云杉属网状物种多样化的研究
发布时间：2019-05-10 14:25
【摘要】：云杉属(Picea)植物是北半球森林植被的重要组成部分,云杉属34个种遍布了整个北半球,其中3个种分布于欧洲,8个种分布于北美,而亚洲是云杉属物种多样性最高的地区分布有23个种。但由于该属物种具有较大的有效群体和较长的世代时间,以及近期的辐射分化和频繁的种间杂交渐渗而导致种间形态趋同,因此传统方法很难建立该属物种的系统发育关系。本研究中,我们采集了26个云杉种(变种)(15个亚洲种、3个欧洲种和8个北美种)并对其进行转录组测序。(1)基于全基因组尺度上利用转录组数据重建云杉系统发育树我们分别利用三种数据集建立系统发育树:数据集一,核基因的直系同源基因(GOD);数据集二,核基因的单核苷酸多态性位点(N-SNP);数据集三,叶绿体基因的单核苷酸多态性位点(C-SNP);基于核基因和叶绿体基因所建立的系统发育树始终聚为四大支系,每支系都由3-11个物种组成,其结果与形态学分类十分相似。然而,每个支系之间及支系内部的系统发育关系却不尽相同。核基因和叶绿体基因的树形冲突主要在支系一和四(lineage I和lineage IV)的系统发育位置不一致。(2)单倍型的共享以及非二歧分支关系的检测在植物的进化过程中,亲缘关系相近的姊妹种与外类群之间普遍存在基因渐渗和杂交等现象,而该现象直接导致了物种间的进化过程并非二歧分化。为了检测云杉属内物种间的非二歧分化的假设,我们首先依据同源单倍型(IBD)的长度来检测支系间多态性共享的情况。基于同源单倍型的结果,我们又利用ABBA-BABA模型对四大支系间基因流的情况做了进一步的验证。最终,我们的研究表明四大支系内部以及四大支系之间共享大量的遗传多态性。同时ABBA-BABA检验也证实了四大支系间确实有明显的基因流存在,且同域物种间比异域物种间共享更多的基因流,而所有ABBA-BABA的假设性检验结果都否定了姊妹种与外类群的二歧拓扑结构。最终,我们的研究表明,云杉属物种分化并非是简单的二歧分化,而是在此过程中存在基因渐渗等导致的网状进化现象。
[Abstract]:Spruce (Picea) is an important part of forest vegetation in the northern hemisphere. 34 species of spruce are distributed throughout the northern hemisphere, of which 3 species are distributed in Europe and 8 species are distributed in North America. There are 23 species in Asia with the highest species diversity in spruce. However, due to the large effective population and long generation time, as well as the recent radiation differentiation and frequent interspecific hybridization, it is difficult to establish the phylogenetic relationship of the genus species by traditional methods, because of its large effective population and long generation time, as well as the recent radiation differentiation and frequent interspecific hybridization gradually leading to the convergence of species morphology. In this study, 26 spruce species (varieties) (15 Asian species) were collected. (1) the phylogenetic tree of Picea spruce was reconstructed on a genome-wide scale by using transcribed set data. We use three data sets to build phylogenetic trees respectively: data set 1, and phylogenetic tree 1, 3 species and 8 species from North America. Direct homologous gene (GOD); of nuclear gene Data set 2, single nucleotide polymorphism site (N-SNP) of nuclear gene, data set 3, single nucleotide polymorphism site of chloroplast gene (C-SNP). The phylogenetic tree based on nuclear gene and chloroplast gene has always been grouped into four branches, each of which is composed of 3 species and 11 species, and the results are very similar to those of morphological classification. However, the phylogenetic relationship between and within each branch is not the same. Tree-shaped conflicts between nuclear genes and chloroplast genes are mainly at different phylogenetic locations between (lineage I and lineage IV). (2) the sharing of haplotypes and the detection of non-dichotomous branching relationships are involved in the evolution of plants. There are many phenomena such as gene infiltration and crossing between sister species and foreign groups with similar kinship, which directly leads to the evolution of species is not dichotomous differentiation. In order to detect the hypothesis of non-dichotomous differentiation among species in spruce, we first detected the polymorphism sharing among branches according to the length of homologous haplotype (IBD). Based on the results of homologous haplotype, we further verified the gene flow among the four branches by using ABBA-BABA model. Finally, our study shows that a large number of genetic polymorphism is shared within and among the four branches. At the same time, ABBA-BABA test also confirmed that there were obvious gene flows among the four branches, and more gene flows were shared among species in the same region than among species in the same region. However, all the hypothetical test results of ABBA-BABA negate the bifid topological structure of sister species and alien groups. Finally, our study shows that the differentiation of spruce species is not a simple dichotomous differentiation, but a reticular evolution caused by gene infiltration and so on.
【学位授予单位】：兰州大学
【学位级别】：博士
【学位授予年份】：2016
【分类号】：S791.18
本文编号：2473716
[Abstract]:Spruce (Picea) is an important part of forest vegetation in the northern hemisphere. 34 species of spruce are distributed throughout the northern hemisphere, of which 3 species are distributed in Europe and 8 species are distributed in North America. There are 23 species in Asia with the highest species diversity in spruce. However, due to the large effective population and long generation time, as well as the recent radiation differentiation and frequent interspecific hybridization, it is difficult to establish the phylogenetic relationship of the genus species by traditional methods, because of its large effective population and long generation time, as well as the recent radiation differentiation and frequent interspecific hybridization gradually leading to the convergence of species morphology. In this study, 26 spruce species (varieties) (15 Asian species) were collected. (1) the phylogenetic tree of Picea spruce was reconstructed on a genome-wide scale by using transcribed set data. We use three data sets to build phylogenetic trees respectively: data set 1, and phylogenetic tree 1, 3 species and 8 species from North America. Direct homologous gene (GOD); of nuclear gene Data set 2, single nucleotide polymorphism site (N-SNP) of nuclear gene, data set 3, single nucleotide polymorphism site of chloroplast gene (C-SNP). The phylogenetic tree based on nuclear gene and chloroplast gene has always been grouped into four branches, each of which is composed of 3 species and 11 species, and the results are very similar to those of morphological classification. However, the phylogenetic relationship between and within each branch is not the same. Tree-shaped conflicts between nuclear genes and chloroplast genes are mainly at different phylogenetic locations between (lineage I and lineage IV). (2) the sharing of haplotypes and the detection of non-dichotomous branching relationships are involved in the evolution of plants. There are many phenomena such as gene infiltration and crossing between sister species and foreign groups with similar kinship, which directly leads to the evolution of species is not dichotomous differentiation. In order to detect the hypothesis of non-dichotomous differentiation among species in spruce, we first detected the polymorphism sharing among branches according to the length of homologous haplotype (IBD). Based on the results of homologous haplotype, we further verified the gene flow among the four branches by using ABBA-BABA model. Finally, our study shows that a large number of genetic polymorphism is shared within and among the four branches. At the same time, ABBA-BABA test also confirmed that there were obvious gene flows among the four branches, and more gene flows were shared among species in the same region than among species in the same region. However, all the hypothetical test results of ABBA-BABA negate the bifid topological structure of sister species and alien groups. Finally, our study shows that the differentiation of spruce species is not a simple dichotomous differentiation, but a reticular evolution caused by gene infiltration and so on.
【学位授予单位】：兰州大学
【学位级别】：博士
【学位授予年份】：2016
【分类号】：S791.18
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