Data from: Ancient climate changes and relaxed selection shape cave colonization in North American cavefishes

Extreme environments serve as natural laboratories for studying
evolutionary processes, with caves offering replicated instances of
independent colonisations. The timing, mode, and genetic underpinnings
underlying cave-obligate organismal evolution remain enigmatic. We
integrate phylogenomics, fossils, paleoclimatic modeling, and newly
sequenced genomes to elucidate the evolutionary history and adaptive
processes of cave colonisation in the study group, the North American
Amblyopsidae fishes. Amblyopsid fishes present a unique system for
investigating cave evolution, encompassing surface, facultative
cave-dwelling, and cave-obligate (troglomorphic) species. Using 1,105 exon
markers and total-evidence dating, we reconstructed a robust phylogeny
that supports the nested position of eyed, facultative cave-dwelling
species within blind cavefishes. We identified three independent cave
colonisations, dated to the Early Miocene (18.5 Mya), Late Miocene (10.0
Mya), and Pliocene (3.0 Mya). Evolutionary model testing supported a
climate-relict hypothesis, suggesting that global cooling trends since the
Early–Middle Eocene may have influenced cave colonisation. Comparative
genomic analyses of 487 candidate genes revealed both relaxed and
intensified selection on troglomorphy-related loci. We found more loci
under relaxed selection, supporting neutral mutation as a significant
mechanism in cave-obligate evolution. Our findings provide empirical
support for climate-driven cave colonisation and offer insights into the
complex interplay of selective pressures in extreme environments.