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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H3K4me1 recruits DNA repair proteins in plants

The Plant Cell, Journal Year: 2024, Volume and Issue: 36(6), P. 2410 - 2426

Published: March 26, 2024

DNA repair proteins can be recruited by their histone reader domains to specific epigenomic features, with consequences on intragenomic mutation rate variation. Here, we investigated H3K4me1-associated hypomutation in plants. We first examined 2 which, plants, contain Tudor domains: PRECOCIOUS DISSOCIATION OF SISTERS 5 (PDS5C), involved homology-directed repair, and MUTS HOMOLOG 6 (MSH6), a mismatch protein. The MSH6 domain of Arabidopsis (Arabidopsis thaliana) binds H3K4me1 as previously demonstrated for PDS5C, which localizes H3K4me1-rich gene bodies essential genes. Mutations revealed ultradeep sequencing wild-type msh6 knockout lines show that functional is critical the reduced single-base substitution (SBS) mutations regions. explored breadth these mechanisms among plants examining large rice (Oryza sativa) data set. conserved are H3K4me1-binding residues PDS5C domains. Recruitment reveals convergent, but distinct, epigenome-recruited from those well described humans. emergent model H3K4me1-recruited consistent evolutionary theory regarding modifier systems offers mechanistic insight into variation

Language: Английский

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Indels: computational methods, evolutionary dynamics, and biological applications

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(9)

Published: Aug. 22, 2024

Abstract Insertions and deletions constitute the second most important source of natural genomic variation. make up to 25% variants in humans are involved complex evolutionary processes including rearrangements, adaptation, speciation. Recent advances long-read sequencing technologies allow detailed inference insertions deletion variation species populations. Yet, despite their importance, studies have traditionally ignored or mishandled due a lack comprehensive methodologies statistical models dynamics. Here, we discuss methods for describing modeling over time. We provide practical advice tackling sequences illustrate our discussion with examples deletion-induced effects human other populations contribution processes. outline promising directions future developments that would researchers analyze large data sets incorporate inference.

Language: Английский

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Structural mutations set an equilibrium non-coding genome fraction

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 5, 2025

Non-coding genome size evolution is poorly understood. While some fraction of non-coding DNA has arguably a regulatory function, large part does not seem to have detectable impact on any phenotypic trait. The abundance non-functional in genomes, observed across the Tree Life, challenges purely adaptationist explanation. Several non-adaptive theories been proposed explain its presence and identify determinants, emphasizing either mutational processes or hazard entailed by DNA. However, those yet integrated into single framework, exact nature fully In this work, we propose simple mathematical model evolution. shows how shaped two factors: unavoidable biases neutrality different mutation types (adding base pairs more likely be neutral than removing some), robustness selection imposed mere existence structural mutations (larger genomes are prone double-strand breaks that can initiate mutations, imposing second-order robustness). Together, these factors ensure an equilibrium fraction. We show depends solely product population rate.

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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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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Mutational robustness and the role of buffer genes in evolvability

The EMBO Journal, Journal Year: 2024, Volume and Issue: 43(12), P. 2294 - 2307

Published: May 8, 2024

Language: Английский

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The rarity of mutations and the inflation of bacterial effective population sizes

Methods in Ecology and Evolution, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 26, 2025

Abstract Mutations are fundamental for evolution, and their mathematical modelling in population genetics heavily relies on our perception of frequency the timescale over which they occur. A common assumption is that mutations infrequent, so when a new mutation arises, previous one has either become fixed or lost. This implies occur exclusively at sites referred to as boundary model. However, can alternatively assume recurrent model, additionally considers contributing shifts allele frequency. In this study, we compare these two models. By examining rates effective sizes across Tree Life, demonstrate model remains valid most species but significantly deviates bacteria. Our analyses further reveal tends overestimate size, particularly bacteria, where estimated be more than five times larger those expected by We address biases proposing Bayesian estimator size accounts mutations. To illustrate how models influence quantification forces other drift, present case study showing exaggerates intensity selective constraints acting three codon positions bacterium Pseudomonas fluorescens . emphasizes importance considering highly diverse accurate inference.

Language: Английский

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Low Mutation Rate and Atypical Mutation Spectrum in Prasinoderma coloniale: Insights From an Early Diverging Green Lineage

Genome Biology and Evolution, Journal Year: 2025, Volume and Issue: 17(3)

Published: March 1, 2025

Mutations are the ultimate source of genetic diversity on which natural selection and drift act, playing a crucial role in evolution long-term adaptation. At molecular level, spontaneous mutation rate (µ), defined as number mutations per base generation, thus determines adaptive potential species. Through accumulation experiment, we estimate spectrum Prasinoderma coloniale, phytoplankton species from an early-branching lineage within Archaeplastida, characterized by unusually high genomic guanine-cytosine (GC) content (69.8%). We find that P. coloniale has very low total µ = 2.00 × 10-10. The insertion-deletion is almost 5 times lesser than single nucleotide with µID 3.40 10-11 µSNM 1.62 also exhibits atypical mutational spectrum: While essentially all other eukaryotes show bias toward GC to AT mutations, no evidence this AT-bias observed coloniale. Since cytosine methylation known be mutagenic, hypothesized may result absence C-methylation. Surprisingly, found levels C-methylation (14% 5mC, 25% 5mCG contexts). Methylated cytosines did not increased rates compared unmethylated ones, supporting prevailing notion universally leads higher rates. Overall, combines GC-rich genome original spectrum, suggesting universal have been present ancestor green lineage.

Language: Английский

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