Phylogenetic discordance arises from incomplete lineage sorting and pre-speciation introgression during erosion-mediated radiation of Asian warty newts

The genus Paramesotriton Chang, 1935, comprising 15 species classified into two groups, exhibits the broadest geographical distribution among modern Asian newts, extending across southern China from west to east and representing a prominent example of adaptive radiation. Despite this success, intrageneric phylogenetic relationships among species remain unresolved, with particularly poor resolution within the Paramesotriton caudopunctatus species group (PCSG). In this study, restriction-site-associated DNA sequencing from five representative PCSG species was combined with previously published mitochondrial genomes to generate a genome-scale phylogenomic framework. The resulting analyses yielded robust support for interspecific relationships within PCSG. Gene tree discordance was primarily attributable to incomplete lineage sorting, with additional contributions from pre-speciation gene flow, as indicated by ASTRAL, HyDe, Dsuite, and PhyloNet. Evidence also supported hybridization between P. longliensis and an unidentified Paramesotriton lineage, consistent with a hybrid origin for P. zhijinensis. Comparative genomic and biogeographic inference further indicated that erosional isolation associated with exposure of carbonate sedimentary rocks facilitated allopatric divergence among PCSG lineages. Moreover, divergence timing aligned PCSG origin and diversification with Miocene paleoclimatic variability and progressive erosion of carbonate substrates, directly implicating karst landscape evolution in lineage formation within Asian warty newts. An erosion-driven speciation framework is therefore supported, in which recurrent episodes of geomorphological restructuring of karst mountain systems repeatedly imposed geographic isolation, driving successive allopatric diversification during both tectonically active and tectonically stable periods.