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.

The impact of bottlenecks and inbreeding on the genome of the endangered Pyrenean desman

“…This ~25% underestimation is probably due to the fact that ddRAD does not capture the most divergent genome sequences. However, the comparative value of heterozygosity rates estimated with ddRAD remains valid, as seen in other works (Wright et al 2020).…”

“…Genomics can help to not only determine which specimens may be more or less appropriate for genetic rescue or captive breeding according to specific genomic health indicators of each individual (Supple and Shapiro 2018;Humble et al 2020;Wright et al 2020), but also to monitor future individuals sampled after the conservation actions to confirm if the measures employed are helping to improve the impoverished genomic health of the Pyrenean desman.…”

Fifty Years of Research on European Mink Mustela lutreola L., 1761 Genetics: Where Are We Now in Studies on One of the Most Endangered Mammals?

“…Conservation genomics helped to identify the conservation implications of admixture in the Eastern wolf Canis lupus lycaon [ 165 ]. Wright et al [ 174 ] identified several candidate genes that may be associated with variation in the breeding success of the Tasmanian devil Sarcophilus harrisii . From the M. lutreola population genetics perspective, the same research demonstrated that individual heterozygosity was not associated with breeding success in captivity but was negatively associated with litter sizes of breeding females [ 174 ].…”

Navigating spaces between conservation research and practice: Are we making progress?

“…Some workshop participants did not believe spatial mismatch is as much of an issue in 2019 as in 2014, likely because local‐level research is increasingly being translated into other contexts and at larger scales. For example, the Australasian Genomics Wildlife Group works to generate species‐specific conservation outcomes, such as for the Tasmanian devil, while also being recognized as a global leader for translating genomic tools to threatened species management around the world (Wright et al., 2020). Likewise, genomics studies of salmonid species demonstrate a range of successful research–practice collaborations that are context relevant while also providing translatable global insights (Garner et al., 2016; Piccolo, 2016).…”