Haplotype-based inference of recent effective population size in modern and ancient DNA samples

Journal article

Holistic insect monitoring needs scalable techniques to overcome taxon biases, determine species abundances, and gather functional traits for all species. This requires that we address taxonomic impediments and the paucity of data on abundance, biomass and functional traits. We here outline how these data deficiencies could be addressed at scale. The workflow starts with large-scale barcoding (megabarcoding) of all specimens from mass samples obtained at biomonitoring sites. The barcodes are then used to group the specimens into molecular operational taxonomic units that are subsequently tested/validated as species with a second data source (e.g. morphology). New species are described using barcodes, images and short diagnoses, and abundance data are collected for both new and described species. The specimen images used for species discovery then become the raw material for training artificial intelligence identification algorithms and collecting trait data such as body size, biomass and feeding modes. Additional trait data can be obtained from vouchers by using genomic tools developed by molecular ecologists. Applying this pipeline to a few samples per site will lead to greatly improved insect monitoring regardless of whether the species composition of a sample is determined with images, metabarcoding or megabarcoding. This article is part of the theme issue ‘Towards a toolkit for global insect biodiversity monitoring’.publishedVersio

Authors: Fournier, R; Tsangalidou, Z; Reich, D; Palamara, PF

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: Nature Research
• Journal: Nature Communications
• Volume: 14
• Issue: 1
• Pages: 7945-7945
• Article number: 7945
• Publication date: 2023-12-01
• DOI: 10.1038/s41467-023-43522-6
• EISSN: 2041-1723
• ISSN: 2041-1723
• Language: English
• Keywords: 1000 Genomes Project; Inference; Population size; Linkage disequilibrium; Demography; Haplotype; Biobank; Demographic history; Effective population size; Ancient DNA; Identity by descent; Genotype; Computer science; Artificial intelligence; Evolutionary biology; Population; Biology; Genetic variation; Genetics