Phylogeography and ecological niche modelling reveal a geographical break in the genetic structure of Boana crepitans (Anura: Hylidae) during the Pleistocene in Eastern Brazil

Integrating evolutionary and ecological approaches provides key insights into diversification processes in Neotropical biomes. Here, we combined phylogeographic analyses and ecological niche modelling (ENM) to investigate the diversification of the treefrog Boana crepitans, a widely distributed species associated with mesic habitats across the Atlantic Forest and Seasonally Dry Tropical Forests (SDTFs). We used mitochondrial and nuclear markers to estimate divergence times, reconstruct ancestral area, and assess population structure, genetic diversity and demographic history. ENMs were used to evaluated niche divergences between lineages, identify potential dispersal corridors, and compare palaeodistributions with historical demography. Our findings revealed two lineages, Eastern and Western, that diverged in the late Pleistocene (∼0.0178 Ma). Both exhibited high haplotype sharing and demographic stability over the last 280,000 years, likely influenced by Quaternary climatic oscillations and the persistence of forest refugia across the Atlantic Forest, Caatinga and Cerrado. Spatial and temporal patterns suggest recurrent connections among mesic habitats during cooler periods, facilitating gene flow and maintaining population stability. Overall, these findings highlight the role of climatic dynamics and landscape connectivity in shaping diversification within B. crepitans and underscore the value of integrative evolutionary-ecological approaches for understanding biogeographic patterns in the Neotropics.