The Yungas, a subtropical mountain rainforest of South America, has been little studied in relation to the evolutionary history of the large‐bodied species of the genus Calomys. Particularly, two species have been synonymized: C. boliviae and C. fecundus; the first is only known from its type locality in the northern Bolivian Yungas, whereas the second is known along the Tucumane–Bolivian Yungas shared by Bolivia and Argentina. In this study, we combined a phylogeographic approach with ecological niche modeling, with samples covering most of the geographic range of C. fecundus. One mitochondrial and two nuclear genes were used for population genetic analyses. Current and paleoclimatic models were obtained. Nuclear genes resulted uninformative by retention of ancestral polymorphism with other species of Calomys. The mitochondrial marker revealed a complex network showing signals of several population expansions. Three genetic clusters in a latitudinal sense were detected, which are coincident with the three stable climatic zones estimated by current and paleoclimatic models. We determined a pattern of expansion during glacial cycles and ancestral refugia during interglacial cycles. None of the potential distribution models predicted the presence of C. fecundus in the type locality of C. boliviae. Therefore, we recommend making integrative taxonomic studies in the Bolivian Yungas, to determine whether or not C. fecundus and C. boliviae correspond to the same species.

The genus Calomys includes several species that have very similar external morphologies, which often leads to confusing field identification and has resulted in conflictive taxonomic histories. One of its clades involves large‐sized body forms, known as the Calomys callosus complex. In a previous study, a biogeographic hypothesis was proposed to explain a south‐to‐north colonisation of South America by species of this complex. However, other studies which not included all members of the complex' members and that used different molecular markers, did not support that biogeographic hypothesis. Here we explore the relationships among C. callosus sensu stricto (s.s.), C. fecundus, C. callidus, C. venustus, C. tocantinsi and Calomys sp. using two mitochondrial genes (Cyt‐b and Control Region) and two nuclear genes (Rhp3 and i7FGB) data. We also applied several gene trees and species delimitation methods to elucidate the taxonomy, distribution and evolutionary relationships among the analysed species. By including sequences of individuals from Argentina, Brazil, Bolivia and Paraguay, we reconstructed the possible ancestral biogeographic origin of the complex. Two main clades were recovered: the western showed the relationships (C. venustus [C. fecundus–Calomys sp.]), while the eastern (C. callidus [C. callosus s.s.–C. tocantinsi]). These results support the original biogeographic hypothesis and suggest the following scenario: in the west, from the Espinal ecoregion, first the Tucumane–Bolivian Yungas and later, the Beni savanna would have been colonised. In the east, from the Espinal, first the Chaco and later the Cerrado ecoregions may have been occupied.

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