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Aim  To comprehend the phylogeographic patterns of genetic variation in anurans at Taiwan Island, this study attempted to examine (1) the existence of various geological barriers (Central Mountain Ranges, CMRs); and (2) the genetic variation of  Bufo bankorensis  using mtDNA sequences among populations located in different regions of Taiwan, characterized by different climates and existing under extreme conditions when compared available sequences of related species  B. gargarizans  of mainland China.    Methodology/Principal Findings  Phylogenetic analyses of the dataset with mitochondrial DNA (mtDNA) D-loop gene (348 bp) recovered a close relationship between  B. bankorensis  and  B. gargarizans , identified three distinct lineages. Furthermore, the network of mtDNA D-loop gene (564 bp) amplified (279 individuals, 27 localities) from Taiwan Island indicated three divergent clades within  B. bankorensis  (Clade W, E and S), corresponding to the geography, thereby verifying the importance of the CMRs and Kaoping River drainage as major biogeographic barriers. Mismatch distribution analysis, neutrality tests and Bayesian skyline plots revealed that a significant population expansion occurred for the total population and Clade W, with horizons dated to approximately 0.08 and 0.07 Mya, respectively. These results suggest that the population expansion of Taiwan Island species  B. bankorensis  might have resulted from the release of available habitat in post-glacial periods, the genetic variation on mtDNA showing habitat selection, subsequent population dispersal, and co-distribution among clades.    Conclusions  The multiple origins (different clades) of  B. bankorensis  mtDNA sequences were first evident in this study. The divergent genetic clades found within  B. bankorensis  could be independent colonization by previously diverged lineages; inferring  B. bankorensis  originated from  B. gargarizans  of mainland China, then dispersal followed by isolation within Taiwan Island. Highly divergent clades between W and E of  B. bankorensis , implies that the CMRs serve as a genetic barrier and separated the whole island into the western and eastern phylogroups.

A New Phylogeographic Pattern of Endemic Bufo bankorensis in Taiwan Island Is Attributed to the Genetic Variation of Populations