Phylogeography of the capybara, Hydrochoerus hydrochaeris, in a large portion of its distribution area in South America

The capybara, Hydrochoerus hydrochaeris, is a semiaquatic herbivorous rodent widely distributed in South American wetlands. Some authors have proposed the existence of two species, several subspecies, and different Evolutionarily Significant Units (ESUs) in the Hydrochoerus genus. However, the available genetic studies of capybaras are limited in their geographical scope. Thus, we examined genetic variation in 387 sequences of the mitochondrial control region (124 generated by the authors and 263 obtained from GenBank) and performed phylogeographic analyses to determine patterns of geographic variation in capybaras sampled in seven South American countries, representing a large portion of the distribution range of the species. Based on these analyses, four ESUs were identified. In addition, within one of these units, two distant geographic populations were identified in the Trans-Andean Colombia (putative H. isthmius population) and the cis-Andean area of the Napo River in Peru and Ecuador. This result and the genetic distances between these ESUs agree with the idea of a unique capybara species. Mismatch distributions and Bayesian skyline plots suggested that capybaras have undergone processes of population decline associated with the adverse weather conditions of the late Pleistocene, followed by population expansions associated with the climatic conditions of the Holocene Climatic Optimum. Phylogenetic trees support the previous hypothesis that the species originated in Western Amazon. However, as our results are based on a single mitochondrial fragment, these results are not conclusive. New studies, including samples from other sites and more mitochondrial and nuclear markers, may elucidate the evolutionarily history of capybaras.