东亚第三纪孑遗落叶林关键类群领春木属物种形成与谱系分化的时空格局与机制

Elucidating the demographic effects of Quaternary climatic oscillations and environmental heterogeneity increases our understanding of the roles of climate change and niche divergence in shaping biodiversity in East Asia. In this study, we will study on the lineage divergence, geographic pattern and genetic diversity of Euptelea, one keystone genus endemic to East Asian Tertiary-relic deciduous forests. Euptelea contains two extant species, E. pleiosperma and E. polyandra.. The samples of Euptelea have been sampled from different regions across the distribution range of the genus in China, Japan and northern India. The sequence variation of both chloroplast DNA (cpDNA) and nuclear ITS as well as nuclear SSR dataset have been used to investigate the geographic distribution patterns, phylogeographic structure, and phylogenetic relationships of haplotypes. Time-calibrated phylogenetic and phylogeographic inferences will be used to trace ancestral areas and biogeographical events. Based on the patterns of lineage diversification, we will further use a genome-wide sampling of SNPs identified within restriction site–associated DNA (RAD) tags to investigate the historical forces responsible for geographic pattern and the mechanisms of speciation and lineage diversification. The population genetics methods and Bayesian and ABC models will be used to infer demorgraphic history of species and lineages. When combining with ecological niche modeling and multivariate niche method, we can address what historical processes, e.g. fragmentation, expansion, long-distance colonization, have the strongest influence on the lineage divergence and geographic pattern of Euptelea. By using genome scan methods, we can identify RAD neutral and outlier loci. Based on landscape genetics methods, we will model environmental data using nonparametric multiple regression to explain lineage divergence and genetic differentiation as a function of spatio-ecological effects. In addition, to identify patterns of adaptive genetic variation on landscapes, and quantify effects of environmental factors on patterns of adaptive genetic variation, we will test the correlations between clines in allele frequencies of individual outlier loci and environmental variation. Based on multi-loci genetic data, evolutionarily important units can be identified. This information will be useful for developing scientific conservation and appropriate management strategies for this endangered genus.

揭示气候动荡与环境异质性对森林关键类群谱系分化与种群动态的影响，有利于理解东亚物种多样性形成机制。本项目拟对第三纪孑遗植物领春木属进行广泛群体取样，基于叶绿体DNA、ITS序列与nSSR变异，利用系统发育与生物地理学方法，分析物种分化时间、历史分布区与生物地理事件、谱系地理结构。利用限制性酶切位点关联DNA测序（RAD-Seq）技术鉴定群体单核苷酸多态性（SNPs），基于整合数据，利用群体遗传学、IMa、ABC模型方法分析物种进化历史与谱系分化过程，结合生态位模型与多变量生态位方法，揭示物种与谱系分化的历史驱动因子。通过基因组扫描方法鉴定RAD中性与outlier位点，利用景观遗传学方法分析地理与景观效应、生态因子对群体\谱系分化以及遗传多样性空间分布格局的影响，解析适应性遗传变异的空间分布格局及影响因子。中性与适应性位点结合鉴定“进化重要单位”，提出领春木属遗传资源保护策略。

本课题对东亚第三纪孑遗落叶林的代表类群大果领春木与多花领春木进行了广泛的野外资源调查与取样，基于叶绿体、ITS序列、微卫星以及简化基因组测序，利用亲缘地理学和群体遗传学方法对领春木属的遗传多样性、遗传结构、物种进化历史与种群动态进行了研究，并利用物种分布模型、景观基因组学方法分析了环境异质性与地理隔离在领春木群体分化中的作用。获得如下研究结果：.（1）野生资源调查、遗传多样性和谱系地理结构。在野外调查的基础上，从物种分布范围内采集了36个群体的样本。基于三个cpDNA片段共检测到35个单倍型，在大果领春木种内存在四个地理谱系，多花领春木种内存在两个地理谱系。基于ITS序列，在领春木属共检测到10种单倍型。基于nSSRs和RAD-SNP标记的遗传结构分析表明：大果领春木和多花领春木由不同的基因池组成，而大果领春木在中国-喜马拉雅和中国-日本植物亚区区系隔离线附近分化为西南谱系和东南谱系，其中西南谱系呈现明显的次级谱系分化，并且拥有较高的遗传多样性；而多花领春木群体间没有明显的近期遗传分化。.（2）物种分化与种群历史。近似贝叶斯计算（ABC）结合地质、气候资料表明中新世末期（c. 9.73 Ma）的气候变化导致领春木属祖先类群局域分布于中国横断山-云贵高原以及日本南部的河岸生境，从而驱使了异域物种形成。大果领春木由于上新世末\更新世初的横断山隆升而发生了原地谱系分化，河道改迁则导致西南谱系向东扩散。.（3）谱系分化的驱动因子和适应性。景观基因组学分析在中国群体中检测到更强的局域适应性信号，其中环境异质性与地理隔离在领春木群体分化中起到了重要作用，而日本的多花领春木群体遗传变异主要受地理隔离的影响。梯度森林模型显示未来 2050 年大果领春木的中东部谱系面临着丧失更多遗传变异的风险，种群衰减幅度要明显高于比西南谱系，这可能与气候变暖河道生境在东部地区散失有关。.最后，根据遗传数据和物种分布区模拟结果，我们提出了领春木属物种遗传资源保护与管理策略。