Genetic variation of common carp Cyprinus carpio L. in China based on mitochondrial COII gene

•Clarify the intraspecific relationship and genetic variability of C. carpio populations.•One maternal ancestral haplotype was identified.•Provide new evidence of East Asia origin of C. carpio.•Estimated the genetic diversity and population dynamic of C. carpio. 196 common carp (Cyprinus carpio L.) samples from five wild populations and ten domestic strains (six Chinese and four European) in China were collected and the genetic variation was analyzed using direct DNA sequencing of mitochondrial Cytochrome c oxidase subunit 2 gene (COII). As a result, a total of 22 haplotypes were identified, and one maternal ancestral haplotype (Hap_1) distributed in all populations exclusive of Songpu carp (SPC) and Hainan wild carp (HWC). For the other two major haplotypes, Hap_3 was mainly shared by German mirror carp (GMC) and populations from Amur River Basin, whereas Hap_16 appeared mainly in scatted scaled mirror carp (SSMC), Xingguo red carp (XGR), Songpu carp (SPC), and part of Yangtze River wild carp (YRWC). Although the genetic variance among populations accounted for only 27.79 % of the total variance, significant differentiation between HWC and other populations were spotted. The apparent split between HWC and other Eurasian populations supported the hypothesis that C. carpio emerged in East Asia as a species. Chinese wild populations exhibited highest genetic diversity (Hd = 0.801 ± 0.032; π = 0.0031 ± 0.0003), followed by introduced European strains (Hd = 0.735 ± 0.036; π = 0.0020 ± 0.0002) and Chinese domestic varieties (Hd = 0.657 ± 0.039, π = 0.0016 ± 0.0003). Significant negative Tajima’s D value was only found in SPC, which was probably the consequence of small founder size and subsequent population expansion.