Genomic data from the Brazilian sibilator frog reveals contrasting Pleistocene dynamics and regionalism in two South American dry biomes

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.