Fig 1.
Localities sampled for mtDNA of Scinax eurydice and mitochondrial gene tree.
The gene tree was obtained by Maximum Likelihood and Bayesian inference for the ND2 locus with support values (Bootstrap/Bayesian Posterior Probabilities) shown by major nodes. The blue circles, green triangles, red hexagons and yellow squares on the map indicate the locations sampled (mtDNA ND2) for each geographic group identified. The area shaded in dark gray on the Brazilian map represents states sampled for present work. The area in light gray in the inset represents the Atlantic Rainforest (based on SOS Mata Atlântica 2013). Haplotypes (H) represented on the tree topology are available in S1 Table. NE (Northeastern) and SE (Southeastern) correspond to populations identified. Numbers inside circles represent rivers listed as possible secondary barrier.
Table 1.
Tamura-Nei distance (Da) within and between clades recognized by genes trees (ND2).
Fig 2.
Median joining networks of the mitochondrial ND2 fragment and nuclear fragments RAG1, β-fibint7 and 28S.
Black dots represent haplotypes not sampled. The colors of the observed haplotypes are based on the grouping of samples of mitochondrial clades (Fig 1): clade NE1 (blue circle), clade NE2 (green triangle), clade SE1 (yellow square), and clade SE2 (red hexagon). Branch lengths are proportional to the number of mutational steps.
Fig 3.
STRUCTURE plots of Scinax eurydice populations.
Population structure between samples of northeast and southeast clades (A), northeast clades and southeast clade (B) and within of northeast and southeast mitochondrial clades (C) of Scinax eurydice. Plots shown represent the best K according to the ad hoc method after Princhard et al. (2000). Panels (A), (B) and (C) results from runs under the allele frequencies and admixture with correlated allele frequencies, respectively. Black lines delimit the mitochondrial clades.
Table 2.
Analyses of molecular variance (AMOVA) of Scinax eurydice.
Table 3.
Diversity indexes for each fragment and clade.
Fig 4.
Chronogram of species tree from the combined mitochondrial and nuclear DNA data generated on *BEAST.
Numbers by nodes represent clade posterior probabilities. Areas where many species trees agree on topology and/or branch lengths are densely colored in blue. The most frequent topologies are represented by shaded consensus tree. White circles with letters at nodes are divergence times and 95% (HPD) of high posterior density of divergence times between clades according to Table 4.
Table 4.
Divergence times and confidence intervals [95% of high posterior density (HPD)].
Fig 5.
Extended Bayesian Skyline Plot (EBSP) results for populations of Scinax eurydice.
The dotted horizontal line shows the median estimate of the EBSP and the gray area shows the upper and lower 95% highest posterior density (HPD). Each graph represents the EBSP analysis for: (A) clade NE1; (B) clade NE2; (C) SE1; (D) clade SE2. The dotted vertical line illustrates the approximate time when events of demographic expansion started in each clade of S. eurydice.