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

Genome biology, Journal Year: 2025, Volume and Issue: 26(1)

Published: April 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.

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

Molecular Biology and Evolution, Journal Year: 2023, Volume and Issue: 40(12)

Published: Nov. 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.

Language: Английский

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Translating genomic advances into biodiversity conservation

Nature Reviews Genetics, Journal Year: 2023, Volume and Issue: 25(5), P. 362 - 373

Published: Nov. 27, 2023

Language: Английский

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A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(3)

Published: Feb. 20, 2024

Abstract The blue whale, Balaenoptera musculus, is the largest animal known to have ever existed, making it an important case study in longevity and resistance cancer. To further this other whale-related research, we report a reference-quality, long-read-based genome assembly of fascinating species. We assembled from PacBio long reads utilized Illumina/10×, optical maps, Hi-C data for scaffolding, polishing, manual curation. also provided read RNA-seq facilitate annotation by NCBI Ensembl. Additionally, annotated both haplotypes using TOGA measured size flow cytometry. then compared whale with cetaceans artiodactyls, including vaquita (Phocoena sinus), world's smallest cetacean, investigate whale's unique biological traits. found dramatic amplification several genes resulting recent burst segmental duplications, though possible connection between giant body requires study. discovered sites insulin-like growth factor-1 gene correlated cetaceans. Finally, our examine heterozygosity historical demography Pacific Atlantic populations, that genomes populations are highly heterozygous their genetic isolation dates last interglacial period. Taken together, these results indicate how high-quality, will serve as resource biology, evolution, conservation research.

Language: Английский

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Demography and environment modulate the effects of genetic diversity on extinction risk in a butterfly metapopulation

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(33)

Published: Aug. 8, 2024

Linking genetic diversity to extinction is a common goal in genomic studies. Recently, debate has arisen regarding the importance of variation conservation as some studies have failed find associations between genome-wide and risk. However, only rarely are fitness measured together wild, typically demographic history environment ignored. It therefore difficult infer whether lack an association real or obscured by confounding factors. To address these shortcomings, we analyzed data from 7,501 individuals with 279 meadows mortality 1,742 larval nests butterfly metapopulation. We found strong negative when considering heterozygosity models. this disappeared accounting for ecological covariates, suggesting demography genetics more complex role Modeling interactions variables revealed that were context-dependent. For example, declined increasing large, but not currently small populations, although heterozygosity, extinction, detected populations recent decline. conclude low important predictor predicting >25% increase beyond factors certain contexts. These results highlight inferences about population viability should rely on alone require investments obtaining environmental natural populations.

Language: Английский

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Limited genomic signatures of population collapse in the critically endangered black abalone (Haliotis cracherodii)

Molecular Ecology, Journal Year: 2024, Volume and Issue: unknown

Published: April 29, 2024

The black abalone, Haliotis cracherodii, is a large, long-lived marine mollusc that inhabits rocky intertidal habitats along the coast of California and Mexico. In 1985, populations were impacted by bacterial disease known as withering syndrome (WS) wiped out >90% individuals, leading to closure all U.S. abalone fisheries since 1993. Current conservation strategies include restoring diminished translocating healthy individuals. However, population collapse on this scale may have dramatically lowered genetic diversity strengthened geographic differentiation, making translocation-based recovery contentious. Additionally, current prevalence WS remains unknown. To address these uncertainties, we sequenced analysed genomes 133 individuals from across their present range. We observed no spatial structure among with exception single chromosomal inversion increases in frequency latitude. Outside inversion, differentiation between sites minimal does not either distance or environmental dissimilarity. Genetic appears uniformly high Demographic inference indicate severe bottleneck beginning just 15 generations past, but decline short lived, present-day size far exceeding pre-bottleneck status quo. Finally, find agent equally sampled range, only 10% lack structure, uniform bacteria indicates translocation could be valid low-risk means restoration for species' recovery.

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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