Analysis of multi-trait evolution across independently evolved cavefish populations reveals shared and independent evolution of suites of traits.

Environmental perturbations often lead to the evolution of multiple traits. Determining whether shared genetic factors underlie multi-trait evolution is a central question in evolutionary biology. In the Mexican tetra, Astyanax mexicanus, cave-dwelling populations have repeatedly evolved multiple traits. The repeated evolution of these traits, paired with robust environmental differences between the surface and cave habitats, provide an opportunity to investigate the genetic basis of multi-trait evolution. Here, we investigate the extent to which shared genetic mechanisms underlie the repeated evolution of multiple traits in cavefish. Across cave populations, we find evidence for shared and distinct genetic mechanisms contributing to the evolution of individual traits. Further, multiple traits covary in cave-surface F2 hybrids. Moreover, many of the same pairs of traits covary in independently evolved cave populations. Finally, multiple traits differ between pigmented and albino F2 fish. Quantification of these traits in surface fish with mutations in the albinism gene oculocutaneous albinism 2 (oca2) reveals that mutations in oca2 reduce bottom-dwelling behaviour in A. mexicanus. Together, these findings suggest that multi-trait evolution occurs repeatedly through shared genetic factors across A. mexicanus cave populations. These results are consistent with pleiotropy and/or linkage playing a large role in multi-trait evolution in this species.