Meeting Abstract
The evolutionary mechanisms governing adaptation to extreme environments remain controversial. In the dark and nutrient-poor cave environment, diverse animals around the world trend towards the loss of eyes and pigmentation. These examples of regressive evolution may evolve through direct selection (e.g., energy conservation), indirect selection (e.g., pleiotropic consequences), and/or neutral forces (e.g., genetic drift). Earlier studies in other systems suggested a principal role for cis-regulatory changes to essential genes involved in dramatic ecological shifts. Hybridization studies in cave- and surface-dwelling Astyanax fish reveals a different pattern of genetic changes, which may imply that regressive loss occurs more frequently through coding rather than regulatory sequence changes. For example, the genes implicated in two Mendelian pigmentation traits (albinism and brown) harbor destructive coding sequence changes in the genes oca2 and mc1r, respectively. To determine the identity and frequency of destructive changes in the Astyanax genome, we performed a genome-wide search for insertions/deletions (“indels”). We aligned millions of short reads from two ancient cavefish populations (Pachón and Tinaja) and surface-dwelling fish to the cavefish reference genome. This analysis yielded several compelling genetic lesions that were variably present in each population. The majority of indels were discovered in the surface populations, by reference to the cavefish genome. At present, we have validated eight genetic mutations arising from genes encoding both structural proteins and transcription factors. Further functional analysis will illuminate the precise role for these genes in cave adaptation and help inform the genetic mechanisms mediating colonization of extreme environments.
