Population genomics for wildlife conservation and management

Hohenlohe, Paul A.; Funk, W. Chris; Rajora, Om P.

doi:10.1111/mec.15720

Cited by 702Genetic diversity and population structureGenetic and phenotypic traits in livestockWildlife Ecology and Conservation

Population genomics for wildlife conservation and management

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Hohenlohe, Paul A., Funk, W. Chris, Rajora, Om P.·2021·Molecular Ecology

DOI 10.1111/mec.15720PMC PMC7894518

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Abstract

Biodiversity is under threat worldwide. Over the past decade, the field of population genomics has developed across nonmodel organisms, and the results of this research have begun to be applied in conservation and management of wildlife species. Genomics tools can provide precise estimates of basic features of wildlife populations, such as effective population size, inbreeding, demographic history and population structure, that are critical for conservation efforts. Moreover, population genomics studies can identify particular genetic loci and variants responsible for inbreeding depression or adaptation to changing environments, allowing for conservation efforts to estimate the capacity of populations to evolve and adapt in response to environmental change and to manage for adaptive variation. While connections from basic research to applied wildlife conservation have been slow to develop, these connections are increasingly strengthening. Here we review the primary areas in which population genomics approaches can be applied to wildlife conservation and management, highlight examples of how they have been used, and provide recommendations for building on the progress that has been made in this field.

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High-quality reference genome assemblies are increasingly recognized as an important foundation of conservation genomics.
“High-quality reference genome assemblies are increasingly recognized as an important foundation of conservation genomics84–91.”
From Chromosomal-level reference genome assembly of muskox (Ovibos moschatus) from Banks Island in the Canadian Arctic, a resource for conservation genomics (2024) · cites this paper as [90]
The Introduction (‘Applications to wildlife’; page not provided) says reference genome assemblies are increasingly available and enable analyses that would otherwise be impossible. ‘Approaches in population genomics’ calls their contribution integral to a genomics study. The paper supports their importance, but these passages do not specifically address the claim’s high-quality qualifier. (LLM, conf=0.82)
Experimental — accuracy not yet measured
Arctic conservation management can be complex with intersecting and conflicting environmental, cultural and socioeconomic issues.
“Arctic conservation management can be complex with intersecting and at times conflicting environmental, cultural and socioeconomic issues90,168,169.”
From Chromosomal-level reference genome assembly of muskox (Ovibos moschatus) from Banks Island in the Canadian Arctic, a resource for conservation genomics (2024) · cites this paper as [90]
The “Informing Management Actions” section (page unavailable) says wildlife managers face difficult management decisions, supporting the general point that conservation management can be complex. It does not address Arctic management or say that environmental, cultural and socioeconomic issues intersect or conflict. (LLM, conf=0.78)
Experimental — accuracy not yet measured

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Population Genomics Provides Key Insights in Ecology and Evolution
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Rajora, O. P. (2019). Population Genomics: Concepts, Approaches, and Applications. Springer Nature Switzerland AG.

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How genomics can help biodiversity conservation
Theissinger, K., Fernandes, C., Formenti, G., Bista, I., Berg, P. R., Bleidorn, C., Bombarely, A., Crottini, A., Gallo, G. R., Godoy, J. A., et al. (2023) · Trends in Genetics · doi:10.1016/j.tig.2023.01.005 · Cited by 401 · see citing works
Conservation genetics as a management tool: The five best-supported paradigms to assist the management of threatened species
Willi, Y., Kristensen, T. N., Sgrò, C. M., Weeks, A. R., Ørsted, M., & Hoffmann, A. A. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2105076119 · Cited by 281 · see citing works
Genomic erosion in the assessment of species’ extinction risk and recovery potential
van Oosterhout, C., Speak, S. A., Birley, T., Hitchings, L. W., Bortoluzzi, C., Percival-Alwyn, L., Urban, L., Groombridge, J. J., Segelbacher, G., & Morales, H. E. (2022) · doi:10.1101/2022.09.13.507768 · Cited by 36 · see citing works
Genomes of critically endangered saola are shaped by population structure and purging
Garcia-Erill, G., Liu, S., Le, M. D., Hurley, M. M., Nguyen, H. D., Nguyen, D. Q., Nguyen, D. H., Santander, C. G., Sánchez Barreiro, F., Gomes Martins, N. F., et al. (2025) · Cell · doi:10.1016/j.cell.2025.03.040 · Cited by 10 · see citing works
Chromosomal-level reference genome assembly of the North American wolverine (<i>Gulo gulo luscus</i>): a resource for conservation genomics
Lok, S., Lau, T. N. H., Trost, B., Tong, A. H. Y., Wintle, R. F., Engstrom, M. D., Stacy, E., Waits, L. P., Scrafford, M., & Scherer, S. W. (2022) · G3 Genes|Genomes|Genetics · doi:10.1093/g3journal/jkac138 · Cited by 6 · see citing works
Chromosomal-level reference genome assembly of muskox (Ovibos moschatus) from Banks Island in the Canadian Arctic, a resource for conservation genomics
Lok, S., Lau, T. N. H., Trost, B., Tong, A. H. Y., Paton, T., Wintle, R. F., Engstrom, M. D., Gunn, A., & Scherer, S. W. (2024) · Scientific Reports · doi:10.1038/s41598-024-67270-9 · Cited by 4 · see citing works

Determining size and dispersion of minimum viable populations for land management planning and species conservation
Lehmkuhl, J. F. (1984) · Environmental Management · doi:10.1007/bf01866938 · Cited by 57 · see citing works
Metapopulation effective size and conservation genetic goals for the Fennoscandian wolf (Canis lupus) population
Laikre, L., Olsson, F. K., Jansson, E., et al. (2016) · Heredity · doi:10.1038/hdy.2016.44 · Cited by 48 · see citing works
Genetic consequences of long‐term small effective population size in the critically endangered pygmy hog
Liu, L., Bosse, M., Megens, H., de Visser, M. C., Groenen, M. A. M., & Madsen, O. (2020) · Evolutionary Applications · doi:10.1111/eva.13150 · Cited by 33 · see citing works
Demographic history and conservation genomics of caribou (Rangifer tarandus) in Québec
Dedato, M. N., Robert, C., Taillon, J., Shafer, A. B. A., & Côté, S. D. (2022) · Evolutionary Applications · doi:10.1111/eva.13495 · Cited by 17 · see citing works
Prediction of the minimum effective size of a population viable in the long term
Pérez-Pereira, N., Wang, J.-L., Quesada, H., & Caballero, A. (2022) · Biodiversity and Conservation · doi:10.1007/s10531-022-02456-z · Cited by 42 · see citing works

Authors: Hohenlohe, P. A., Funk, W. C., & Rajora, O. P.
Affiliations: University of Idaho (US)
Colorado State University (US)
University of New Brunswick (CA)
Corresponding author: Hohenlohe, Paul A.
ORCID: Hohenlohe, Paul A.
Funk, W. Chris
Venue: Molecular Ecology
Publisher: Wiley
Published: 2020-11-18
Volume: 30
Issue: 1
Pages: 62-82
ISSN: 0962-1083 (ISSN-L)
1365-294X
DOI: 10.1111/mec.15720
PMC: PMC7894518
OpenAlex: W3095529345
Cited by: 702
References: 168
Citations by year: 2026: 137 · 2025: 144 · 2024: 138 · 2023: 127 · 2022: 112 · 2021: 38 · 2020: 3 · 2019: 1 · 2017: 1
FWCI: 10.01
Type: journal article
Language: en
Open access: hybrid
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0/ (vor)
Locations: Molecular Ecology (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
Physical Sciences › Environmental Science › Ecology › Wildlife Ecology and Conservation
Keywords: population genomics, wildlife conservation, wildlife management, effective population size, inbreeding, demographic history, population structure, inbreeding depression, adaptation to environmental change, adaptive genetic variation, non-model organisms
MeSH terms: Animals, Animals, Wild, Conservation of Natural Resources, Genetics, Population, Biodiversity, Metagenomics

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Population genomics for wildlife conservation and management

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