A demonstration of conservation genomics for threatened species management
Abstract
As species extinction rates increase, genomics provides a powerful tool to support intensive management of threatened species. We use the Tasmanian devil (Sarcophilus harrisii) to demonstrate how conservation genomics can be implemented in threatened species management. We conducted whole genome sequencing (WGS) of 25 individuals from the captive breeding programme and reduced‐representation sequencing (RRS) of 98 founders of the same programme. A subset of the WGS samples was also sequenced by RRS, allowing us to directly compare genome‐wide heterozygosity with estimates from RRS data. We found good congruence in interindividual variation and gene‐ontology classifications between the two data sets, indicating that our RRS data reflect the genome well. We also attempted genome‐wide association studies with both data sets (regarding breeding success), but the genomic data suffered from small sample size, while the RRS data suffered from lack of precision, highlighting a key trade‐off in the design of conservation genomic research. Nevertheless, we identified a number of candidate genes that may be associated with variation in breeding success. Individual heterozygosity, as measured by WGS or RRS, was not associated with breeding success in captivity but was negatively associated with litter sizes of breeding females in the RRS data set. Our findings enable conservation managers to have confidence in RRS data while understanding its limitations, and provide avenues for further investigation into which processes underlie variation in breeding success in captive Tasmanian devils. We caution, however, that deep functional insights using RRS may be impaired by a lack of precision, especially when marker density is low.
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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 [86]
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González‐Pech, R. A., Stephens, T. G., Chen, Y., Mohamed, A. R., Cheng, Y., Shah, S., Dougan, K. E., Fortuin, M. D. A., Lagorce, R., Burt, D. W., et al. (2021) · BMC Biology · doi:10.1186/s12915-021-00994-6 · Cited by 110 · see citing works
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Self-citationNavigating spaces between conservation research and practice: Are we making progress?
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GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species
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Self-citationIannucci, A., Benazzo, A., Natali, C., Arida, E. A., Zein, M. S. A., Jessop, T. S., Bertorelle, G., & Ciofi, C. (2021) · Molecular Ecology · doi:10.1111/mec.16121 · Cited by 30 · see citing works
von Takach, B., Ranjard, L., Burridge, C. P., Cameron, S. F., Cremona, T., Eldridge, M. D. B., Fisher, D. O., Frankenberg, S., Hill, B. M., Hohnen, R., et al. (2022) · Molecular Ecology · doi:10.1111/mec.16680 · Cited by 30 · see citing works
Vekemans, X., Castric, V., Hipperson, H., Müller, N. A., Westerdahl, H., & Cronk, Q. (2021) · Molecular Ecology · doi:10.1111/mec.16020 · Cited by 29 · see citing works
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Podsiadłowski, L., Tunström, K., Espeland, M., & Wheat, C. W. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evab122 · Cited by 28 · see citing works
Big Data in Conservation Genomics: Boosting Skills, Hedging Bets, and Staying Current in the Field
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Tao, Y., Chen, B., Kang, M., Liu, Y., & Wang, J. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.717200 · Cited by 25 · see citing works
Genomic signatures of inbreeding in a critically endangered parrot, the kākāpō
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Escoda, L., & Castresana, J. (2021) · Evolutionary Applications · doi:10.1111/eva.13249 · Cited by 23 · see citing works
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Bock, S. L., Smaga, C. R., McCoy, J. A., & Parrott, B. B. (2022) · Molecular Ecology · doi:10.1111/mec.16670 · Cited by 24 · see citing works
Batley, K. C., Sandoval‐Castillo, J., Kemper, C. M., Zanardo, N., Tomo, I., Beheregaray, L. B., & Möller, L. M. (2021) · Molecular Ecology · doi:10.1111/mec.15873 · Cited by 22 · see citing works
A reference genome for the critically endangered woylie, Bettongia penicillata ogilbyi
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Self-citationBaveja, P., Garg, K. M., Chattopadhyay, B., Sadanandan, K. R., Prawiradilaga, D. M., Yuda, P., Lee, J. G. H., & Rheindt, F. E. (2020) · Evolutionary Applications · doi:10.1111/eva.13149 · Cited by 21 · see citing works
Teixeira, T. M., & Nazareno, A. G. (2021) · Frontiers in Plant Science · doi:10.3389/fpls.2021.730258 · Cited by 20 · see citing works
Skorupski, J. (2020) · Genes · doi:10.3390/genes11111332 · Cited by 20 · see citing works
Preadapted to adapt: underpinnings of adaptive plasticity revealed by the downy brome genome
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Self-citationA Chromosome-Scale Hybrid Genome Assembly of the Extinct Tasmanian Tiger ( Thylacinus cynocephalus )
Feigin, C. Y., Frankenberg, S., & Pask, A. J. (2022) · Genome Biology and Evolution · doi:10.1093/gbe/evac048 · Cited by 18 · see citing works
Mochales‐Riaño, G., Fontsere, C., de Manuel, M., Talavera, A., Burriel‐Carranza, B., Tejero‐Cicuéndez, H., AlGethami, R. H. M., Shobrak, M. Y., Marquès‐Bonet, T., & Carranza, S. (2023) · iScience · doi:10.1016/j.isci.2023.107481 · Cited by 18 · see citing works
Metapopulation management of a critically endangered marsupial in the age of genomics
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Self-citationGenomic Approaches for Conservation Management in Australia under Climate Change
Onley, I. R., Moseby, K. E., & Austin, J. J. (2021) · Life · doi:10.3390/life11070653 · Cited by 21 · see citing works
la Puente, A. B., Ventura, J., Miñarro, M., Somoano, A., Hey, J., & Castresana, J. (2022) · Scientific Reports · doi:10.1038/s41598-022-07877-y · Cited by 17 · see citing works
Zhang, S., Li, C., Li, Y., Chen, Q., Hu, D., Cheng, Z., Wang, X. L., Shan, Y., Bai, J., & Liu, G. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.705337 · Cited by 14 · see citing works
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Wit, J., Workentine, M. L., Redman, E., Laing, R., Stevens, L., Cotton, J. A., Chaudhry, U. N., Ali, Q., Andersen, E. C., Yeaman, S., et al. (2022) · International Journal for Parasitology · doi:10.1016/j.ijpara.2022.07.004 · Cited by 9 · see citing works
Benefit-Sharing by Design: A Call to Action for Human Genomics Research
Cartney, A. M. M., Scholz, A. H., Groussin, M., & Staunton, C. (2024) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-021623-104241 · Cited by 9 · see citing works
Chen, S. H., Yap, J. S., Viler, V., Stehn, C., Sandhu, K. S., Percival, J., Pegg, G. S., Menzies, T., Jones, A., Guo, K., et al. (2025) · Molecular Ecology · doi:10.1111/mec.70030 · Cited by 9 · see citing works
Conservation genomics of urban populations of Streamside Salamander (Ambystoma barbouri)
Hubbs, N. W., Hurt, C. R., Niedzwiecki, J. H., Leckie, B., & Withers, D. I. (2022) · PLoS ONE · doi:10.1371/journal.pone.0260178 · Cited by 8 · see citing works
Characterization of reproductive gene diversity in the endangered Tasmanian devil
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Bužan, E., de Guttry, C., Bortoluzzi, C., Street, N. R., Lucek, K., Rosling, A., Ometto, L., Mouton, A., Marins, L. S., Ruiz‐López, M. J., et al. (2025) · Molecular Ecology · doi:10.1111/mec.70001 · Cited by 15 · see citing works
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
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Haplotype-resolved genome and population genomics of the threatened garden dormouse in EuropePreprint
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Genomic Erosion Through the Lens of Comparative GenomicsPreprint
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Seven reasons why threatened species managers must consider genetic health
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Olawoye, O. O., Salami, K. K., Azeez, A., Adebola, P., Sarimiye, T. F., Imaledo, J. A., Realini, T., Hauser, M. A., & Ashaye, A. O. (2022) · PLoS ONE · doi:10.1371/journal.pone.0278286 · Cited by 3 · see citing works
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Evolutionary genetics of translocated island populations of birds: data and opportunities
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Optimized In Vitro Restriction Digestion Protocol for Preparing Maize and Barley ddRAD-Seq Libraries
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Comparing the methods in sample collection and storage for genomic research
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- Authors
- Wright, B. R., Farquharson, K. A., McLennan, E. A., Belov, K., Hogg, C. J., & Grueber, C. E.
- Affiliations
- The University of Sydney (AU)
- Corresponding author
- Grueber, Catherine E.
- ORCID
- Venue
- Molecular Ecology Resources
- Publisher
- Wiley
- Published
- 2020-07-24
- Volume
- 20
- Issue
- 6
- Pages
- 1526-1541
- ISSN
- 1755-098X (ISSN-L)
- 1755-0998
- OpenAlex
- W3036313957
- Cited by
- 69
- References
- 101
- Citations by year
- 2026: 1 · 2025: 12 · 2024: 7 · 2023: 5 · 2022: 19 · 2021: 19 · 2020: 6
- FWCI
- 7.48
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- Locations
- Molecular Ecology Resources (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Australian Research Council (DP170101253, LP140100508)
- 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
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- conservation genomics, Tasmanian devil, threatened species management, captive breeding programs, reduced representation sequencing, whole genome sequencing, heterozygosity, genome-wide association study, breeding success, litter size, candidate genes, marker density, small sample size
- MeSH terms
- Animals, Conservation of Natural Resources, Female, Marsupialia, Genome, Genomics, Genetic Association Studies, Endangered Species
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