長(zhǎng)江及珠江流域的中華沙塘鱧種群遺傳多樣性分析
發(fā)布時(shí)間：2018-07-29 06:32
【摘要】：本論文采集了中華沙塘鱧(Odontobutis sinensis)的9個(gè)種群,用線粒體(Cyt b)及核基因(EPICs、微衛(wèi)星)多種分子標(biāo)記,全面分析了長(zhǎng)江及珠江流域的中華沙塘鱧種群遺傳結(jié)構(gòu),探討了這種遺傳差異的成因。主要結(jié)果如下:1.Cyt b基因?qū)﹂L(zhǎng)江及珠江流域中華沙塘鱧的遺傳多樣性分析從宜都(YD)、當(dāng)陽(yáng)(DY)、荊州(JZ)、洪湖(HH)、鷹潭(YT)、桂林(GL)、鷹潭(DTH)、全州(QZ)、湘潭(XT)等9個(gè)地區(qū)采集108尾中華沙塘鱧個(gè)體,擴(kuò)增線粒體Cyt b基因全長(zhǎng)用于序列分析,并選取其中的1127 bp進(jìn)行遺傳學(xué)分析,結(jié)果如下:(1)從108尾中華沙塘鱧樣本中,共獲得29個(gè)Cyt b基因單倍型(序列長(zhǎng)度1 127 bp),總的單倍型多樣性(Hd)、核苷酸多樣性(π)值分別為0.929 0、0.009 41,呈現(xiàn)出較高的遺傳多樣性和較低的核苷酸多樣性的特點(diǎn);(2)中華沙塘鱧9種群間的FST值在0.110 6~0.998 8間(P0.01),K2-P遺傳距離在0.002~0.022間,揭示各種群間存在顯著的遺傳分化;而多數(shù)種群間的基因交流值(Nm)小于1(P0.05),表明這些中華沙塘鱧種群間的基因交流有限。(3)中性進(jìn)化檢測(cè)和網(wǎng)絡(luò)親緣關(guān)系分析表明,中華沙塘鱧的桂林(GL)和洞庭湖(DTH)種群經(jīng)歷過(guò)種群擴(kuò)張事件,推測(cè)中華沙塘鱧基因交流的方向?yàn)橛砷L(zhǎng)江水系種群流向珠江水系種群。通過(guò)以上研究為中華沙塘鱧的資源保護(hù)、開發(fā)與利用提供科學(xué)的理論依據(jù)。2基于核基因EPICs分子標(biāo)記的種群遺傳多樣性及遺傳結(jié)構(gòu)分析本研究克隆并測(cè)序了一個(gè)EPICs標(biāo)記即55305E1的基因序列,用于中華沙塘鱧9個(gè)種群的遺傳多樣性和遺傳結(jié)構(gòu)分析。(1)序列分析。研究中,我們選取55305E1基因的1070bp,對(duì)長(zhǎng)江及珠江流域共9個(gè)種群進(jìn)行遺傳多樣性分析。結(jié)果表明,共有178個(gè)變異位點(diǎn),變異比例為16.7%,其中單變異位點(diǎn)有105個(gè),占總變異的59%,簡(jiǎn)約信息位點(diǎn)為63且占總變異的35%。堿基的平均含量為T32.6%,C 18.4%,A 31.7%,G17.7%。A+T(64.3%)G+C(36.1%),表明中華沙塘鱧中線粒體與核基因均呈現(xiàn)AT偏好性。(2)遺傳多樣性分析。中華沙塘鱧9個(gè)種群的種群總的單倍型多樣性(Hd)為0.99330,變化范圍在0.6-1之間。核苷酸多樣性(π)為0.01370,變化范圍為在0.0035-0.0132之間。(3)種群親緣關(guān)系及遺傳結(jié)構(gòu)分析。從9個(gè)種群的108個(gè)個(gè)體中,共檢測(cè)到82個(gè)單倍型(H)。每個(gè)種群都有多個(gè)單倍型,其中DTH單倍型最多(19個(gè)),而GL單倍型最少(4個(gè))較少。其中H3、H14為GL和QZ的共享單倍型,H13為GL、QZ、XT的共享單倍型。系統(tǒng)進(jìn)化樹顯示長(zhǎng)江及珠江流域中華沙塘鱧共分為兩大支,即:YD的種群?jiǎn)为?dú)聚為一支,而其它的8個(gè)種群聚為另外一支,包GL、DTH、XT、QZ、YD、JZ、HH、YT種群。珠江流域的GL與QZ先聚類,然后再與XT和DTH聚類。單倍型網(wǎng)狀結(jié)構(gòu)關(guān)系顯示該9個(gè)種群并沒有按照地理位置進(jìn)行聚類,表明中華沙塘鱧種群處于譜系重排的狀態(tài)。AMOVA分析中華沙塘鱧最佳的分組方法,即YD種群?jiǎn)为?dú)分為一組而其它群體分為一組為最好的分組方法。(4)中華沙塘鱧種群歷史動(dòng)態(tài)檢測(cè)。分析發(fā)現(xiàn),Tajima's D、Fu's Fs小于0(P0.05),加上單倍型最小網(wǎng)狀圖顯示出星狀散布的特點(diǎn),表明長(zhǎng)江及珠江流域的中華沙塘鱧可能經(jīng)歷了種群擴(kuò)張事件。3、基于微衛(wèi)星的中華沙塘鱧種群遺傳多樣性與遺傳結(jié)構(gòu)分析本章用13對(duì)微衛(wèi)星引物,分析了以上9個(gè)種群的遺傳多樣性與遺傳結(jié)構(gòu)。主要結(jié)果如下:(1)種群遺傳多樣性。NA種群平均等位基因(Na)數(shù)為6,其中XT的等位基因數(shù)最多,而YD等位基因數(shù)最少。QZ的等位基因豐富度(AR)最高,而YD的最低。所有種群的觀測(cè)雜合度(Ho)為0.347,期望雜合度(HE)為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)。各種群的近交系數(shù)Fis變化范圍為0.713-0.745,都大于0.5,說(shuō)明中華沙塘鱧的9個(gè)種群間分化較大,種群總的遺傳多樣性較高。(2)種群遺傳差異分析。分析發(fā)現(xiàn),種群間遺傳距離較大,如DY和YT遺傳距離最大為0.0458,而最小的為GL和QZ為0.101。不同種群的AMOVA分析顯示,無(wú)論是將種群按地理距離分組還是系統(tǒng)進(jìn)化樹分支分組,種群間遺傳差異都大于種群內(nèi)的遺傳差異,表明差異主要來(lái)源于種群間。NJ樹顯示,GL、QZ、XT、DTH聚為一類,而JZ、HH、YT、DY、YD聚為一類,顯示出按照地理位置聚類的特征。(3)種群主成分分析。GL、QZ、XT、DTH聚為一組,而JZ、HH、YT、DY、YD聚為一組,且PC1為34.94%,PC2為20.87%。Structure顯示K=2時(shí)為最佳分組。(4)種群的瓶頸效應(yīng)。根據(jù)種群是否雜合度過(guò)剩來(lái)判斷種群是否經(jīng)歷過(guò)瓶頸效應(yīng),(Sign test和Wilcoxon’s test)檢測(cè)模型發(fā)現(xiàn)GL、DY、JZ種群經(jīng)歷顯著的瓶頸效應(yīng)。
[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.
【學(xué)位授予單位】：上海海洋大學(xué)
【學(xué)位級(jí)別】：碩士
【學(xué)位授予年份】：2017
【分類號(hào)】：S917.4
本文編號(hào)：2151829
[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.
【學(xué)位授予單位】：上海海洋大學(xué)
【學(xué)位級(jí)別】：碩士
【學(xué)位授予年份】：2017
【分類號(hào)】：S917.4
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