A Pipeline and Recommendations for Population and Individual Diagnostic SNP Selection in Non‐Model Species
Despite substantial reductions in the cost of sequencing over the last decade, genetic panels remain relevant due to their cost-effectiveness and flexibility across a variety of sample types. In particular, single nucleotide polymorphism (SNP) panels are increasingly favoured for conservation applications. SNP panels are often used because of their adaptability, effectiveness with low-quality samples, and cost-efficiency for population monitoring and forensics. However, the selection of diagnostic SNPs for population assignment and individual identification can be challenging. The consequences of poor SNP selection are under-powered panels, inaccurate results, and monetary loss. Here, we develop a novel and user-friendly SNP selection pipeline (mPCRselect) that can be used to select SNPs for population assignment and/or individual identification. mPCRselect allows any researcher, who has sufficient SNP-level data, to design a successful and cost-effective SNP panel for a diploid species of conservation concern.
Authors
- Tessa Ferrari (ORCID: https://orcid.org/0009-0009-7692-4465)
- Ellie E. Armstrong (ORCID: https://orcid.org/0000-0001-7107-6318)
- Joanna L. Kelley (ORCID: https://orcid.org/0000-0002-7731-605X)
- Chenyang Li (ORCID: https://orcid.org/0000-0002-4406-9224)
- Dmitri A. Petrov (ORCID: https://orcid.org/0000-0002-3664-9130)
- Michael G. Campana (ORCID: https://orcid.org/0000-0003-0461-6462)
- Jazlyn A. Mooney (ORCID: https://orcid.org/0000-0002-2369-0855)
- Katherine A. Solari (ORCID: https://orcid.org/0000-0001-7029-6554)
Institutions
- University of California, Riverside (US)
- University of Southern California (US)
- University of California, Santa Cruz (US)
- Smithsonian Conservation Biology Institute (US)
- Chan Zuckerberg Biohub San Francisco (US)
- Evolutionary Genomics (United States) (US)
- National Zoological Park (US)
- Chan Zuckerberg Initiative (United States) (US)
- Conservation Biology Institute
- Washington State University (US)
- Stanford University (US)
Publication Details
- Journal
- Molecular Ecology Resources
- Published
- 2024-11-29
- DOI
- https://doi.org/10.1111/1755-0998.14048
- Citations
- 4
- Primary Topic
- Genetic diversity and population structure
- Type
- article
- Field-Weighted Citation Impact
- 2.20
Funders
- Smithsonian Institution
- Washington Research Foundation
- Women in Science and Engineering, University of Southern California