Genomic insights into the conservation status of the world’s last remaining Sumatran rhinoceros populations

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: April 26, 2021

Abstract Small populations are often exposed to high inbreeding and mutational load that can increase the risk of extinction. The Sumatran rhinoceros was widespread in Southeast Asia, but is now restricted small isolated on Sumatra Borneo, most likely extinct Malay Peninsula. Here, we analyse 5 historical 16 modern genomes from these investigate genomic consequences recent decline, such as increased load. We find Peninsula population experienced shortly before extirpation, which possibly accompanied by purging. Borneo instead show low inbreeding, currently sizes may thus near future lead depression. Moreover, little evidence for differences local adaptation among populations, suggesting depression could potentially be mitigated assisted gene flow populations.

Language: Английский

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Neutral genetic diversity as a useful tool for conservation biology

Conservation Genetics, Journal Year: 2021, Volume and Issue: 22(4), P. 541 - 545

Published: June 28, 2021

Language: Английский

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Navigating the temporal continuum of effective population size

Methods in Ecology and Evolution, Journal Year: 2021, Volume and Issue: 13(1), P. 22 - 41

Published: Oct. 20, 2021

Abstract Effective population size, Ne, is a key evolutionary parameter that determines the levels of genetic variation and efficacy selection. Estimation interpretation Ne are essential in diverse areas conservation biology, ranging from assessing potential or extinction risk to empowering research on genomic basis adaptation. The applications concept resulted largely independent methodological developments using different definitions focusing estimation either contemporary long‐term Ne. Recently, several novel approaches appeared allow temporal trends at various parts continuum. Here, we provide an overview aspects asking whether existing methods available data estimates for entire We outline apparent division into literature, review across continuum navigate reader through it pointing important biological limitations inherent procedures. Finally, examples recent future perspectives. conclude can now be inferred complementary approaches, bringing together Further rapid progress field expected wide adoption machine learning transition haplotype‐resolved data. notwithstanding, interpretational difficulties likely remain, emphasising need thorough understanding theory behind methods, their assumptions limitations.

Language: Английский

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Purging of deleterious burden in the endangered Iberian lynx

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(11)

Published: March 1, 2022

SignificanceThe dynamics of deleterious variation under contrasting demographic scenarios remain poorly understood in spite their relevance evolutionary and conservation terms. Here we apply a genomic approach to study differences the burden alleles between endangered Iberian lynx (Lynx pardinus) widespread Eurasian lynx). Our analysis unveils significantly lower former species that should be ascribed genetic purging, is, increased opportunities selection against recessive homozygotes due inbreeding caused by its smaller population size, as illustrated our analytical predictions. This research provides theoretical empirical evidence on purging certain conditions.

Language: Английский

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New developments in the field of genomic technologies and their relevance to conservation management

Conservation Genetics, Journal Year: 2021, Volume and Issue: 23(2), P. 217 - 242

Published: Nov. 11, 2021

Abstract Recent technological advances in the field of genomics offer conservation managers and practitioners new tools to explore for applications. Many these are well developed used by other life science fields, while others still development. Considering possibilities, choosing right tool(s) from toolbox is crucial can pose a challenging task. With this mind, we strive inspire, inform illuminate on how efforts benefit current genomic biotechnological revolution. inspirational case studies show technologies help resolve some main challenges, also informing implementable different are. We here focus specifically small population management, highlight potential genetic rescue, discuss opportunities gene editing with adaptation changing environments. In addition, delineate applications drives controlling invasive species. that offers added efforts, but comes limitations use novel emerging techniques.

Language: Английский

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Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(7)

Published: Feb. 7, 2023

Sea turtles represent an ancient lineage of marine vertebrates that evolved from terrestrial ancestors over 100 Mya. The genomic basis the unique physiological and ecological traits enabling these species to thrive in diverse habitats remains largely unknown. Additionally, many populations have drastically declined due anthropogenic activities past two centuries, their recovery is a high global conservation priority. We generated analyzed high-quality reference genomes for leatherback ( Dermochelys coriacea ) green Chelonia mydas turtles, representing extant sea turtle families. These are highly syntenic homologous, but localized regions noncollinearity were associated with higher copy numbers immune, zinc-finger, olfactory receptor (OR) genes ORs related waterborne odorants greatly expanded turtles. Our findings suggest divergent evolution key gene families may underlie immunological sensory adaptations assisting navigation, occupancy neritic versus pelagic environments, diet specialization. Reduced collinearity was especially prevalent microchromosomes, greater content, heterozygosity, genetic distances between species, supporting critical role vertebrate evolutionary adaptation. Finally, diversity demographic histories starkly contrasted indicating had low yet stable effective population size, exhibit extremely compared other reptiles, harbor load reinforcing concern persistence under future climate scenarios. provide invaluable resources advancing our understanding best practices imperiled lineage.

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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Selection, recombination and population history effects on runs of homozygosity (ROH) in wild red deer (Cervus elaphus)

Heredity, Journal Year: 2023, Volume and Issue: 130(4), P. 242 - 250

Published: Feb. 17, 2023

The distribution of runs homozygosity (ROH) may be shaped by a number interacting processes such as selection, recombination and population history, but little is known about the importance these mechanisms in shaping ROH wild populations. We combined an empirical dataset >3000 red deer genotyped at >35,000 genome-wide autosomal SNPs evolutionary simulations to investigate influence each factors on ROH. assessed focal comparison effect history. investigated role using both physical map genetic linkage search for found differences between populations types indicating that history local rate have Finally, we ran forward with varying histories, rates levels allowing us further interpret our data. These showed has greater than either or selection. show selection can cause genomic regions where common, only when effective size (N

Language: Английский

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Whole‐Genome Evaluation of Genetic Rescue: The Case of a Curiously Isolated and Endangered Butterfly

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 27, 2025

Genetic rescue, or the translocation of individuals among populations to augment gene flow, can help ameliorate inbreeding depression and loss adaptive potential in small isolated populations. rescue is currently under consideration for an endangered butterfly Canada, Half-moon Hairstreak (Satyrium semiluna). A small, unique population persists Waterton Lakes National Park, Alberta, from other by more than 400 km. However, whether genetic would actually be helpful has not been evaluated. Here, we generate first chromosome-level genome assembly whole-genome resequence data species. We find that Alberta maintains extremely low diversity genetically very divergent nearest British Columbia Montana. Runs homozygosity suggest this due a long history inbreeding, coalescent analyses show isolated, yet stable, up 40k years. When like its viability despite diversity, it likely undergone purging deleterious recessive alleles could threatened reintroduction such via rescue. Ecological niche modelling indicates also exhibits environmental associations are atypical Together, these evolutionary ecological divergences crosses may result outbreeding depression. therefore infer relatively harmful rather at present. because reduced potential, still benefit future as climate habitat conditions change. Proactive experimental should completed assess reproductive compatibility progeny fitness.

Language: Английский

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Genomes of Galápagos Mockingbirds Reveal the Impact of Island Size and Past Demography on Inbreeding and Genetic Load in Contemporary Populations

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 6, 2025

ABSTRACT Restricted range size brings about noteworthy genetic consequences that may affect the viability of a population and eventually its extinction. Particularly, question if an increase in inbreeding can avert accumulation load via purging is hotly debated conservation field. Insular populations with limited sizes represent ideal setup for relating to these factors. Leveraging set eight differently sized Galápagos mockingbirds ( Mimus ), we investigated how island shaped effective N e load. We assembled genome M. melanotis genotyped three individuals per by whole‐genome resequencing. Demographic inference showed most remained high after colonisation archipelago 1–2 Mya. decline parvulus happened only 10–20 Kya, whereas critically endangered trifasciatus longer history reduced . Despite historical fluctuations, current determines linear fashion. In contrast, significant coefficients, derived from runs homozygosity, were identified four smallest populations. The index additive suggested , where lowest By carried highest load, possibly due recent rapid bottleneck. Overall, our study demonstrates complex effect demography on providing implications genetics general project particular.

Language: Английский

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