Mitogenomics of the jaguarundi (Puma yagouaroundi, Felidae, Carnivora): Disagreement between morphological subspecies and molecular data

We analyzed 80 mitogenomes of the elusive jaguarundi (Puma yagouaroundi, Felidae, Carnivora), representing seven of the eight putative morphological subspecies traditionally described. The mitochondrial genetic diversity levels were very high in this cat species and therefore similar to other Neotropical cats. Nonetheless, the number of significantly different molecular clusters did not align well with putative morphological subspecies. We detected three possible molecular subspecies: P. y. yagouaroundi (wide distribution in Central and South America), P. y. melantho (Central Andean, and their inter-valleys, Peruvian area) and P. y. eyra (Paraguay and northern Argentina). There were also small geographical clusters with no correspondence with the morphological subspecies, especially in Costa Rica, northern and eastern Colombia, and Pacific trans-Andean Colombia and Ecuador. Thus, the number of molecular subspecies in jaguarundi could be less than the number defined morphologically. However, well-differentiated mitochondrial lineages could exist in the area of the putative P. y. panamensis and correspond to undescribed subspecies. The temporal split of the ancestors of the puma and jaguarundi and the initial mitochondrial diversification within the jaguarundi occurred during the late Pliocene, but the major fraction of haplotype proliferation happened during the Pleistocene. All the procedures we used detected a strong population expansion for the jaguarundi during the Günz-Mindel interglacial period of the Pleistocene. The spatial genetic analyses showed that the isolation-by-distance patterns are not well developed in this species. In contrast, we detected a very significant circular cline with spatial autocorrelation. Therefore, from a molecular perspective some of the individuals far removed from each other geographically are also very similar. This new information may be very helpful to conservation ecologists and managers of jaguarundi habitats as we continue to improve our understanding of the evolutionary history of this cat species.