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

The Plant Journal, Journal Year: 2023, Volume and Issue: 114(4), P. 743 - 766

Published: Feb. 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.

Language: Английский

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Phylogenomics shed light on the complex evolutionary history of a gymnosperm genus showing East Asian–Tethyan disjunction

Journal of Systematics and Evolution, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 3, 2025

Abstract When and how disjunct distributions of biological taxa arose has long attracted interest in biogeography, yet the East Asian–Tethyan disjunction is understudied. Cupressus (Cupressaceae) shows this disjunction, with 10 species Asia three Mediterranean region. Here we used target‐capture sequencing obtained 1991 single‐copy nuclear genes, plus complete plastomes, to infer evolutionary history . Our phylogenomic reconstruction resolved four well supported clades , but revealed significant phylogenetic conflicts, inter‐lineage gene flow, incomplete lineage sorting tree estimation error all making important contributions. The Chengiana clade most likely originated by hybridization between ancestors Himalayan–Hengduan Mountains subtropical clades, whereas orogenic climatic changes may have facilitated flow within clade. Molecular dating suggested that recent common ancestor appeared around middle Eocene period then became continuously distributed across Eurasia. when diverged, been driven Eocene/Oligocene declines global temperature, reinforced ecogeographic barrier created uplift Qinghai–Tibet Plateau. Niche shifts clade, signatures selection genes for drought salt tolerance, probably indicate adaptation local conditions. Overall, our study in‐depth analyses are powerful tools deciphering complex origin organisms, especially gymnosperms.

Language: Английский

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Genomic insights into adaptive evolution of the species-rich cosmopolitan plant genus Rhododendron

Cell Reports, Journal Year: 2024, Volume and Issue: 43(10), P. 114745 - 114745

Published: Sept. 19, 2024

Language: Английский

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The paradox of extremely fast evolution driven by genetic drift in multi-copy gene systems

Published: March 6, 2025

Multi-copy gene systems that evolve within, as well between, individuals are common. They include viruses, mitochondrial DNAs, multi-gene families etc. The paradox is neutral evolution in two stages should be far slower than single-copy but the opposite often true, thus leading to suggestion of natural selection. We now apply new Generalized Haldane (GH) model quantify genetic drift mammalian ribosomal RNA genes (or rDNAs). On average, rDNAs have C ∼ 150 - 300 copies. A mutation rDNA take 4 NC * generations become fixed ( N , population size; effective copy number). While > >> 1 expected, observed fixation time mouse and human < hence 1. Genetic appears much 100 times stronger for rRNA genes. large increases driven by a host molecular mechanisms such conversion unequal crossover. Although each mechanism has been extremely difficult quantify, GH permits estimation their total effects on drift. In conclusion, can generally applicable multi-copy without being burdened tracking diverse individually.

Language: Английский

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Chromosome‐level genome assembly of a rare karst‐growing Rhododendron species provides insights into its evolution and environmental adaptation

Journal of Systematics and Evolution, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 29, 2024

Abstract Rhododendron is a significant plant genus, with over 600 identified species in China. The subgenus Hymenanthes holds the largest number of germplasms and showcases strong environmental adaptability. However, there remains lack understanding regarding 's evolution adaptations. bailiense Y.P.Ma, C.Q.Zhang & D.F.Chamb., an exceedingly rare species, thrives alkaline karst landforms Guizhou, southwest China, different from typical growing environment other species. In this study, we present chromosome‐level genome assembly R. , revealing size 923.3 Mb, contig N50 24.5 total 47 567 predicted genes. An evolutionary analysis indicated that diverged its ancestors prior to rhododendrons, expanded contracted genes being notably enriched “stress response” “growth,” respectively. predominantly found on limestone soil mountains only two wild populations known. contained high copy ankyrin repeat (ANK) Ca 2+ ‐ATPase (CAP) genes, primarily involved transport, shedding light how copes high‐calcium stress. contrast, structures ANKs displayed unique characteristics, while CAPs showed conservatism. provides new insights into adaptation history plants environments, potentially offering valuable information for adaptive breeding ecological enhancement such challenging settings.

Language: Английский

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Genetic and ecophysiological evidence that hybridization facilitated lineage diversification in yellow Camellia (Theaceae) species: a case study of natural hybridization between C. micrantha and C. flavida

BMC Plant Biology, Journal Year: 2023, Volume and Issue: 23(1)

Published: March 22, 2023

Hybridization is generally considered an important creative evolutionary force, yet this process still poorly characterized in karst plants. In study, we focus on natural hybridization yellow Camellia species, a group of habitat specialists confined to karst/non-karst habitats southwestern China.Based population genome data obtain from double digest restriction-site associated DNA (ddRAD) sequencing, found evidence for and introgression between C. micrantha flavida, specifically confirmed their hybrid population, "ptilosperma". Ecophysiological results suggested that extreme hydraulic traits were fixed "ptilosperma", these being consistent with its distinct ecological niche, which lies outside parental ranges.The identified event expected have played role generating novel variation during, the displays different phenological characteristics ecophysiological colonization new niche limestone karst.

Language: Английский

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A new species of Populus and the extensive hybrid speciation arising from it on the Qinghai-Tibet Plateau

Molecular Phylogenetics and Evolution, Journal Year: 2024, Volume and Issue: 196, P. 108072 - 108072

Published: April 12, 2024

Language: Английский

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Integrated analyses reveal extensive cytonuclear discordance and two new members of Rhodiola

Journal of Systematics and Evolution, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 6, 2025

Abstract Our knowledge of species diversity in biodiversity hotspots remains incomplete. The Qinghai–Tibet Plateau (QTP) and the mountainous region southwestern China have long been regarded as hotspots. However, despite considerable efforts, numerous plant may still elude formal description. Rhodiola L. (Crassulaceae) encompasses ca . 58 perennial herb species, which used an important traditional medicinal for centuries. Rampant exploitation has put some at risk extinction. also recognized a promising model investigating radiation speciation QTP. phylogenetic relationships among major clades genus are not well resolved, underlying causes cytonuclear discordance briefly mentioned previous studies remain unexplored. Through phylogenomic analyses utilizing data from both nuclear genome plastome 42 we identified six found extensive discordance, was primarily attributed to hybridization introgression occurring or closely related species. In addition, integration morphological, phylogenomic, population genomic, ecological evidence resulted identification description new : R. renii sp. nov., reclassification previously Pseudosedum merged into results highlight significant role evolution probably other rapid‐radiated groups QTP, emphasize need increased discovery efforts such QTP its adjacent areas.

Language: Английский

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Divergence of alpine plant populations of three Gentianaceae species in the Qinling sky Island

BMC Plant Biology, Journal Year: 2025, Volume and Issue: 25(1)

Published: Feb. 4, 2025

Known for their unique biodiversity, the Qinling Mountains are considered only area in which alpine biomes occur central China. Given that particularly sensitive to global warming, understanding how plants respond climatic fluctuations is essential evolution and conservation of biodiversity. To address this issue, three species Gentianaceae (Gentiana crassuloides, G. hexaphylla Swertia bifolia) represent different life types diverse genera were selected. Genetic clustering analysis according around 33,317 185,133 SNPs showed population was a separate lineage within each species. A high level genetic differentiation observed among populations other Divergence time estimation based on plastomes approximate Bayesian computation genomic originated at periods under various patterns including primary source hybridization. Significant signals isolation by distance environment found all The redundancy gradient forest analyses revealed several temperature- precipitation-related variables mainly contributed shaping others, indicating exhibited similar pattern adaptations local environments. This study unveiled evolutionary features these elucidated contributing role both environmental geographical differentiation, scientifically supports future efforts.

Language: Английский

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Integration of De Novo Chromosome‐Level Genome and Population Resequencing of Peganum (Nitrariaceae): A Case Study of Speciation and Evolutionary Trajectories in Arid Central Asia

Molecular Ecology Resources, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 10, 2025

ABSTRACT Natural hybridization is a significant driving force in plant evolution and speciation. Understanding the genetic mechanism dynamic evolutionary trajectories of divergence between species hybrids remains central goal biology. Here, we examined Peganum their intermittent hybrid entities (IHEs) from large‐scale sympatric allopatric regions. We sequenced genomes Arid Central Asia (ACA) region its surrounding areas, discovering that origin could be traced to Hexi Corridor eastern Asia, where migration led geographic environmental isolation, giving rise new based on natural selection. Different species, exhibiting excellent dispersal abilities, migrated same regions underwent hybridization. The descendant inherited developed adaptive traits parent through gene flow introgression, particularly DNA repair wax layer formation, leading speciation IHEs. This study clarified transition stages identified Mixing‐Isolation‐Mixing cycles (MIM) model as framework suitable for , marking initial identification this unique ACA region.

Language: Английский

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