Phylogenomics and eDNA to study interaction networks of insects across tropical rainforests

热带雨林生态系统通常被认为是生物多样性最高的热点，但在地理和生态环境之间的总物种丰富度存在巨大差异。我们对这些差异及其原因的了解非常有限，主要是因为巨大的多样性禁止在不同地点之间进行严格的比较，也许除了研究得最好的脊椎动物群。更不为人所知的是这些生态系统中复杂的相互作用，例如食草昆虫与其宿主植物之间的相互作用。该项目将通过一种将全生态系统基因组学与生物遗传学相结合的新方法来应对全球比较的挑战。我们将使用鞘翅目（甲虫）的具体情况，可以说是地球上最大的辐射，在比较三大洲的原始森林，代表东方，新热带和非洲热带地区。我们会问：这些群落的系统发育多样性是什么，多样性是近代的还是古代的（即雨林是多样性的“摇篮”还是“博物馆”）？地球上哪里是谱系地方性最高的地方，有谱系起源的热点吗？在种群水平上，我们会问，在不同的大陆上，种群规模作为衡量物种年龄的标准，遗传多样性最丰富的群落是否也拥有较高的物种遗传多样性。最后，eDNA方法允许研究之间的相互作用：草食动物和寄主植物，树皮甲虫和树木病原真菌，和金龟子和它们的哺乳动物粪便资源。该学生将成为SITE-100项目（www.site100.org）的一部分，用于研究全球节肢动物多样性，该项目提供了一个大型未发表的基因组和成像数据库，可用于该项目。高通量分类学领域的进展是迅速的，但在现阶段，他们很少超越方法开发的问题。它的应用，热带甲虫组合横跨大陆允许生物多样性的一个基本上未知的领域的分类特征和全球模式和保护优先事项的研究，在生态系统的规模。

Tropical rainforest ecosystems are generally recognised as top biodiversity hotspots, but there are huge differences in the total species richness among biogeographic and ecographic settings. We only have minimal understanding of these differences and their causes, mostly because the great diversity prohibits strict comparisons among sites, except perhaps for the most well studied groups of vertebrates. Even less well known are the complex interactions within these ecosystems, e.g. between herbivorous insects and their host plants. This project will tackle the challenge of global comparisons through a novel approach that combines ecosystem-wide genomics with phylogenetics. We will use the specific case of Coleoptera (beetles), the arguably largest radiation of Earth, in a comparison of primary forests across three continents, representing the Oriental, Neotropical, and Afrotropical regions. We will ask: what is the phylogenetic diversity of these communities and is diversity recent or ancient (i.e. are rainforests 'cradles' or 'museums' of diversity)? Where on Earth is the highest endemicity of lineages, and are there hotspots of lineage origin? At the population level, we will ask if the most phylogenetically diverse communities also hold high genetic diversity within the species, using population size as a measure of age of species in different continents. Finally, eDNA methods allow to study interactions: between herbivores and hostplants, bark beetles and tree-pathogenic fungi, and dung beetles and their mammalian dung resource. The student will be part of the SITE-100 project (www.site100.org) for the study of global arthropod diversity, which provides a large unpublished database of genomic and imaging data that can be exploited for this project. Progress in the field of high-throughput taxonomy is rapid, but at this stage they rarely go beyond issues of method development. Its application to tropical beetle assemblages across continents allows the taxonomic characterisation of a largely unknown realm of biodiversity and the study of global patterns and conservation priorities, on an ecosystem scale.