Biology subjects

Chuven, J.

Publications and source records attributed to Chuven, J..

3 recordsLinked to original sources

bioRxiv2022

Genetic diversity in global populations of the Critically Endangered addax (Addax nasomaculatus) and its implications for conservation

Threatened species are frequently patchily distributed across small wild populations, ex situ populations managed with varying levels of intensity, and reintroduced populations. Best practice advocates for integrated management across in situ and ex situ populations. Wild addax (Addax nasomaculatus) now number fewer than 100 individuals, yet thousands of addax remain in ex situ populations, which can provide addax for reintroductions, as has been the case in Tunisia in the mid-1980s. However, integrated management requires genetic data to ascertain the relationships between wild and ex situ populations that have incomplete knowledge of founder origins, management histories and pedigrees. We undertook a global assessment of genetic diversity across wild, ex situ, and reintroduced populations in Tunisia to assist conservation planning for this Critically Endangered species. We show that the remnant wild populations retain more mitochondrial haplotypes which are more evolutionarily diverse than the entirety of the ex situ populations across Europe, North America and the United Arab Emirates, and the reintroduced Tunisian population. Additionally, 1704 SNPs revealed that whilst population structure within the ex situ population is minimal, each population carries unique diversity. Finally, we show that careful selection of founders and subsequent genetic management is vital to ensure genetic diversity is provided to, and minimise drift and inbreeding within, reintroductions. Our results highlight a vital need to conserve the last remaining wild addax population, and we provide a genetic foundation for determining integrated conservation strategies to prevent extinction and optimise future reintroductions.

genetics↗

bioRxiv2022

Conservation management strategy impacts inbreeding and genetic load in scimitar-horned oryx

In an age of habitat loss and overexploitation, small populations, both captive and wild, are increasingly facing the effects of isolation and inbreeding. Genetic management has therefore become a vital tool for ensuring population viability. However, little is known about how the type and intensity of intervention shape the genomic landscape of inbreeding and mutation load. We address this using whole genome sequence data of scimitar-horned oryx (Oryx dammah), an iconic antelope that has been subject to contrasting management strategies since it was declared extinct in the wild. We show that unmanaged populations are enriched for long runs of homozygosity (ROH) and have significantly higher inbreeding coefficients than managed populations. Additionally, despite the total number of deleterious alleles being similar across management strategies, the burden of homozygous deleterious genotypes was consistently higher in unmanaged groups. These findings emphasise the risks associated with deleterious mutations through multiple generations of inbreeding. As wildlife management strategies continue to diversify, our study reinforces the importance of maintaining genome-wide variation in vulnerable populations and has direct implications for one of the largest reintroduction attempts in the world. Significance statementConservation genetic management is becoming increasingly important for safeguarding and restoring wildlife populations. Understanding how the intensity of intervention influences genomic components of fitness is therefore essential for supporting species viability. We investigate the impact of contrasting management strategies on the genomic landscape of inbreeding and mutation load in captive populations of scimitar-horned oryx. We reveal how several decades of management have prevented the formation of long runs of homozygosity and masked the expression of deleterious mutations. Our findings highlight the dynamics between inbreeding, mutation load and population size and have direct implications for future management of threatened species.

evolutionary biology↗

bioRxiv2019

Chromosomal-level genome assembly of the scimitar-horned oryx: insights into diversity and demography of a species extinct in the wild

Captive populations provide a valuable insurance against extinctions in the wild. However, they are also vulnerable to the negative impacts of inbreeding, selection and drift. Genetic information is therefore considered a critical aspect of conservation management planning. Recent developments in sequencing technologies have the potential to improve the outcomes of management programmes however, the transfer of these approaches to applied conservation has been slow. The scimitar-horned oryx (Oryx dammah) is a North African antelope that has been extinct in the wild since the early 1980s and is the focus of a long-term reintroduction project. To enable the selection of suitable founder individuals, facilitate post-release monitoring and improve captive breeding management, comprehensive genomic resources are required. Here, we used 10X Chromium sequencing together with Hi-C contact mapping to develop a chromosomal-level genome assembly for the species. The resulting assembly contained 29 chromosomes with a scaffold N50 of 100.4 Mb, and displayed strong chromosomal synteny with the cattle genome. Using resequencing data from six additional individuals, we demonstrated relatively high genetic diversity in the scimitar-horned oryx compared to other mammals, despite it having experienced a strong founding event in captivity. Additionally, the level of diversity across populations varied according to management strategy. Finally, we uncovered a dynamic demographic history that coincided with periods of climate variation during the Pleistocene. Overall, our study provides a clear example of how genomic data can uncover valuable insights into captive populations and contributes important resources to guide future management decisions of an endangered species.

genomics↗