Comparison of genetic diversity and population structure of eight Macrobrachium nipponense populations in China based on D-loop sequences

Abstract

This study was performed by using D-loop region sequences to investigate genetic diversity and population structure across eight representative groups of M. nipponense from south to north China. Eight populations comprising a total of 144 individuals were from Songhua River (SHJ), Yellow River (HH), Yangtze River (YZ), Pearl River (ZJ), Weishan Lake (WSH), Taihu Lake (TH), Bosten Lake (BH) and Wanquan River (WQH). The 1130-bp D-loop region exhibited a higher content of A + T (79.04%) than C + G (20.95%). In addition, 239 variable sites and 73 haplotypes were detected. The population haplotype diversity (h) were ranked as follows: WQH (0.9810) > YZ (0.9571) > WSH (0.9429) > ZJ (0.8901) > SHJ (0.8791) > HH (0.8693) > TH (0.8667) > BH (0.3684); the nucleotide diversity (π) were ranked as: WQH (0.0607) > YZ (0.0299) > SHJ(0.0236) > WSH(0.0221) > TH(0.0132) > ZJ(0.0131) > HH(0.0118) > BH(0.0011). The pairwise FST values reached highly significant level (P < 0.01). The gene flow (Nm) results revealed abundant gene exchange between WSH and TH (11.057), HH (7.226) and ZJ (6.255). The maximum likelihood (ML) phylogenetic tree showed that 73 haplotypes were divided into two main branches. Only the haplotypes of the BH population clustered together, indicating the low genetic diversity of this population, whereas a high diversity was observed in other populations. Network results were consistent with phylogenetic tree results. The analysis of mismatch distribution showed that all eight populations presented multimodal distribution. Fu’s Fs test and Tajima’s D tests were applied to determine the population expansion. All eight populations showed non-significant negative values, which suggests that the M. nipponense population in China did not experience population expansion.