劳亚大陆与冈瓦纳大陆地理分离与生态系统重建：中国至澳大拉西亚地域的樟科植物系统基因组学研究

Tropical forest ecosystems are amongst the most species-rich habitat on the planet, providing ecosystem services to millions of people and acting as important climate regulators. Genomic, evolutionary and biogeographical studies of species-rich tropical forest groups are hampered, however, by extensive geographic ranges, a general paucity of diagnostic morphological characters and limited success of previous studies due to the use of low-informative molecular markers. This has resulted in fragmented knowledge on the evolutionary history, genetic diversity and ecological functioning of key plant families of tropical ecosystems, while we are facing a global loss of biodiversity due to unsustainable use of biological resources, climate change and deforestation..Here, we propose a comprehensive study coupling the latest next-generation genomic sequencing techniques and recent advances in molecular dating and biogeographical reconstruction analyses to unravel the origin, evolutionary diversification, historical biogeography and causes for genomic diversity in Lauraceae, a dominant plant family in the Sino-Australasian region which is at the forefront of the current biodiversity crisis. We will establish a representative species dataset for 200 species of Sino-Australasian Lauraceae, sampling from former continental fragments, islands and tropical mountains to incorporate as much evolutionary information as possible, including a globally representative set of Lauraceae outgroups. Latest high throughput sequencing techniques will be used to obtain complete chloroplast genomes supplemented with thousands of newly developed nuclear markers for our study taxa. Phylogenomics, stratified molecular dating (using time slices) and biogeographical reconstructions will be performed to create a high-resolution phylogeographic hypothesis for the historical diversification, dispersal and ecological adaptations of the family. Results will enable us to assess the palaeogeographical origin of Sino-Australasian Lauraceae, assess causes and temporal properties of geographic disjunctions and compare timing, tempo and modes of diversification. We will evaluate responses in evolutionary rates to changes in palaeogeographic configurations, climate, eustatic sea-level conditions, and the development of the tropical biome in Asia..This project will conduct one of the first major phylogenomic studies combining new genomic approaches with phylogenetic and historical biogeographic analyses, molecular dating and diversification rates analyses. No major studies on the phylogenomics of Sino-Australasian Lauraceae have been performed to date, and no cross-regional comprehensive phylogeographic studies based on genomic data exist. This research will serve as a corner stone in understanding the geographic distribution of genomic diversity within China, and its evolutionary connections to South-East Asia, Malesia and Australasia. In the face of overwhelming evidence for an anthropogenic biodiversity crisis, this improved understanding will inform conservation strategies for tropical forests biomes across tropical Asia.

热带森林是全球物种最丰富的生态系统，为亿万人提供生态服务功能并作为重要的气候调节子。但其基因组学、进化及生物地理学的研究滞后，受其广阔的地理分布、缺乏可分辨的形态特征以及合适的分子标记限制。本项目拟在生物多样性危机背景下，解开植物的起源，进化多样性、历史生物地理学以及基因组的多样性。结合最新基因组测序技术、数据组装、分子定年与生物地理学重建分析。建立中国至澳大拉西亚地区樟科代表物种数据库（200种），在劳亚和冈瓦纳大陆分裂后的岛屿、热带山区取样获取樟科物种的进化信息，以评定中澳樟科古地理来源及遗传多样化模式。同时确定该类群在地理配置上的进化速率，气候适应、海平面变化的机制，以及亚洲热带生物群系的传播和发展。本项目结合分子系统学、基因组学、系统发育和古生物地理学，运用分子确定物种起源和的形态建模，评定中国热带树木的基因组多样性的起源和地理分布，及与东南亚、马来群岛和澳大利亚进化史上的关系。

复杂，多样和分布广泛的植物群的基因组，进化和生物地理研究受到许多技术和实践难题的阻碍。广泛的地理范围，加上栖息地隔离和栖息地多样性，使得收集所需的生物材料变得费时。由于缺乏诊断形态学特征，通常无法获得大型热带植物属的知识，这使得无法容易地鉴定物种，特别是在不育的情况下。该项目分析并比较了三个核心地理区域之间的植物学多样性：1）中国和东南亚（25个属中> 600 pppp。）； Malesia（在22属中> 1500 pppp。）；和大洋洲（在7个属中> 110 pppp。）。我们为樟科创建了一​​个具有地区代表性的跨科系谱系统框架，随后用于回答中澳拉美地区的重要进化和生物地理问题。然后，将该框架应用于将来的研究，以支持其他数据集的构建，并为植物科系的关系和进化创建全局系统发育假说。通过这项研究，我们确定了与Malesia湿润雨林的起源和组装有关的许多因素，主要集中在樟科和壳斗科。此外，我们的项目为GenBank当前提供了大量完整的叶绿体序列，从而允许使用植物学方法来了解该家族进化多样化的模式和过程。该项目产生了两份出版物和一份硕士论文。为该项目开发的资源已提供给科学界，并被允许大大加快对这一重要热带森林群的研究。

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