Genomic landscape of the global oak phylogeny

New Phytologist, Год журнала: 2019, Номер 226(4), С. 1198 - 1212

Опубликована: Окт. 14, 2019

Summary The tree of life is highly reticulate, with the history population divergence emerging from populations gene phylogenies that reflect histories introgression, lineage sorting and divergence. In this study, we investigate global patterns oak diversity test hypothesis there are regions genome broadly informative about phylogeny. We utilize fossil data restriction‐site associated DNA sequencing ( RAD ‐seq) for 632 individuals representing nearly 250 Quercus species to infer a time‐calibrated phylogeny world's oaks. use reversible‐jump Markov chain Monte Carlo method reconstruct shifts in diversification rates, accounting among‐clade sampling biases. then map > 20 000 ‐seq loci back an annotated genomic distribution introgression phylogenetic support across Oak lineages have diversified among geographic regions, followed by ecological within Americas Eurasia. Roughly 60% traces four clades experienced increases net diversification, probably response climatic transitions or opportunity. strong contrasts high heterogeneity signal introgression. Oaks phylogenomic mosaics, their may fact depend on flow shapes genome.

Язык: Английский

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Oaks: an evolutionary success story

New Phytologist, Год журнала: 2019, Номер 226(4), С. 987 - 1011

Опубликована: Окт. 20, 2019

Summary The genus Quercus is among the most widespread and species‐rich tree genera in northern hemisphere. extraordinary species diversity America Asia together with continuous continental distribution of a limited number European raise questions about how macro‐ microevolutionary processes made an evolutionary success. Synthesizing conclusions reached during past three decades by complementary approaches phylogenetics, phylogeography, genomics, ecology, paleobotany, population biology quantitative genetics, this review aims to illuminate leading radiation expansion oaks. From opposing scales time geography, we converge on four overarching explanations success oaks: accumulation large reservoirs within populations species; ability for rapid migration contributing ecological priority effects lineage diversification; high rates divergence clades combined convergent solutions problems across clades; propensity hybridization, adaptive introgression facilitating migration. Finally, explore potential future research avenues, emphasizing integration macroevolutionary perspectives.

Язык: Английский

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Phylogenomic analyses highlight innovation and introgression in the continental radiations of Fagaceae across the Northern Hemisphere

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

Опубликована: Март 14, 2022

Northern Hemisphere forests changed drastically in the early Eocene with diversification of oak family (Fagaceae). Cooling climates over next 20 million years fostered spread temperate biomes that became increasingly dominated by oaks and their chestnut relatives. Here we use phylogenomic analyses nuclear plastid genomes to investigate timing pattern major macroevolutionary events ancient genome-wide signatures hybridization across Fagaceae. Innovation related seed dispersal is implicated triggering waves continental radiations beginning rapid lineages resulting unparalleled transformation forest dynamics within 15 following K-Pg extinction. We detect introgression at multiple time scales, including predating origination genus-level diversity. As moved into newly available habitats Miocene, secondary contact between previously isolated species occurred. This resulted adaptive introgression, which may have further amplified white Eurasia.

Язык: Английский

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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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Modern Strategies to Assess and Breed Forest Tree Adaptation to Changing Climate

Frontiers in Plant Science, Год журнала: 2020, Номер 11

Опубликована: Окт. 21, 2020

Studying the genetics of adaptation to new environments in ecologically and industrially important tree species is currently a major research line fields plant science genetic improvement for tolerance abiotic stress. Exploring genomic basis local imperative assessing conditions under which trees will successfully adapt situ global climate change. However, this knowledge has scarcely been used conservation forest because woody perennials face limitations such as their outcrossing reproductive systems, long juvenile phase, huge genome sizes. Therefore, review we discuss predictive approaches that promise increasing selection accuracy shortening generation intervals. They may also assist detection novel allelic variants from germplasm, disclose potential different environments. For instance, natural populations allow using tools population genomics field study signatures adaptation. Conventional markers whole sequencing both help identifying genes diverge between more than expected neutrality, exhibit unique diversity indicative 'selective sweeps'. Ultimately, these efforts inform breeding status capable pivoting health, ecosystem services, sustainable production. Key long-term perspectives include understanding how trees' phylogeographic history affect adaptive relevant variation available environmental Encouraging 'big data' (machine learning –ML) comprehensively merging heterogeneous ecological datasets becomes imperative, too.

Язык: Английский

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Adaptation Strategies and Approaches for Managing Fire in a Changing Climate

Climate, Год журнала: 2022, Номер 10(4), С. 58 - 58

Опубликована: Апрель 8, 2022

As the effects of climate change accumulate and intensify, resource managers juggle existing goals new mandates to operationalize adaptation. Fire contend with direct on resources in addition climate-induced disruptions fire regimes subsequent ecosystem effects. In systems stressed by warming drying, increased activity amplifies pace scale severe disturbance events, heightening urgency for management action. are asked integrate information impacts their professional expertise determine how achieve objectives a changing altered regimes. This is difficult task, need support as they incorporate adaptation into planning operations. We present list strategies approaches specific based co-produced knowledge from science–management partnership pilot-tested two-day workshop natural regional stakeholders. “menu” flexible useful tool who connect dots between ecology, science, intent, implementation. It was created tested part an framework used widely across United States should be applicable many fire-prone forest ecosystems.

Язык: Английский

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The application gap: Genomics for biodiversity and ecosystem service management

Biological Conservation, Год журнала: 2023, Номер 278, С. 109883 - 109883

Опубликована: Янв. 4, 2023

The conservation of biodiversity from the genetic to community levels is fundamental for continual provision ecosystem services (ES), benefits that ecosystems provide people. Genetic and genomic diversity enhance resilience populations communities underpin functions services. We show genomics applications are mostly limited flagship species their ES management underachieved. propose a framework on how can guide sustainable bridge this genomics-ES 'application gap'. review knowledge in single (relatedness, potentially adaptive variants) or interacting (host-microorganism coevolution, hybridization) effective actions. These include population supplementation, assisted migration hybridization promote climate-adapted variants potential, control invasives, delimitation areas, provenancing strategies restoration, managing microbial function solving trade-offs. Genomics-informed actions improved outcomes supported through synergies between scientists managers at local, regional international levels, development standardized workflows, training incorporation local information. Such facilitate implementation policies such as UN 2030 goals EU Biodiversity strategy 2030, support inclusion ambitious new CBD post-2020 Global Framework hybrids.

Язык: Английский

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Phylogenomics reveals extreme gene tree discordance in a lineage of dominant trees: hybridization, introgression, and incomplete lineage sorting blur deep evolutionary relationships despite clear species groupings in Eucalyptus subgenus Eudesmia

Molecular Phylogenetics and Evolution, Год журнала: 2023, Номер 187, С. 107869 - 107869

Опубликована: Июль 8, 2023

Язык: Английский

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Genomic vulnerability to climate change in Quercus acutissima, a dominant tree species in East Asian deciduous forests

Molecular Ecology, Год журнала: 2023, Номер 32(7), С. 1639 - 1655

Опубликована: Янв. 10, 2023

Understanding the evolutionary processes that shape landscape of genetic variation and influence response species to future climate change is critical for biodiversity conservation. Here, we sampled 27 populations across distribution range a dominant forest tree, Quercus acutissima, in East Asia, applied genome-wide analyses track history predict fate under climate. We found two groups (East West) Q. acutissima diverged during Pliocene. also heterogeneous genomic this species, which may have been shaped by population demography linked selections. Using genotype-environment association analyses, identified climate-associated SNPs diverse set genes functional categories, indicating model polygenic adaptation acutissima. further estimated three offset metrics quantify vulnerability due complex interplay between local migration. marginal are higher risk extinction because change, not be able suitable habitats maintain gene-environment relationships observed current detected reverse offsets northern China, currently present whole adapt conditions area. Overall, study illustrates how variation, provides comprehensive view maladaptation

Язык: Английский

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Introgression and incomplete lineage sorting blurred phylogenetic relationships across the genomes of sclerophyllous oaks from southwest China

Cladistics, Год журнала: 2024, Номер 40(4), С. 357 - 373

Опубликована: Янв. 10, 2024

Resolving evolutionary relationships among closely related species with interspecific gene flow is challenging. Genome-scale data provide opportunities to clarify complex in and observe variations across the genomes of such species. The Himalayan-Hengduan subalpine oaks have a nearly completely sympatric distribution southwest China probably constitute syngameon. In this study, we mapped resequencing from different group Quercus aquifolioides reference genome obtain high-quality filtered single nucleotide polymorphism (SNP) dataset. We also assembled their plastomes. reconstructed phylogenetic relationships, explored level pattern introgression these investigated tree variation using sliding windows. same or plastomes were found be shared extensively within specific geographical area. Phylogenomic analyses genome-wide SNP that most clade showed genetic coherence, but several connected by introgression. trees obtained windows are highly heterogeneous therefore obscured. Our study all form obscured observed empirically best explained conjunction incomplete lineage sorting.

Язык: Английский

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