Molecular genetic structure and relationship of Chinese and Hungarian common carp (Cyprinus carpio L.) strains based on mitochondrial sequence

China and Hungary are major providers of the common carp (Cyprinus carpio L.) in East Asia and Europe respectively. However, the genetic variation and relationship of this species in the two countries have been poorly understood. In this study, mitochondrial COII‐tRNA^Lys and D‐loop sequences were analysed to investigate the genetic structure and relationships of the representative wild and domesticated common carps distributed in China and Hungary. The results indicated that the genetic diversities of the Chinese common carps are higher than those of Hungarian common carps, and the diversities of the wild common carps are higher than those of domesticated common carps in both the countries. Analysis of molecular variance and pairwise F_ST demonstrated a significant genetic divergence between the Chinese and the Hungarian common carps, and between the wild and the domesticated common carps. Bayesian phylogenetic analysis and statistical parsimony network showed an obvious genetic differentiation between the Chinese and the Hungarian common carps, between the wild and the domesticated common carps. However, a few specimens and haplotypes from the Chinese wild common carps appeared in the Hungarian common carps, demonstrating that there was no absolutely isolated and possible genetic linker between the Chinese and the Hungarian common carps.