An evolutionary perspective on genetic load in small, isolated populations as informed by whole genome resequencing and forward-time simulations

Evolution, Год журнала: 2022, Номер 77(3), С. 690 - 704

Опубликована: Дек. 19, 2022

Small populations are vulnerable to increased genetic load and drift that can lead reductions in fitness adaptive potential. By analyzing 66 individual whole genomes of Montezuma Quail (Cyrtonyx montezumae) from multiple populations, we illustrate how is dynamic over evolutionary time. We show evolving like a ring species, where the terminal extant Arizona Texas have been separated for ~16,500 years. The remained small but stable since separation, whereas population much larger today has contracting thousands Most deleterious mutations across genome young segregating privately each greater number alleles present population. Our data indicate ancestral purged during strong bottlenecks, reduced efficiency selection means more likely rise frequency Forward-time simulations severe declines historically large detrimental fitness, long-term at risk potential population-level fitness. study highlights intimate connections among history, historical demography, load, wild populations.

Язык: Английский

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

Molecular Ecology, Год журнала: 2022, Номер 32(7), С. 1567 - 1580

Опубликована: Дек. 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.

Язык: Английский

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Genomic Underpinnings of Population Persistence in Isle Royale Moose

Molecular Biology and Evolution, Год журнала: 2023, Номер 40(2)

Опубликована: Фев. 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.

Язык: Английский

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Genomic signatures of inbreeding depression for a threatened Aotearoa New Zealand passerine

Molecular Ecology, Год журнала: 2023, Номер 32(8), С. 1893 - 1907

Опубликована: Янв. 19, 2023

For small and isolated populations, the increased chance of mating between related individuals can result in a substantial reduction individual population fitness. Despite increasing availability genomic data to measure inbreeding accurately across genome, depression studies for threatened species are still scarce due difficulty measuring fitness wild. Here, we investigate extensively monitored Tiritiri Mātangi island Aotearoa New Zealand passerine, hihi (Notiomystis cincta). First, using custom 45 k single nucleotide polymorphism (SNP) array, explore patterns by inferring homozygous segments genome. Although all have similar levels ancient inbreeding, highly inbred affected recent which probably be explained bottleneck effects such as habitat loss after European arrival their translocation 1990s. Second, on fitness, measured lifetime reproductive success, its three components, juvenile survival, adult annual survival 363 hihi. We find that global significantly affects but none remaining traits. Finally, employ genome-wide association approach test locus-specific identify 13 SNPs associated with success. Our findings suggest does impact hihi, at different scales traits, purging has therefore failed remove variants deleterious from this conservation concern.

Язык: Английский

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Genetic Load and Adaptive Potential of a Recovered Avian Species that Narrowly Avoided Extinction

Molecular Biology and Evolution, Год журнала: 2023, Номер 40(12)

Опубликована: Ноя. 23, 2023

Abstract High genetic diversity is a good predictor of long-term population viability, yet some species persevere despite having low diversity. Here we study the genomic erosion Seychelles paradise flycatcher (Terpsiphone corvina), that narrowly avoided extinction after declined to 28 individuals in 1960s. The recovered unassisted over 250 1990s and was downlisted from Critically Endangered Vulnerable International Union for Conservation Nature Red List 2020. By comparing historical, prebottleneck (130+ years old) modern genomes, uncovered 10-fold loss Highly deleterious mutations were partly purged during bottleneck, but mildly accumulated. genome shows signs historical inbreeding bottleneck 1960s, levels recent demographic recovery. Computer simulations suggest small Ne reduced masked load made more resilient extinction. However, reduction due chronically severe likely have adaptive potential face environmental change, which together with higher load, compromises its viability. Thus, ancestral offers short-term resilience hampers adaptability shifts. In light rapid global rates decline, our work can continue suffer effect their decline even recovery, highlighting importance considering computer modeling conservation assessments.

Язык: Английский

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Landmarks in the history of selective sweeps

Animal Genetics, Год журнала: 2023, Номер 54(6), С. 667 - 688

Опубликована: Сен. 14, 2023

Abstract Half a century ago, seminal article on the hitchhiking effect by Smith and Haigh inaugurated concept of selection signature. Selective sweeps are characterised rapid spread an advantageous genetic variant through population hence play important role in shaping evolution research diversity. The process which beneficial allele arises becomes fixed population, leading to increase frequency other linked alleles, is known as or draft. Kimura's neutral theory complementary, with ‘null model’ positive ‘signal’. Both widely accepted evolution, especially genomics enabling precise measurements. Significant advances genomic technologies, such next‐generation sequencing, high‐density SNP arrays powerful bioinformatics tools, have made it possible systematically investigate signatures variety species. Although history relatively recent, progress has been last two decades, owing increasing availability large‐scale data development computational methods. In this review, we embark journey selective sweeps, ranging from early theoretical work recent empirical studies that utilise data.

Язык: Английский

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The chromosome-scale genome of Magnolia sinica (Magnoliaceae) provides insights into the conservation of plant species with extremely small populations (PSESP)

GigaScience, Год журнала: 2024, Номер 13

Опубликована: Янв. 1, 2024

Magnolia sinica (Magnoliaceae) is a highly threatened tree endemic to southeast Yunnan, China. In this study, we generated for the first time high-quality chromosome-scale genome sequence from M. sinica, by combining Illumina and ONT data with Hi-C scaffolding methods. The final assembled size of was 1.84 Gb, contig N50 ca. 45 Mb scaffold 92 Mb. Identified repeats constituted approximately 57% genome, 43,473 protein-coding genes were predicted. Phylogenetic analysis shows that magnolias form sister clade eudicots order Ceratophyllales, while monocots are other core angiosperms. our total 21 individuals 5 remnant populations as well 22 specimens belonging 8 related Magnoliaceae species, resequenced. results showed had higher genetic diversity (θw = 0.01126 θπ 0.01158) than species in Magnoliaceae. However, population structure suggested differentiation among very low. Analyses demographic history using different models consistently revealed 2 bottleneck events occurred. contemporary effective estimated be 10.9. patterns loads (inbreeding numbers deleterious mutations) constructive strategies conservation these sinica. Overall, will valuable genomic resource

Язык: Английский

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Genetic architecture of inbreeding depression may explain its persistence in a population of wild red deer

Molecular Ecology, Год журнала: 2024, Номер 33(9)

Опубликована: Март 28, 2024

Inbreeding depression is of major concern in declining populations, but relatively little known about its genetic architecture wild such as the degree to which it composed large or small effect loci and their distribution throughout genome. Here, we combine fitness genomic data from a population red deer investigate inbreeding effects. Based on runs homozygosity (ROH)-based coefficient, F

Язык: Английский

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Population genomics reveals strong impacts of genetic drift without purging and guides conservation of bull and giant kelp

Current Biology, Год журнала: 2025, Номер unknown

Опубликована: Янв. 1, 2025

Язык: Английский

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Genomic evidence for low genetic diversity but purging of strong deleterious variants in snow leopards

Genome biology, Год журнала: 2025, Номер 26(1)

Опубликована: Апрель 14, 2025

Long-term persistence of species with low genetic diversity is the focus widespread attention in conservation biology. The snow leopard, Panthera uncia, a big cat from high-alpine regions Asia. However, its subspecies taxonomy, evolutionary history, potential, and survival strategy remain unclear, which greatly hampers their conservation. We sequence high-quality chromosome-level genome leopard genomes 52 wild leopards. Population genomics reveal existence two large lineages global leopards, northern southern lineages, supported by biogeography. Last Glacial Maximum drove divergence lineages. Microclimate differences rivers between western central Himalayas likely maintain differentiation EPAS1 positively selected lineage almost fixed amino acid substitutions shows an increased allele frequency elevation. Compared to lineage, exhibits lower level genomic higher levels inbreeding load, consistent recent population decline. find that leopards have extremely than other Carnivora species; however, strong deleterious mutations been effectively purged historical bottlenecks inbreeding, may be vital mechanism for viability. Our findings highlight importance unveiling both burden threatened species.

Язык: Английский

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