Cavefish genomes resolve the ages of North American subterranean ecosystems

Genomes provide tools for reconstructing organismal evolution and larger Earth-system processes. Here, we reconstruct the genomic evolution of cave-adapted amblyopsid fishes. Although microcomputed tomography reveals the strikingly similar skeletons of cave-adapted lineages, analyses of the genomes of all species suggest that amblyopsids independently colonized caves and degenerated their eyes at least four times after descending from populations that already possessed adaptations to low-light environments. By examining pseudogenization through loss-of-function mutations in amblyopsids, we infer that the genomic bases of their vision degenerated over millions of years. We leverage these data to pinpoint the ages of subterranean karstic ecosystems in eastern North America, which are difficult to date using traditional geochronologic techniques. Our results demonstrate how genomes can be used to reconstruct the timescale of Earth system evolution.