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The most accepted hypothesis has suggested that the fauna in Taiwan Island originated from South China, but some studies supported the Japan, Ryukyu Archipelago, and Taiwan Islands as a unique biogeographical district. This study examines whether the populations of freshwater snail Semisulcospira libertina in Taiwan are closer to those in Japan based on the mitochondrial cytochrome c oxidase subunit I (COI) gene sequences. Our study shows the populations in North Taiwan originated from Japan and the cyclic glacial caused the migrations among islands and continent repeatedly; the populations in South Taiwan might originate from South China or South Asia. Our results will not only affect the conclusions in phylogeography of freshwater species in Taiwan but also change the sampling plans in the future studies about evolutionary of freshwater species in East Asia.

Little has been known about the impacts of past vicariance events on the phylogeography and population structure of freshwater fishes in East Asia. The aims of this study are to assess the genetic variability with extensive sampling throughout the range of Chinese spiny loach, Cobitis sinensis, and to infer the genetic structure and evolutionary history of populations. Cobitis sinensis in China may have initiated from two ancestral populations, namely Yangtze and Pearl Rivers, which diverged about 7.24 MYA likely due to drainage systems alteration. In the phylogroup I, a southward dispersal event occurred from East China (Yangtze River) to south ZheMin and Hainan subregions, followed by eastward dispersal from ZheMin to south Taiwan. In the phylogroup II, eastward colonization took place from Pearl River to north Taiwan in the late Pliocene, coupled with loss of genetic diversity in the island populations. This study showed that Cenozoic tectonic movements and climatic and sea‐level fluctuations may have shaped the genetic structure of C. sinensis in concert. Highly diverged mtDNA sequences suggest existence of cryptic species in morphospecies C. sinensis.

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The mitochondrial DNA cytochrome c oxidase subunit I sequences from 95 specimens of Semisulcospira libertina in Taiwan were identified as two major phylogroups, exhibiting a southern and northern distribution, north of Formosa Bank and south of Miaoli Plateau. The genetic distance between these two phylogroups was 12.20%, and the distances within-phylogroups were 4.97 and 5.56%. According to a molecular clock of 1.56% per lineage per million years, the divergence time between these two major phylogroups was estimated at 4.94 million years ago (mya), with the two phylogroups forming at 3.64 and 3.75 mya, respectively. Moreover, the geological events have suggested that Taiwan Island emerged above sea level at 4-5 mya, and became its present shape at 2 mya. These results suggested that these two phylogroups might originate from two independent ancestral populations or divergent before colonizing Taiwan. Within South phylogroup, the initial colonization was hypothesized to be in Kaoping River (WT), followed by its northward. The high divergence between south- and north of WT River was influenced by the formation of the Kaoping foreland basins. Within North phylogroup, the colonization was from central sub-region through paleo-Miaoli Plateau to northern and northeastern sub-regions. This study showed that the landform changes might have shaped the genetic structure of S. libertina in concert. Apparently, two cryptic species or five different genetic stocks of S. libertina could be identified; these results are useful for the evaluation and conservation of S. libertina in Taiwan.