长江及珠江流域的中华沙塘鳢种群遗传多样性分析

发布时间：2018-07-29 06:32

【摘要】：本论文采集了中华沙塘鳢(Odontobutis sinensis)的9个种群,用线粒体(Cyt b)及核基因(EPICs、微卫星)多种分子标记,全面分析了长江及珠江流域的中华沙塘鳢种群遗传结构,探讨了这种遗传差异的成因。主要结果如下:1.Cyt b基因对长江及珠江流域中华沙塘鳢的遗传多样性分析从宜都(YD)、当阳(DY)、荆州(JZ)、洪湖(HH)、鹰潭(YT)、桂林(GL)、鹰潭(DTH)、全州(QZ)、湘潭(XT)等9个地区采集108尾中华沙塘鳢个体,扩增线粒体Cyt b基因全长用于序列分析,并选取其中的1127 bp进行遗传学分析,结果如下:(1)从108尾中华沙塘鳢样本中,共获得29个Cyt b基因单倍型(序列长度1 127 bp),总的单倍型多样性(Hd)、核苷酸多样性(π)值分别为0.929 0、0.009 41,呈现出较高的遗传多样性和较低的核苷酸多样性的特点;(2)中华沙塘鳢9种群间的FST值在0.110 6~0.998 8间(P0.01),K2-P遗传距离在0.002~0.022间,揭示各种群间存在显著的遗传分化;而多数种群间的基因交流值(Nm)小于1(P0.05),表明这些中华沙塘鳢种群间的基因交流有限。(3)中性进化检测和网络亲缘关系分析表明,中华沙塘鳢的桂林(GL)和洞庭湖(DTH)种群经历过种群扩张事件,推测中华沙塘鳢基因交流的方向为由长江水系种群流向珠江水系种群。通过以上研究为中华沙塘鳢的资源保护、开发与利用提供科学的理论依据。2基于核基因EPICs分子标记的种群遗传多样性及遗传结构分析本研究克隆并测序了一个EPICs标记即55305E1的基因序列,用于中华沙塘鳢9个种群的遗传多样性和遗传结构分析。(1)序列分析。研究中,我们选取55305E1基因的1070bp,对长江及珠江流域共9个种群进行遗传多样性分析。结果表明,共有178个变异位点,变异比例为16.7%,其中单变异位点有105个,占总变异的59%,简约信息位点为63且占总变异的35%。碱基的平均含量为T32.6%,C 18.4%,A 31.7%,G17.7%。A+T(64.3%)G+C(36.1%),表明中华沙塘鳢中线粒体与核基因均呈现AT偏好性。(2)遗传多样性分析。中华沙塘鳢9个种群的种群总的单倍型多样性(Hd)为0.99330,变化范围在0.6-1之间。核苷酸多样性(π)为0.01370,变化范围为在0.0035-0.0132之间。(3)种群亲缘关系及遗传结构分析。从9个种群的108个个体中,共检测到82个单倍型(H)。每个种群都有多个单倍型,其中DTH单倍型最多(19个),而GL单倍型最少(4个)较少。其中H3、H14为GL和QZ的共享单倍型,H13为GL、QZ、XT的共享单倍型。系统进化树显示长江及珠江流域中华沙塘鳢共分为两大支,即:YD的种群单独聚为一支,而其它的8个种群聚为另外一支,包GL、DTH、XT、QZ、YD、JZ、HH、YT种群。珠江流域的GL与QZ先聚类,然后再与XT和DTH聚类。单倍型网状结构关系显示该9个种群并没有按照地理位置进行聚类,表明中华沙塘鳢种群处于谱系重排的状态。AMOVA分析中华沙塘鳢最佳的分组方法,即YD种群单独分为一组而其它群体分为一组为最好的分组方法。(4)中华沙塘鳢种群历史动态检测。分析发现,Tajima's D、Fu's Fs小于0(P0.05),加上单倍型最小网状图显示出星状散布的特点,表明长江及珠江流域的中华沙塘鳢可能经历了种群扩张事件。3、基于微卫星的中华沙塘鳢种群遗传多样性与遗传结构分析本章用13对微卫星引物,分析了以上9个种群的遗传多样性与遗传结构。主要结果如下:(1)种群遗传多样性。NA种群平均等位基因(Na)数为6,其中XT的等位基因数最多,而YD等位基因数最少。QZ的等位基因丰富度(AR)最高,而YD的最低。所有种群的观测杂合度(Ho)为0.347,期望杂合度(HE)为0.601。其中GL的Ho最高(0.471),而DY的Ho最低(0.212),而GL的HE最高(0.588),XT的最低(0.398)。各种群的近交系数Fis变化范围为0.713-0.745,都大于0.5,说明中华沙塘鳢的9个种群间分化较大,种群总的遗传多样性较高。(2)种群遗传差异分析。分析发现,种群间遗传距离较大,如DY和YT遗传距离最大为0.0458,而最小的为GL和QZ为0.101。不同种群的AMOVA分析显示,无论是将种群按地理距离分组还是系统进化树分支分组,种群间遗传差异都大于种群内的遗传差异,表明差异主要来源于种群间。NJ树显示,GL、QZ、XT、DTH聚为一类,而JZ、HH、YT、DY、YD聚为一类,显示出按照地理位置聚类的特征。(3)种群主成分分析。GL、QZ、XT、DTH聚为一组,而JZ、HH、YT、DY、YD聚为一组,且PC1为34.94%,PC2为20.87%。Structure显示K=2时为最佳分组。(4)种群的瓶颈效应。根据种群是否杂合度过剩来判断种群是否经历过瓶颈效应,(Sign test和Wilcoxon’s test)检测模型发现GL、DY、JZ种群经历显著的瓶颈效应。
[Abstract]:In this paper, 9 populations of Odontobutis sinensis were collected. The genetic structure of the population in the Yangtze and Pearl River basins was analyzed with mitochondrial (Cyt b) and nuclear gene (EPICs, microsatellite). The main results were as follows: the 1.Cyt B gene was used for the Yangtze River and the Pearl River Flow. The analysis of genetic diversity of the region of Chinese sand pond SNA from Yidu (YD), Dangyang (DY), Jingzhou (JZ), Honghu (HH), Yingtan (YT), Guilin (GL), Yingtan (DTH), whole state (QZ), Xiangtan (XT) and so on. The whole length of the Cyt B gene of the amplified linear granular Cyt was used for sequence analysis, and 1127 of them were selected to carry out genetic analysis. The results were as follows. (1) 29 Cyt B gene haplotypes (sequence length 1127 BP), total haplotype diversity (Hd), nucleotide diversity (PI) value were 0.929 0,0.009 41 respectively, and the diversity of genetic diversity and lower ribonucleic acid diversity was higher, and (2) the FST value of 9 population of Chinese sand pond SNA was in 0.110 6~ 0.9988 (P0.01), K2-P genetic distance between 0.002~0.022, revealed that there were significant genetic differentiation among the groups, and the gene exchange values (Nm) among the majority of the population were less than 1 (P0.05), indicating that the genetic exchange among these populations was limited. (3) the neutral evolution test and the network relationship analysis showed that the Guilin (GL) of the Chinese sand pond (GL) The population of Dongting Lake (DTH) has experienced a population expansion event. It is speculated that the direction of genetic communication is from the Yangtze River water system to the Pearl River water system. Through the above study, the resources conservation, development and utilization of the Chinese sand pond SNA is provided with a scientific basis for the development and utilization of.2 based on the genetic diversity and remains of the population based on the nuclear based EPICs molecular markers. In this study, the genetic diversity and genetic structure of a EPICs marker, 55305E1, were cloned and sequenced. (1) sequence analysis. In the study, we selected the 1070bp of the 55305E1 gene and analyzed the genetic diversity of 9 populations in the Yangtze River and the Pearl River Basin. The results showed that the genetic diversity of 9 populations in the Yangtze River and the Pearl River Basin. There were 178 variation sites, the proportion of variation was 16.7%, of which 105, 59% of the total variation, and the average content of the simple information loci 63 and the total variation of 35%. base was T32.6%, C 18.4%, A 31.7%, G17.7%.A+T (64.3%) G+C (36.1%), indicating that both mitochondria and nuclear genes in snakehead snakehead of China showed AT preference. (2) genetic diversity. Analysis. The total haplotype diversity (Hd) of the population of 9 populations was 0.99330, the range of variation was between 0.6-1. The nucleotide diversity (PI) was 0.01370, the range of variation was between 0.0035-0.0132. (3) genetic relationship and genetic structure analysis. 82 haplotypes (H) were detected from 108 individuals of 9 populations. There are multiple haplotypes, of which DTH haplotypes are the most (19), while GL haplotypes are the least (4). H3, H14 are shared haplotypes of GL and QZ, H13 is the shared haplotype of GL, QZ, XT. The phylogenetic tree shows that the Yangtze River and Pearl River Basin are divided into two branches, that is, YD population alone is one, and the other 8 populations gather into another. GL, DTH, XT, QZ, YD, JZ, HH, YT population. The GL and QZ first cluster in the Pearl River Basin, and then cluster with XT and DTH. The relationship between the haplotype reticular formation showed that the 9 populations did not cluster according to geographical location. The population is divided into one group and the other groups are divided into the best grouping methods. (4) the historical dynamic detection of the population of the Chinese sand pond SNA head. The analysis found that Tajima's D, Fu's Fs is less than 0 (P0.05), and the smallest reticulation chart of haplotype shows the characteristics of star spread, which indicates that the Chinese sand pond of the Yangtze River and Pearl River basin may experience the population expansion Event.3, based on microsatellite genetic diversity and genetic structure analysis in this chapter, 13 pairs of microsatellite primers were used to analyze the genetic diversity and genetic structure of the above 9 populations. The main results are as follows: (1) the average number of alleles (Na) of the population genetic diversity.NA population is 6, of which the number of alleles of the population is the most, and the YD allele is in the YD allele. The allele richness (AR) of the least.QZ was the highest, while the YD was the lowest. The observed heterozygosity (Ho) of all populations was 0.347, and the expected heterozygosity (HE) was the highest (0.471) of GL Ho of 0.601., while DY Ho was the lowest (0.212), while GL HE (0.588) was the lowest (0.398). The results showed that the differentiation of 9 populations was larger and the total genetic diversity of the population was high. (2) the genetic diversity of the population was analyzed. It was found that the genetic distance between the populations was larger, such as the maximum genetic distance of DY and YT was 0.0458, and the smallest AMOVA analysis of GL and QZ for different 0.101. populations showed that the population was grouped by geographical distance. It is the branch group of phylogenetic tree, and the genetic difference between population is greater than the genetic difference within the population. It shows that the difference mainly comes from.NJ tree display among the population, GL, QZ, XT, DTH are clustered into one class, and JZ, HH, YT, DY, YD are clustered into one class, showing the characteristics of clustering according to the geographical location. (3) D is a group, and PC1 is 34.94%, and PC2 is the best group for 20.87%.Structure to display K=2. (4) the bottleneck effect of the population. Whether the population has experienced the bottleneck effect based on whether the population is miscellaneous or not, (Sign test and Wilcoxon 's test) detection model found GL, DY, experienced significant bottleneck effect.
【学位授予单位】：上海海洋大学
【学位级别】：硕士
【学位授予年份】：2017
【分类号】：S917.4

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