Adaptive molecular convergence: Molecular evolution versus molecular phylogenetics.

Definitive identification of convergent evolution, the acquisition of the same biological trait in unrelated lineages, provides one of the most compelling sources of evidence for natural selection. Although numerous examples of convergent morphological evolution are well known (such as the independent development of wings in birds and mammals), cases of convergent evolution at the molecular-genetic level appear to be quite rare. We recently discovered a remarkable case of convergent molecular evolution involving more than 100 parallel amino-acid changes across all 13 mitochondrially-encoded proteins of snakes and agamid lizards. Just a few of these convergent substitutions were sufficient to positively mislead the inference of phylogeny, even with thousands of sites providing latent support for the correct underlying relationships. Since this example demonstrates that molecular convergence can happen en masse in nature, affecting multiple genes, it is important to consider the threat this poses to molecular systematics, and careful genome-wide assays for convergent molecular evolution are warranted. This result implies that the protein adaptive landscape is sometimes highly constrained.