Cytochrome b phylogeny of North American hares and jackrabbits (Lepus, lagomorpha) and the effects of saturation in outgroup taxa

Jackrabbits and hares, members of the genus Lepus, comprise over half of the species within the family Leporidae (Lagomorpha). Despite their ecological importance, potential economic impact, and worldwide distribution, the evolution of hares and jackrabbits has been poorly studied. We provide an initial phylogenetic framework for jackrabbits and hares so that explicit hypotheses about their evolution can be developed and tested. To this end, we have collected DNA sequence data from a 702-bp region of the mitochondrial cytochrome b gene and reconstructed the evolutionary history (via parsimony, neighbor joining, and maximum likelihood) of 11 species of Lepus, focusing on North American taxa. Due to problems of saturation, induced by multiple substitutions, at synonymous coding positions between the ingroup taxa and the outgroups (Oryctolagus and Sylvilagus), both rooted and unrooted trees were examined. Variation in tree topologies generated by different reconstruction methods was observed in analyses including the outgroups, but not in the analyses of unrooted ingroup networks. Apparently, substitutional saturation hindered the analyses when outgroups were considered. The trees based on the cytochrome b data indicate that the taxonomic status of some species needs to be reassessed and that species of Lepus within North America do not form a monophyletic entity.