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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Three problems in the genetics of speciation by selection

Proceedings of the National Academy of Sciences, Год журнала: 2022, Номер 119(30)

Опубликована: Июль 18, 2022

Speciation is the process by which barriers to gene flow evolve between populations. Although we now know that speciation largely driven natural selection, knowledge of agents selection and genetic genomic mechanisms facilitate divergence required for a satisfactory theory speciation. In this essay, highlight three advances/problems in our understanding have arisen from studies genes regions underlie evolution reproductive isolation. First, describe how identification “speciation” makes it possible identify causing isolation, while also noting link genetics phenotypic intrinsic postzygotic remains tenuous. Second, discuss important role recombination suppressors facilitating with flow, but point out means timing become associated cold spots uncertain. Third, establish importance ancient variation speciation, although argue focus on evolutionarily young groups may bias conclusions favor relative new mutations.

Язык: Английский

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Genomics of plant speciation

Plant Communications, Год журнала: 2023, Номер 4(5), С. 100599 - 100599

Опубликована: Апрель 12, 2023

Studies of plants have been instrumental for revealing how new species originate. For several decades, botanical research has complemented and, in some cases, challenged concepts on speciation developed via the study other organisms while also additional ways which can form. Now, ability to sequence genomes at an unprecedented pace and scale allowed biologists settle decades-long debates tackle emerging challenges research. Here, we review these recent genome-enabled developments plant speciation. We discuss complications related identification reproductive isolation (RI) loci using analyses landscape genomic divergence highlight important role that structural variants speciation, as increasingly revealed by sequencing technologies. Further, genomics advanced what know routes formation, like hybridization or whole-genome duplication, casting doubt others, population bottlenecks genetic drift. While fast-track genes mutations confer RI, emphasize follow-up molecular field experiments remain critical. Nonetheless, clarified outsized ancient rather than mutations, particularly early during conclude highlighting promising avenues future study. These include expanding so far about epigenetic changes broadening scope taxonomic breadth studies, synthesizing information from extensive data already generated community.

Язык: Английский

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Evolutionary genomics of oceanic island radiations

Trends in Ecology & Evolution, Год журнала: 2023, Номер 38(7), С. 631 - 642

Опубликована: Март 2, 2023

Язык: Английский

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Genomic insights into rapid speciation within the world’s largest tree genus Syzygium

Nature Communications, Год журнала: 2022, Номер 13(1)

Опубликована: Сен. 12, 2022

Species radiations, despite immense phenotypic variation, can be difficult to resolve phylogenetically when genetic change poorly matches the rapidity of diversification. Genomic potential furnished by palaeopolyploidy, and relative roles for adaptation, random drift hybridisation in apportionment remain understood factors. Here, we study these aspects a model radiation, Syzygium, most species-rich tree genus worldwide. Genomes 182 distinct species 58 unidentified taxa are compared against chromosome-level reference genome sea apple, Syzygium grande. We show that while shares an ancient doubling event with other Myrtales, little evidence exists recent polyploidy events. Phylogenomics confirms originated Australia-New Guinea diversified multiple migrations, eastward Pacific westward India Africa, bursts speciation visible as resolved branches on phylogenies. Furthermore, some sublineages demonstrate genomic clines recapitulate cladogenetic events, suggesting stepwise geographic speciation, neutral process, has been important

Язык: Английский

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Unraveling the extensive phylogenetic discordance and evolutionary history of spurless taxa within the Aquilegia ecalcarata complex

New Phytologist, Год журнала: 2025, Номер unknown

Опубликована: Март 7, 2025

Parallel evolution of the same, or at least very similar, phenotype(s) in different lineages is often interpreted as evidence for action natural selection. However, caution required when inferring parallel based on uncertain potentially incorrect phylogenetic frameworks. Here, by conducting extensive phylogenomic and population genetic analyses, we aim to clarify evolutionary history spurless taxa within Aquilegia ecalcarata complex. We observed substantial discordance patterns across entire genome, primarily attributed ancient introgression incomplete lineage sorting. Additionally, identified several whose positions were distorted admixture events. Using a backbone tree demographic modeling, determined that these independently originated twice this group. Intriguingly, our investigation revealed experienced expansion during global cooling, while their spurred sister groups underwent contraction. The losses petal spurs, therefore, may be linked adaptations low-temperature conditions. These findings emphasize importance comprehensive population-level analyses inference provide valuable insights into dynamics trait loss its implications adaptive strategies.

Язык: Английский

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Ancient hybridization leads to the repeated evolution of red flowers across a monkeyflower radiation

Evolution Letters, Год журнала: 2023, Номер 7(5), С. 293 - 304

Опубликована: Июнь 5, 2023

The reuse of old genetic variation can promote rapid diversification in evolutionary radiations, but most cases, the historical events underlying this divergence are not known. For example, ancient hybridization generate new combinations alleles that sort into descendant lineages, potentially providing raw material to initiate divergence. In Mimulus aurantiacus species complex, there is evidence for widespread gene flow among members radiation. addition, allelic MaMyb2 responsible differences flower color between closely related ecotypes subspecies puniceus, contributing reproductive isolation by pollinators. Previous work suggested was introgressed red-flowered ecotype puniceus. However, additional taxa within radiation have independently evolved red flowers from their yellow-flowered ancestors, raising possibility introgression had a more origin. study, we used repeated tests admixture whole-genome sequence data across diverse demonstrate has been both and recurrent group. signal removed due selection, suggesting barriers place taxa. Yet, roughly 30 kb region contains currently shared only Patterns admixture, divergence, extended haplotype homozygosity confirm history hybridization, where functional variants preserved positive selection lost counterparts. results study reveal against reduce genomic signatures provide essential facilitates evolution phenotypic traits lineages.

Язык: Английский

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Chromosome‐level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long‐reads, linked‐reads and Hi‐C

Molecular Ecology Resources, Год журнала: 2022, Номер 22(5), С. 1836 - 1854

Опубликована: Янв. 11, 2022

Telopea speciosissima, the New South Wales waratah, is an Australian endemic woody shrub in family Proteaceae. Waratahs have great potential as a model clade to better understand processes of speciation, introgression and adaptation, are significant from horticultural perspective. Here, we report first chromosome-level genome for T. speciosissima. Combining Oxford Nanopore long-reads, 10x Genomics Chromium linked-reads Hi-C data, assembly spans 823 Mb (scaffold N50 69.0 Mb) with 97.8% Embryophyta BUSCOs "Complete". We present new method Diploidocus (https://github.com/slimsuite/diploidocus) classifying, curating QC-filtering scaffolds, which combines read depths, k-mer frequencies BUSCO predictions. also tool, DepthSizer (https://github.com/slimsuite/depthsizer), size estimation depth single-copy orthologues estimate be approximately 900 Mb. The largest 11 scaffolds contained 94.1% assembly, conforming expected number chromosomes (2n = 22). Genome annotation predicted 40,158 protein-coding genes, 351 rRNAs 728 tRNAs. investigated CYCLOIDEA (CYC) role determination floral symmetry, confirm presence two copies genome. Read analysis 180 "Duplicated" genes using DepthKopy (https://github.com/slimsuite/depthkopy), suggests almost all real duplications, increasing confidence highlighting possible need revise set this lineage. speciosissima reference (Tspe_v1) provides important genomic resource Proteaceae support conservation flora Australia further afield.

Язык: Английский

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The Role of Introgression During the Radiation of Endemic Fishes Adapted to Living at Extreme Altitudes in the Tibetan Plateau

Molecular Biology and Evolution, Год журнала: 2023, Номер 40(6)

Опубликована: Май 29, 2023

Abstract Recent genomic analyses of evolutionary radiations suggest that ancient introgression may facilitate rapid diversification and adaptive radiation. The loach genus Triplophysa, a with most species endemic to Tibetan Plateau, shows ecological diversity evolution represents potential example radiation linked the uplift Plateau. Here, we interrogate complex history Triplophysa fishes through analysis whole-genome sequences. By reconstructing phylogeny quantifying across this clade, simulating speciation migration processes, confirm extensive gene flow events occurred disparate species. Our results plays more substantial role than incomplete lineage sorting in underpinning phylogenetic discordance Triplophysa. also indicate regions affected by exhibit characteristics lower recombination rates nucleotide associate selection. Simulation tibetana suggests have been Gonghe Movement third resulting founder effects subsequent reduction Ne.

Язык: Английский

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Allopolyploid origin and diversification of the Hawaiian endemic mints

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Апрель 10, 2024

Abstract Island systems provide important contexts for studying processes underlying lineage migration, species diversification, and organismal extinction. The Hawaiian endemic mints (Lamiaceae family) are the second largest plant radiation on isolated Islands. We generated a chromosome-scale reference genome one species, Stenogyne calaminthoides , resequenced 45 relatives, representing 34 to uncover continental origins of this group their subsequent diversification. further 109 individuals two purported hybrids, found high Mauna Kea volcano island Hawai’i. three distinct genera, Haplostachys Phyllostegia nested inside fourth genus, Stachys . uncovered four independent polyploidy events within including allopolyploidy event direct western North American ancestors. While taxa may have principally diversified by parapatry drift in small fragmented populations, localized admixture played an role early Our genomic analyses view into how organisms radiated chains, settings that provided principal natural laboratories Darwin’s thinking about evolutionary process.

Язык: Английский

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