Jungle Genomics - overcoming the Linnean shortfall with Nanopore sequencing in biodiversity hotspots

栖息地的急剧丧失要求分类学家显著加快发现物种的速度。在SPP的第一阶段，我们开发了一个基于分类类群的所有描述名称的类型材料的专著管道，该管道可用于区分遗传上不同的物种和同义词，并产生全面的专著。然而，由于只包括已命名的分类群，因此对物种的发现没有贡献。为了解决这个问题，我们提出了一种基于纳米孔的植物物种发现测序方法，该方法集成在我们现有的管道中。纳米孔测序可用于快速筛选收集的未知物质，重要的是，它允许在现场直接检测未命名的物种。通过这种方式，我们打算克服林奈开花植物的短缺，并大大加快植物物种的发现。我们计划在马达加斯加测试我们的方法，马达加斯加是最濒危的生物多样性热点之一。我们将再次关注葫芦科（葫芦科），它在马达加斯加的形态、栖息地和传粉者方面极其多样化。然而，马达加斯加葫芦谱系的物种数量惊人地少，至少在用所描述的物种计算时，物种形成率显著放缓。对这些低多样化率最可能的解释是林奈短缺效应，这意味着马达加斯加瓜类的大部分多样性仍有待发现。我们将为已描述的70种马达加斯加葫芦建立一个基因组参考数据库，然后使用廉价的纳米孔测序直接在现场筛选多达1000个样本。在现场查询我们的参考数据库将使我们能够指导对新物种的收集工作，这将使实地工作非常有效。我们项目的结果将是一个完整的马达加斯加葫芦科专著和一个全面的基因组数据集，结合我们的全球基因组数据集，将用于推断系统发育估计和分析马达加斯加葫芦的生物地理历史和多样化率。我们简单的丛林基因组学方法允许包括和培训当地科学家，这增加了实地工作的成功率，并将使发展中国家的分类学家几乎不依赖于外国的支持。

The loss of habitats at dramatic scales requires that taxonomists increase significantly the speed of discovery of species. In the first phase of the SPP, we developed a monograph-pipeline based on type material of all described names for a taxonomic group, which can be used to distinguish genetically distinct species from synonyms and results in comprehensive monographs. However, it cannot contribute to discovery of species since only named taxa are included. To account for this problem, we propose a Nanopore-based sequencing approach for plant species discovery integrated in our existing pipeline. Nanopore-sequencing can be used to rapidly screen unidentified material in collections and, importantly, allows detection of unnamed species directly in the field. In this way, we intend to overcome the Linnean shortfall in flowering plants and drastically speed up plant species discovery.We plan to test our approach in Madagascar, one of the most endangered biodiversity hotspots. We will focus again on the gourd family (Cucurbitaceae), which is extremely diverse in morphology, habitat, and pollinators in Madagascar. However, Malagasy cucurbit lineages are surprisingly species-poor with a significant slow-down in speciation rates at least when calculated with the described species. The most likely explanation for these low diversification rates is a Linnean shortfall effect, meaning that the bulk of the Malagasy cucurbit diversity is still awaiting discovery. We will build a genomic reference database for the 70 described Malagasy cucurbit species and then use cheap Nanopore sequencing to screen up to 1000 samples directly in the field. Querying our reference database on-site will allow us to guide collecting efforts towards the new species, which will make the field work very efficient. The result of our project will be a full monograph for the Cucurbitaceae of Madagascar and a comprehensive genomic dataset, which combined with our global genomic dataset for the family will be used to infer phylogeny estimates and analyse the biogeographic history, and diversification rates of Malagasy cucurbits. Our simple jungle-genomics approach allows inclusion and training of local scientists, which increases the success rate of fieldwork and will make taxonomists in developing countries almost independent from foreign support.