Data from: Cryptic genetic diversity is paramount in small-bodied amphibians of the genus Euparkerella (Anura: Craugastoridae) endemic to the Brazilian Atlantic Forest

Morphological similarity associated to restricted distributions and low
dispersal abilities make the direct developing “Terrarana” frogs of the
genus Euparkerella a good model for examining diversification processes.
We here infer phylogenetic relationships within the genus Euparkerella,
using DNA sequence data from one mitochondrial and four nuclear genes
coupled with traditional Bayesian phylogenetic reconstruction approaches
and more recent coalescent methods of species tree inference. We also used
Bayesian clustering analysis and a recent Bayesian coalescent-based
approach specifically to infer species delimitation. The analysis of 39
individuals from the four known Euparkerella species uncovered high levels
of genetic diversity, especially within the two previously
morphologically-defined E. cochranae and E. brasiliensis. Within these
species, the gene trees at five independent loci and trees from combined
data (concatenated dataset and the species tree) uncovered six deeply
diverged and geographically coherent evolutionary units, which may have
diverged between the Miocene and the Pleistocene. These six units were
also uncovered in the Bayesian clustering analysis, and supported by the
Bayesian coalescent-based species delimitation (BPP), and Genealogical
Sorting Index (GSI), providing thus strong evidence for underestimation of
the current levels of diversity within Euparkerella. The cryptic diversity
now uncovered opens new opportunities to examine the origins and
maintenance of microendemism in the context of spatial heterogeneity
and/or human induced fragmentation of the highly threatened Brazilian
Atlantic forest hotspot.