羌活与宽叶羌活的种间基因流和物种分化研究
发布时间：2019-03-14 20:17
【摘要】：羌活(Notopterygium incisum)和宽叶羌活(N.franchetii)是邻域分布于我国青藏高原及其临近高山地区的两种多年生珍惜濒危草本植物,两种植物的物种形成和群体历史进化可能受到了过去高原隆升以及第四纪冰期气候波动的影响。本研究取样两个物种高原地区青海、甘肃、四川及陕西等地的21个群体共122个个体材料为研究对象,同时选取羌活属近缘物种青海当归(Angelica nitida)、东当归(A.acutiloba)和白芷(A.dahurica)作为外类群,利用单亲遗传的叶绿体基因片段和线粒体基因片段以及双亲遗传的多个核基因片段作为分子标记,通过群体水平上的DNA测序检测羌活和宽叶羌活自然群体遗传变异的地理分布模式,分析两物种的遗传多样性和群体结构,进行探讨两物种间基因流和物种分化历史,主要结果如下：(1)叶绿体(cpDNA)和线粒体基因(mtDNA)序列分析得出：选用的一个叶绿体片段OG28079长261 bp,分离得到3个变异位点,都集中在羌活中；鉴定到4种单倍型,其中有3种单倍型是羌活的特有单倍型,宽叶羌活只有1种mtDNA单倍型；两个线粒体基因(OG537和OG917)长度总和872 bp,序列中共有3个变异位点,其中1个在羌活中,2个在宽叶羌活中,共统计出4种单倍型,其中有1个羌活的特有单倍型,2个宽叶羌活的特有单倍型,并且有1个单倍型为两个物种所共有。在谱系分化和系统发育分析的研究中,发现羌活与宽叶羌活物种有紧密的亲缘关系。单倍型地理分布图显示,两个物种在叶绿体、线粒体和核基因序列上都存在有单倍型共享的现象,且这两个物种在青藏高原东南边缘有重叠的分布区,可能是发生了二次接触(Secondary contact)及基因渐渗(Introgression)事件。(2)由8个核DNA序列的研究发现,羌活和宽叶羌活的基因多态性水平较低；但宽叶羌活(πT=0.00303;πs=0.00422)的核苷酸多态性水平略高于羌活(πT= 0.00367;πs=0.00408).AMOVA和Permut分析表明两个物种的遗传变异主要存在于群体间,两物群体体间的平均分化比率为79.02%,其中羌活群体间的分化比率平均值达到了89.94%；宽叶羌活群体间的分化比率平均值为75.28%,而群体内变异较少。两物种在所研究的核DNA序列中单倍型种类较多,羌活及宽叶羌活的特有单倍型也较多,且在Network图中有各自明显的区分区域,两物种共享单倍型的现象较少,说明两物种间的分化程度较大。(3)应用隔离-迁移模型进行基因流分析,发现在羌活和宽叶羌活之间检测到了明显不对等的双向基因流,从宽叶羌活迁移至羌活的基因流大于从羌活迁移至宽叶羌活的基因流。分化时间T=4.635×105年,推测两物种进化历史与青藏高原隆升相关。羌活的平均有效群体大小Ne1=7.824x106,宽叶羌活的有效群体大小Ne2=6.792×106,祖先群体的大小NeA=4.249x107,两物种的有效群体大小有明显的收缩；单个核DNA序列的进化时间相近,由此推测两物种的物种形成符合异域物种形成模式,并伴随近期的二次接触及基因渐渗事件。同时相对于祖先群体,两物种的群体大小都有明显的收缩；结合Mismatch的分析结果,暗示在羌活和宽叶羌活进化历史上有可能经历过分布区反复收缩及扩张的事件。(4)根据三种基因片段的单倍型地理分布,发现羌活和宽叶羌活中单倍型多样性较高的群体大多集中在青海西部阿坝自治州的东部河湟谷地,青藏高原与黄土高原接壤处的互助、大通地区,四川西北部的高海拔山区及秦岭山脉的太白山地区。据此推测羌活和宽叶羌活的冰期避难所可能在青藏高原东北部与黄土高原接壤处、青藏高原东部边缘及秦岭西部地区。
[Abstract]:Notopterygium incisum and Notopterygium root (N. franchetii) are two kinds of rare and endangered herb which are distributed in the Qinghai-Tibet plateau and adjacent high-mountain areas of China. The species formation and the evolution of the population history of the two plants may be affected by the uplift of the past plateau and the climatic fluctuation of the Quaternary. In this study,122 individual materials of 21 groups in Qinghai, Gansu, Sichuan and Shaanxi were taken as the research objects in the two species of Qinghai, Gansu, Sichuan and Shaanxi. the geographical distribution mode of the genetic variation of the notopterygium root and the broad-leaf notopterygium root natural population is detected by the DNA sequencing on the population level by using the chloroplast gene fragment and the mitochondrial gene fragment and the plurality of nuclear gene fragments of the parent to be used as the molecular marker, The genetic diversity and population structure of the two species were analyzed, and the history of the gene flow and the species differentiation between the two species was studied. The main results are as follows: (1) the sequence analysis of the chloroplast (cpDNA) and the mitochondrial gene (mtDNA): one of the selected chloroplast fragments OG28079 is 261bp, 3 mutation sites were isolated and concentrated in the notopterygium root;4 single-fold types were identified, among which three single-fold types were the unique haplotypes of the notopterygium, only one mtDNA haplotype was found in the broad-leaf notopterygium, and the total length of the two mitochondrial genes (OG537 and OG917) was 872 bp, and the total number of the two mitochondrial genes (OG537 and OG917) was 872 bp, and there were 3 mutation sites in the sequence. Among them,1 of notopterygium root and 2 were in the notopterygium root of broad leaf, four single-fold types were counted, one of which had the unique haplotype of notopterygium root, the unique haplotype of 2 broad-leaf notopterygium, and one haplotype was common to both species. In the study of lineage differentiation and phylogenetic analysis, it was found that notopterygium root was closely related to the notopterygium root species. The haplotype geographical distribution map shows that the two species have a haplotype-sharing phenomenon in the chloroplast, the mitochondria and the nuclear gene sequence, and the two species have overlapping distribution areas on the southeast edge of the Qinghai-Tibet Plateau. Secondary contact and the progression of the gene may be the case. (2) The genetic polymorphism of notopterygium root and notopterygium root is lower than that of notopterygium root (IGT = 0.00303;% s = 0.00422), which is slightly higher than that of notopterygium root (IGT = 0.00367;% s = 0.00408), according to the eight nuclear DNA sequences. AMOVA and Permut analysis showed that the genetic variation of the two species was mainly present in the group, the average differentiation rate among the two groups was 79.02%, the average value of the differentiation ratio among the notopterygium was 89.94%, and the average value of the differentiation ratio among the notopterygium root groups was 75.28%. And the intra-population variation is less. The single-fold type of the two species in the studied nuclear DNA sequence is more, the unique haplotype of the notopterygium root and the notopterygium root is more, and there is a distinct distinguishing region in the network graph, the phenomenon that the two species share the haplotype is less, and the differentiation degree between the two species is relatively large. And (3) carrying out gene flow analysis by using an isolation-migration model, and finding that a two-way gene flow is detected between the notopterygium root and the notopterygium root and the notopterygium root, and the gene flow from the notopterygium root to the notopterygium root is larger than the gene flow from the notopterygium root to the notopterygium root. The differentiation time T = 4.635-105 years, and the evolution history of the two species is presumed to be related to the uplift of the Qinghai-Tibet Plateau. The mean effective population size of Notopterygium root is Ne1 = 7.824x106, the effective population size of Notopterygium root is Ne2 = 6.792-106, the size of the ancestor group is NeA = 4.249x107, the effective population size of the two species is obviously contracted, and the evolution time of the single nuclear DNA sequence is similar, It is presumed that the species formation of two species is in conformity with the formation pattern of the alien species and is accompanied by the recent secondary contact and the gene gradual infiltration. At the same time, the population size of the two species is obviously contracted with respect to the group of the ancestors, and the results of the analysis of Mismatch suggest that it is possible to experience the repeated contraction and expansion of the distribution area in the history of notopterygium root and notopterygium root. (4) according to the single-type geographical distribution of the three gene fragments, most of the groups of the notopterygium root and the notopterygium root in the broad-leaved notopterygium root are found to be mostly concentrated in the eastern river, the valley of the east river of the Abba autonomous prefecture of the western Qinghai, the mutual aid of the Qinghai-Tibet plateau and the loess plateau of the Loess Plateau, and the Datong area, The high-altitude mountainous area in the northwest of Sichuan and the Taibai Mountain area of the Qinling Mountains. Based on this, it is estimated that the ice age shelters of notopterygium root and notopterygium root may be located in the northeast of the Qinghai-Tibet Plateau and the Loess Plateau, the eastern edge of the Qinghai-Tibet Plateau and the western part of the Qinling Mountains.
【学位授予单位】：西北大学
【学位级别】：硕士
【学位授予年份】：2016
【分类号】：Q943
本文编号：2440334
[Abstract]:Notopterygium incisum and Notopterygium root (N. franchetii) are two kinds of rare and endangered herb which are distributed in the Qinghai-Tibet plateau and adjacent high-mountain areas of China. The species formation and the evolution of the population history of the two plants may be affected by the uplift of the past plateau and the climatic fluctuation of the Quaternary. In this study,122 individual materials of 21 groups in Qinghai, Gansu, Sichuan and Shaanxi were taken as the research objects in the two species of Qinghai, Gansu, Sichuan and Shaanxi. the geographical distribution mode of the genetic variation of the notopterygium root and the broad-leaf notopterygium root natural population is detected by the DNA sequencing on the population level by using the chloroplast gene fragment and the mitochondrial gene fragment and the plurality of nuclear gene fragments of the parent to be used as the molecular marker, The genetic diversity and population structure of the two species were analyzed, and the history of the gene flow and the species differentiation between the two species was studied. The main results are as follows: (1) the sequence analysis of the chloroplast (cpDNA) and the mitochondrial gene (mtDNA): one of the selected chloroplast fragments OG28079 is 261bp, 3 mutation sites were isolated and concentrated in the notopterygium root;4 single-fold types were identified, among which three single-fold types were the unique haplotypes of the notopterygium, only one mtDNA haplotype was found in the broad-leaf notopterygium, and the total length of the two mitochondrial genes (OG537 and OG917) was 872 bp, and the total number of the two mitochondrial genes (OG537 and OG917) was 872 bp, and there were 3 mutation sites in the sequence. Among them,1 of notopterygium root and 2 were in the notopterygium root of broad leaf, four single-fold types were counted, one of which had the unique haplotype of notopterygium root, the unique haplotype of 2 broad-leaf notopterygium, and one haplotype was common to both species. In the study of lineage differentiation and phylogenetic analysis, it was found that notopterygium root was closely related to the notopterygium root species. The haplotype geographical distribution map shows that the two species have a haplotype-sharing phenomenon in the chloroplast, the mitochondria and the nuclear gene sequence, and the two species have overlapping distribution areas on the southeast edge of the Qinghai-Tibet Plateau. Secondary contact and the progression of the gene may be the case. (2) The genetic polymorphism of notopterygium root and notopterygium root is lower than that of notopterygium root (IGT = 0.00303;% s = 0.00422), which is slightly higher than that of notopterygium root (IGT = 0.00367;% s = 0.00408), according to the eight nuclear DNA sequences. AMOVA and Permut analysis showed that the genetic variation of the two species was mainly present in the group, the average differentiation rate among the two groups was 79.02%, the average value of the differentiation ratio among the notopterygium was 89.94%, and the average value of the differentiation ratio among the notopterygium root groups was 75.28%. And the intra-population variation is less. The single-fold type of the two species in the studied nuclear DNA sequence is more, the unique haplotype of the notopterygium root and the notopterygium root is more, and there is a distinct distinguishing region in the network graph, the phenomenon that the two species share the haplotype is less, and the differentiation degree between the two species is relatively large. And (3) carrying out gene flow analysis by using an isolation-migration model, and finding that a two-way gene flow is detected between the notopterygium root and the notopterygium root and the notopterygium root, and the gene flow from the notopterygium root to the notopterygium root is larger than the gene flow from the notopterygium root to the notopterygium root. The differentiation time T = 4.635-105 years, and the evolution history of the two species is presumed to be related to the uplift of the Qinghai-Tibet Plateau. The mean effective population size of Notopterygium root is Ne1 = 7.824x106, the effective population size of Notopterygium root is Ne2 = 6.792-106, the size of the ancestor group is NeA = 4.249x107, the effective population size of the two species is obviously contracted, and the evolution time of the single nuclear DNA sequence is similar, It is presumed that the species formation of two species is in conformity with the formation pattern of the alien species and is accompanied by the recent secondary contact and the gene gradual infiltration. At the same time, the population size of the two species is obviously contracted with respect to the group of the ancestors, and the results of the analysis of Mismatch suggest that it is possible to experience the repeated contraction and expansion of the distribution area in the history of notopterygium root and notopterygium root. (4) according to the single-type geographical distribution of the three gene fragments, most of the groups of the notopterygium root and the notopterygium root in the broad-leaved notopterygium root are found to be mostly concentrated in the eastern river, the valley of the east river of the Abba autonomous prefecture of the western Qinghai, the mutual aid of the Qinghai-Tibet plateau and the loess plateau of the Loess Plateau, and the Datong area, The high-altitude mountainous area in the northwest of Sichuan and the Taibai Mountain area of the Qinling Mountains. Based on this, it is estimated that the ice age shelters of notopterygium root and notopterygium root may be located in the northeast of the Qinghai-Tibet Plateau and the Loess Plateau, the eastern edge of the Qinghai-Tibet Plateau and the western part of the Qinling Mountains.
【学位授予单位】：西北大学
【学位级别】：硕士
【学位授予年份】：2016
【分类号】：Q943
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