Cave evolution on repeat: reuse of the same genomic regions across lineages of Astyanax mexicanus

Abstract Similar traits repeatedly evolve across independent populations in response to similar environmental conditions. For many repeatedly evolved traits, it is unknown if populations evolve similar traits through the same or different genetic mechanisms. To address this question, we leveraged the Mexican tetra fish, Astyanax mexicanus, which has repeatedly evolved many traits including reduced sleep duration, eye degeneration, and metabolic shifts to accommodate limited nutrient availability. We defined whether shared or independent genetic architecture governs the repeated evolution of sleep loss, increased food consumption, early onset adipose deposition, and eye loss in different evolutionary origins of the cavefish phenotype by using quantitative trait locus (QTL) mapping across 3 cave × surface F2 hybrid populations. We found that, among the traits evaluated, eye loss exhibits the most genetic repeatability, with ∼43% of QTL shared across lineages. Sleep loss and metabolic traits (ie feeding, adiposity) were genetically less repeatable, with only ∼25% to 33% of QTL shared across lineages. Next, we explored whether QTL for metabolism, eye loss, and sleep traits in cavefish colocalize in the cavefish genome and are inherited together to facilitate potential cavefish adaptation. Although these traits have repeatedly co-evolved in cave populations, we did not find evidence for extensive genetic linkage among them. Overall, we found that genetic repeatability is a common feature in the repeated evolution of cave traits, the extent of genetic repeatability varies across cave traits, and there is little evidence for widespread colocalization of sleep, eye loss, and metabolic traits within the genome.