Zoological Studies 46(5): 547-560 (2007) Phylogeography of the Taiwanese Endemic Hillstream Loaches, Hemimyzon formosanus and H. taitungensis (Cypriniformes: Balitoridae) Tzi-Yuan Wang1,2, Te-Yu Liao1,3, and Chyng-Shyan Tzeng1,* 1Department of Life Science, National Tsing Hua University, 101 Kuang-Fu Road, Sec. 2, Hsinchu 300, Taiwan 2Genomics Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Nankang, Taipei 115, Taiwan. Tel: 886-2-27898756. Fax: 886-2-27898757. E-mail:
[email protected] 3Department of Vertebrate Zoology, Swedish Museum of Natural History, SE-104 05 Stockholm, Sweden (Accepted January 23, 2007) Tzi-Yuan Wang, Te-Yu Liao, and Chyng-Shyan Tzeng (2007) Phylogeography of the Taiwanese endemic hill- stream loaches, Hemimyzon formosanus and H. taitungensis (Cypriniformes: Balitoridae). Zoological Studies 46(5): 547-560. Variations in nucleotide sequences within the mitochondrial control region were used to deter- mine the paleogeography of speciation and diversification of 2 balitorids endemic to Taiwan. Examination of 11 populations of Hemimyzon formosanus and 5 populations of H. taitungensis respectively revealed 23 and 11 haplotypes within the mitochondrial control regions. Utilizing the neighbor-joining method and maximum-parsi- mony trees, we showed the presence of 3 groups and 2 subgroups in H. formosanus, and 1 group in H. taitun- gensis. The nested clade analysis, a method with a higher resolution, revealed that the 1 group of H. taitun- gensis could be further divided into 2 subgroups on the minimum spanning network. The nested clade analysis predicted the evolutionary divergence of populations in H. formosanus due to past fragmentation; furthermore, dispersion among populations of H.