云杉屬網(wǎng)狀物種多樣化的研究
發(fā)布時間：2019-05-10 14:25
【摘要】：云杉屬(Picea)植物是北半球森林植被的重要組成部分,云杉屬34個種遍布了整個北半球,其中3個種分布于歐洲,8個種分布于北美,而亞洲是云杉屬物種多樣性最高的地區(qū)分布有23個種。但由于該屬物種具有較大的有效群體和較長的世代時間,以及近期的輻射分化和頻繁的種間雜交漸滲而導(dǎo)致種間形態(tài)趨同,因此傳統(tǒng)方法很難建立該屬物種的系統(tǒng)發(fā)育關(guān)系。本研究中,我們采集了26個云杉種(變種)(15個亞洲種、3個歐洲種和8個北美種)并對其進行轉(zhuǎn)錄組測序。(1)基于全基因組尺度上利用轉(zhuǎn)錄組數(shù)據(jù)重建云杉系統(tǒng)發(fā)育樹我們分別利用三種數(shù)據(jù)集建立系統(tǒng)發(fā)育樹:數(shù)據(jù)集一,核基因的直系同源基因(GOD);數(shù)據(jù)集二,核基因的單核苷酸多態(tài)性位點(N-SNP);數(shù)據(jù)集三,葉綠體基因的單核苷酸多態(tài)性位點(C-SNP);基于核基因和葉綠體基因所建立的系統(tǒng)發(fā)育樹始終聚為四大支系,每支系都由3-11個物種組成,其結(jié)果與形態(tài)學(xué)分類十分相似。然而,每個支系之間及支系內(nèi)部的系統(tǒng)發(fā)育關(guān)系卻不盡相同。核基因和葉綠體基因的樹形沖突主要在支系一和四(lineage I和lineage IV)的系統(tǒng)發(fā)育位置不一致。(2)單倍型的共享以及非二歧分支關(guān)系的檢測在植物的進化過程中,親緣關(guān)系相近的姊妹種與外類群之間普遍存在基因漸滲和雜交等現(xiàn)象,而該現(xiàn)象直接導(dǎo)致了物種間的進化過程并非二歧分化。為了檢測云杉屬內(nèi)物種間的非二歧分化的假設(shè),我們首先依據(jù)同源單倍型(IBD)的長度來檢測支系間多態(tài)性共享的情況。基于同源單倍型的結(jié)果,我們又利用ABBA-BABA模型對四大支系間基因流的情況做了進一步的驗證。最終,我們的研究表明四大支系內(nèi)部以及四大支系之間共享大量的遺傳多態(tài)性。同時ABBA-BABA檢驗也證實了四大支系間確實有明顯的基因流存在,且同域物種間比異域物種間共享更多的基因流,而所有ABBA-BABA的假設(shè)性檢驗結(jié)果都否定了姊妹種與外類群的二歧拓撲結(jié)構(gòu)。最終,我們的研究表明,云杉屬物種分化并非是簡單的二歧分化,而是在此過程中存在基因漸滲等導(dǎo)致的網(wǎng)狀進化現(xiàn)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.
【學(xué)位授予單位】：蘭州大學(xué)
【學(xué)位級別】：博士
【學(xué)位授予年份】：2016
【分類號】：S791.18
本文編號：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.
【學(xué)位授予單位】：蘭州大學(xué)
【學(xué)位級別】：博士
【學(xué)位授予年份】：2016
【分類號】：S791.18
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