Project Details
Projekt
Jungle Genomics - overcoming the Linnean shortfall with Nanopore sequencing in biodiversity hotspots
Applicant
Professor Dr. Hanno Schaefer
Subject Area
Evolution and Systematics of Plants and Fungi
Term
from 2017 to 2024
Project identifier
Deutsche Forschungsgemeinschaft (DFG) - Project number 351790369
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.
DFG Programme
Priority Programmes
