Odorrana schmackeri sensu lato, a group of montane stream-dwelling amphibians in southern China, provides an ideal model for deciphering how Cenozoic geological and climatic dynamics drive cryptic diversification. By integrating mitochondrial 12S/16S rRNA sequences from 1,398 samples spanning 107 populations and genome-wide SNP data from 193 individuals across 18 populations, we reconstruct the geographic structure and speciation history of O. schmackeri sensu lato. Our analyses resolved six evolutionarily distinct lineages in O. schmackeri sensu lato, i.e., Odorrana hejiangensis, Odorrana ichangensis, Odorrana kweichouensis, Odorrana schmackeri, Odorrana tianmuii, and Odorrana huanggangensis. A pronounced east–west geographic break aligned with the stepped topography shaped by Qinghai-Tibetan Plateau uplift, while Late Miocene-Pleistocene climatic oscillations and drainage reorganizations drove lineage diversification through cyclical habitat fragmentation and secondary contact. We observed topological incongruence between mitochondrial and SNP-based phylogenies. Multiple lines of evidence provided strong support for historical gene flow and hybridization events, primarily between O. huanggangensis, O. schmackeri, O. tianmuii, and O. kweichowensis. The initial divergence within O. schmackeri sensu lato dates to the late Miocene, with subsequent speciation events occurring throughout the Pliocene and early Pleistocene. Demographic expansions during the Early Pleistocene facilitated niche differentiation and Ecological Niche Modeling indicated that each species has maintained distinct geographical distributions across different climatic periods (LIG, LGM, Current), with suitable habitats responding differently to Pleistocene climatic fluctuations. This study resolved the taxonomic complexity of O. schmackeri sensu lato and contributed to biogeographic theory by demonstrating how heterogeneous landscapes drive speciation through cyclical isolation, secondary contact, and adaptive radiation.
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