The geographical distribution and population genetic structure of the endangered freshwater goby Gymnogobius sp. 2 sensu Akihito et al. (2013) (formerly known as Gymnogobius cf. castaneus “Toyama-endemic”) were investigated via extensive field surveys in the Hokuriku District, on the Sea of Japan side of central Honshu, Japan. This species was widely distributed over the western Hokuriku region, including the Toyama Plain, Noto Peninsula/Kaga Plain (Ishikawa Prefecture), and Fukui Plain. Analyses of mitochondrial DNA and nuclear DNA indicated that the Ishikawa and Fukui populations of Gymnogobius sp. 2, which formed a monophyletic group, were clearly divergent from other species of the G. castaneus species complex. In addition, there was a clear genetic divergence between these populations. However, the complete mtDNA replacement has occurred in the Toyama populations of Gymnogobius sp. 2, almost certainly via historical introgressive hybridization with the G. castaneus–taranetzi complex. Thus, this species forms at least three isolated lineages with unique and divergent evolutionary histories.
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