Cited by 71Genetic diversity and population structureGenetic and phenotypic traits in livestockGenetic Mapping and Diversity in Plants and Animals

A demonstration of conservation genomics for threatened species management

Wright, Belinda R., Farquharson, Katherine A., McLennan, Elspeth A., Belov, Katherine, Hogg, Carolyn J., Grueber, Catherine E.·2020·Molecular Ecology Resources

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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Crossref · 10.1111/1755-0998.13211

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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.
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
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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