Experimental estimates of germline mutation rate in eukaryotes: a phylogenetic meta-analysis

Evolution Letters, Journal Year: 2023, Volume and Issue: 7(4), P. 216 - 226

Published: June 19, 2023

Mutation is the ultimate source of all genetic variation, and over last 10 years ready availability whole-genome sequencing has permitted direct estimation mutation rate for many non-model species across tree life. In this meta-analysis, we make a comprehensive search literature estimates in eukaryotes, identifying 140 accumulation (MA) parent-offspring (PO) studies covering 134 species. Based on these data, revisit differences single-nucleotide (SNM) between different phylogenetic lineages update known relationships generation time, genome size, nucleotide diversity-while accounting nonindependence. We do not find significant difference MA PO estimated rates, but confirm that mammal plant have higher rates than arthropods unicellular eukaryotes lowest rates. are with longer times larger sizes, even when relationships. Moreover, although diversity positively correlated rate, gradient relationship significantly less one (on logarithmic scale), consistent populations smaller effective size. For 29 which data available, indel short deletions generally more common insertions. Nevertheless, despite recent progress, no either SNM or available majority deeply branching eukaryotic lineages-or most animal phyla. Even among charismatic megafauna, experimental remain unknown amphibia scarce reptiles fish.

Language: Английский

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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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A gene-based model of fitness and its implications for genetic variation: Genetic and inbreeding loads

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

Published: Feb. 21, 2025

Abstract In the companion paper to this, we examined consequences for patterns of linkage disequilibrium “gene” model fitness, which postulates that effects recessive or partially deleterious mutations located at different sites within a gene fail complement each other. Here, examine genetic and inbreeding loads, using both analytical simulation methods, contrast it with frequently used “sites” allows allelic complementation. We show results in slightly lower load, but much smaller than model, implying standard predictions mutational contributions depression may be overestimates. Synergistic epistasis between pairs was also modeled, shown considerably reduce load models. The theoretical are discussed relation data on Drosophila melanogaster .

Language: Английский

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Causes and Consequences of Varying Transposable Element Activity: An Evolutionary Perspective

Annual Review of Genomics and Human Genetics, Journal Year: 2024, Volume and Issue: 25(1), P. 1 - 25

Published: April 11, 2024

Transposable elements (TEs) are genomic parasites found in nearly all eukaryotes, including humans. This evolutionary success of TEs is due to their replicative activity, involving insertion into new locations. TE activity varies at multiple levels, from between taxa within individuals. The rapidly accumulating evidence the influence on human health, as well rapid growth tools study it, motivated an evaluation what we know about thus far. Here, discuss why varies, and consequences this variation, perspective. By studying nonhuman organisms context theories, can shed light factors that affect activity. While usually deleterious, some have lasting impacts by conferring benefits host or affecting other processes.

Language: Английский

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Double trouble: two retrotransposons triggered a cascade of invasions in Drosophila species within the last 50 years

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Jan. 9, 2025

Abstract Horizontal transfer of genetic material in eukaryotes has rarely been documented over short evolutionary timescales. Here, we show that two retrotransposons, Shellder and Spoink , invaded the genomes multiple species melanogaster subgroup within last 50 years. Through horizontal transfer, spread D. during 1980s, while both simulans 1990s. Possibly following hybridization, infected island endemic mauritiana (Mauritius) sechellia (Seychelles) with TEs after 1995. In same approximate time-frame, also teissieri a confined to sub-Saharan Africa. We find donors are likely American Drosophila from willistoni cardini repleta groups. Thus, described cascade TE invasions could only become feasible extended their distributions into Americas 200 years ago, aided by human activity. Our work reveals cascades invasions, initiated human-mediated range expansions, have an impact on genomic phenotypic evolution geographically dispersed species. Within few decades, invade many species, including endemics, very distant donor TE.

Language: Английский

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The adaptive value of recombination in resolving intralocus sexual conflict by gene duplication

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2025, Volume and Issue: 292(2039)

Published: Jan. 1, 2025

Recombination plays a key role in increasing the efficacy of selection. We investigate whether recombination can also play resolving adaptive conflicts at loci coding for traits shared between sexes. Errors during events resulting gene duplications may provide long-term evolutionary advantage if those experience sexually antagonistic (SA) selection since, after duplication, sex-specific expression profiles will be free to evolve, thereby reducing load on population fitness and conflict. The potential duplication tempered by short-term deleterious effects gamete zygote survival, which tolerable species with high reproductive output but not low output. used datasets candidate SA from Drosophila melanogaster humans test these ideas. As humans, alleles flies net positive across two sexes occurred higher frequencies than negative effects. In flies, rates were associated more intense levels sexual conflict genes paralogues occur regions rates, indicating are history Genes experiencing showed both proportion numbers paralogues. Together, our findings reveal multiple lines evidence possible route towards resolution an via that is facilitated rates.

Language: Английский

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On the origin of the P-element invasion in Drosophila simulans

Mobile DNA, Journal Year: 2025, Volume and Issue: 16(1)

Published: Feb. 26, 2025

Language: Английский

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Variation in the Spectrum of New Mutations among Inbred Strains of Mice

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(8)

Published: Aug. 1, 2024

The mouse serves as a mammalian model for understanding the nature of variation from new mutations, question that has both evolutionary and medical significance. Previous studies suggest rate single-nucleotide mutations (SNMs) in mice is ∼50% humans. However, information largely comes involving C57BL/6 strain, there little other strains. Here, we study accumulated 59 lines derived four inbred strains are commonly used genetics clinical research (BALB/cAnNRj, C57BL/6JRj, C3H/HeNRj, FVB/NRj), maintained eight to nine generations by brother-sister mating. By analyzing Illumina whole-genome sequencing data, estimate average SNMs ∼μ = 6.7 × 10-9. substantial spectrum among strains, so burden also varies For example, FVB strain markedly skewed toward C→A transversions likely experience higher deleterious load than due an increased frequency nonsense glutamic acid codons. Finally, observe DNA sequence contexts, CpG sites, their adjacent nucleotides playing important role.

Language: Английский

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The fitness consequences of genetic divergence between polymorphic gene arrangements

Genetics, Journal Year: 2023, Volume and Issue: 226(3)

Published: Dec. 26, 2023

Inversions restrict recombination when heterozygous with standard arrangements, but often have few noticeable phenotypic effects. Nevertheless, there are several examples of inversions that can be maintained polymorphic by strong selection under laboratory conditions. A long-standing model for the source such is divergence between arrangements respect to recessive or partially deleterious mutations, resulting in a selective advantage heterokaryotypic individuals over homokaryotypes. This paper uses combination analytical and numerical methods investigate this model, simple case an autosomal inversion multiple independent nucleotide sites subject mildly mutations. complete lack heterokaryotypes assumed, as well constancy frequency space time. It shown significantly higher mutational load will develop less frequent arrangement. only expected two alternative nearly equal frequency, so their loads very similar size. The effects some Drosophila pseudoobscura on fitness traits seem too large explained process, although it may contribute observed Several population genomic statistics provide evidence signatures reduced efficacy associated rarer currently little published data relevant theoretical predictions.

Language: Английский

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Effects ofWolbachiaon Transposable Element Expression Vary BetweenDrosophila melanogasterHost Genotypes

Genome Biology and Evolution, Journal Year: 2023, Volume and Issue: 15(3)

Published: Feb. 28, 2023

Abstract Transposable elements (TEs) are repetitive DNA sequences capable of changing position in host genomes, thereby causing mutations. TE insertions typically have deleterious effects but they can also be beneficial. Increasing evidence the contribution TEs to adaptive evolution further raises interest understanding what factors impact activity. Based on previous studies associating bacterial endosymbiont Wolbachia with changes abundance piRNAs, a mechanism for repression, and transposition specific TEs, we hypothesized that infection would interfere We tested this hypothesis by studying expression 14 panel 25 Drosophila melanogaster genotypes, naturally infected annotated insertions. The genotypes differed significantly titers inside individual flies, broad-sense heritability around 20%, number insertions, which depended greatly identity. By removing from target generated pairs Wolbachia-positive Wolbachia-negative lines quantified transcription levels our TEs. found variation was dependent status, identity, genotype. Comparing between removal affected 21.1% TE-genotype combinations tested, up 2.3 times differences median level transcript. Our data show activity underscoring importance generation genetic novelty hosts.

Language: Английский

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