薜荔基因组分化及其驱动因素研究

Speciation is the core issue of evolutionary ecology, and is the cornerstone of species diversity and ecosystem diversity. Genome sequencing provides important information of driving forces of speciation, and had become a powerful tool to reveal speciation mechanism. Gene flow is critical to distinguish the classical allopatric speciation with the recently proposed speciation-with-gene flow theory, but very few studies had focused on the specific mechanisms causing speciation via combining checks of genomic signals and analyses of spatiotemporal pattern of historical gene flow. .In this project, we will focus on the two varieties of Ficus pumila and its closely related species in subseries Plagiostigmaticae, which form a speciation continuum. We will re-sequence the complete genome of selected species and populations of Ficus pumila varieties. Based on the genomic data, we will identify the phylogenetic relationship of target species and estimate the genetic divergence between the two varieties of Ficus pumila at genome level to detect highly divergent regions and the genomic signals of potential driving forces. We will also infer population demography, including effective population size and its variation before and after the formation of the two varieties, spatiotemporal gene flow pattern, as well as potential introgression from closely related species. Combining our results with biogeographic information, we will conclude the predominant forces driving the divergence of the two varieties and provide a better understanding of how the high species diversity was generated in genus Ficus.

物种形成长期以来是进化生态学研究的核心问题，近年来快速发展的基因组测序可提供物种形成驱动因素的重要信息，成为阐释成种机制的有力工具。基因流强弱是区别经典的异域成种与新近提出的基因流存在下成种理论的关键，然而结合检验基因组信号、分化过程中基因流及其发生时间以阐明物种形成机制的实证研究甚少。本项目以处于成种连续谱不同阶段的薜荔2个变种及薜荔榕亚系的近缘种为对象，拟采用基因组重测序获得单核苷酸多态性等数据，在确定薜荔及其近缘种间的系统进化关系基础上，分析薜荔种内基因组不同区域的多样性和分化，检验镶嵌分化格局形成原因的基因组信号，揭示种间基因渗入对薜荔种内分化的贡献，结合种群统计和进化历史分析，反演有效种群大小及其变化，确定基因流在薜荔变种形成中的作用，明确变种分化模式，从而检验基因流存在下成种理论在薜荔中是否成立，研究成果也可为理解榕属植物丰富物种多样性提供依据。

基因流存在下的物种形成是近20年来关注的热点问题，其重要特征是基因组呈现分化高度异质性，其中分化很高的区域称为分化基因组岛，然而影响高分化区的因素很多，甄别影响分化基因组形成的因素成为检验基因流存在下的物种形成的关键。我们构建了分析分化基因组岛鉴别以及影响因素检验的流程，以薜荔两个变种（薜荔和爱玉子)以及其近缘种(匍茎榕、藤榕）为对象，通过基因组重测序，筛选cpDNA和nDNA SNPs，得到如下结论：1）核基因组的系统进化树上不存在类群间的混杂现象，但叶绿体基因组的系统进化树存在类群间的混杂，显示薜荔和爱玉子间存在基因流；2）主成分分析可有效区分薜荔、爱玉子和匍茎榕，聚类分析显示薜荔和爱玉子基因组存在匍茎榕成分，基因渐渗分析显示匍茎榕至爱玉子的渐渗强度大于至薜荔的渐渗；3）在基因组中发现106个分化基因组岛，最大的为50kb；4）经排除基因组特征以及多种因素影响后，确认基因流存在下的歧化选择在薜荔和爱玉子的分化中起主导作用；5）来自匍茎榕的基因渐渗也对分化基因组岛的形成有重要贡献；6）分化基因组岛含191个基因，GO条目有19个，其中不少与果胶代谢有关，而果胶代谢与耐寒性有关，表明薜荔和爱玉子的分化可能与低温适应有关。已发表和录用9篇学术论文，其中SCI收录源7篇，含Entomologia Generalis、Ecological Entomology、Journal of Systematics & Evolution等生态与进化重要刊物。培养博士后、博士和硕士各1名。