Genetic rescue without genomic swamping in wild populations

Fitzpatrick, Sarah W.; Bradburd, Gideon S.; Kremer, Colin T.; Salerno, Patricia E.; Angeloni, Lisa M.; Funk, W. Chris

doi:10.1101/701706

Cited by 10 publications

(10 citation statements)

References 39 publications

(52 reference statements)

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“…Studies of selection in contemporary hybridizing populations offer another route to merge pattern and process, and to tease apart forms of selection acting in admixed populations. For example, Chen et al, 2019 ; Chen et al, 2016 and Fitzpatrick, 2019 studied weakly differentiated populations and found that genome-wide selection broadly favored ancestry derived from migrants in small populations, consistent with the idea that in small populations foreign ancestry can be favored to lighten the genetic load. In contrast, we recently found little evidence that hybridization load shapes genome-wide ancestry in hybrid swordtail populations formed between species with substantial differences in historical effective population size ( Schumer et al, 2018 ).…”

Section: Ways Forwardmentioning

confidence: 53%

The genomic consequences of hybridization

Moran

Payne

Langdon

et al. 2021

eLife

169

189

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In the past decade, advances in genome sequencing have allowed researchers to uncover the history of hybridization in diverse groups of species, including our own. Although the field has made impressive progress in documenting the extent of natural hybridization, both historical and recent, there are still many unanswered questions about its genetic and evolutionary consequences. Recent work has suggested that the outcomes of hybridization in the genome may be in part predictable, but many open questions about the nature of selection on hybrids and the biological variables that shape such selection have hampered progress in this area. We synthesize what is known about the mechanisms that drive changes in ancestry in the genome after hybridization, highlight major unresolved questions, and discuss their implications for the predictability of genome evolution after hybridization.

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Section: Ways Forwardmentioning

confidence: 53%

The genomic consequences of hybridization

Moran

Payne

Langdon

et al. 2021

eLife

169

189

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“…Potential concerns about outbreeding depression and/or genomic swamping of the AENP buffalo population following this proposed genetic supplementation could be alleviated by considering the current support for an estimated short time since isolation (~100 years) [ 17 , 49 ] and by conducting regular genetic monitoring of the population. Furthermore, recent studies showed local genes, and alleles related to local adaptation, were maintained in the recipient population after genetic supplementation, while the benefits of genetic rescue were still observed [ 50 – 52 ].…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity, relatedness and inbreeding of ranched and fragmented Cape buffalo populations in southern Africa

2020

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Wildlife ranching, although not considered a conventional conservation system, provides a sustainable model for wildlife utilization and could be a source of valuable genetic material. However, increased fragmentation and intensive management may threaten the evolutionary potential and conservation value of species. Disease-free Cape buffalo (Syncerus caffer caffer) in southern Africa exist in populations with a variety of histories and management practices. We compared the genetic diversity of buffalo in national parks to private ranches and found that, except for Addo Elephant National Park, genetic diversity was high and statistically equivalent. We found that relatedness and inbreeding levels were not substantially different between ranched populations and those in national parks, indicating that breeding practices likely did not yet influence genetic diversity of buffalo on private ranches in this study. High genetic differentiation between South African protected areas highlighted their fragmented nature. Structure analysis revealed private ranches comprised three gene pools, with origins from Addo Elephant National Park, Kruger National Park and a third, unsampled gene pool. Based on these results, we recommend the Addo population be supplemented with disease-free Graspan and Mokala buffalo (of Kruger origin). We highlight the need for more research to characterize the genetic diversity and composition of ranched wildlife species, in conjunction with wildlife ranchers and conservation authorities, in order to evaluate the implications for management and conservation of these species across different systems.

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“…Whether characterized using reduced-representation sequence data or whole-genome sequence (WGS) data, SNP-based estimates of genome-wide diversity are being used to better inform conservation by delineating species (e.g., Quattrini et al, 2019;but see Stanton et al, 2019), detecting hybridisation and introgression (Dufresnes & Dubey, 2020;Peters et al, 2016; but see Forsdick et al, 2021 preprint;Hauser, Athrey, & Leberg, 2021 preprint), identifying conservation units (e.g., Liddell et al, 2020), identifying source populations for conservation translocations (e.g., Dresser, Ogle, & Fitzpatrick, 2017), and guiding conservation breeding programs (e.g., Galla et al, 2020;Wright et al, 2020). Beyond genome-wide diversity, there is a growing consensus around the importance of considering functional genomic diversity in conservation management (Fitzpatrick et al, 2020;Hoelzel, Bruford, & Fleischer, 2019;S. Li et al, 2014;Willi, Van Buskirk, & Hoffmann, 2006).…”

Section: Structural Variants: a New Tool In The Conservation Genomics Toolboxmentioning

confidence: 99%

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

Wold

Galla

Santure

et al. 2021

Preprint

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Structural variants (SVs) are large rearrangements (> 50 bp) within the genome that impact the form and structure of chromosomes. As a result, SVs are a significant source of functional genomic diversity, i.e. variation at genomic regions underpinning phenotype differences, that can have large effects on individual and population fitness. While there are increasing opportunities to investigate functional genomic diversity in threatened species via single nucleotide polymorphism (SNP) datasets, SVs remain understudied despite their potential influence on complex traits of conservation interest. In this future-focused Opinion, we contend that characterizing SVs offers the conservation genomics community an exciting opportunity to complement SNP-based approaches to enhance species recovery. We identify three critical resources to characterize SVs de novo: 1) High-quality, contiguous, annotated reference genome(s); 2) Whole genome resequence data from representative individuals of the target species/populations; and 3) Well-curated metadata including pedigrees. We also leverage the existing literature–predominantly in human health, agriculture and eco-evol biology–to identify pangenomic approaches for readily characterizing SVs and consider how integrating these into the conservation genomics toolbox may transform the way we intensively manage some of the world’s most threatened species.

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Genetic rescue without genomic swamping in wild populations

Cited by 10 publications

References 39 publications

The genomic consequences of hybridization

The genomic consequences of hybridization

Genetic diversity, relatedness and inbreeding of ranched and fragmented Cape buffalo populations in southern Africa

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

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