Phylogenetics and phylogeography of two large Neotropical rodents (Capybara, Hydrochoerus hydrochaeris, hydrochaeridae and paca, Cunniculis paca, agoutidae; Rodentia) by means of mitochondrial genes: Opposite patterns

We analyzed mitochondrial genes (D-loop and Cyt-b) to compare the genetic structure and phylogeography between the capybara (Hydrochoerus hydrochoeris, n = 78) and the paca (Cunniculus paca, n = 120). The two species presented very high levels of gene diversity for both mitochondrial markers, but the paca yielded higher levels than the capybara. The capybara showed a noteworthy and significant amount of genetic heterogeneity among different populations, although the mt D-loop gene was more useful in differentiating the populations than was mt Cyt-b. In contrast, the paca yielded low levels of gene heterogeneity among different populations. In this case, both mitochondrial genes had inconspicuous and similar genetic heterogeneities. Estimations of Bayesian female effective numbers, indicated the paca as having higher values than the capybara. For both species, mt Cyt-b yielded higher effective sizes than did mt D-loop. Similarly, the Bayesian gene flow estimates were considerably greater among paca populations than among capybara populations. Different analyses revealed population expansions in both species. Only the capybara population of Northern Colombia showed some evidence of a population bottleneck. An isolation by distance analysis showed that the capybara yielded a very positive and significant relationship between genetic and geographic distances, whereas among paca populations there was no significant relationship. Our phylogenetic analyses suggest the capybara to be effected by geographical barriers. This agrees quite well with the fact that the dispersion of the capybara is restricted by the existence of rivers. Our results did not support similar findings for the paca, and therefore could not confirm any putative ESUs or subspecies for the paca. Furthermore, our results suggest the mitochondrial haplotype splits of both species to have occurred during the Miocene, but were older in capybara than in paca. In the case of the capybara, the original focus of dispersion seems to be the Western Amazon, whereas for the paca, this origin is not clear. Although many authors consider the trans-Andean capybara population as a different species (H. isthmus), our molecular results suggest this population to be a geographical subspecies.