A molecular supermatrix of the rabbits and hares (Leporidae) allows for the identification of five intercontinental exchanges during the Miocene

The hares and rabbits belonging to the family Leporidae have a nearly worldwide distribution and approximately 72% of the genera have geographically restricted distributions. Despite several attempts using morphological, cytogenetic, and mitochondrial DNA evidence, a robust phylogeny for the Leporidae remains elusive. To provide phylogenetic resolution within this group, a molecular supermatrix was constructed for 27 taxa representing all 11 leporid genera. Five nuclear (SPTBN1, PRKCI, THY, TG, and MGF) and two mitochondrial (cytochrome b and 12S rRNA) gene fragments were analyzed singly and in combination using parsimony, maximum likelihood, and Bayesian inference. The analysis of each gene fragment separately as well as the combined mtDNA data almost invariably failed to provide strong statistical support for intergeneric relationships. In contrast, the combined nuclear DNA topology based on 3601 characters greatly increased phylogenetic resolution among leporid genera, as was evidenced by the number of topologies in the 95% confidence interval and the number of significantly supported nodes. The final molecular supermatrix contained 5483 genetic characters and analysis thereof consistently recovered the same topology across a range of six arbitrarily chosen model specifications. Twelve unique insertion-deletions were scored and all could be mapped to the tree to provide additional support without introducing any homoplasy. Dispersal-vicariance analyses suggest that the most parsimonious solution explaining the current geographic distribution of the group involves an Asian or North American origin for the Leporids followed by at least nine dispersals and five vicariance events. Of these dispersals, at least three intercontinental exchanges occurred between North America and Asia via the Bering Strait and an additional three independent dispersals into Africa could be identified. A relaxed Bayesian molecular clock applied to the seven loci used in this study indicated that most of the intercontinental exchanges occurred between 14 and 9 million years ago and this period is broadly coincidental with the onset of major Antarctic expansions causing land bridges to be exposed.