The complete mitogenome reveals genetic diversity and differentiation among wild and farmed black carp (Mylopharyngodon piceus) populations

Abstract

Black carp (Mylopharyngodon piceus) is an important freshwater fish species in China, and fishery resources have been severely depleted for decades. Understanding the population genetic background is a prerequisite for conservation of black carp genetic resources. Complete mitogenome was analyzed for the first time to study the population genetic diversity and structure of black carp across China. The complete mitochondrial genomes obtained from six wild and three farmed populations ranged from 16,598 to 16,614 base pairs. Black carp populations across China are characterized by moderate to high genetic differentiation (0.08 ≤ F_ST ≤ 0.55, P ＜ 0.05), with a low overall degree of gene flow (0.34 ≤ N_m ≤ 2.61) individuals per generation. The nucleotide diversity (Pi) ranged from 0.0010 to 0.0024 and the average number of pairwise nucleotide differences (K) ranged from 17.4 to 40.2, with the minimum Pi and K values (0.0010 and 17.4) observed in the Foshan population. Compared to farmed populations, wild populations exhibited high average genetic diversity. Neighbor-joining phylogenetic reconstructions revealed two main genetic lineages, one represented by wild populations from the middle reaches of the Yangtze River and the other by populations from the lower reaches of the Yangtze River and farmed populations. The results of Tajima's D and Fu's F neutrality tests and the nucleotide mismatch distribution indicated that wild populations expanded rapidly after undergoing a historic genetic bottleneck. Demographic decline over recent generations has resulted in a bottleneck effect upon black carp populations and genetic connectivity across its distribution has become limited. Poorly designed artificial propagation, long-term inbreeding and random genetic drift probably were the main causes of low genetic diversity in cultured populations. Our results provide baseline information crucial for conservation of black carp genetic resources in China.