Mitogenomic phylogeny revealed the fine population structure of an endangered cyprinid fish Pseudorasbora pugnax in the Tokai region, central Japan

The complete mitochondrial genome sequences (mitogenomes) from 19 populations (originating from 15 localities) of Pseudorasbora pugnax , covering almost all known populations of the endangered species, were determined to clarify their genetic population structure and evolutionary history. The 211 cytochrome b (cyt b ) gene sequences indicated low intrapopulation genetic diversity, and each population had only one or two haplotypes. The 37 mitogenome sequences also indicated low intrapopulation diversity, and the haplotypes were unique to every population. The phylogenetic relationships among the mitogenomic haplotypes indicated three groups, including subgroups, and the groups and subgroups were distributed in different geographic areas. These results suggest that the unique haplotypes in each population had not been randomly fixed by recent population fragmentation of this species, and the geographic distribution reflects the historical population structure. The divergence time estimated by mitogenomic data indicates that the genetic divergence of mtDNA groups occurred in the Pleistocene.