Characterization of reproductive gene diversity in the endangered Tasmanian devil

Brandies, Parice A.; Wright, Belinda; Hogg, Carolyn J.; Grueber, Catherine E.; Belov, Katherine

doi:10.1111/1755-0998.13295

Cited by 8 publications

(9 citation statements)

References 87 publications

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“…The SNP diversity is considered to re ect the genetic diversity of the population (Brandies et al 2021). Thus, preserving SNPs is one way to increase the long-term survival of the population.…”

Section: Single-nucleotide Polymorphism Composition Between Subpopula...mentioning

confidence: 99%

Evaluating the importance of translocations in rescuing the genetic diversity of the endemic Saimaa ringed seal

Sundell

Kammonen

Mustanoja

et al. 2022

Preprint

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Fragmentation of isolated populations increases the risk of inbreeding and loss of genetic diversity. The endemic Saimaa ringed seal (Pusa hispida saimensis) is one of the most endangered pinnipeds in the world with a population of only ~400 individuals. The current genetic diversity of this subspecies, isolated in Lake Saimaa in Finland for ca. 1,000 generations, is alarmingly low. The population is further divided into semi-isolated subpopulations in the labyrinthine landscape of the lake, which exposes the population to deleterious genomic effects. We performed whole-genome sequencing on Saimaa ringed seals (N=30) and analyzed the level of homozygosity and genetic composition across the individual genomes. Our results show that the Saimaa ringed seal population has a high number of runs of homozygosity (RoH) compared with the neighboring Baltic ringed seal (Pusa hispida botnica) reference population (p<0.001). We found a general signal of differentiation in homozygosity within Lake Saimaa subpopulations (p<0.05) and detected thousands of unique single-nucleotide polymorphisms (SNPs) in all subpopulations. The observed high levels of inbreeding and the risk of losing indispensable SNPs may directly affect fitness in individuals. These results support augmented gene flow as a genetic conservation action. Based on our results, we recommend Pihlajavesi as a potential source and Southern Saimaa as a potential recipient subpopulation for translocating individuals. The Saimaa ringed seal is a recognized subspecies and therefore translocations should be considered only within the lake to avoid an unpredictable risk of disease, the introduction of deleterious alleles, and severe ecological issues for the population.

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Section: Single-nucleotide Polymorphism Composition Between Subpopula...mentioning

confidence: 99%

Evaluating the importance of translocations in rescuing the genetic diversity of the endemic Saimaa ringed seal

Sundell

Kammonen

Mustanoja

et al. 2022

Preprint

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“…In the genomics era, there is an opportunity to incorporate functional genomic information including SVs into conservation management. To date, functional genomics has illuminated our understanding of immunocompetence (e.g., Grogan et al, 2017;Morrison et al, 2020) and reproductive fitness (e.g., Brandies et al, 2020) in threatened species. On its own, this information provides a helpful context for how inbreeding or direct management efforts may affect the population diversity and persistence (Robinson et al 2019).…”

Section: Integrating Functional Genomics Into Applied Conservationmentioning

confidence: 99%

Expanding the conservation genomics toolbox: incorporating structural variants to enhance functional studies for species of conservation concern

Wold

Galla

Eccles

et al. 2021

Preprint

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Increased capability in the conservation genomics community, combined with decreased sequencing costs, is providing new opportunities for the application of whole-genome sequence data to enhance species recovery. Indeed, assessments of genome-wide diversity based on SNP data are already informing the conservation management of threatened species around the world. However, SNP data alone may not sufficiently capture all of the information necessary for the effective conservation management of critically endangered species that suffer from severe inbreeding depression. For threatened species that require significant intervention, it is critical that we as conservation genomicists expand our repertoire to include assessments of functional diversity. Structural variants are a likely source of functional diversity, as their frequency and genomic context affect the dosage and regulation of gene expression through mechanisms that alter genome organization and impact fitness. In this future-focused Opinion, we leverage the existing literature - predominantly focused on model and agricultural species - to identify pan-genomic and chromosomic approaches for readily characterizing structural variants and to consider how integrating these into the conservation genomics toolbox will transform the way we manage some of the world’s most threatened species.

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“…Functional variation refers to the genetic basis of phenotypic variation-traits that influence survival and reproductive fitness of individuals. While efforts have been made to characterize functional variation in model organisms, small sample sizes inherent in threatened populations, limited genomic resources (i.e., reference genomes and annotations) for non-model species, and the complexities of polygenic traits (those determined by the combination of multiple loci) remain limiting factors for broad application of these methods for species of conservation concern (but see Batley et al, 2019;Brandies et al, 2020). In a primary production context where specific traits are targeted in breeding programmes, pedigrees are used to inform a trait mapping approach to identify quantitative trait loci (QTLs), or genomic regions associated with specific phenotypic traits.…”

Section: Functional Variationmentioning

confidence: 99%

Current applications and future promise of genetic/genomic data for conservation in an Aotearoa New Zealand context

Forsdick¹,

Adams²,

Alexander³

et al. 2021

Preprint

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1.To achieve the vision outlined in the national strategy for biodiversity, Te Mana o te Taiao, we will need to unite diverse disciplines, including conservation genetics/genomics.2.As conservation genetic/genomic data generated for—and associated with—taonga (treasured) species is also taonga, we highlight the need for collaborative research partnerships that centre the needs, aspirations and expertise of mana whenua.3.As a team of predominantly early-career conservation genetics and genomics researchers working across institutions as Te Tiriti o Waitangi partners, each speaking to our own expertise, we review available and emerging tools in the conservation genetics/genomics toolbox.4.To support practitioners in identifying appropriate and affordable tools from the toolbox, we present a table that encompasses resource requirements (including finances, time, and skill) to assist conservation practitioners in assessing the associated costs and benefits of these tools for informing conservation management.5.To support researchers and practitioners in establishing long-lasting partnerships with mana whenua, we highlight key aspects of data management and data sovereignty for consideration.6.Intended as a platform to initiate discussion within and among conservation practitioners and researchers, mana whenua, and local communities, the development of government policies is beyond the scope of this contribution.7.To meet the vision of Te Mana o te Taiao, we conclude by calling for a transdisciplinary approach that includes conservation genetics/genomics.

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Characterization of reproductive gene diversity in the endangered Tasmanian devil

Cited by 8 publications

References 87 publications

Evaluating the importance of translocations in rescuing the genetic diversity of the endemic Saimaa ringed seal

Evaluating the importance of translocations in rescuing the genetic diversity of the endemic Saimaa ringed seal

Expanding the conservation genomics toolbox: incorporating structural variants to enhance functional studies for species of conservation concern

Current applications and future promise of genetic/genomic data for conservation in an Aotearoa New Zealand context

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