Convergent Evolution in Amblyopsid Cavefishes and the Age of Eastern North American Subterranean Ecosystems

Genomes provide tools for reconstructing organismal evolution and larger Earth system processes. Although genome sequences have been jointly analyzed with geological data to understand links between biological evolution and geological phenomena such as erosion and uplift, genomic and natural history observations have seldom been leveraged to reconstruct the timescale of landscape change in cases where traditional methods from the Earth sciences cannot. Here, we reconstruct the genomic evolution of cave-adapted amblyopsid fishes. Although high-resolution computed tomography reveals the strikingly similar skeletons of cave-adapted lineages, our analyses of the genomes of all species in this clade 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 infer the ages of subterranean karstic ecosystems in eastern North America, which are difficult to date using standard geochronologic techniques. Our results support ancient ages for imperiled North American cave biotas and show how genomes can be used to inform the timescale of landscape evolution.