Mitochondrial genetic diversity and gene flow of common carp from main river drainages in China

1. The common carp (Cyprinus carpio L.) is one of the most widely distributed and important freshwater fishes in the world. In China, the common carp has been recognised as three subspecies: C. carpio haematopterus, C. carpio rubrofuscus and C. carpio carpio. The Nanling Mountains have been suggested as providing the dividing line between C. carpio haematopterus and C. carpio rubrofuscus. However, the demographic history and gene flow of the common carp in China is not clear. 2. We collected mitochondrial COII and D‐loop sequences (1494 bp) from 241 individuals distributed in eight major river drainages across China. The objective was to provide the first investigation into population genetic structure, demographic history and migration patterns of the common carp from these river drainages, and to assess the validity of the three subspecies. 3. Phylogenetic analysis did not result in three major monophyletic lineages corresponding to the three subspecies. The Nanling Mountains do not form a border separating C. carpio haematopterus and C. carpio rubrofuscus. amova showed low population differentiation, with 11.60% of the molecular variance found among river drainages. Pairwise F_ST values between river drainages were moderate (0.0331–0.2617). Substantial gene flow detected in coalescent analysis between drainages showed that the Yangtze drainage was the centre from which migrants moved northward, southward and north‐westward. Human‐mediated translocation has confounded our ability to identify subspecies of common carp in China.