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

Humble, Emily; Dobrynin, Pavel; Senn, Helen; Chuven, Justin; Scott, Alan F.; Mohr, David; Dudchenko, Olga; Omer, Arina D.; Colaric, Zane; Aiden, E; Dhaheri, Shaikha Salem Al; Wildt, David E.; Oliaji, Shireen; Tamazian, Gaik; Pukazhenthi, Budhan S.; Ogden, Rob; Koepfli, Klaus Peter

doi:10.1111/1755-0998.13181

Cited by 32 publications

(58 citation statements)

References 114 publications

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“…In addition to high‐resolution genetic diversity data, the chromosomal‐level genome assembly generated by Humble et al. (2020) also facilitates the development of single nucleotide polymorphism (SNP) genotyping arrays for effective post‐release monitoring. Humble et al.…”

Section: Figurementioning

confidence: 99%

“…Conservation is never more pressing than for a species that has gone extinct in the wild, and Humble et al. (2020) highlight how a better understanding of a species’ genome can enhance applied conservation.…”

Section: Figurementioning

confidence: 99%

“…In both zoos and private collections, populations can be more effectively managed through integrated management strategies informed by genomic data and modelling (Giglio, Ivy, Jones, & Latch, 2016;Wildt et al, 2019). As the scimitar-horned oryx reintroduction programme continues and populations become established, SNP arrays developed from the genomic resources presented in Humble et al (2020) can be used to effectively monitor wild populations. Conservation is never more pressing than for a species that has gone extinct in the wild, and Humble et al (2020) highlight how a better understanding of a species' genome can enhance applied conservation.…”

mentioning

confidence: 99%

“…As the scimitar-horned oryx reintroduction programme continues and populations become established, SNP arrays developed from the genomic resources presented in Humble et al (2020) can be used to effectively monitor wild populations. Conservation is never more pressing than for a species that has gone extinct in the wild, and Humble et al (2020) highlight how a better understanding of a species' genome can enhance applied conservation.…”

mentioning

confidence: 99%

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Integrating genomics into conservation management

Latch

2020

Molecular Ecology Resources

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Reintroductions are a powerful tool in species conservation. Hundreds of species have benefited from reintroductions, and they have been effective in curbing the accelerating loss of biodiversity (Soorae, 2018, Brichieri-Colombi and Moehrenschlager 2019). The ultimate goal of a reintroduction is to attain long-term persistence without human intervention. Genetic diversity is central to this goal, contributing to a species' adaptive potential and promoting biodiversity and ecosystem integrity. Seeded with abundant genetic diversity, a reintroduced population can grow and become self-sustaining. Initial sampling of founders is a critical component of population establishment. Founding a reintroduction with a large number of unrelated individuals maximizes genetic diversity and provides a solid foundation for a successful reintroduction. Mixing founders from genetically differentiated source populations can better represent species-wide genetic variation (McLennan, Grueber, Wise, Belov, & Hogg, 2020; Ralls et al., 2018). To identify valuable source populations and develop a plan to sample them, it is necessary to survey potential source populations. Surveys naturally include any remnant populations in the wild, and frequently incorporate studbook-managed captive populations (e.g., in zoos). Zoo-based captive breeding programmes aim to maintain gene diversity in populations over the long term through prioritized pairings that minimize mean kinship and thus sustain a valuable reservoir of genetic variation. Broadening our view to consider the entire in situ/ex situ spectrum reveals the potential value of semicaptive populations in private collections or ranches. These animals are typically managed using less stringent (or no) genetic management practices compared to zoo breeding programmes, yet they conceivably represent an untapped reservoir of genetic variation for conservation management. Humble et al. (2020) apply a genomics approach to survey genetic variation in source populations of the scimitar-horned oryx (Oryx dammah), a species declared extinct in the wild (Figure 1). Captive populations exist in European, North American and Australian zoos, but most remaining animals are held within

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Section: Figurementioning

confidence: 99%

Section: Figurementioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Integrating genomics into conservation management

Latch

2020

Molecular Ecology Resources

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“…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.…”

Section: Lessons From the Genome Of A Species With Extraordinary Inbrmentioning

confidence: 99%

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

Escoda

Castresana

2020

Preprint

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The Pyrenean desman (Galemys pyrenaicus) is a small semiaquatic mammal endemic to the Iberian Peninsula. Despite its limited range, this species presents a strong genetic structure due to past isolation in glacial refugia and subsequent bottlenecks. Additionally, some populations are highly fragmented today as a consequence of river barriers, causing substantial levels of inbreeding. These features make the Pyrenean desman a unique model in which to study the genomic footprints of differentiation, bottlenecks and extreme isolation in an endangered species. The complete genome of the Pyrenean desman was assembled using a Bloom filter-based approach. An analysis of the 1.83 Gb reference genome and the sequencing of five additional individuals from different evolutionary units allowed us to detect its main genomic characteristics. The population differentiation of the species was reflected in highly distinctive demographic trajectories. A severe population bottleneck during the postglacial recolonization of the eastern Pyrenees created the lowest genomic heterozygosity ever recorded in a mammal. Moreover, isolation and inbreeding gave rise to a high proportion of runs of homozygosity (ROH). Despite these extremely low levels of genetic diversity, two key multigene families from an eco-evolutionary perspective that need to be genetically variable, the major histocompatibility complex and olfactory receptor genes, showed heterozygosity excess in the majority of individuals. Furthermore, these two classes of genes were significantly less abundant than expected within ROH. These results allow us to characterize important genomic health indicators for each individual, information that may be crucial for the conservation and management of the species.

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