Evolution of the germline mutation rate across vertebrates

Nature, Journal Year: 2023, Volume and Issue: 615(7951), P. 285 - 291

Published: March 1, 2023

The germline mutation rate determines the pace of genome evolution and is an evolving parameter itself1. However, little known about what its evolution, as most studies rates have focused on single species with different methodologies2. Here we quantify across vertebrates by sequencing comparing high-coverage genomes 151 parent-offspring trios from 68 mammals, fishes, birds reptiles. We show that per-generation varies among a factor 40, being higher for males than females in mammals birds, but not reptiles fishes. generation time, age at maturity species-level fecundity are key life-history traits affecting this variation species. Furthermore, long-term effective population sizes tend to lower per generation, providing support drift barrier hypothesis3. exceptionally high yearly domesticated animals, which been continually selected including shorter times, further importance time rates. Overall, our comparative analysis pedigree-based provides ecological insights vertebrates.

Language: Английский

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The Mutationathon highlights the importance of reaching standardization in estimates of pedigree-based germline mutation rates

eLife, Journal Year: 2022, Volume and Issue: 11

Published: Jan. 12, 2022

In the past decade, several studies have estimated human per-generation germline mutation rate using large pedigrees. More recently, estimates for various nonhuman species been published. However, methodological differences among in detecting mutations and estimating rates make direct comparisons difficult. Here, we describe many different steps involved pedigree-based rates, including sampling, sequencing, mapping, variant calling, filtering, appropriately accounting false-positive false-negative rates. For each step, review methods parameter choices that used recent literature. Additionally, present results from a 'Mutationathon,' competition organized five research labs to compare single pedigree of rhesus macaques. We report almost twofold variation final groups post-alignment processing, filtering criteria, provide details into sources across studies. Though difference is not statistically significant, this discrepancy emphasizes need standardized estimations difficulty comparing Finally, work aims guidelines computational statistical benchmarks future interested identifying

Language: Английский

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A paternal bias in germline mutation is widespread in amniotes and can arise independently of cell division numbers

eLife, Journal Year: 2022, Volume and Issue: 11

Published: Aug. 2, 2022

In humans and other mammals, germline mutations are more likely to arise in fathers than mothers. Although this sex bias has long been attributed DNA replication errors spermatogenesis, recent evidence from points the importance of mutagenic processes that do not depend on cell division, calling into question our understanding basic phenomenon. Here, we infer ratio paternal-to-maternal mutations,

Language: Английский

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De novo Mutations in Domestic Cat are Consistent with an Effect of Reproductive Longevity on Both the Rate and Spectrum of Mutations

Molecular Biology and Evolution, Journal Year: 2022, Volume and Issue: 39(7)

Published: June 30, 2022

The mutation rate is a fundamental evolutionary parameter with direct and appreciable effects on the health function of individuals. Here, we examine this important in domestic cat, beloved companion animal as well valuable biomedical model. We estimate 0.86 × 10-8 per bp generation for cat (at an average parental age 3.8 years). find evidence significant paternal effect, more mutations transmitted by older sires. Our analyses suggest that human have accrued similar numbers germline before reaching sexual maturity. per-generation 28% lower than what has been observed humans, but consistent shorter time cat. Using model reproductive longevity, which takes into account differences to maturity, are able explain much difference rates between species. further apply our longevity novel analysis spectra spectrum resembles at younger reproduction. Together, these results implicate changes life-history driver evolution As first observation effect outside rodents primates, also phenomenon may be universal among mammals.

Language: Английский

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Characterizing the rates and patterns ofde novogermline mutations in the aye-aye (Daubentonia madagascariensis)

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 11, 2024

Given the many levels of biological variation in mutation rates observed to date primates - spanning from species individuals genomic regions future steps our understanding rate evolution will be aided by both a greater breadth coverage across primate clade, but also depth as afforded an evaluation multiple trios within individual species. In order help bridge these gaps, we here present analysis representing one most basal splits on tree (aye-ayes), combining whole-genome sequencing seven parent-offspring three-generation pedigree with novel computational pipeline that takes advantage recently developed pan-genome graphs, thereby circumventing application (highly subjective) quality metrics has previously been shown result notable differences detection

Language: Английский

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A whole-genome scan for evidence of recent positive and balancing selection in aye-ayes (Daubentonia madagascariensis) utilizing a well-fit evolutionary baseline model

Published: Nov. 11, 2024

The aye-aye (

Language: Английский

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Inferring the demographic history of aye-ayes (Daubentonia madagascariensis) from high-quality, whole-genome, population-level data

Published: Nov. 11, 2024

The nocturnal aye-aye,

Language: Английский

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Inferring the demographic history of aye-ayes (Daubentonia madagascariensis) from high-quality, whole-genome, population-level data

Genome Biology and Evolution, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 3, 2025

Abstract The nocturnal aye-aye, Daubentonia madagascariensis, is one of the most elusive lemurs on island Madagascar. timing its activity and arboreal lifestyle has generally made it difficult to obtain accurate assessments population size using traditional census methods. Therefore, alternative estimates provided by genetic inference are essential for yielding much needed information conservation measures enabling ecological evolutionary studies this species. Here, we utilize genomic data from 17 individuals—including 5 newly sequenced, high-coverage genomes—to estimate history. Essential estimation recently published annotations aye-aye genome which allow variation at putatively neutral regions be included in procedures, subject selective constraints, or linkage such sites, excluded owing biasing effects selection demographic inference. By comparing a variety tools develop well-supported model history, find strong support two demes, separating northern Madagascar rest island. Additionally, that experienced severe reductions size. first occurred rapidly, approximately 3,000 5,000 years ago, likely corresponded with arrival humans second over past few decades related substantial habitat loss, suggesting species still undergoing decline remains great risk extinction.

Language: Английский

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Direct Measurement of the Mutation Rate and Its Evolutionary Consequences in a Critically Endangered Mollusk

Molecular Biology and Evolution, Journal Year: 2025, Volume and Issue: 42(1)

Published: Jan. 1, 2025

Abstract The rate at which mutations arise is a fundamental parameter of biology. Despite progress in measuring germline mutation rates across diverse taxa, such estimates are missing for much Earth's biodiversity. Here, we present the first estimate from phylum Mollusca. We sequenced three pedigreed families white abalone Haliotis sorenseni, long-lived, large-bodied, and critically endangered mollusk, estimated de novo 8.60 × 10−9 single nucleotide per site generation. This similar to measured vertebrates with comparable generation times longevity abalone, higher than faster-reproducing invertebrates. spectrum also that seen vertebrate species, although an excess rare C > A polymorphisms wild individuals suggests modifier allele or environmental exposure may have once increased rates. use our infer baseline effective population sizes (Ne) multiple Pacific find persisted over most their evolutionary history as large stable populations, contrast extreme fluctuations recent small census day. then timing pattern evolution genus Haliotis, was previously unknown due few fossil calibrations. Our findings important step toward understanding they establish key conservation genomics research mollusks.

Language: Английский

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Unprecedented female mutation bias in the aye-aye, a highly unusual lemur from Madagascar

PLoS Biology, Journal Year: 2025, Volume and Issue: 23(2), P. e3003015 - e3003015

Published: Feb. 7, 2025

Every mammal studied to date has been found have a male mutation bias: parents transmit more de novo mutations offspring than female parents, contributing increasingly with age. Although male-biased for 75 years, its causes are still debated. One obstacle understanding this pattern is near universality—without variation in bias, it difficult find an underlying cause. Here, we present new data on multiple pedigrees from two primate species: aye-ayes ( Daubentonia madagascariensis ), member of the strepsirrhine primates, and olive baboons Papio anubis ). In stark contrast across mammals, much larger effect maternal age paternal rates aye-aye. addition, older aye-aye mothers substantially fathers. We carry out both computational experimental validation our results, contrasting them results other primates using same methodologies. Further, analyze set DNA repair replication genes identify candidate that may be responsible change bias observed aye-ayes. Our demonstrate not immutable trait, but rather one can evolve between closely related species. Further work (and possibly lemuriform primates) should help explain molecular basis sex-biased mutation.

Language: Английский

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