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的顶级热点，但在生物地理和生态环境中，总物种丰富度存在巨大差异。我们对这些差异及其原因只有很少的了解，主要是因为巨大的多样性阻碍了地点之间的严格比较，也许除了研究最充分的脊椎动物群体。更不为人所知的是这些生态系统内的复杂相互作用，例如食草性昆虫与其寄主植物之间的相互作用。该项目将通过一种新的方法解决全球比较的挑战，该方法将生态系统全基因组学与系统发育学相结合。我们将以鞘翅目(甲虫)为例，对代表东方、新热带和非洲热带地区的三大洲的原始森林进行比较，甲虫是地球上辐射最大的物种。我们会问：这些群落的系统发育多样性是什么？多样性是最近的还是古老的(即热带雨林是多样性的摇篮还是博物馆)？究竟哪里是宗族地方性最高的地方，有没有宗族起源的热点？在种群水平上，我们将问，是否最具系统发育多样性的群落也在物种内保持着高度的遗传多样性，使用种群规模作为不同大陆物种年龄的衡量标准。最后，EDNA方法允许研究：草食动物和寄主植物、树皮甲虫和树木病原真菌之间的相互作用，以及屎甲虫和它们的哺乳动物粪便资源之间的相互作用。这名学生将成为Site-100项目(www.site100.org)的一部分，该项目旨在研究全球节肢动物多样性，该项目提供了一个可用于该项目的大型未发表的基因组和成像数据数据库。高通量分类学领域的进展很快，但在这个阶段，他们很少超越方法开发的问题。将其应用于各大洲的热带甲虫群落，可以在生态系统范围内对基本上未知的生物多样性领域进行分类描述，并研究全球模式和保护优先事项。

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be part of the SITE-100 project (www.site100.org) for the study of global arthropod diversity, which provides a large unpublished database of genomic and imaging data that can be exploited for this project.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.