Hybridization and polyploidy are particular characteristics of biodiversity among cypriniform fish. To infer ancient parentage of the tetraploids found among Japanese Cobitis loaches, we compare mitochondrial and four nuclear loci from two tetraploids with several diploid populations of C. biwae, C. striata and related species. Mitochondrial gene tree showed monophyletic diploid C. striata and paraphyletic C. biwae relative to C. striata. On the contrary, nuclear sequence analysis recovered both monophyletic diploid C. biwae and C. striata. Disagreement in mitochondrial and nuclear gene trees indicates an ancient hybridization event and mitochondrial gene introgression. The tetraploid C. biwae includes both mitochondrial and nuclear sequences close to diploid C. biwae, indicating autotetraploidy. The tetraploid C. striata has nuclear alleles of both C. biwae and C. striata and mtDNA of C. biwae. It is an allotetraploid with C. biwae as the mother. Our analyses also reveal an onset of genome reshaping after the allotetraploidization.
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