Abstract
The high biodiversity and strong population structure of freshwater fauna has often been attributed to historical geological and climatic alterations. The impact of these historical changes on obligate freshwater species on a small geographical scale has not been well understood due to the lack of fine-scale comparative phylogeographic studies. Strong population structure has been reported in a goby and a caridean shrimp in Hong Kong, a small but highly developed city in South China, but the common drivers of population differentiation in freshwater fauna in this region remain unclear. This study examined the fine-scale phylogeographic patterns of two freshwater loaches, Schistura fasciolata and Pseudogastromyzon myersi in Hong Kong, using sequence data of mitochondrial control region and two nuclear markers (interphotoreceptor retinoid binding protein gene 2 and ribosomal protein S13 gene). Results show that they exhibit pronounced population structure as supported by high and significant Φ(ST). Phylogenetic analyses based on the control region reveal six and three distinct lineages in S. fasciolata and P. myersi, respectively. Phylogeographic structure of both species generally follows the paleodrainage pattern, though P. myersi shows a shallower structure on the Mainland, perhaps due to their higher mobility. Most of these lineages diverged during the Pliocene and Late Pleistocene, a period with marked sea-level fluctuations. In a broader context, this suggests that sea-level fluctuation played an important role in shaping even the fine-scale population structure of freshwater fish in South China, implying that the genetic diversity of this fauna may be higher than expected.