Common to rare transfer learning (CORAL) enables inference and prediction for a quarter million rare Malagasy arthropods
DNA-based biodiversity surveys result in massive-scale data, including up to millions of species-of which, most are rare. Making the most of such data for inference and prediction requires modeling approaches that can relate species occurrences to environmental and spatial predictors, while incorporating information about their taxonomic or phylogenetic placement. Even if the scalability of joint species distribution models to large communities has greatly advanced, incorporating hundreds of thousands of species has not been feasible to date, leading to compromised analyses. Here we present a 'common to rare transfer learning' (CORAL) approach, based on borrowing information from the common species to enable statistically and computationally efficient modeling of both common and rare species. We illustrate that CORAL leads to much improved prediction and inference in the context of DNA metabarcoding data from Madagascar, comprising 255,188 arthropod species detected in 2,874 samples.
Authors
- Steven L. Winter (ORCID: https://orcid.org/0000-0003-0268-5667)
- Panu Somervuo (ORCID: https://orcid.org/0000-0003-3121-4047)
- Eric Tsiriniaina Rajoelison (ORCID: https://orcid.org/0000-0001-7716-006X)
- Otso Ovaskainen (ORCID: https://orcid.org/0000-0001-9750-4421)
- Tomas V. Roslin (ORCID: https://orcid.org/0000-0002-2957-4791)
- Nerea Abrego (ORCID: https://orcid.org/0000-0001-6347-6127)
- Brian Lee Fisher (ORCID: https://orcid.org/0000-0002-4653-3270)
- Deirdre Kerdraon (ORCID: https://orcid.org/0000-0002-8780-6044)
- Evgeny V. Zakharov (ORCID: https://orcid.org/0000-0002-2310-7738)
- Bess Hardwick (ORCID: https://orcid.org/0000-0001-5195-6115)
- Gleb Tikhonov (ORCID: https://orcid.org/0000-0003-3040-0307)
- Brendan Furneaux (ORCID: https://orcid.org/0000-0003-3522-7363)
- Sujeevan Ratnasingham (ORCID: https://orcid.org/0000-0002-3694-0171)
- Mikko Pentinsaari (ORCID: https://orcid.org/0000-0001-7241-3873)
- Paul D. N. Hebert (ORCID: https://orcid.org/0000-0002-3081-6700)
- Jeremy R deWaard (ORCID: https://orcid.org/0000-0001-9778-5454)
- Sten Anslan (ORCID: https://orcid.org/0000-0002-2299-454X)
- Dimby Raharinjanahary (ORCID: https://orcid.org/0000-0003-2464-6298)
- David B. Dunson
- Stephanie deWaard
- Jayme E Sones (ORCID: https://orcid.org/0009-0007-6078-1688)
Institutions
- Agriculture and Agri-Food Canada (CA)
- University of Helsinki (FI)
- National Museum of Natural History (US)
- Duke University (US)
- Tsimbazaza Zoo (MG)
- California Academy of Sciences (US)
- Swedish University of Agricultural Sciences (SE)
- University of Guelph (CA)
- University of Jyväskylä (FI)
Publication Details
- Journal
- Nature Methods
- Published
- 2025-09-23
- DOI
- https://doi.org/10.1038/s41592-025-02823-y
- Citations
- 1
- Primary Topic
- Environmental DNA in Biodiversity Studies
- Type
- article
- Field-Weighted Citation Impact
- 1.72