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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Human generation times across the past 250,000 years

Science Advances, Journal Year: 2023, Volume and Issue: 9(1)

Published: Jan. 6, 2023

The generation times of our recent ancestors can tell us about both the biology and social organization prehistoric humans, placing human evolution on an absolute time scale. We present a method for predicting historical male female based changes in mutation spectrum. Our analyses whole-genome data reveal average 26.9 years across past 250,000 years, with fathers consistently older (30.7 years) than mothers (23.2 years). Shifts sex-averaged have been driven primarily by to age paternity, although we report substantial increase past. also find large difference among populations, reaching back when all humans occupied Africa.

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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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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Pedigree-based and phylogenetic methods support surprising patterns of mutation rate and spectrum in the gray mouse lemur

Heredity, Journal Year: 2021, Volume and Issue: 127(2), P. 233 - 244

Published: July 16, 2021

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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The genome of the black-footed cat: Revealing a rich natural history and urgent conservation priorities for small felids

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(2)

Published: Jan. 2, 2024

Habitat degradation and loss of genetic diversity are common threats faced by almost all today’s wild cats. Big cats, such as tigers lions, great concern have received considerable conservation attention through policies international actions. However, knowledge actions for small cats lagging considerably behind. The black-footed cat, Felis nigripes , one the smallest felid species, is experiencing increasing with a rapid reduction in population size. there lack information to assist developing effective A de novo assembly high-quality chromosome-level reference genome cat was made, comparative genomics analyses were carried out. These revealed that most significant changes evolution sensory metabolic-related genes, reflecting adaptations its characteristic nocturnal hunting high metabolic rate. Genomes exhibit level inbreeding, especially signals recent inbreeding events, which suggest they may experienced severe isolation caused habitat fragmentation. More importantly, associated two deleterious mutated genes exacerbate risk amyloidosis, dominant disease causes mortality about 70% captive individuals. Our research provides comprehensive documentation evolutionary history suggests an urgent need investigate genomic variations felids worldwide support

Language: Английский

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The Evolutionary Interplay of Somatic and Germline Mutation Rates

Annual Review of Biomedical Data Science, Journal Year: 2024, Volume and Issue: 7(1), P. 83 - 105

Published: April 26, 2024

Novel sequencing technologies are making it increasingly possible to measure the mutation rates of somatic cell lineages. Accurate germline rate measurement have also been available for a decade, assess how this fundamental evolutionary parameter varies across tree life. Here, we review some classical theories about and evolution that were formulated using principles population genetics biology aging cancer. We find measurements, while still limited in phylogenetic diversity, seem consistent with theory selection preserve soma is proportional life span. However, make conflicting predictions regarding which species should most accurate DNA repair. Resolving conflict will require carefully measuring scale time division achieving better understanding pleiotropy among types.

Language: Английский

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The ‘faulty male’ hypothesis for sex-biased mutation and disease

Current Biology, Journal Year: 2023, Volume and Issue: 33(22), P. R1166 - R1172

Published: Nov. 1, 2023

Language: Английский

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