Deep reticulation: the long legacy of hybridization in vascular plant evolution

The Plant Journal, Год журнала: 2023, Номер 114(4), С. 743 - 766

Опубликована: Фев. 13, 2023

Hybridization has long been recognized as a fundamental evolutionary process in plants but, until recently, our understanding of its phylogenetic distribution and biological significance across deep scales largely obscure. Over the past decade, genomic phylogenomic datasets have revealed, perhaps not surprisingly, that hybridization, often associated with polyploidy, common throughout history plants, particularly various lineages flowering plants. However, studies also highlighted challenges disentangling signals ancient hybridization from other sources conflict (in particular, incomplete lineage sorting). Here, we provide critical review vascular outlining well-documented cases plant phylogeny, well unique to documenting versus recent hybridization. We definition for which, knowledge, explicitly attempted before. Further extent reticulation should remain an important research focus, especially because published examples likely represent tip iceberg terms total future increasingly explore macroevolutionary this process, impact on trajectories (e.g. how does influence trait evolution or generation biodiversity over time scales?), life ecological factors shape, shaped, frequency geologic phylogeny. Finally, consider implications ubiquitous conceptualize, analyze, classify Networks, opposed bifurcating trees, more accurate representations many cases, although ability infer, visualize, use networks comparative analyses is highly limited. Developing improved methods generation, visualization, represents direction biology. Current classification systems do generally allow recognition reticulate lineages, classifications themselves are based evidence chloroplast genome. Updating better reflect nuclear phylogenies, considering whether recognize systems, will challenge systematics community.

Язык: Английский

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Genome-wide analyses of introgression between two sympatric Asian oak species

Nature Ecology & Evolution, Год журнала: 2022, Номер 6(7), С. 924 - 935

Опубликована: Май 5, 2022

Язык: Английский

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Population genomics unravels the Holocene history of bread wheat and its relatives

Nature Plants, Год журнала: 2023, Номер 9(3), С. 403 - 419

Опубликована: Март 16, 2023

Язык: Английский

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Comparative genomics reveals the dynamics of chromosome evolution in Lepidoptera

Nature Ecology & Evolution, Год журнала: 2024, Номер 8(4), С. 777 - 790

Опубликована: Фев. 21, 2024

Chromosomes are a central unit of genome organization. One-tenth all described species on Earth butterflies and moths, the Lepidoptera, which generally possess 31 chromosomes. However, some display dramatic variation in chromosome number. Here we analyse 210 chromosomally complete lepidopteran genomes show that chromosomes extant lepidopterans derived from 32 ancestral linkage groups, term Merian elements. elements have remained largely intact through 250 million years evolution diversification. Against this stable background, eight lineages undergone extensive reorganization either numerous fissions or combination fusion fission events. Outside these lineages, fusions rare rarer still. Fusions often involve small, repeat-rich sex-linked element. Our results reveal constraints architecture Lepidoptera provide deeper understanding chromosomal rearrangements eukaryotic evolution.

Язык: Английский

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Chromosome evolution in Lepidoptera

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Май 14, 2023

Abstract Chromosomes are a central unit of genome organisation. One tenth all described species on Earth Lepidoptera, butterflies and moths, these generally possess 31 holocentric chromosomes. However, subset lepidopteran display dramatic variation in chromosome counts. By analysing 210 chromosomally-complete genomes, the largest analysis eukaryotic chromosomal-level reference genomes to date, we show that diverse karyotypes extant derived from 32 ancestral linkage groups, which term Merian elements. elements have remained largely intact across 250 million years evolution diversification. Against this stable background, identify eight independent lineages evaded constraint undergone extensive reorganisation - either by numerous fissions or combination fusion fission events. Outside lineages, fusions rare rarer still. Fusions tend involve small, repeat-rich and/or Z chromosome. Together, our results reveal constraints architecture Lepidoptera enable deeper understanding importance chromosomal rearrangements shaping genomes.

Язык: Английский

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Genome assemblies of 11 bamboo species highlight diversification induced by dynamic subgenome dominance

Nature Genetics, Год журнала: 2024, Номер 56(4), С. 710 - 720

Опубликована: Март 15, 2024

Abstract Polyploidy (genome duplication) is a pivotal force in evolution. However, the interactions between parental genomes polyploid nucleus, frequently involving subgenome dominance, are poorly understood. Here we showcase analyses of bamboo system (Poaceae: Bambusoideae) comprising series lineages from diploid (herbaceous) to tetraploid and hexaploid (woody), with 11 chromosome-level de novo genome assemblies 476 transcriptome samples. We find that woody subgenomes exhibit stunning karyotype stability, parallel dominance two clades gradual shift clade. Allopolyploidization have shaped evolution tree-like lignified culms, rapid growth synchronous flowering characteristic bamboos as large grasses. Our work provides insights into remarkable system, including its dependence on genomic context ability switch which dominant over evolutionary time.

Язык: Английский

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Hybrid speciation driven by multilocus introgression of ecological traits

Nature, Год журнала: 2024, Номер 628(8009), С. 811 - 817

Опубликована: Апрель 17, 2024

Abstract Hybridization allows adaptations to be shared among lineages and may trigger the evolution of new species 1,2 . However, convincing examples homoploid hybrid speciation remain rare because it is challenging demonstrate that hybridization was crucial in generating reproductive isolation 3 Here we combine population genomic analysis with quantitative trait locus mapping species-specific traits examine a case Heliconius butterflies. We show elevatus sympatric both parents has persisted as an independently evolving lineage for at least 180,000 years. This despite pervasive ongoing gene flow one parent, pardalinus , which homogenizes 99% their genomes. The remaining 1% introgressed from other melpomene scattered widely across H. genome islands divergence These contain multiple are under disruptive selection, including colour pattern, wing shape, host plant preference, sex pheromones mate choice. Collectively, these place on its own adaptive peak permit coexistence parents. Our results driven by introgression ecological traits, possible multilocus genetic architecture.

Язык: Английский

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Ancestral Hybridization Facilitated Species Diversification in the Lake Malawi Cichlid Fish Adaptive Radiation

Molecular Biology and Evolution, Год журнала: 2019, Номер 37(4), С. 1100 - 1113

Опубликована: Дек. 6, 2019

The adaptive radiation of cichlid fishes in East African Lake Malawi encompasses over 500 species that are believed to have evolved within the last 800,000 years from a common founder population. It has been proposed hybridization between ancestral lineages can provide genetic raw material fuel such exceptionally high diversification rates, and evidence for this recently presented Victoria region superflock. Here, we report genomes also show two split 3-4 Ma, today represented by cichlids riverine Astatotilapia sp. "ruaha blue." ancestries present large blocks several kilobases, but there is little variation pattern species, suggesting large-scale mosaic structure was largely established prior radiation. Nevertheless, tens thousands polymorphic variants apparently derived interspersed genomes. These loci striking excess differentiation across ecological subgroups assemblage, parental alleles sort differentially into benthic pelagic lineages, consistent with strong differential selection on these during divergence. Furthermore, enriched genes involved immune response vision, including opsin previously identified as important speciation. Our results reinforce role explosive demonstrating its significance one largest recent vertebrate radiations.

Язык: Английский

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Genomics of Evolutionary Novelty in Hybrids and Polyploids

Frontiers in Genetics, Год журнала: 2020, Номер 11

Опубликована: Июль 28, 2020

It has long been recognized that hybridization and polyploidy are prominent processes in plant evolution. Although classically as significant speciation adaptation, recognition of the importance interspecific gene flow dramatically increased during genomics era, concomitant with an unending flood empirical examples, or without genome doubling. Interspecific is thus increasingly thought to lead evolutionary innovation diversification, via adaptive introgression, homoploid hybrid allopolyploid speciation. Less well understood, however, suite genetic genomic mechanisms set motion by merger differentiated genomes, temporal scale over which recombinational complexity mediated might be expressed exposed natural selection. We focus on these issues here, considering types molecular saltational event between two diverged species, either doubling, how various can contribute novel phenotypes. Genetic include infusion new alleles genesis structural variation including translocations inversions, homoeologous exchanges, transposable element mobilization insertional effects, presence-absence copy number variation. Polyploidy generates massive transcriptomic regulatory alteration, presumably disrupted stoichiometries factors, small RNAs other interactions cascade from single-gene expression change up through entire networks transformed modules. highlight both combinatorial possibilities range scales such generated, selection drift.

Язык: Английский

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Adaptive Introgression across Semipermeable Species Boundaries between Local Helicoverpa zea and Invasive Helicoverpa armigera Moths

Molecular Biology and Evolution, Год журнала: 2020, Номер 37(9), С. 2568 - 2583

Опубликована: Апрель 23, 2020

Abstract Hybridization between invasive and native species has raised global concern, given the dramatic increase in range shifts pest outbreaks due to anthropogenic dispersal. Nevertheless, secondary contact sister lineages of local provides a natural laboratory understand factors that determine introgression maintenance or loss barriers. Here, we characterize early evolutionary outcomes following Helicoverpa armigera H. zea Brazil. We carried out whole-genome resequencing moths from Brazil two temporal samples: during outbreak 2013 2017. There is evidence for burst hybridization widespread into coinciding with expansion 2013. However, armigera, admixture proportion length introgressed blocks were significantly reduced 2017, suggesting selection against admixture. In contrast genome-wide pattern, there was striking adaptive single region zea, including an insecticide resistance allele increased frequency over time. summary, despite extensive gene flow after contact, boundaries are largely maintained except containing insecticide-resistant locus. document worst-case scenario species, which now instead one, acquired pyrethroid insecticides through introgression.

Язык: Английский

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