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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Genomic Underpinnings of Population Persistence in Isle Royale Moose

Molecular Biology and Evolution, Journal Year: 2023, Volume and Issue: 40(2)

Published: Feb. 1, 2023

Island ecosystems provide natural laboratories to assess the impacts of isolation on population persistence. However, most studies persistence have focused a single species, without comparisons other organisms they interact with in ecosystem. The case study moose and gray wolves Isle Royale allows for direct contrast genetic variation isolated populations that experienced dramatically differing trajectories over past decade. Whereas wolf recently declined nearly extinction due severe inbreeding depression, has thrived continues persist, despite having low diversity being ∼120 years. Here, we examine patterns genomic underlying continued population. We document high levels population, roughly as at time its decline. manifests form intermediate-length runs homozygosity suggestive historical purging, contrasting long observed smaller Using simulations, confirm substantial purging likely occurred also notable increases load, which could eventually threaten viability term. Overall, our results demonstrate complex relationship between inbreeding, diversity, highlights use datasets computational simulation tools understanding factors enabling populations.

Language: Английский

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Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations

eLife, Journal Year: 2023, Volume and Issue: 12

Published: March 3, 2023

Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic datasets remains major obstacle. Today, more realistic are possible thanks to large increases quantity quality available genetic data, sophistication inference simulation software. However, implementing these still requires substantial time specialized knowledge. These challenges especially pronounced simulating genomes species not well-studied, since it always clear what information required produce with level realism sufficient confidently answer given question. The community-developed framework stdpopsim seeks lower this barrier by facilitating complex models using up-to-date information. initial version focused on establishing six well-characterized model (Adrion et al., 2020). Here, we report improvements made new release (version 0.2), which includes significant expansion catalog additions capabilities. Features added improve simulated include non-crossover recombination provision species-specific annotations. Through community-driven efforts, expanded number than threefold broadened coverage across tree life. During process expanding catalog, have identified common sticking points developed best practices setting up genome-scale simulations. We describe input data generating simulation, suggest good obtaining relevant from literature, discuss pitfalls considerations. aim further promote use whole-genome simulations, non-model organisms, making them available, transparent, accessible everyone.

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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Genomic erosion in the assessment of species extinction risk and recovery potential

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Sept. 15, 2022

Abstract Many species are facing unprecedented population size declines and deterioration of their environment. This exposes to genomic erosion, which we define here as the damage inflicted a species’ genome or gene pool due loss genetic diversity, an increase in expressed load, maladaptation, and/or introgression. The International Union for Conservation Nature (IUCN) bases its extinction risk assessments on direct threats habitat. However, it does not assess long-term impacts hence, is likely underestimate many species. High-quality whole sequence data that currently being generated could help improve assessments. Genomic contains information about past demography, genome-wide incidence introgression, well load deleterious mutations. Computer modelling these enables forecasting trajectories under different management scenarios. In this Perspective, discuss posed by erosion. Using evolutionary simulations, argue provides critical assessing recovery potential Genomics-informed complement IUCN Red List, such genomics-informed conservation invaluable guiding programs UN’s Decade Ecosystem Restoration beyond.

Language: Английский

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Quantifying the fraction of new mutations that are recessive lethal

Evolution, Journal Year: 2023, Volume and Issue: 77(7), P. 1539 - 1549

Published: April 19, 2023

Abstract The presence and impact of recessive lethal mutations have been widely documented in diploid outcrossing species. However, precise estimates the proportion new that are remain limited. Here, we evaluate performance Fit∂a∂i, a commonly used method for inferring distribution fitness effects (DFE), mutations. Using simulations, demonstrate both additive cases, inference deleterious nonlethal portion DFE is minimally affected by small (<10%) Additionally, while Fit∂a∂i cannot estimate fraction mutations, can accurately infer Finally, as an alternative approach to lethal, employ models mutation–selection–drift balance using existing genomic parameters segregating lethals humans Drosophila melanogaster. In species, load be explained very (<1%) nonsynonymous being lethal. Our results refute recent assertions much higher (4%–5%), highlighting need additional information on joint selection dominance coefficients.

Language: Английский

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When birds of a feather flock together: Severe genomic erosion and the implications for genetic rescue in an endangered island passerine

Evolutionary Applications, Journal Year: 2024, Volume and Issue: 17(7)

Published: June 28, 2024

Abstract The Seychelles magpie‐robin's (SMR) five island populations exhibit some of the lowest recorded levels genetic diversity among endangered birds, and high inbreeding. These collapsed during 20th century, species was listed as Critically Endangered in IUCN Red List 1994. An assisted translocation‐for‐recovery program initiated 1990s increased number mature individuals, resulting its downlisting to 2005. Here, we explore temporal genomic erosion SMR based on a dataset 201 re‐sequenced whole genomes that span past ~150 years. Our sample set includes individuals predate bottleneck by up 100 years, well from contemporary established recovery program. Despite SMR's recent demographic recovery, our data reveal marked increase both load realized extant when compared historical samples. Conservation management may have reduced intensity selection increasing juvenile survival relaxing intraspecific competition between accumulation loss‐of‐function mutations (i.e. severely deleterious variants) rapidly recovering population. In addition, found 3‐fold decrease While low modern limit species' adaptability future environmental changes, conservation efforts (including assessments) also need assess threats posed their load. computer simulations highlight value translocations for rescue show how this could halt threatened such SMR.

Language: Английский

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Models based on best-available information support a low inbreeding load and potential for recovery in the vaquita

Heredity, Journal Year: 2023, Volume and Issue: 130(4), P. 183 - 187

Published: March 20, 2023

Language: Английский

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Genetic diversity loss in the Anthropocene will continue long after habitat destruction ends

Published: Oct. 22, 2024

Genetic diversity within species is the basis for evolutionary adaptive capacity and has recently been included as a target protection in United Nations’ Global Biodiversity Framework (GBF). However, there lack of reliable large-scale predictive frameworks to quantify how much genetic already lost, let alone quantitatively predict future losses under different conservation scenarios 21st century. Combining spatio-temporal population theory with genomic data 18 plant animal species, we studied dynamics after habitat area losses. We show reacts slowly declines, but lagged will continue many decades even habitats are fully protected. To understand magnitude this problem, combined our method species’ monitoring reported Living Planet Index, Red List, new GBF indicators. then project loss 13,808 short-term 13 – 22% long-term 42 48% substantial deviations depending on level fragmentation. These results highlight that only current insufficient ensure health continuous likely underestimates long term impacts. provide an area-based framework develop quantitative global biodiversity.

Language: Английский

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Digital image processing to detect adaptive evolution

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(12)

Published: Nov. 20, 2024

In recent years, advances in image processing and machine learning have fueled a paradigm shift detecting genomic regions under natural selection. Early techniques employed population-genetic summary statistics as features, which focus on specific patterns expected by adaptive neutral processes. Though such engineered features are important when training data limited, the ease at simulated can now be generated has led to development of approaches that take representations haplotype alignments automatically extract using convolutional neural networks. Digital methods termed α-molecules class for multiscale representation objects diverse set from images. One α-molecule method, wavelet decomposition, lends greater control over high-frequency components Another curvelet is an extension concept considers events occurring along curves within We show application these yield high true positive rate accuracy detect hard soft selective sweep signatures with both linear nonlinear classifiers. Moreover, we find models easy visualize interpret, performance rivaling those contemporary deep sweeps.

Language: Английский

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