Phylogenetic discordance is due to incomplete lineage sorting and pre-speciation introgression in the erosion-mediated radiation of Asian warty newts

The genus<i> Paramesotriton</i>, comprising 15 species classified into two groups, exhibits the broadest geographical distribution among modern Asian newts, spanning southern China from west to east. The group represents a successful example of adaptive radiation. The intrageneric phylogenetic relationships among the species, however, remain unresolved, particularly within the <i>P. caudopunctatus</i> group (PCSG). In this study, we employed restriction-site associated DNA sequencing across five representative PCSG species and integrated data from previously published mitochondrial genomes to conduct a comprehensive phylogenomic analysis. Our results provide robust support for resolving interspecific relationships within the PCSG. Incomplete lineage sorting was identified as the primary cause of gene tree discordance, supplemented by gene flow events predating speciation (e.g., ASTRAL, HyDe, Dsuite, and PhyloNet). We also found evidence of hybridization between<i> P. longliensis</i> and an unidentified<i> Paramesotriton</i> lineage, suggesting that<i> P. zhijinensis</i> may be of hybrid origin. Our findings further suggest that erosional isolation caused by the exposure of carbonate sedimentary rocks has facilitated allopatric divergence among the PCSG species. Moreover, our results integrate the origin and diversification of the PCSG with Miocene paleoclimatic conditions and the erosion of carbonate sedimentary rocks, providing crucial insights into the speciation mechanisms of Asian warty newts. We propose an erosion-driven speciation model, wherein repeated episodes of allopatric diversification were promoted by the dynamic geomorphological processes in karst mountain ecosystems during both tectonically active and quiescent periods.