Phylogenetic Analysis of Combined Mitochondrial Genome and 32 Nuclear Genes Provides Key Insights into Molecular Systematics and Historical Biogeography of Asian Warty Newts of the Genus (Caudata: Salamandridae)

The Chang, 1935 genus of Asian warty newts is the second most diverse genus in the family Salamandridae, currently containing 14 recognized species from northern Vietnam to southwest-central and southern China. Although species of this genus have been included in previous phylogenetic studies, the origin and interspecific relationships of the genus are still not fully resolved, especially at key nodes in the phylogeny. In this study, we sequenced mitochondrial genomes and 32 nuclear genes from 27 samples belonging to 14 species to reconstruct the interspecific phylogenetic relationships within and explore its historical biogeography in southern China. Both Bayesian inference and maximum-likelihood analyses highly supported the monophyly of and its two recognized species groups ( and groups) and further identified five hypothetical phylogenetic cryptic species. Biogeographic analyses indicated that originated in southwestern China (Yunnan-Guizhou Plateau/South China) during the late Oligocene. The time of origin of corresponded to the second uplift of the Himalayan/Qinghai-Xizang (Tibetan) Plateau (QTP), rapid lateral extrusion of Indochina, and formation of karst landscapes in southwestern China. Principal component analysis (PCA), independent sample -tests, and niche differentiation using bioclimatic variables based on locations of occurrence suggested that habitat conditions in the three current regions (West, South, and East) differ significantly, with different levels of climatic niche differentiation. Species distribution model (SDM) predictions indicated that the most suitable distribution areas for the and species groups are western and southern/eastern areas of southern China. This study increases our knowledge of the taxonomy, biodiversity, origin, and suitable distribution areas of the genus based on phylogenetic, biogeographic, and species distribution models.