Determining the Null Model for Detecting Adaptive Convergence from Genomic Data: A Case Study using Echolocating Mammals

Convergent evolution occurs when the same trait arises independently in multiple lineages. In most cases of phenotypic convergence such transitions are adaptive, so finding the underlying molecular causes of convergence can provide insight into the process of adaptation. Convergent evolution at the genomic level also lends itself to study by comparative methods, although molecular convergence can also occur by chance, adding noise to this process. Parker et al. studied convergence across the genomes of several mammals, including echolocating bats and dolphins (Parker J, Tsagkogeorga G, Cotton JA, Liu Y, Provero P, Stupka E, Rossiter SJ. 2013. Genome-wide signatures of convergent evolution in echolocating mammals. Nature 502:228-231). On the basis of a null distribution of site-specific likelihood support (SSLS) generated using simulated topologies, they concluded that there was evidence for genome-wide adaptive convergence between echolocating taxa. Here, we demonstrate that methods based on SSLS do not adequately measure convergence, and reiterate the use of an empirical null model that directly compares convergent substitutions between all pairs of species. We find that when the proper comparisons are made there is no surprising excess of convergence between echolocating mammals, even in sensory genes.