Crossover Interference: Shedding Light on the Evolution of Recombination

Annual Review of Genetics, Journal Year: 2019, Volume and Issue: 53(1), P. 19 - 44

Published: Aug. 20, 2019

Through recombination, genes are freed to evolve more independently of one another, unleashing genetic variance hidden in the linkage disequilibrium that accumulates through selection combined with drift. Yet crossover numbers evolutionarily constrained, at least and not many than per bivalent most taxa. Crossover interference, whereby a reduces probability neighboring crossover, contributes this homogeneity. The mechanisms by which interference is achieved crossovers regulated major current subject inquiry, facilitated novel methods visualize pinpoint recombination events. Here, we review patterns models built describe process. We then discuss selective forces have likely shaped regulation numbers.

Language: Английский

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Patterns of recombination in snakes reveal a tug-of-war between PRDM9 and promoter-like features

Science, Journal Year: 2024, Volume and Issue: 383(6685)

Published: Feb. 22, 2024

In some mammals, notably humans, recombination occurs almost exclusively where the protein PRDM9 binds, whereas in vertebrates lacking an intact

Language: Английский

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Understanding the Genetic Basis of Variation in Meiotic Recombination: Past, Present, and Future

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(7)

Published: July 1, 2024

Meiotic recombination is a fundamental feature of sexually reproducing species. It often required for proper chromosome segregation and plays important role in adaptation the maintenance genetic diversity. The molecular mechanisms are remarkably conserved across eukaryotes, yet meiotic genes proteins show substantial variation their sequence function, even between closely related Furthermore, rate distribution shows huge diversity within chromosomes, individuals, sexes, populations, This has implications many evolutionary processes, how why this evolved not well understood. A key step understanding trait evolution to determine its basis-that is, number, effect sizes, loci underpinning variation. In perspective, I discuss past current knowledge on basis distribution, explore implications, present open questions future research.

Language: Английский

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Fine-Scale Map Reveals Highly Variable Recombination Rates Associated with Genomic Features in the Eurasian Blackcap

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(1)

Published: Jan. 1, 2024

Abstract Recombination is responsible for breaking up haplotypes, influencing genetic variability, and the efficacy of selection. Bird genomes lack protein PR domain-containing 9, a key determinant recombination dynamics in most metazoans. Historical maps birds show an apparent stasis positioning events. This highly conserved pattern over long timescales may constrain evolution birds. At same time, extensive variation rate observed across genome between different species Here, we characterize fine-scale historical map iconic migratory songbird, Eurasian blackcap (Sylvia atricapilla), using linkage disequilibrium–based approach that accounts population demography. Our results reveal variable rates among within chromosomes, which associate positively with nucleotide diversity GC content negatively chromosome size. increased significantly at regulatory regions but not necessarily gene bodies. CpG islands are associated strongly rates, though their specific position local DNA methylation patterns likely influence this relationship. The association retrotransposons varied according to family location. also provide evidence heterogeneous intrachromosomal conservation its closest sister taxon, garden warbler. These findings highlight considerable variability scales role genomic features shaping variation. study opens possibility further investigating impact on population-genomic features.

Language: Английский

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PRDM9 drives the location and rapid evolution of recombination hotspots in salmonid fish

PLoS Biology, Journal Year: 2025, Volume and Issue: 23(1), P. e3002950 - e3002950

Published: Jan. 6, 2025

In many eukaryotes, meiotic recombination occurs preferentially at discrete sites, called hotspots. various lineages, hotspots are located in regions with promoter-like features and evolutionarily stable. Conversely, some mammals, driven by PRDM9 that targets away from promoters. Paradoxically, induces the self-destruction of its this triggers an ultra-fast evolution mammalian is ancestral to all animals, suggesting a critical importance for program, but has been lost lineages surprisingly little effect on meiosis success. However, it unclear whether function described mammals shared other species. To investigate this, we analyzed landscape several salmonids, genome which harbors one full-length truncated paralogs. We identified initiation sites Oncorhynchus mykiss mapping DNA double-strand breaks (DSBs). found DSBs clustered positioned promoters, enriched H3K4me3 H3K36me3 location depended genotype Prdm9 . observed high level polymorphism zinc finger domain , indicating diversification positive selection. Moreover, population-scaled maps O kisutch Salmo salar revealed rapid turnover caused target motif erosion. Our results imply conserved across vertebrates peculiar evolutionary runaway active hundred million years.

Language: Английский

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Sex Differences in the Recombination Landscape

The American Naturalist, Journal Year: 2019, Volume and Issue: 195(2), P. 361 - 379

Published: June 14, 2019

Sex differences in overall recombination rates are well known, but little theoretical or empirical attention has been given to how and why sexes differ their landscapes: the patterns of along chromosomes. In first scientific review this phenomenon, we find that is biased toward telomeres males more uniformly distributed females most vertebrates many other eukaryotes. Notable exceptions pattern exist, however. Fine-scale also frequently between females. The molecular mechanisms responsible for sex remain unclear, chromatin landscapes play a role. Why these evolve unclear. Hypotheses suggest they may result from sexually antagonistic selection acting on coding genes regulatory elements, meiotic drive females, during haploid phase life cycle, against aneuploidy, mechanistic constraints. No single hypothesis, however, can adequately explain evolution all cases. Sex-specific have important consequences population differentiation chromosome evolution.

Language: Английский

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Recombination-Aware Phylogenomics Reveals the Structured Genomic Landscape of Hybridizing Cat Species

Molecular Biology and Evolution, Journal Year: 2019, Volume and Issue: 36(10), P. 2111 - 2126

Published: June 10, 2019

Current phylogenomic approaches implicitly assume that the predominant phylogenetic signal within a genome reflects true evolutionary history of organisms, without assessing confounding effects postspeciation gene flow can produce mosaic signals interact with recombinational variation. Here, we tested validity this assumption analysis 27 species cat family, local recombination rate on tree inference and divergence time estimation across their genomes. We found prevailing autosomes is not always representative most probable speciation history, due to ancient hybridization throughout felid evolution. Instead, was concentrated regions low recombination, notably enriched large X chromosome cold spots exhibited recurrent patterns strong genetic differentiation selective sweeps mammalian orders. By contrast, high were for signatures flow, these sequences inflated crown-lineage times by ∼40%. conclude existing infer Tree Life may be highly misleading considering genomic architecture relative its interplay historical hybridization.

Language: Английский

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From molecules to populations: appreciating and estimating recombination rate variation

Nature Reviews Genetics, Journal Year: 2020, Volume and Issue: 21(8), P. 476 - 492

Published: May 29, 2020

Language: Английский

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The genomic impact of historical hybridization with massive mitochondrial DNA introgression

Genome biology, Journal Year: 2018, Volume and Issue: 19(1)

Published: July 17, 2018

The extent to which selection determines interspecific patterns of genetic exchange enlightens the role adaptation in evolution and speciation. Often reported extensive introgression could be selection-driven, but also result from demographic processes, especially cases invasive species replacements, can promote at their invasion front. Because selective sweeps similarly mold variation, population genetics evidence for only gathered an explicit framework. Iberian hare, Lepus granatensis, displays its northern range mitochondrial DNA L. timidus, arctic/boreal that it replaced locally after last glacial maximum. We use whole-genome sequencing infer geographic genomic nuclear fit a neutral model replacement with hybridization, allowing us evaluate how influenced genome-wide, including mtDNA.Although average mtDNA contrast strongly, they single post-glacial timidus by granatensis. Outliers elevated include several genes related immunity, spermatogenesis, metabolism. Introgression is reduced on X chromosome low recombining regions.General explained purely processes. Hybrid incompatibilities interplay between recombination modulate levels introgression. Selection promoted some involved conflicts, either (parasites) or possibly cytonuclear. In latter case, mitigate potential negative effects alien metabolism male-specific traits.

Language: Английский

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Efficiently Summarizing Relationships in Large Samples: A General Duality Between Statistics of Genealogies and Genomes

Genetics, Journal Year: 2020, Volume and Issue: 215(3), P. 779 - 797

Published: May 2, 2020

Abstract As a genetic mutation is passed down across generations, it distinguishes those genomes that have inherited from not, providing glimpse of the genealogical tree relating to each other at site. Statistical summaries variation therefore also describe underlying genealogies. We use this correspondence define general framework efficiently computes single-site population statistics using succinct sequence encoding genealogies and genome sequence. The approach accumulates sample weights within position on genome, which are then combined summary function; different result choices weight function. Results can be reported in three ways: by site, corresponds calculated as usual sequence; branch, gives expected value dual site statistic under infinite sites model mutation, node, summarizes contribution ancestor these statistics. implement many currently defined (making statistics’ relationship trees concrete explicit), well corresponding branch shape. evaluate computational performance simulated data, show calculating sequences several orders magnitude more efficient than optimized matrix-based methods terms both run time memory requirements. explore how duality between holds practice inferred 1000 Genomes Project data set, discuss ways deviations may encode interesting biological signals.

Language: Английский

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