豆科系统发育基因组学

	豆科系统发育基因组学
	张荣
导师	伊廷双
关键词	豆科，叶绿体基因组，线粒体基因组，转录组，深度和族级分支，冲突，系统发育基因组学，快速辐射演化 Legumimosae, plastome, mitochondrial genome, transcriptome, deep and tribal lineages, conflict, phylogenomics, rapid radiation
摘要	重建生命之树是开展几乎所有进化生物学研究的基础。解析快速辐射分化类群的系统发育关系一直是系统学研究的难点和挑战。豆科是被子植物第三大科，也是生态和经济价值最大科之一。由于豆科主要分支经历了快速辐射分化，是典型的分类和系统发育重建困难类群，其中很多关键节点系统发育关系难以解析，很多族级分支分类范畴和系统发育关系尚不清楚。博士后期间主要开展两项研究，一是开展豆科质体系统发育基因组学研究，利用代表豆科所有6 个亚科和主要分支的165 属187 种的质体基因组进行全面分析，获得了该科具有高分辨和高支持的系统树，解析了云实亚科和蝶形花亚科的早期分支内一些长期存在争议的深度系统发育关系；证实了质体基因组存在冲突的系统发育信号；创新性地提出质体基因组可能存在复杂的进化模式，高度异质的系统发育信号可能产生错误的系统发育关系，分析冲突系统发育信号是质体系统发育基因组学研究中的必要环节。二是基于多组学数据的系统发育基因组学研究，选择代表豆科所有74 个族级分支485 属909 种的质体和线粒体基因组、转录组数据重建了豆科系统发育关系，解析了豆科难以解析的关键节点及绝大多数族级分支的系统发育关系，确定了部分快速辐射分支的系统发育关系；明确了其中69 个族为单系分支（含13 个建议新拟定的族），确认了豆科族级分类范畴；揭示了ILS 和基因流是造成豆科主要分支关系核质冲突的主要生物因素，且在不同程度上影响了它们间关系的解析。基因树估计误差、基因流和不完全谱系分选能解释大部分的基因树变异。基因的相对组成频率、基因树的分子钟违背程度和位点进化速率异质性是造成基因树与物种树之间冲突的其它主要因素。难以解析的系统发育关系主要由于不完全谱系分选和基因流造成，但也不能排除分析过程中的其它系统误差。本研究首次构建的豆科族级分支的高分辨和高支持的系统发育框架不仅为该科的分类、物种多样化、形态和功能演化、固氮历史等研究奠定了基础，也为辐射类群的系统发育关系解析提供了新思路。; Tree of Life supplies basis for almost all studies in evolutionary biology. It is a challenging task to resolve the phylogenetic relationships of lineages that have undergone rapid evolutionary radiations. Fabaceae (Leguminosae) is the third largest and one of the most ecologically and economically important angiosperm families. Most major lineages of legumes have undergone rapid radiations, which make both phylogenetic inference and classification of this family challenging. In Leguminosae, relationships of many key lineages and nodes remain contentious, category and relationships of some tribe/tribal lineages are still unresolved. During the post-doctoral period, I mainly carried out two studies. Based on the plastomes of 187 species (165 genera) representing all six subfamilies and major lineages of Leguminosae, this study firstly produced well resolved trees with strong statistical support, thus providing strong support for resolution of some long-controversial deep relationships among the early diverging lineages of the subfamilies Caesalpinoideae and Papilionoideae. In addition, this study confirmed the existence of conflicting phylogenetic signals in the plastome. This study suggests the plastomes of many legumes might have complex evolutionary histories. Highly conflicting phylogenetic signals might result in misleading phylogenetic inferences, it is therefore necessary to thoroughly examine in plastid phylogenomics. Secondly, we integrated data from all three plant genomes (including plastomes, mitochondrial genes and transcriptome data) of 485 genera (909 species) representing all 74 tribe/tribal lineages to reconstruct the maximum likelihood and coalescent trees of Leguminosae. Some recalcitrant deep and most tribal relationships were resolved with strong support, especially, some parts of rapid radiations were identified and their relationships were resolved. There are 69 tribe/tribal lineages resolved to be monophyletic with robust support, and 13 out of them were proposed as new tribes. We also summarized all these tribal categories of Leguminosae. Our results indicated that gene flow and ILS could be the main biological factors of nucleocytoplasmic or other conflicts within main lineages in Leguminosae and affected the resolution of their relationships to varying degrees; gene tree estimation error, gene flow and incomplete lineage sorting can explain most of the gene tree variation. The other main factors causing the phylogenetic conflicts of gene-species trees include relative composition frequency variability (RCFV), degree of violation of a molecular clock (DVMC), and heterogeneity of evolutionary rate within one gene. The difficulties of resolving phylogenetic relationships of clade with rapid radiations can be mainly attributed to ILS and gene flow, but other systematic errors can not be excluded. This study reconstructs a robustly supported tribal phylogenetic backbone for future studies on classification.
语种	中文
	2022-01
学位授予单位	中国科学院大学
文献类型	学位论文
条目标识符	http://ir.kib.ac.cn/handle/151853/75088
专题	昆明植物所硕博研究生毕业学位论文
推荐引用方式 GB/T 7714	张荣. 豆科系统发育基因组学[D]. 中国科学院大学,2022.

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