Species delimitation and intraspecific diversification in recently diverged South American foxes

The divergence between the Andean fox (Lycalopex culpaeus) and the South American gray fox (L. griseus) represents a recent speciation event in South America. These taxa are partially sympatric and share biological, morphological, and ecological traits. Previous studies failed to recover reciprocal monophyly, suggesting the occurrence of introgression or incomplete lineage sorting (ILS). Here, we obtained mitochondrial and nuclear markers for 140 L. culpaeus and 134 L. griseus from the Southern Cone of South America to assess their inter and intraspecific divergence. We recovered reciprocal monophyly of L. culpaeus and L. griseus, with mild signatures of introgression or ILS. Therefore, taxonomic misidentification and the use of a limited number of markers may be the main reason behind the past debate about the delimitation of both species. Two main divergent clades were found in L. culpaeus with a phylogeographical boundary in the High Plateau of northeastern Chile. The southern clade along with three northern sub-clades corresponded to four morphological subspecies. Less genetic differentiation was found in L. griseus with a spatial population structure that does not support the occurrence of distinct subspecies. The results found in this study suggest the extant evolutionary significant units that need to be considered for biological conservation management of these species.