The Comparative Phylogeography Of Two Labeoninae Species Based On Nuclear Genes

Garra orientalis, belongs to Cypriniformes, Cyprinidae, Labeoninae, Garra. G. orientalis is widely distributed in the Pearl River, Minjiang, Jiulongjiang, Yuanjiang, Hanjiang and drainage in Hainan Island of south China. Osteochilus salsburyi, belongs to Cypriniformes, Cyprinidae, Labeoninae, Osteochilus. O. salsburyi is distributed in Pearl River, Minjiang, Jiulongjiang, Yuanjiang and other drainages, as well as Hainan Island. It is also found in Vietnam. We would like to choose the molecular markers of nuclear genes(S7 and Rag2) to analyse phylogeography and population genetic structure of G. orientalis and O. salsburyi populations, G. orientalis got the number of 8 populations while O. salsburyi got the number of 12 populations.Results showed as follows:1. The appropriate primers were designed to amplify S7 and Rag2 gene of G. orientalis and O. salsburyi. We obtained 103 sequences of S7 gene and Rag2 gene of 8 populations of G. orientalis and 213 sequences of S7 gene and Rag2 gene of 12 popuations of O. salsburyi. The length of S7 gene was 635 bp and the length of Rag2 gene was 990 bp of G. orientalis, while the length of S7 gene was 762 bp and the length of Rag2 gene was 814 bp of O. salsburyi.2. We analysed the differences between S7 and Rag2 sequences. Compared the base composition of S7 gene and Rag2 gene. G. orientalis’ S7 gene contained 27 variable sites, the total variation rate was 4.25%. Among all of the variable sites, there were 26 parsimony informative sites in total, accounting for 4.09%. G. orientalis’ Rag2 gene contained 34 variable sites, the total variation rate was 3.43%. Among all of the variable sites, there were 20 parsimony informative sites in total, accounting for 2.02%. O. salsburyi’ S7 gene contained 37 variable sites, the total variation rate was 4.86%. Among all of the variable sites, there were 36 parsimony informative sites in total, accounting for 4.72%. O. salsburyi’ Rag2 gene contained 15 variable sites, the total variation rate was 1.84%. Among all of the variable sites, there were 10 parsimony informative sites in total, accounting for 1.23%. The statistic showed that S7 gene got a higher variable rate than Rag2 gene. The total variation rate of these two genes of G. orientalis were higher than O. salsburyi.3. Genetic diversity of G. orientalis and O. salsburyi: The haplotype diversity of G. orientalis population was from 0.2222 to 1.0000, the average was 0.95793; the nucleotide diversity was from 0.000684 to 0.006051, the average was 0.006256. The haplotype diversity of O. salsburyi was from0.9670~1.0000, the average was 0.99889; the nucleotide diversity was from 0.004096 to 0.007369, the average was 0.006835. Both of the two species had a high haplotype diversity and a relatively low nucleotide diversity.4. Phylogenetic relationship: We used Neighbor-Joining to reconstruct the phylogenetic tree of these two species. Eight populations of G. orientalis could be divided into two major clades A, B. B can be divided into B1, B2, B3. A included populations from Jianou(JO), Jingxiu(JX), Huaan(HA), Heyuan(HY) and Chunxi(CX); B1 just contained minority populations from Qionghai(QH), Baisha(BS), Heyuan(HY) and Chunxi(CX); B2 included majority populations from Qionghai(QH) and Baisha(BS); B3 included some populations from Qionghai(QH) and Baisha(BS), and all of the populations from Ledong(LD). The haplotype network of G. orientalis was divided into three lineages. Both of the NJ tree and the haplotype network showed obvious clustering among geographical populations. The NJ tree of O. salsburyi divided into six main clades, named A, B, C, D, E, F. A included majority populations from Ledong(LD), Raoping(RP), Xinyi(XY), and some populations from Heyuan(HY), Huaan(HA), Jiexi(JH), Sihui(SH), Haifeng(HF), Chunxi(CX), Jinxiu(JX). Qionghai(QH), Baisha(BS), Chunxi(CX) and Jinxiu(JX); B included populations major from Qionghai(QH), Chunxi(CX), Jiexi(JH), Haifeng(HF), as well as some populations from Baisha(BS), Ledong(LD), Huaan(HA), Jinxiu(JX); C included minority populations from Qionghai(QH), Baisha(BS), Ledong(LD), Chunxi(CX); D included some populations from Qionghai(QH), Baisha(BS), Ledong(LD); E included minority populations from Qionghai(QH), Baisha(BS), Huaan(HA), Jinxiu(JX); F included some populations from Baisha(BS), Ledong(LD), Heyuan(HY), Sihui(SH), Haifeng(HF). The haplotype network is accordance with the phylogenetic tree. Both of the NJ tree and the haplotype network showed clustering among geographical populations to some degree, but not as abviously as G. orientalis.5. Genetic differentiation and population genetic structure analysis. The genetic differentiation index(FST) of G. orientalis populations ranged from-0.049 to 0.7376 what was relatively high. The genetic distance among different groups ranged from 0.001 to 0.010, which means a large variation range. AMOVA and SAMOVA analysis showed that G. orientalis populations can be divided into three groups, variation among groups was 43.18% while that within populations was 52.54%. The FST of O. salsburyi ranged from 0.01470 to 0.33744 and genetic differentiation index was relatively low. The genetic distance was in a relatively average state among different groups ranged from 0.005 to 0.008, which means a small variation range. AMOVA and SAMOVA analysis showed O. salsburyi population can be divided into five groups. Variation among groups was 10.43% while that within populations was 83.85%.6. Population demographical history. Eight geographic populations of G. orientalis were tested with Tajima’s D and Fu ’S Fs, combined with the nucleotide mismatch distribution. The result showed that the four populations from Qionghai(QH), Baisha(BS), Heyuan(HY) and Chunxi(CX) had probably exprienced population expansion in the recently history. The 12 geographical populations of O. salsburyi were tested with neutral detection as well as nucleotide mismatch distribution of each population, The result showed that the vast majority populations of O. salsburyi had probably expienced expansion.The mitochondrial genes were usually used to analyze the phylogeography of primary freshwater fishes in Southern China region. In our study, we used only nuclear genes to analysis the population genetic structure of two primary freshwater fishes in this region, for the purpose of further understanding the correlation between genetic differentiation and geographical distribution in this area. In addition, our results also can be a good supplements for the previous reserch.