Species divergence with gene flow and hybrid speciation on the Qinghai–Tibet Plateau

New Phytologist, Год журнала: 2022, Номер 234(2), С. 392 - 404

Опубликована: Янв. 12, 2022

Summary The Qinghai–Tibet Plateau (QTP) sensu lato ( sl ), comprising the platform, Himalaya and Hengduan Mountains, is characterized by a large number of endemic plant species. This evolutionary cradle may have arisen from explosive species diversification because geographic isolation. However, gene flow has been widely detected during speciation processes all groups examined, suggesting that natural selection also played an important role divergence in this region. In addition, hybrids recovered almost species‐rich genera. suggests numerous region are still ‘on pathway to complete reproductive isolation (RI)’. Such could directly develop into new through hybrid polyploidization homoploid (HHS). HHS take place more easily than previously thought alternate inheritance alleles parents at multiple RI loci. Therefore, isolation, hybridization together promoted genera on QTP . We emphasize need for identification functional analysis major genes speciation, especially encourage investigations parallel adaptive causing across different lineages within similar but specific habitats

Язык: Английский

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Evolutionary origin of species diversity on the Qinghai–Tibet Plateau

Journal of Systematics and Evolution, Год журнала: 2021, Номер 59(6), С. 1142 - 1158

Опубликована: Авг. 25, 2021

Abstract The Qinghai–Tibet Plateau (QTP) sensu lato ( sl ) houses an exceptional species diversity in Asia. To develop a comprehensive understanding of this fascinating region, we reviewed recent progress from biogeographic, paleogeographic, paleontological and genomic research both plants animals the QTP . Numerous studies have been conducted to examine whether uplift triggered production rich there, Quaternary “unified ice sheet” eliminated on central plateau how high‐altitude developed extreme environment adaptations. Major disputes arose about first issue, mainly different circumscriptions related uplift, inaccurate dating molecular phylogenetic trees, non‐causal correlations between diversification. is spatially temporally heterogeneous, abundant fossils reported recently similarly support such asynchronous upheaval model across entire region. Available phylogeographic alpine suggested their glacial refugia , rejecting unified sheet during Last Glacial Maximum. Genomic evidence limited number has identified numerous candidate genes for adaptation. In future, more should be focused speciation adaptation mechanisms based cutting‐edge methods.

Язык: Английский

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Genome–Environment Associations, an Innovative Tool for Studying Heritable Evolutionary Adaptation in Orphan Crops and Wild Relatives

Frontiers in Genetics, Год журнала: 2022, Номер 13

Опубликована: Авг. 5, 2022

Leveraging innovative tools to speed up prebreeding and discovery of genotypic sources adaptation from landraces, crop wild relatives, orphan crops is a key prerequisite accelerate genetic gain abiotic stress tolerance in annual such as legumes cereals, many which are still species despite advances major row crops. Here, we review novel, interdisciplinary approach combine ecological climate data with evolutionary genomics under the paradigm new field study: genome–environment associations (GEAs). We first exemplify how GEA utilizes situ georeferencing genotypically characterized, gene bank accessions pinpoint genomic signatures natural selection. later discuss necessity update current models predict both regional- local- or micro-habitat–based mechanistic ecophysiological indices cutting-edge GWAS-type association models. Furthermore, account for polygenic adaptation, encourage community start gathering estimated adaptive values (GEAVs) prediction (GP) multi-dimensional machine learning (ML) The latter two should ideally be weighted by de novo GWAS-based estimates optimized scalable marker subset. end envisioning avenues make inferences more robust through merging high-resolution sources, environmental remote sensing summary statistics site frequency spectrum, epigenetic molecular functionality responsible plastic inheritance wild. Ultimately, believe that coupling predictions innovations will help capture hidden adaptations stresses based on germplasm resources assist responses change. “I shall endeavor find out nature’s forces act upon one another, what manner geographic environment exerts its influence animals plants. In short, I must about harmony nature” Alexander von Humboldt— Letter Karl Freiesleben, June 1799 .

Язык: Английский

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Cryptic divergences and repeated hybridizations within the endangered “living fossil” dove tree (Davidia involucrata) revealed by whole genome resequencing

Plant Diversity, Год журнала: 2024, Номер 46(2), С. 169 - 180

Опубликована: Фев. 12, 2024

The identification and understanding of cryptic intraspecific evolutionary units (lineages) are crucial for planning effective conservation strategies aimed at preserving genetic diversity in endangered species. However, the factors driving evolution maintenance these lineages most species remain poorly understood. In this study, we conducted resequencing 77 individuals from 22 natural populations Davidia involucrata, a "living fossil" dove tree endemic to central southwest China. Our analysis revealed presence three distinct local within species, which emerged approximately 3.09 0.32 million years ago. These divergence events align well with geographic climatic oscillations that occurred across distributional range. Additionally, observed frequent hybridization between lineages, resulting formation hybrid their adjacent as disjunct regions. hybridizations likely arose climate-driven population expansion and/or long-distance gene flow. Furthermore, identified numerous environment-correlated variants total many other genes exhibited signals positive during two major lineages. findings shed light on highly dynamic underlying remarkably similar phenotype Importantly, results not only provide guidance development plans but also enhance our past histories.

Язык: Английский

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Genomic Data Reveals Population Genetic and Demographic History of Magnolia fistulosa (Magnoliaceae), a Plant Species With Extremely Small Populations in Yunnan Province, China

Frontiers in Plant Science, Год журнала: 2022, Номер 13

Опубликована: Фев. 17, 2022

Elucidating the genetic background of threatened species is fundamental to their management and conservation, investigating demographic history these helpful in determination threats facing them. The woody genus Magnolia (Magnoliaceae) have high economic, scientific ecological values. Although nearly half all been evaluated as threatened, date there has no population study employing Next Generation Sequencing (NGS) technology this genus. In present study, we investigate conservation genomics fistulosa, a endemic limestone area along Sino-Vietnamese border, using double digest restriction-site-associated DNA-sequencing (ddRAD-seq) approach. To increase reliability our statistical inferences, employed two approaches, Stacks ipyrad, for SNP calling. A total 15,272 18,960, respectively, putatively neutral SNPs were generated by ipyrad. Relatively diversity large divergence detected M. fistulosa. higher absolute values calculated ipyrad data set, sets showed same trends (π, He), differentiation (FST) inbreeding coefficients (FIS). change effective size fistulosa within last 1 Ma was detected, including decline about 0.5-0.8 ago, bottleneck event 0.2-0.3 fluctuations during glacial stage, recovery after maximum. Our findings not only lay foundation future species, but also provide new insights into evolutionary southeastern Yunnan, China.

Язык: Английский

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Genomic divergence of Stellera chamaejasme through local selection across the Qinghai–Tibet plateau and northern China

Molecular Ecology, Год журнала: 2022, Номер 31(18), С. 4782 - 4796

Опубликована: Июль 23, 2022

Abstract Understanding how populations diverge and new species arise is a central question in evolutionary biology. “Allopatric” divergence through geographical isolation considered to be the commonest mechanism generating biodiversity mountain ecosystems. However, underlying genomic dynamics, especially islands of elevated genes that are highly diverged as result lineage‐specific selection, remain poorly understood. Stellera chamaejasme has wide range across Qinghai–Tibet Plateau northern China, making it good model with which explore during speciation We assembled high‐quality, chromosome‐level genome for this resequenced genomes 24 its major distribution. Our population analyses recovered four distinct genetic lineages corresponding distributions contrasting environments. we revealed continuous gene flow historical divergences these lineages. Interlineage hybrids plastome introgressions were frequently found regions contact, further increased between two contacting recent past. The heterogeneous selection ancestral polymorphisims hitchhiking contributed greatly formation islands. positively selected within outside annotated mainly involved local adaptation. results suggest S. likely have been triggered maintained by together isolation.

Язык: Английский

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Genomic population structure and local adaptation of the wild strawberry Fragaria nilgerrensis

Horticulture Research, Год журнала: 2022, Номер 9

Опубликована: Янв. 1, 2022

Abstract The crop wild relative Fragaria nilgerrensis is adapted to a variety of diverse habitats across its native range in China. Thus, discoveries made this species could serve as useful guide the development new superior strawberry cultivars that are resilient or variable environments. However, genetic diversity and architecture traits underlying important adaptive remain poorly understood. Here, we used whole-genome resequencing data from 193 F. individuals spanning distribution China investigate diversity, population structure genomic basis local adaptation. We identified four groups, with western group located Hengduan Mountains exhibiting highest diversity. Redundancy analysis suggested both environment geographic variables shaped significant proportion variation. Our analyses revealed environmental difference explains more observed variation than distance. This suggests adaptation distinct habitats, which present unique combination abiotic factors, likely drove differentiation. Lastly, by implementing selective sweep scans genome–environment association throughout genome, associated investigated functions putative candidate genes nilgerrensis.

Язык: Английский

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The genomic and epigenetic footprint of local adaptation to variable climates in kiwifruit

Horticulture Research, Год журнала: 2023, Номер 10(4)

Опубликована: Фев. 21, 2023

Abstract A full understanding of adaptive genetic variation at the genomic level will help address questions how organisms adapt to diverse climates. Actinidia eriantha is a shade-tolerant species, widely distributed in southern tropical region China, occurring spatially heterogeneous environments. In present study we combined population genomic, epigenomic, and environmental association analyses infer structure positive selection across climatic gradient, assess offset change for A. eriantha. The strongly shaped by geography influenced restricted gene flow resulting from isolation distance due habitat fragmentation. total, identified 102 outlier loci annotated 455 candidate genes associated with basis climate adaptation, which were enriched functional categories related development processes stress response; both temperature precipitation are important factors driving variation. addition single-nucleotide polymorphisms (SNPs), total 27 single-methylation variants (SMVs) had significant correlation least one four variables 16 SMVs located or adjacent genes, several predicted be involved plant response abiotic biotic stress. Gradient forest analysis indicated that central/east populations higher risk future maladaptation under change. Our results demonstrate local impose strong pressures lead adaptation. Such information adds our mechanisms variable climates revealed genome epigenome analysis.

Язык: Английский

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Genetic divergence and local adaptation of Liriodendron driven by heterogeneous environments

Molecular Ecology, Год журнала: 2021, Номер 31(3), С. 916 - 933

Опубликована: Ноя. 13, 2021

Abstract Ecological adaptive differentiation alters both the species diversity and intraspecific genetic in forests, thus affecting stability of forest ecosystems. Therefore, knowledge underpinnings ecological is critical for effective conservation. In this study, single‐nucleotide polymorphisms (SNPs) from population transcriptomes were used to investigate spatial distribution variation Liriodendron assess whether environmental variables can explain divergence. We examined contributions divergence explored local adaptation using a landscape genomic approach. Niche models statistical analyses showed significant niche between L . chinense tulipifera , suggesting that may play crucial role driving interspecific detected new fine‐scale structure six groups occurred during late Pliocene early Pleistocene. Redundancy analysis (RDA) revealed associations multiple variables. Environmental association identified 67 loci (EALs; nonsynonymous SNPs) underwent or differentiation, 28 which associated with genes. These candidate provide substantial evidence Our findings reveal pattern novel insight into heterogeneous environments shaping among populations, informing future conservation efforts.

Язык: Английский

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Genomic insights into differentiation and adaptation of Amorphophallus yunnanensis in the mountainous region of Southwest China

Ecology and Evolution, Год журнала: 2024, Номер 14(1)

Опубликована: Янв. 1, 2024

Abstract The role of geographical isolation and environmental adaptation in driving the differentiation radiation species has been a hotspot evolutionary biology. extremely complicated fragmented geography mountainous region Southwest China provides an excellent system for investigating process divergence heterogeneous habitats. Amorphophallus yunnanensis is extreme habitat preference that resides mainly China. Here, we used restriction site‐associated DNA sequencing (RAD‐seq) to characterize geographic pattern genetic variation among 19 populations A. as well genomic basis adaptation. A low population diversity high level was observed. data revealed clear east–west differentiation, with two distinct lineages corresponding Guizhou plateau Yunnan plateau, respectively. However, discovered demographic expansion Plateau lineage recent hybridization at contact region. Significant levels by distance along environment were detected. Outlier tests genome–environment association analyses identified 89 putatively adaptive loci might play Our results suggest attributed together divergent selection

Язык: Английский

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