Impact of whole-genome duplications on structural variant evolution in Cochlearia

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: June 25, 2024

Abstract Polyploidy, the result of whole-genome duplication (WGD), is a major driver eukaryote evolution. Yet WGDs are hugely disruptive mutations, and we still lack clear understanding their fitness consequences. Here, study whether in greater diversity genomic structural variants (SVs) how they influence evolutionary dynamics plant genus, Cochlearia (Brassicaceae). By using long-read sequencing graph-based pangenome, find both negative positive interactions between SVs. Masking recessive mutations due to leads progressive accumulation deleterious SVs across four ploidal levels (from diploids octoploids), likely reducing adaptive potential polyploid populations. However, also discover putative benefits arising from SV accumulation, as more ploidy-specific harbor signals local adaptation polyploids than diploids. Together, our results suggest that play diverse contrasting roles trajectories young polyploids.

Language: Английский

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The emerging importance of cross‐ploidy hybridisation and introgression

Molecular Ecology, Journal Year: 2024, Volume and Issue: 33(8)

Published: March 19, 2024

Abstract Natural hybridisation is now recognised as pervasive in its occurrence across the Tree of Life. Resurgent interest natural fuelled by developments genomics has led to an improved understanding genetic factors that promote or prevent species cross‐mating. Despite this body work overturning many widely held assumptions about barriers hybridisation, it still thought ploidy differences between will be absolute barrier and introgression. Here, we revisit assumption, reviewing findings from surveys polyploidy wild. In a case study British flora, 203 hybrids representing 35% with suitable data have formed via cross‐ploidy matings, while wider literature search revealed 59 studies (56 plants 3 animals) which been confirmed data. These results show readily overlooked, potentially common some groups. General these include strong directionality introgression usually towards higher parent, being more likely involve allopolyploids than autopolyploids. Evidence for adaptive cases hybrid speciation shows potential important evolutionary outcomes.

Language: Английский

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Adaptive introgression: how polyploidy reshapes gene flow landscapes

New Phytologist, Journal Year: 2021, Volume and Issue: 230(2), P. 457 - 461

Published: Jan. 17, 2021

Summary Rare yet accumulating evidence in both plants and animals shows that whole genome duplication (WGD, leading to polyploidy) can break down reproductive barriers, facilitating gene flow between otherwise isolated species. Recent population genomic studies wild, outcrossing Arabidopsis arenosa lyrata indicate this WGD‐potentiated be adaptive highly specific response particular environmental intracellular challenges. The mechanistic basis of WGD‐mediated easing species barrier strength seems primarily lie the relative dosage each parental endosperm. While generalisations about polyploids fraught, indicates breakdown these combined with diploid polyploid polyploids, allows some act as adaptable ‘allelic sponges’, enjoying increased potential respond challenging environments.

Language: Английский

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Novelty and Convergence in Adaptation to Whole Genome Duplication

Molecular Biology and Evolution, Journal Year: 2021, Volume and Issue: 38(9), P. 3910 - 3924

Published: March 29, 2021

Abstract Whole genome duplication (WGD) can promote adaptation but is disruptive to conserved processes, especially meiosis. Studies in Arabidopsis arenosa revealed a coordinated evolutionary response WGD involving interacting proteins controlling meiotic crossovers, which are minimized an autotetraploid (within-species polyploid) avoid missegregation. Here, we test whether this surprising flexibility of essential process, meiosis, recapitulated independent system, Cardamine amara, 17 My diverged from A. arenosa. We assess stability and perform population-based scans for positive selection, contrasting the genomic C. amara with that found strongest selection signals at genes predicted functions thought important WGD: chromosome remodeling, cell cycle, ion transport. However, responses two species differ: minimal ortholog-level convergence emerged, none meiosis exhibiting strong signal amara. This consistent our observations lower occasional clonal spreading diploid suggesting nascent lineages were preadapted by their lifestyle survive while enduring reduced fidelity. contrast lack ortholog convergence, see process-level network DNA management, organization, stress signaling, homeostasis processes. gives first insight into salient adaptations required meet challenges state shows autopolyploids utilize multiple trajectories adapt WGD.

Language: Английский

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Parallel adaptation in autopolyploid Arabidopsis arenosa is dominated by repeated recruitment of shared alleles

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: Aug. 17, 2021

Relative contributions of pre-existing vs de novo genomic variation to adaptation are poorly understood, especially in polyploid organisms. We assess this high resolution using autotetraploid Arabidopsis arenosa, which repeatedly adapted toxic serpentine soils that exhibit skewed elemental profiles. Leveraging a fivefold replicated invasion, we selection on SNPs and structural variants (TEs) 78 resequenced individuals discover significant parallelism candidate genes involved ion homeostasis. further model parallel infer repeated sweeps shared pool nearly all these loci, supporting theoretical expectations. A single striking exception is represented by TWO PORE CHANNEL 1, exhibits convergent evolution from independent mutations at an identical, otherwise conserved site the calcium channel selectivity gate. Taken together, suggests populations can rapidly adapt environmental extremes, calling both novel polymorphisms.

Language: Английский

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Robustness and the generalist niche of polyploid species: Genome shock or gradual evolution?

Current Opinion in Plant Biology, Journal Year: 2022, Volume and Issue: 69, P. 102292 - 102292

Published: Sept. 2, 2022

The prevalence of polyploidy in wild and crop species has stimulated debate over its evolutionary advantages disadvantages. Previous studies have focused on changes occurring at the polyploidization events, including genome-wide termed "genome shock," as well ancient polyploidy. Recent bioinformatics advances empirical Arabidopsis wheat relatives are filling a research gap: functional study polyploid using RNA-seq, DNA polymorphism, epigenomics. Polyploid can become generalists natura through environmental robustness by inheriting merging parental stress responses. Their evolvability is enhanced mutational working inherited standing variation. identification key genes responsible for gradual adaptive evolution will encourage synthetic biological approaches to transfer other species.

Language: Английский

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Deleterious Mutations Accumulate Faster in Allopolyploid Than Diploid Cotton (Gossypium) and Unequally between Subgenomes

Molecular Biology and Evolution, Journal Year: 2022, Volume and Issue: 39(2)

Published: Jan. 26, 2022

Whole-genome duplication (polyploidization) is among the most dramatic mutational processes in nature, so understanding how natural selection differs polyploids relative to diploids an important goal. Population genetics theory predicts that recessive deleterious mutations accumulate faster allopolyploids than due masking effect of redundant gene copies, but this prediction hitherto unconfirmed. Here, we use cotton genus (Gossypium), which contains seven derived from a single polyploidization event 1-2 Million years ago, investigate mutation accumulation. We two methods identifying at nucleotide and amino acid level, along with whole-genome resequencing 43 individuals spanning six allopolyploid species their diploid progenitors, demonstrate progenitors. find that, unlike what would be expected under models demographic changes alone, strongly show biggest difference between ploidy levels, diminishes for moderately mildly mutations. further proportion nonsynonymous are coresident subgenomes allopolyploids, suggesting homoeologous acts unequally subgenomes. Our results provide genome-wide perspective on classic notions significance likely broadly applicable implications our evolutionary fate Finally, note some measures (e.g., dN/dS, πN/πS) may biased when different levels compared.

Language: Английский

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Demographic history inference and the polyploid continuum

Genetics, Journal Year: 2023, Volume and Issue: 224(4)

Published: June 5, 2023

Polyploidy is an important generator of evolutionary novelty across diverse groups in the Tree Life, including many crops. However, impact whole-genome duplication depends on mode formation: doubling within a single lineage (autopolyploidy) versus after hybridization between two different lineages (allopolyploidy). Researchers have historically treated these scenarios as completely separate cases based patterns chromosome pairing, but represent ideals continuum chromosomal interactions among duplicated genomes. Understanding history polyploid species thus demands quantitative inferences demographic and rates exchange subgenomes. To meet this need, we developed diffusion models for genetic variation polyploids with subgenomes that cannot be bioinformatically separated potentially variable inheritance patterns, implementing them dadi software. We validated our using forward SLiM simulations found inference approach able to accurately infer parameters (timing, bottleneck size) involved formation auto- allotetraploids, well segmental allotetraploids. then applied empirical data allotetraploid shepherd's purse (Capsella bursa-pastoris), finding evidence allelic Taken together, model provides foundation modeling equations, which will help increase understanding demography selection lineages.

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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Autopolyploid lineage shows climatic niche expansion but not divergence inArabidopsis arenosa

American Journal of Botany, Journal Year: 2019, Volume and Issue: 106(1), P. 61 - 70

Published: Jan. 1, 2019

Premise of the Study Successful establishment neopolyploids, and therefore polyploid speciation, is thought to be contingent on environmental niche shifts from their progenitors. We explore this shift hypothesis in obligate outcrosser Arabidopsis arenosa complex, which includes diploid recently formed autotetraploid populations. Methods To characterize climatic niches for both cytotypes arenosa, we first gathered data localities with known ploidy types. then estimated diploids autotetraploids calculated overlap. Using overlap statistic, tested equivalency similarity. explored differences by estimating comparing optimum breadth indices expansion unfilling. Key Results Climatic between substantial. Although two models are not significantly divergent, they identical as differ along gradients. Autotetraploids fill nearly entire space have expanded into novel environments. Conclusions find but divergence, together a moderate change optimum, lineage . These results indicate that alone cannot explain coexistence tetraploid cytotypes.

Language: Английский

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