Subterranean Fishes of the World

3213

2013

AIM 2013

The precise genetic mechanisms accompanying the regression of phenotypic characters, and whether one mechanism explains all regressive phenotypes, remain largely unknown. Cave animals represent salient examples of regressive evolution, owing to the recurrent loss of pigmentation and eye reduction in organisms living amidst the dark subterranean environment. Among these cave-dwelling examples, the blind Mexican cavefish Astyanax mexicanus has converged on depigmented phenotypes in at least 7 known cave populations. Although the mechanism through which these traits regress is poorly understood, one possibility is that the genes responsible for maintaining pigmentation become non-functional through loss-of-function mutations. An alternative scenario is that genes acquire regulatory mutations leading to altered expression levels that may account for degenerative phenotypes in caves. We set out to determine if a pattern exists between the accumulation of coding sequence mutations in genes of exclusive function, supported by prior QTL studies identifying the genes Oca2 and Mc1r in the evolution of albinism and brown, respectively. We hypothesized that genes with pleiotropic functions may be constrained from the accumulation of loss-of-function coding alterations because of antagonistic effects on other phenotypes. We utilized an integrated de novo Astyanax transcriptome to perform large-scale genetic comparisons specifically evaluating pigmentation gene expression differences between surface and Pachón cave-dwelling fish. From this transcriptome, we identified ~440 genes with pigmentation-related functions. We then evaluated these for potential loss-of-function coding mutations in Pachón cavefish. This gene set was then assessed for robust expression level differences between morphotypes using RNA-seq. Our preliminary data indicate that by 3 dpf, more than 50 pigmentation-related genes are downregulated in cave-dwelling forms. Additionally, we found evidence of both coding and regulatory alterations affecting pigmentation genes having accumulated in cavefish lineages. Future studies will clarify whether genes acting exclusively on pigmentation are more likely to harbor destructive loss-of-function coding sequence mutations, while regulatory alterations are more frequently associated with pleiotropic genes.

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