LAUSR

Common carp (Cyprinus carpio) is an important valuable cyprinid in China and has been a popular cultured aquaculture species around the globe. Understanding the genetic diversity of wild native common carp not only provides basic data for the protection and utilization of common carp resources, but assesses the effect of human activities on the genetic diversity of this species. In this study, genetic diversity and population structure of the common carp from fifteen sampling populations in the Pearl River and Nandujiang River was conducted using a coalescent mitochondrial locus including mitochondrial cytochrome b gene (Cytb) and a control region (D-loop) segment. The haplotype diversity and nucleotide diversity were 0.962 and 0.00628 in the Pearl River and 0.808 and 0.00376 in the Nandujiang River, repectively. Phylogenetic and haplotype network analyses indicated that three subspecie C. carpio rubrofuscus, C. c. haematopterus, and C. c. carpio all occurs in both rivers. The analysis of molecular variance revealed that the variation within populations (86.2%) was the main source of the total variation. Statistically significant genetic differentiation among different Pearl River populations of C. c. rubrofuscus (Fst  = 0.05-0.25), and relatively high genetic differentiation between the Nandujiang River population and the Pearl River populations (Fst  >0.238) is apparent. Bayesian clustering analyses detected that global populations comprised of eight genetic clusters and examined that Nandujiang River population included relatively pure genetic clusters. Neutrality tests suggested that native populations experienced recent population expansion and Extended Bayesian Skyline Plot (EBSP) indicated that the common carp populations likely experienced a historical expansion during 0.125-0.250 million years ago (Ma). Artificial fish propagation and release, escaping from fish farms, and Fang Sheng may explain the invasion of non-native subspecies in many river sections, such as Laibin, Rongjiang, Huizhou, Heyuan, and Zhaoqing river sections. To conserve the native common carp populations, release station should be established to culture native common carp fry. Overall, our findings can be contributed to complementing scientific knowledge for conservation and management of the wild native common carp. This article is protected by copyright. All rights reserved.