The crucial role of genome-wide genetic variation in conservation

Proceedings of the National Academy of Sciences, Journal Year: 2021, Volume and Issue: 118(48)

Published: Nov. 12, 2021

The unprecedented rate of extinction calls for efficient use genetics to help conserve biodiversity. Several recent genomic and simulation-based studies have argued that the field conservation biology has placed too much focus on conserving genome-wide genetic variation, should instead managing subset functional variation is thought affect fitness. Here, we critically evaluate feasibility likely benefits this approach in conservation. We find population theory empirical results show generally best prevent inbreeding depression loss adaptive potential from driving populations toward extinction. Focusing efforts presumably will only be feasible occasionally, often misleading, counterproductive when prioritized over variation. Given increasing habitat other environmental changes, failure recognize detrimental effects lost long-term viability worsen biodiversity crisis.

Language: Английский

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The long‐standing significance of genetic diversity in conservation

Molecular Ecology, Journal Year: 2021, Volume and Issue: 30(17), P. 4147 - 4154

Published: July 1, 2021

Abstract Since allozymes were first used to assess genetic diversity in the 1960s and 1970s, biologists have attempted characterize gene pools conserve observed domestic crops, livestock, zoos (more recently) natural populations. Recently, some authors claimed that importance of conservation biology has been greatly overstated. Here, we argue a voluminous literature indicates otherwise. We address four main points made by detractors diversity's role using published firmly establish is intimately tied evolutionary fitness, associated demographic consequences are paramount many efforts. think responsible management Anthropocene should, whenever possible, include ecosystems, communities, populations individuals, their underlying diversity.

Language: Английский

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Genetic load: genomic estimates and applications in non-model animals

Nature Reviews Genetics, Journal Year: 2022, Volume and Issue: 23(8), P. 492 - 503

Published: Feb. 8, 2022

Language: Английский

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Landscape Genomics to Enable Conservation Actions: The California Conservation Genomics Project

Journal of Heredity, Journal Year: 2022, Volume and Issue: 113(6), P. 577 - 588

Published: April 8, 2022

Abstract The California Conservation Genomics Project (CCGP) is a unique, critically important step forward in the use of comprehensive landscape genetic data to modernize natural resource management at regional scale. We describe CCGP, including all aspects project administration, collection, current progress, and future challenges. CCGP will generate, analyze, curate single high-quality reference genome 100–150 resequenced genomes for each 153 species projects (representing 235 individual species) that span ecological phylogenetic breadth California’s marine, freshwater, terrestrial ecosystems. resulting portfolio roughly 20 000 be analyzed with identical informatic genomic pipelines, providing overview hotspots within-species diversity, potential realized corridors connecting these hotspots, regions reduced diversity requiring rescue, distribution variation critical rapid climate adaptation. After 2 years concerted effort, full funding ($12M USD) has been secured, identified, funds distributed 68 laboratories 114 investigators drawn from 10 University campuses. remaining phases include completion collection analyses, delivery inferences state federal regulatory agencies help stabilize declines. aspirational goals are identify geographic long-term preservation biodiversity, prioritize those based on defensible criteria, provide foundational knowledge informs strategies both ecosystem levels.

Language: Английский

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Purging and accumulation of genetic load in conservation

Trends in Ecology & Evolution, Journal Year: 2023, Volume and Issue: 38(10), P. 961 - 969

Published: June 19, 2023

Our ability to assess the threat posed by genetic load small and declining populations has been greatly improved advances in genome sequencing computational approaches. Yet, considerable confusion remains around definitions of its dynamics, how they impact individual fitness population viability. We illustrate both selective purging drift affect distribution deleterious mutations during size decline recovery. show this impacts composition load, affects extinction risk recovery potential populations. propose a framework examine dynamics advocate for introduction estimates management endangered

Language: Английский

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Genetic load has potential in large populations but is realized in small inbred populations

Evolutionary Applications, Journal Year: 2021, Volume and Issue: 14(6), P. 1540 - 1557

Published: March 8, 2021

Abstract Populations with higher genetic diversity and larger effective sizes have greater evolutionary capacity (i.e., adaptive potential) to respond ecological stressors. We are interested in how the variation captured protein‐coding genes fluctuates relative overall genomic whether smaller populations suffer costs due their load of deleterious mutations compared populations. analyzed individual whole‐genome sequences ( N = 74) from three different Montezuma quail Cyrtonyx montezumae ), a small ground‐dwelling bird that is sustainably harvested some portions its range but conservation concern elsewhere. Our historical demographic results indicate United States exhibit low levels large part long‐term declines population over nearly million years. The more isolated Texas significantly inbred than Arizona intermediate‐sized New Mexico we surveyed. gene pool has proportion strongly variants segregating pool. demonstrate even populations, highly effectively purged and/or lost drift. However, find realized elevated because inbreeding coupled frequency slightly manifested homozygotes. Overall, our study illustrates genomics can be used proactively assess both neutral functional aspects contemporary framework while simultaneously considering deeper histories.

Language: Английский

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What Have We Learned from the First 500 Avian Genomes?

Annual Review of Ecology Evolution and Systematics, Journal Year: 2021, Volume and Issue: 52(1), P. 611 - 639

Published: Sept. 9, 2021

The increased capacity of DNA sequencing has significantly advanced our understanding the phylogeny birds and proximate ultimate mechanisms molding their genomic diversity. In less than a decade, number available avian reference genomes to over 500—approximately 5% bird diversity—placing in privileged position advance fields phylogenomics comparative, functional, population genomics. Whole-genome sequence data, as well indels rare changes, are further resolving tree life. accumulation genomes, increasingly with long-read greatly improves resolution features such germline-restricted chromosomes W chromosome, is facilitating comparative integration genotypes phenotypes. Community-based initiatives Bird 10,000 Genomes Project Vertebrate Genome playing fundamental role amplifying coalescing vibrant international program

Language: Английский

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The impact of habitat loss and population fragmentation on genomic erosion

Conservation Genetics, Journal Year: 2023, Volume and Issue: 25(1), P. 49 - 57

Published: Aug. 8, 2023

Abstract Habitat loss and population fragmentation pose severe threats to biodiversity the survival of many species. Population isolation decline in effective size lead increased genetic drift inbreeding. In turn, this reduces neutral diversity, it also affects load deleterious mutations. Here, we analyse effect such genomic erosion by designing a spatially explicit, individual based model SLiM, simulating effects recorded habitat Mauritius over past ~ 250 years. We show that diversity (genome-wide heterozygosity) was barely noticeable during first 100 years loss. Changes took even more time register, they only became apparent circa 200 after start decline. Although considerable number mutations were lost drift, others frequency. The masked thus converted into realised load, which compromised fitness viability much native had been lost. Importantly, continued metapopulation stabilised at low numbers. Our study shows historic can sustained threat populations future generations, without further UN’s Decade on Ecosystem Restoration needs transformative change save species from extinction, requires urgent restoration natural habitats.

Language: Английский

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

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(18)

Published: April 25, 2023

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

Language: Английский

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Species-wide genomics of kākāpō provides tools to accelerate recovery

Nature Ecology & Evolution, Journal Year: 2023, Volume and Issue: 7(10), P. 1693 - 1705

Published: Aug. 28, 2023

Language: Английский

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