Abstract

Complex organs such as eyes are commonly lost during evolution, but the time scale on which lost phenotypes could be reactivated is a matter of long-standing debate, with important implications for the molecular mechanisms of trait loss. Two phylogenetic approaches have been used to test whether regain of traits has occurred. One way is by comparison of nested, continuous time Markov models of trait evolution, an approaches that we term a tree-based tests. A second way to demonstrate statistical support for trait regain through use of node-based tests, using explicit estimation of ancestral node states. Here, we estimate new molecular and morphological phylogenies and use them to examine the possibility of eye regain and dispersal between shallow and abyssal seas during the history of cylindroleberidid ostracods, a family of about 200 species, comprising ed of both eyeless and sighted species. First, we confirmed that eye presence/absence is correlated with habitat depth. Parameter estimates from a phylogenetic model indicate that speciation is more rapid in deep-sea, eyeless clades compared to shallow sighted clades. In addition, we found that tree-based statistical tests usually indicated reversals, including both transitions from deep to shallow seas and re-gain of eyes. In contrast, node-based statistical tests usually failed to show significant support for reversals. These results also hold for simulated phylogenies, indicating they are not unique to the current dataset. We recommend that both tree-based and node-based tests should be examined before making conclusions about character reversal, and that ideally, alternative character histories should be tested using additional data, besides just the phylogenetic distribution of presence/absence of the characters.