million years. Moreover, a genome-wide analysis of protein-coding genes suggests weaker purifying selection on mildly deleterious mutations in this cavefish than in other catfish lineages, likely reflecting a long-term small effective population size.
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BibTeX
@article{policarpo2026evidence,
title = {{Evidence of genome-wide relaxed selection on mildly deleterious mutations in an ancient subterranean catfish}},
author = {Maxime Policarpo and Julien Fumey and Marine Milhes and Céline Bonillo and Alejandra Campos and Max Hidalgo and Sylvie Rétaux and Marc Pouilly and Didier Casane},
journal = {Evolution - International Journal of Organic Evolution},
year = {2026},
month = sep,
doi = {10.1093/evolut/qpag158},
url = {https://hal.science/hal-05802238v1},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Evidence of genome-wide relaxed selection on mildly deleterious mutations in an ancient subterranean catfish
AU - Maxime Policarpo
AU - Julien Fumey
AU - Marine Milhes
AU - Céline Bonillo
AU - Alejandra Campos
AU - Max Hidalgo
AU - Sylvie Rétaux
AU - Marc Pouilly
AU - Didier Casane
PY - 2026
DA - 2026/09/08
JO - Evolution - International Journal of Organic Evolution
DO - 10.1093/evolut/qpag158
UR - https://hal.science/hal-05802238v1
AB - About 100 subterranean catfish species have been described, resulting from repeated colonization of cave environments by multiple surface lineages. Most cave-dwelling species are found in the Americas, in particular in South America, but a few species also live in Central and North America. Despite the availability of high-quality genome assemblies for two cave species, the Mexican blind catfish Prietella phreatophila and the Colombian blind catfish Trichomycterus rosablanca, genomic approaches to investigate genetic changes associated with subterranean life or to estimate cave colonization times remain largely unexplored. To fill this gap, we additionally sequenced the genomes of four blind and depigmented subterranean catfishes from Peru (three Trichomycterus and one Astroblepus), as well as the genomes of four close surface relatives. We first extracted a large set of light-related genes, such as phototransduction and crystallin genes, and found contrasting decays of these sequences in different cave species, from 1% of pseudogenes in T. rosablanca to 48% in P. phreatophila. Two independent molecular dating methods gave congruent ages, indicating that these catfishes colonized subterranean habitats at different times, ranging from Early Pliocene to Late Pleistocene, supporting the hypothesis that surface catfishes repeatedly and rapidly adapted to subterranean habitats. The oldest cave species, P. phreatophila, appears to have been thriving in the dark for over 3.5 million years. Moreover, a genome-wide analysis of protein-coding genes suggests weaker purifying selection on mildly deleterious mutations in this cavefish than in other catfish lineages, likely reflecting a long-term small effective population size.
SN - 0014-3820
SN - 1558-5646
ER -