Recombination and selection against introgressed DNA

Evolution, Journal Year: 2023, Volume and Issue: 77(4), P. 1131 - 1144

Published: Feb. 13, 2023

Abstract Introgressed DNA is often deleterious at many loci in the recipient species’ genome, and therefore purged by selection. Here, we use mathematical modeling whole-genome simulations to study influence of recombination on this process. We find that aggregate controls genome-wide rate purging early generations after admixture, when most rapid. Aggregate influenced number chromosomes heterogeneity their size, crossovers locations along chromosomes. A comparative prediction species with fewer should purge introgressed ancestry more profoundly, exhibit weaker genomic signals historical introgression. Turning within-genome patterns, show that, autosomal both sexes, expected sex than autosomes, all else equal. The opposite holds for without heterogametic sex. Finally, positive correlations between have recently been observed within genomes several species. these are likely driven not recombination’s effect unlinking neutral from alleles, but alleles themselves.

Language: Английский

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Five millennia of mitonuclear discordance in Atlantic bluefin tuna identified using ancient DNA

Heredity, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 7, 2025

Mitonuclear discordance between species is readily documented in marine fishes. Such may either be the result of past natural phenomena or recent introgression from previously seperated after shifts their spatial distributions. Using ancient DNA spanning five millennia, we here investigate long-term presence Pacific bluefin tuna (Thunnus orientalis) and albacore alalunga) -like mitochondrial (MT) genomes Atlantic thynnus), a with extensive exploitation history observed abundance age structure. Comparing (n = 130) modern 78) MT most its range, detect no significant temporal population structure, which implies ongoing gene flow populations large effective sizes over millennia. Moreover, identify discordant haplotypes specimens up to 5000 years old find that frequency these has remained similar through time. We therefore conclude not driven by introgression. Our observations provide oldest example directly environment, highlighting utility obtain insights persistence such phenomena.

Language: Английский

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Re-evaluating Homoploid Reticulate Evolution in Helianthus Sunflowers

Molecular Biology and Evolution, Journal Year: 2023, Volume and Issue: 40(2)

Published: Jan. 17, 2023

Abstract Sunflowers of the genus Helianthus are models for hybridization research and contain three best-studied examples homoploid hybrid speciation. To understand a broader picture within annual sunflowers, we used whole-genome resequencing to conduct phylogenomic analysis test gene flow between lineages. We find that all sunflower species tested have evidence admixture, suggesting was common during radiation genus. Support major tree decreases with increasing recombination rate, consistent introgression contributing discordant topologies. Admixture graphs found be associated origins putative (Helianthus anomalus, deserticola, paradoxus). However, events more ancient than suggested by previous work. Furthermore, H. anomalus deserticola appear arisen from single event involving an unexpected donor, rather through multiple independent as previously proposed. This means our results with, but not definitive proof of, two speciation in Using data set covers whole genus, including perennial species, signals span beyond, highly divergent and/or sorting haplotypes. Thus, can viewed syngameon which largely reproductively isolated linked together occasional or frequent flow.

Language: Английский

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Leveraging shared ancestral variation to detect local introgression

PLoS Genetics, Journal Year: 2024, Volume and Issue: 20(1), P. e1010155 - e1010155

Published: Jan. 8, 2024

Introgression is a common evolutionary phenomenon that results in shared genetic material across non-sister taxa. Existing statistical methods such as Patterson's D statistic can detect introgression by measuring an excess of derived alleles between populations. The effective to genome-wide patterns but give spurious inferences when applied local regions. We propose new statistic, D+, leverages both ancestral and infer introgressed Incorporating increases the number informative sites per region, improving our ability identify introgression. use coalescent framework derive expected value this function different demographic parameters under instantaneous admixture model simulations compute power precision D+. While D+ comparable, has better than D. apply empirical data from 1000 Genome Project Heliconius butterflies targets humans butterflies.

Language: Английский

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Ploidy as a leaky reproductive barrier: mechanisms, rates and evolutionary significance of interploidy gene flow

Annals of Botany, Journal Year: 2024, Volume and Issue: unknown

Published: June 13, 2024

Abstract Background Whole-genome duplication (polyploidization) is a dominant force in sympatric speciation, particularly plants. Genome doubling instantly poses barrier to gene flow owing the strong crossing incompatibilities between individuals differing ploidy. The strength of barrier, however, varies from species and recent genetic investigations revealed cases rampant interploidy introgression multiple ploidy-variable species. Scope Here, we review novel insights into frequency natural systems summarize underlying mechanisms promoting flow. Field surveys, occasionally complemented by experiments, suggest frequent opportunities for flow, direction diploid tetraploid, (higher) polyploids. However, scarcity accompanying population evidence virtual lack integration these approaches leave levels realized nature largely unknown. Finally, discuss potential consequences genome permeability on polyploid speciation adaptation highlight avenues that have just recently been opened very first genomic studies Standing stark contrast with rapidly accumulating evolutionary importance homoploid introgression, similar are yet be documented. Conclusions genomics era provides opportunity re-evaluate role adaptation. To achieve this goal, interdisciplinary bordering ecology genetics needed.

Language: Английский

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Fisher's Geometric Model as a Tool to Study Speciation

Cold Spring Harbor Perspectives in Biology, Journal Year: 2024, Volume and Issue: 16(7), P. a041442 - a041442

Published: Jan. 22, 2024

Hilde Schneemann1, Bianca De Sanctis1,2 and John J. Welch1 1Department of Genetics, University Cambridge, Cambridge CB2 3EH, United Kingdom 2Department Zoology, 3EJ, Correspondence: hilde.schneemann{at}evobio.eu

Language: Английский

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Phylogenomic comparative methods: Accurate evolutionary inferences in the presence of gene tree discordance

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(22)

Published: May 22, 2023

Phylogenetic comparative methods have long been a mainstay of evolutionary biology, allowing for the study trait evolution across species while accounting their common ancestry. These analyses typically assume single, bifurcating phylogenetic tree describing shared history among species. However, modern phylogenomic shown that genomes are often composed mosaic histories can disagree both with and each other-so-called discordant gene trees. trees describe not captured by tree, therefore unaccounted in classic approaches. The application standard to containing discordance leads incorrect inferences about timing, direction, rate evolution. Here, we develop two approaches incorporating into methods: one constructs an updated variance-covariance matrix from trees, another applies Felsenstein's pruning algorithm over set calculate likelihoods. Using simulation, demonstrate our generate much more accurate estimates tree-wide rates than methods. We apply clades wild tomato genus Solanum varying discordance, demonstrating contribution variation floral traits. Our potential be applied broad range inference problems phylogenetics, including ancestral state reconstruction lineage-specific shifts.

Language: Английский

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Interploidy Introgression Shaped Adaptation during the Origin and Domestication History of Brassica napus

Molecular Biology and Evolution, Journal Year: 2023, Volume and Issue: 40(9)

Published: Sept. 1, 2023

Polyploidy is recurrent across the tree of life and known as an evolutionary driving force in plant diversification crop domestication. How polyploid plants adapt to various habitats has been a fundamental question that remained largely unanswered. Brassica napus major cultivated worldwide, resulting from allopolyploidy between unknown accessions diploid B. rapa oleracea. Here, we used whole-genome resequencing data representing majority morphotypes ecotypes species rapa, oleracea, investigate role polyploidy during To do so, first reconstructed phylogenetic history napus, which supported hypothesis emergence derived hybridization European turnip wild These analyses also showed swede Siberian kale (used vegetable fodder) were domesticated before rapeseed (oil crop). We next observed frequent interploidy introgressions sympatric diploids prominent throughout domestication napus. Introgressed genomic regions shown increase overall genetic diversity tend be localized high recombination. detected numerous candidate adaptive introgressed found evidence some genes these contributed phenotypic adaptation different morphotypes. Overall, our results shed light on origin demonstrate introgression important mechanism fuels rapid species.

Language: Английский

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The fitness of an introgressing haplotype changes over the course of divergence and depends on its size and genomic location

PLoS Biology, Journal Year: 2023, Volume and Issue: 21(7), P. e3002185 - e3002185

Published: July 17, 2023

The genomic era has made clear that introgression, or the movement of genetic material between species, is a common feature evolution. Examples both adaptive and deleterious introgression exist in variety systems. What unclear how fitness an introgressing haplotype changes as species diverge size changes. In simple model, we show may more easily occur into parts genome which have not diverged heavily from ancestor. key insight alleles shared background are likely to positive epistatic interactions, increasing larger block. regions where few existing substitutions disrupted, this epistasis can be than incompatibilities with recipient genome. Further, early process divergence, large haplotypes favored individual alleles. This model consistent observations relationship recombination rate frequency across genome; however, it generates several novel predictions. First, suggests exist, negative, recently pairs. Furthermore, replaces derived variation will at sites carrying ancestral variants. These predictions tested example Drosophila melanogaster , some support for both. Finally, provides potential alternative explanation asymmetry direction expectations higher rapidly populations slowly evolving ones.

Language: Английский

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Uncovering ghost introgression through genomic analysis of a distinct eastern Asian hickory species

The Plant Journal, Journal Year: 2024, Volume and Issue: 119(3), P. 1386 - 1399

Published: June 6, 2024

SUMMARY Ghost introgression, or the transfer of genetic material from extinct unsampled lineages to sampled species, has attracted much attention. However, conclusive evidence for ghost especially in plant remains scarce. Here, we newly assembled chromosome‐level genomes both Carya sinensis and cathayensis , additionally re‐sequenced whole 43 C. individuals as well 11 representing diploid hickory species. These genomic datasets were used investigate reticulation bifurcation patterns within genus (Juglandaceae), with a particular focus on beaked . By combining D ‐statistic BPP methods, obtained compelling that supports occurrence introgression an ancestral lineage. This conclusion was reinforced through phylogenetic network analysis genome scan method VolcanoFinder, latter which can detect signatures adaptive unknown donors. Our results not only dispel certain misconceptions about history but also further refine our understanding 's biogeography via divergence estimates. Moreover, successful integration methods demonstrates their efficacy facilitating more precise identification types.

Language: Английский

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