Mitochondrial DNA reveals evolutionary status and population genetics of two closely related fish (Misgurnus bipartitus and Misgurnus mohoity) in northeast China

• Misgurnus mohoity and Misgurnus nikolskyi was embedded in the Paramisgurnus dabryanus lineage.
• High h and low π were found in Misgurnus bipartitus, and M. mohoity exhibited both high h and π.
• Significant population subdivisions were detected in these two species in northeast China.

To provide valuable insights into the taxonomic relationship and germplasm resource of Misgurnus mohoity and Misgurnus bipartitus, phylogenetic and population structure analysis were performed based on mitochondrial DNA. The phylogenetic tree reconstructed from genera Misgurnus and Paramisgurnus revealed the species in genus Misgurnus were not in a monophyletic group and divided into two divergent clades; M. bipartitus and Misgurnus anguillicaudatus were clustered into a monophyletic group; M. mohoity was embedded in the Paramisgurnus dabryanus lineage. Totally, 19 and 21 haplotypes were identified from the individuals of M. bipartitus and M. mohoity based on COI gene, respectively. High haplotype diversity and low nucleotide diversity were found within the populations of M. bipartitus, and the populations of M. mohoity exhibited both high levels of haplotype diversity and nucleotide diversity. Meanwhile, high levels of genetic differentiation and genetic variation between populations in Liao River basin (PAJ, FUS and HUR) and populations in Songhua river basin (MDJ, FUY and FUJ) were observed in M. bipartitus; the populations of M. mohoity also revealed high genetic differentiation and high among-population genetic variation. The results of this study can be potentially exploited to conservation and management strategies of wild loach resources.