Trends in loss and retention of vision-related genes are similar between two trechine beetles independently colonizing caves

Whether evolution is predictable has been tested in evolutionary biology by comparing lineages that experienced parallel evolution. For example, the repeatability of gene expression between strains was examined in the experimental evolution of bacteria. However, whether it is possible to predict the evolutionary fate of a gene (i.e., loss or retention) after an organism colonizes a new habitat and experiences a long period is not sufficiently clear. Here, we investigate a visual gene set in two species of eyeless trechine beetles (Coleoptera: Carabidae: Trechinae), which are thought to have colonized caves independently, and show that many of the lost genes and retained genes are common between them. We also estimate the pleiotropy that represents the extent to which these genes act in several tissues, using gene expression data in a model organism, and show that commonly lost genes have low pleiotropy. Our results suggest that the loss and retention of a visual gene set are relatively easy to predict in cave-dwelling trechine beetles. Furthermore, this study supports the possibility that even evolutionary fates of genes, which occur after a long period, are influenced by the functional constraints of these genes.