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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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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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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From high masked to high realized genetic load in inbred Scandinavian wolves

Molecular Ecology, Journal Year: 2022, Volume and Issue: 32(7), P. 1567 - 1580

Published: Dec. 2, 2022

Abstract When new mutations arise at functional sites they are more likely to impair than improve fitness. If not removed by purifying selection, such deleterious will generate a genetic load that can have negative fitness effects in small populations and increase the risk of extinction. This is relevant for highly inbred Scandinavian wolf ( Canis lupus ) population, founded only three wolves 1980s suffering from inbreeding depression. We used annotation evolutionary conservation scores study variation total 209 genomes both neighbouring northern Europe. The masked (deleterious heterozygote state) was highest Russia Finland with alleles segregating lower frequency neutral variation. Genetic drift population led loss ancestral alleles, fixation variants significant per‐individual realized homozygote state; an 45% protein‐coding genes) over five generations inbreeding. Arrival immigrants gave temporary rescue effect re‐entering thereby shifting homozygous into genotypes. However, absence permanent connectivity Finnish Russian populations, has then again exposure mutations. These observations provide genome‐wide insight magnitude molecular level, relation history. They emphasize importance securing gene flow management endangered populations.

Language: Английский

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Prediction of the minimum effective size of a population viable in the long term

Biodiversity and Conservation, Journal Year: 2022, Volume and Issue: 31(11), P. 2763 - 2780

Published: July 11, 2022

Abstract The establishment of the minimum size for a viable population (MVP) has been used as guidance in conservation practice to determine extinction risks populations and species. A consensus MVP rule 50/500 individuals attained, according which effective N e = 50 is needed avoid due inbreeding depression short term, 500 survive long term. However, large loads ( B ) usually found nature, well consideration selection affecting genetic diversity, have led suggestion that those numbers should be doubled (100/1000). Purging deleterious mutations can also main factor suggested rules. In previous simulation study, reduction by action purging pointed towards an intermediate between two rules term survival. Here, we focused on consequences MVPs We performed computer simulations under purging, drift, new mutation, environmental effects fitness investigate times loss diversity range sizes. Our results indicate reduce persist with estimates close species moderately reproductive rates. values appear at least 1000 when species´ rates are low.

Language: Английский

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Runs of homozygosity reveal past bottlenecks and contemporary inbreeding across diverging populations of an island‐colonizing bird

Molecular Ecology, Journal Year: 2023, Volume and Issue: 32(8), P. 1972 - 1989

Published: Jan. 27, 2023

Genomes retain evidence of the demographic history and evolutionary forces that have shaped populations drive speciation. Across island systems, contemporary patterns genetic diversity reflect population demography, including colonization events, bottlenecks, gene flow drift. Here, we investigate genome-wide distribution runs homozygosity (ROH) using whole-genome resequencing individuals (>22× coverage) from six across three archipelagos Berthelot's pipit (Anthus berthelotii)-a passerine has recently undergone We show most dramatic reduction in occurs between mainland sister species (the tawny pipit) is lowest experienced sequential bottlenecks (i.e., Madeiran Selvagens populations). Pairwise Markovian coalescent (PSMC) analyses estimated diverged its ~2 million years ago, with archipelago founded 50,000 colonized 8000 ago. identify many long ROH (>1 Mb) these populations. Population expansion within last 100 may eroded archipelago, resulting a prevalence short (<1 Mb). However, extensive detected suggest strong recent inbreeding bottleneck effects, as much 38% autosomes consisting >250 kb. These findings highlight importance history, well selection drift, shaping genomic diverging

Language: Английский

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The influence of gene flow on population viability in an isolated urban caracal population

Molecular Ecology, Journal Year: 2024, Volume and Issue: 33(9)

Published: April 5, 2024

Abstract Wildlife populations are becoming increasingly fragmented by anthropogenic development. Small and isolated often face an elevated risk of extinction, in part due to inbreeding depression. Here, we examine the genomic consequences urbanization a caracal ( Caracal ) population that has become Cape Peninsula region City Town, South Africa, is thought number ~50 individuals. We document low levels migration into over past ~75 years, with estimated rate 1.3 effective migrants per generation. As consequence this isolation small size, contemporary (mean F ROH = 0.20). Inbreeding primarily manifests as long runs homozygosity >10 Mb, consistent effects rapid recent growth Town. To explore how reduced may impact future dynamics, parameterized eco‐evolutionary simulation model. find if rates do not change future, expected decline, though projected extinction. However, decline or mortality increase, potential extinction greatly elevated. avert suggest translocating initiate genetic rescue be warranted near future. Our analysis highlights utility datasets coupled computational models for investigating influence gene flow on viability.

Language: Английский

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Multi-generational benefits of genetic rescue

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: July 30, 2024

Abstract Genetic rescue—an increase in population fitness following the introduction of new alleles—has been proven to ameliorate inbreeding depression small, isolated populations, yet is rarely applied as a conservation tool. A lingering question regarding genetic rescue wildlife how long beneficial effects persist admixed populations. Using data collected over 40 years from 1192 endangered Florida panthers ( Puma concolor coryi ) across nine generations, we show that experimental implemented 1995—via release eight female pumas Texas—alleviated morphological, genetic, and demographic correlates depression, subsequently preventing extirpation population. We present unequivocal evidence, for first time any terrestrial vertebrate, phenotypic benefits remain this after five generations admixture, which helped panther abundance (> fivefold) effective size 20-fold). Additionally, even with extensive microsatellite allele frequencies continue support distinctness other North American puma including Texas. Although threats habitat loss, human-wildlife conflict, infectious diseases are challenges many imperiled our results suggest can serve an effective, multi-generational tool populations facing extinction inbreeding.

Language: Английский

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Using Computational Simulations to Model Deleterious Variation and Genetic Load in Natural Populations

The American Naturalist, Journal Year: 2023, Volume and Issue: 202(6), P. 737 - 752

Published: July 17, 2023

AbstractDeleterious genetic variation is abundant in wild populations, and understanding the ecological conservation implications of such an area active research. Genomic methods are increasingly used to quantify impacts deleterious natural populations; however, these approaches remain limited by inability accurately predict selective dominance effects mutations. Computational simulations offer a complementary tool that can help overcome limitations, although have yet be widely employed. In this perspective article, we aim encourage genomics researchers adopt greater use computational aid deepening our populations. We first provide overview components simulation variation, describing key parameters involved models. Next, discuss several for validating Finally, compare validate recently proposed mutation models, demonstrating models based on estimates selection from experimental systems biased toward highly describe new model supported multiple orthogonal lines evidence example scripts implementing (https://github.com/ckyriazis/simulations_review).

Language: Английский

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Using computational simulations to quantify genetic load and predict extinction risk

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

Published: Aug. 15, 2022

Abstract Small and isolated wildlife populations face numerous threats to extinction, among which is the deterioration of fitness due an accumulation deleterious genetic variation. Genomic tools are increasingly used quantify impacts variation in small populations; however, these approaches remain limited by inability accurately predict selective dominance effects individual mutations. Computational simulations offer alternative complementary tool that can help overcome limitations, though such have yet be widely employed. In this Perspective, we aim encourage conservation genomics researchers adopt greater use computational aid quantifying predicting threat poses extinction. We first provide overview components a simulation variation, describing key parameters involved models. Next, clarify several misconceptions about essential parameter, distribution (DFE) new mutations, review recent debates over what most appropriate DFE are. conclude comparing modern those long been employed population viability analysis, weighing pros cons ‘genomics-informed’ approach, discussing areas for future research. Our Perspective will facilitate broader genomics, enabling deeper understanding biodiversity.

Language: Английский

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