Pseudocongruent phylogeography reflects unique responses to environmental perturbations in a biodiversity hotspot

Aim: Comparative phylogeographic studies provide important insights into the biogeographical processes shaping regional patterns of diversity. Yet, comparative studies are lacking for southern African herpetofauna, despite their high diversity. We statistically compare phylogeographic structure and divergence-time estimates among five co-distributed forest-living herpetofaunal taxa to assess rivers, climatic refugia, and climatic gradients as congruent drivers of phylogeographic diversity. Location: Maputoland-Pondoland-Albany biodiversity hotspot, Southern Africa. Taxon: herpetofauna (reptiles and amphibians). Methods: Phylogeographic structure and divergence-times within species were estimated from mitochondrial and nuclear DNA sequence data. Phylogeographic concordance factors were used to estimate the degree of phylogeographic congruence among sympatric localities. Full-likelihood Bayesian comparisons were used to estimate synchronous divergence between phylogeographic regions and across a putative river barrier. Paleoclimatic niche models were compared among taxa to identify congruent climatic refugia. Non-parametric statistics were used to identify climatic differences between regions and among populations within each species. Finally, redundancy analyses were used to assess geographic distance, climate, and the putative river barrier as explanatory variables to genetic diversity. Results: There is comprehensive phylogeographic structuring within each species, comprising distinct northerly and southerly clades. Phylogeographic concordance factors generally support co-diversification in a north/south axis. Yet, analyses of the divergence-time estimates through the Mio/Plio/Pleistocene indicate asynchronous phylogeographic histories. Climatic niche models identified idiosyncratic responses to paleoclimatic change. Climatic variables are significantly different among populations in all species and correlated with latitude. A combined model of distance, climate, and rivers explained the greatest proportion of genetic diversity in most taxa, of which climate explained the highest variance. Main Conclusions: Ancient and recent species-specific responses to climatic and geological processes resulted in pseudo-congruent phylogeographic histories among the five co-distributed species. The presence of a congruent north/south pattern in multiple taxonomic groups occupying different forested microhabitats, from fossorial to arboreal, supports latitudinal gradients as global drivers of phylogeographic diversity along the east coast of South Africa.Occurrence data used to generate Maxent models for each of the five co-distributed forest herpetofaunal species. All datasets were spatially filtered by ~5km