The divergence of mutation rates and spectra across the Tree of Life

EMBO Reports, Journal Year: 2023, Volume and Issue: 24(10)

Published: Aug. 24, 2023

Abstract Owing to advances in genome sequencing, stability has become one of the most scrutinized cellular traits across Tree Life. Despite its centrality all things biological, mutation rate (per nucleotide site per generation) ranges over three orders magnitude among species and several‐fold within individual phylogenetic lineages. Within major organismal groups, rates scale negatively with effective population size a amount functional DNA genome. This relationship is parsimoniously explained by drift‐barrier hypothesis, which postulates that natural selection typically operates reduce until further improvement thwarted power random genetic drift. this constraint, molecular mechanisms underlying replication fidelity repair are free wander, provided performance entire system maintained at prevailing level. The evolutionary flexibility bears on resolution several prior conundrums population‐genetic analysis raises challenges for future applications these areas.

Language: Английский

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Variation in mutation, recombination, and transposition rates inDrosophila melanogasterandDrosophila simulans

Genome Research, Journal Year: 2023, Volume and Issue: 33(4), P. 587 - 598

Published: April 1, 2023

The rates of mutation, recombination, and transposition are core parameters in models evolution. They impact genetic diversity, responses to ongoing selection, levels load. However, even for key evolutionary model species such as Drosophila melanogaster simulans, few estimates these available, we have little idea how vary between individuals, sexes, or populations. Knowledge this variation is fundamental parameterizing genome Here, provide direct their a West African European population D. simulans Across 89 flies, observe 58 single-nucleotide mutations, 286 crossovers, transposable element (TE) insertions. Compared the melanogaster, find has lower mutation rate (1.67 × 10-9 site-1 gen-1 vs. 4.86 gen-1) (8.99 10-5 copy-1 23.36 gen-1), but higher recombination (3.44 cM/Mb 2.06 cM/Mb). similar significantly lower, not different, rate. Overall, paternal-derived mutations more frequent than maternal ones both species. Our study quantifies among different populations our will benefit future studies genetics.

Language: Английский

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Characterizing the Rates and Patterns of De Novo Germline Mutations in the Aye-Aye (Daubentonia madagascariensis)

Molecular Biology and Evolution, Journal Year: 2025, Volume and Issue: 42(3)

Published: March 1, 2025

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 not only be aided by 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 de novo mutations and ultimately estimates rates. This deep sampling enabled both detailed picture parental age effects sex dependency rates, which compare studied primates, provided unique insights into nature genetic endangered primates planet.

Language: Английский

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Convergent evolution of epigenome recruited DNA repair across the Tree of Life

Published: April 17, 2025

Mutations fuel evolution while also causing diseases like cancer. Epigenome-targeted DNA repair can help organisms protect important genomic regions from mutation. However, the adaptive value, mechanistic diversity, and of epigenome-targeted systems across tree life remain unresolved. Here, we investigated histone reader domains fused to protein MSH6 (MutS Homolog 6) over 4,000 eukaryotes. We uncovered a paradigmatic example convergent evolution: has independently acquired distinct domains; PWWP (metazoa) Tudor (plants), previously shown target modifications in active genes humans (H3K36me3) Arabidopsis (H3K4me1). Conservation shows signatures natural selection, particularly for amino acids that bind specific modifications. Species have gained or retained readers tend larger genome sizes, especially marked by significantly more introns genic regions. These patterns support previous theoretical predictions about co-evolution architectures mutation rate heterogeneity. The implications evolution, health, mutational origins genetic diversity life.

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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Background Selection From Unlinked Sites Causes Nonindependent Evolution of Deleterious Mutations

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(3)

Published: March 1, 2024

Abstract Background selection describes the reduction in neutral diversity caused by against deleterious alleles at other loci. It is typically assumed that purging of affects linked variants, and indeed simulations only treat a genomic window. However, background unlinked loci also depresses diversity. In agreement with previous analytical approximations, our human-like genome realistically high genome-wide mutation rate, effects exceed those selection. reduces genetic factor independent census population size. Outside genic regions, strength increases mean coefficient, contradicting theory but theory. Neutral within regions fairly Deleterious load among haploid individuals underdispersed, indicating nonindependent evolution mutations. Empirical evidence for underdispersion was previously interpreted as global epistasis, we recover it from non-epistatic model.

Language: Английский

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Effects of urban-induced mutations on ecology, evolution and health

Nature Ecology & Evolution, Journal Year: 2024, Volume and Issue: 8(6), P. 1074 - 1086

Published: April 19, 2024

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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Effective population size does not explain long-term variation in genome size and transposable element content in animals

Published: Sept. 11, 2024

Animal genomes exhibit a remarkable variation in size, but the evolutionary forces responsible for such are still debated. As effective population size (N e ) reflects intensity of genetic drift, it is expected to be key determinant fixation rate nearly-neutral mutations. Accordingly, Mutational Hazard Hypothesis postulates lineages with low N have bigger genome sizes due accumulation slightly deleterious transposable elements (TEs), and those high maintain streamlined as consequence more selection against TEs. However, existence both empirical confirmation refutation using different methods scales precludes its general validation. Using high-quality public data, we estimated TE content non-synonymous synonymous substitutions (dN/dS) proxy 807 species including vertebrates, molluscs insects. After collecting available life-history traits, tested associations among proxies, while accounting phylogenetic non-independence. Our results confirm TEs major drivers variation, endorse traits dN/dS reliable proxies . do not find any evidence increased drift result an across animals. Within closely related clades, only few isolated weak emerge fishes birds. outline scenario where dynamics vary according lineage-specific patterns, lending no support predominant force driving long-term evolution

Language: Английский

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Summary Tests of Introgression Are Highly Sensitive to Rate Variation Across Lineages

Systematic Biology, Journal Year: 2023, Volume and Issue: 72(6), P. 1357 - 1369

Published: Sept. 12, 2023

The evolutionary implications and frequency of hybridization introgression are increasingly being recognized across the tree life. To detect from multi-locus genome-wide sequence data, a popular class methods based on summary statistics subsets 3 or 4 taxa. However, these often carry assumption constant substitution rate lineages genes, which is commonly violated in many groups. In this work, we quantify effects variation D test (also known as ABBA-BABA test), D3 test, HyDe. All tests used widely range taxonomic groups, part because they very fast to compute. We consider species lineages, their lineage-by-gene interaction, gene-tree edges. simulated networks according birth-death-hybridization process, so capture realistic phylogenies. For all tested, found marked increase false discovery reticulation (type-1 error rate) when there lineages. was most sensitive, with around 80% type-1 error, such that appears more sensitive departure clock than presence reticulation. tests, power events decreased number increased, indicating multiple can obscure one another if occur within small subset Our study highlights need using site-based statistics, points advantages do not require assumptions rates genes.

Language: Английский

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