Aim: Knowledge about the Neotropical dry formations, particularly the Caatinga, remains rudimentary compared to other biotas in the region. Here we address several biogeographical hypotheses by combining intense geographic and genomic sampling obtained for the Brazilian sibilator frog. We specifically test predictions related to the putative roles of past climate shifts (Pleistocene and Holocene) and local geographic barriers (past and current courses of the São Francisco river, SFR) in causing population differentiation in this species.

Location: Caatinga and eastern Cerrado.

Taxon: Brazilian sibilator frog Leptodactylus troglodytes.

Methods: We sequenced up to ~15,000 single nucleotide polymorphisms for 159 samples from 61 locations. We inferred genetic structure using spatial clustering and examined population sizes through time. We estimated the relationship among populations using phylogenetic reconstruction, estimated historical distributions with ecological niche modelling, and inferred demographic history under isolation-with-migration models.

Results: Genetic diversity in L. troglodytes corresponds to biome boundaries, with one population in the Cerrado and two populations in the Caatinga, separated by the SFR. Demographic model selection indicates the Caatinga populations expanded since the end of the Pleistocene while the Cerrado population declined. Within the Caatinga, population expansion began earlier and was more extreme in the north. A continuous stability area maintained the two Caatinga populations, which share a common origin and began diverging in the mid-Pleistocene, first with symmetric gene flow and later under pronounced migration from the north.

Main Conclusions: We could not reject a role of past climate change in causing diversification of relictual populations in the Cerrado, but we found no evidence of multiple refuges or long-term isolation within the Caatinga. Instead, diversification in this biome appears to be caused by the SFR acting as a "soft barrier" that constrains migration over an extended period of time.