Phylogeography of Habia fuscicauda (Cardinalidae) indicates population isolation, genetic divergence and demographic changes during the Quaternary climate shifts in the Mesoamerican rainforest

High diversity, complex topography and geological factors make the Neotropics an interesting region for the study of avian diversification. Phylogeography, in conjunction with ecological niche modeling, offers an interesting complementary approach to identify the tempo and mode of diversification in different species. In this work, we analyzed the genetic structure of Habia fuscicauda based on multilocus analyses using mtDNA (ND2 and ND4) and nuDNA (ACOI-I9 and ODC) sequences. Additionally, we transferred the optimal conditions for current distribution to the Mid-Holocene, Last Glacial Maximum and the Last Inter-Glacial in order to evaluate the shift in species distribution and compare with the genetic data. Our results indicate that H. fuscicauda comprises two clades: one with genetic correspondence to south-east Mexico to the Nicaragua Depression and the other from the south of the Nicaragua Depression to Central Panama. Within these clades, we identified genetic differentiation between populations across the Isthmus of Tehuantepec, Costa Rica—associated with the Talamanca Cordillera—and Central Panama. The two principal clades showed contrasting demographic histories, with the northern clade showing demographic changes and the southern clade demographic stasis. The ecological niche models identified areas as refugia for the northern clade fin Central America and for the southern clade in the Talamanca Cordillera and Central Panama, supporting the hypothesis that these clades were isolated from each other during the climate shifts of the Pleistocene.