Over the past century,anthropogenic greenhouse gas emissions have continuously increased global temperature and triggered climate change,significantlyimpacting species distributions and biodiversity patterns.Understan...Over the past century,anthropogenic greenhouse gas emissions have continuously increased global temperature and triggered climate change,significantlyimpacting species distributions and biodiversity patterns.Understanding how climate-driven shifts in species distributions reshape diversity patterns is crucial for formulating effective future conservation strategies.Based on the distribution data of 314 Rhododendron species in China,along with 16 environmental variables,we examined spatial diversity patterns and assessed regional and biome differences in species responses using ensembled species distribution models.Our results indicated that climatic variables significantlyinfluencedspecies distributions,with ongoing climate change expected to concentrate Rhododendron distribution patterns and alter species composition.Regional topography played a critical role in shaping species responses to global warming.In the mountainous areas of southwestern China,species exhibited heightened sensitivity to temperature fluctuations,shifting upward as temperature increased.This region also had a higher proportion of threatened species and showed an overall contraction in primary distribution range.Conversely,in southern China,species were more influencedby precipitation,exhibiting a notable northward shift and expansion in primary distribution areas.Notably,alpine species,occurring in habitats above the treeline,may face severe survival risks due to the high degree of habitat loss and fragmentation.We identifiedseven priority conservation areas,predominantly situated in highly fragmented mountainous regions that were inadequately protected by existing nature reserves.Our findingscontribute to a better understanding of changes in Rhododendron diversity patterns under climate change,providing valuable insights for developing comprehensive,flora-wideconservation plans in China.展开更多
The Miombo ecoregion covers eastern and southern Africa,with variations in plant species composition,structure,and biomass across a broad precipitation gradient.Most studies of woody plant communities focus exclusivel...The Miombo ecoregion covers eastern and southern Africa,with variations in plant species composition,structure,and biomass across a broad precipitation gradient.Most studies of woody plant communities focus exclusively on larger overstorey trees(≥5 or≥10cm stem diameter),overlooking the contribution of small trees and shrubs in the understorey,which can comprise a significant portion of total biomass and diversity.Here,we evaluate the contribution of both large overstorey and small understorey woody plants to species diversity and above-ground biomass(AGB),with 17 plots(0.5-1ha)across five sites representing both extremes of rainfall gradient spanning the Miombo ecoregion,in northeast Namibia(500-700mm mean annual precipitation,MAP)and southern Democratic Republic of Congo(DRC)(>1,200mm MAP).Mean AGB per site ranged from 21 to 119Mg·ha^(-1),increasing with rainfall,while the proportional AGB contribution of small trees,saplings,and shrubs decreased.In dry Namibia,small trees,saplings,and shrubs(<5cm DBH)contributed up to 28.2%of total AGB(mean±standard deviation:18.3%±3.4%),whereas in wet DRC,they contributed only up to 2.5%(2.3%±1.4%).Namibian sites,on average,contained a large proportion of woody species diversity exclusively in small trees and shrubs(<5cm DBH),with 55 species representing 59.4%of the total diversity.In contrast,DRC sites had higher overall small woody plant diversity(66 species)but fewer species found exclusively as small individuals(25.2%),with many saplings that grow to larger trees.Understorey composition also differed,with saplings of overstorey trees dominating in DRC,while shrubs dominated in Namibia.Our findings show that woody biomass and diversity in dry woodlands are substantially underestimated when studies focus only on larger trees.This highlights the need to consider all woody vegetation to better understand woody plant diversity and biomass variation.展开更多
Deep genome skimming(DGS)has emerged as a promising approach to recover orthologous nuclear genes for large-scale phylogenomic analyses.However,its reliability with low DNA quality and quantity typical of archival spe...Deep genome skimming(DGS)has emerged as a promising approach to recover orthologous nuclear genes for large-scale phylogenomic analyses.However,its reliability with low DNA quality and quantity typical of archival specimens,such as herbarium material,remains largely unexplored.We used Rhododendron as a case study to evaluate best practices for DGS in phylogenetic analyses at both deep and shallow scales.We first investigated locus recovery variation with sequencing depth,before evaluating the phylogenetic utility of different sets of loci,including Angiosperms353,target nuclear exons,and extended exon-flanking regions.We found DGS effectively recovered nuclear genes from herbarium specimens,with~15coverage performing similarly to deeper sequencing.The recovery of target exon and flanking regions was improved by using supercontigs as a reference,offering a potential solution to limited sequencing depth.The high-integrity nuclear sequences recovered robust phylogenetic relationships within Rhododendron.Notably,exon-flanking regions showed significant potential for resolving relationships at shallow scales.Genes recovered with taxon-specific references had less missing data than those recovered by Angiosperms353 and generated higher-resolution phylogenetic trees.This study demonstrates the utility of DGS data for obtaining numerous nuclear genes from herbarium specimens for phylogenetic studies,and makes recommendations for best practices regarding sequencing coverage,locus selection,and bioinformatic approaches.展开更多
出版于2006年9月的最新版的《国际植物命名法规》,即维也纳法规(Vienna Code),取代了圣路易斯法规(Saint Louis Code)而成为管理植物学(包括藻类学和真菌学)科学命名的唯一有效法规。本文报道了维也纳法规和圣路易斯法规之间的主要区别...出版于2006年9月的最新版的《国际植物命名法规》,即维也纳法规(Vienna Code),取代了圣路易斯法规(Saint Louis Code)而成为管理植物学(包括藻类学和真菌学)科学命名的唯一有效法规。本文报道了维也纳法规和圣路易斯法规之间的主要区别。这些区别包括两版法规在起始日期、有效发表、合格发表、化石植物、多型真菌、拼写和附录诸方面的不同。展开更多
Leaf development involves many complex genetic interactions,signals between adjacent cells or between more distant tissues and consequent changes in cell fate.This review describes three stages in leaf development whe...Leaf development involves many complex genetic interactions,signals between adjacent cells or between more distant tissues and consequent changes in cell fate.This review describes three stages in leaf development where regulation by small RNAs have been used to modulate gene expression patterns.展开更多
The strength of phylogeographic breaks can vary among species in the same area despite being subject to the same geological and climate history due to differences in biological traits.Several important phylogeographic...The strength of phylogeographic breaks can vary among species in the same area despite being subject to the same geological and climate history due to differences in biological traits.Several important phylogeographic breaks exist around the Sichuan Basin in Southwest China but few studies have focused on wind-dispersed plants.Here,we investigated the phylogeographic patterns and the evolutionary history of Populus lasiocarpa,a wind-pollinated and wind-dispersed tree species with a circum-Sichuan Basin distribution in southwest China.We sequenced and analyzed three plastid DNA fragments(ptDNA)and eight nuclear microsatellites(nSSRs)of 265 individuals of P.lasiocarpa from 21 populations spanning the entire distribution range.Distribution patterns based on nSSR data revealed that there are three genetic groups in P.lasiocarpa.This is consistent with the three phylogeographic breaks(Sichuan Basin,the Kaiyong Line and the 105°E line),where the Sichuan basin acts as the main barrier to gene flow between western and eastern groups.However,the distribution pattern based on ptDNA haplotypes poorly matched the phylogeographic breaks,and wind-dispersed seeds may be one of the main contributing factors.Species distribution modelling suggested a larger potential distribution in the last glacial maximum with a severe bottleneck during the last interglacial.A DIYABC model also suggested a population contraction and expansion for both western and eastern lineages.These results indicate that biological traits are likely to affect the evolutionary history of plants,and that nuclear molecular markers,which experience higher levels of gene flow,might be better indicators of phylogeographic breaks.展开更多
Chinese Assam tea(Camellia sinensis var.assamica)is an important tea crop with a long history of cultivation in Yunnan,China.Despite its potential value as a genetic resource,its genetic diversity and domestication/br...Chinese Assam tea(Camellia sinensis var.assamica)is an important tea crop with a long history of cultivation in Yunnan,China.Despite its potential value as a genetic resource,its genetic diversity and domestication/breeding history remain unclear.To address this issue,we genotyped 469 ancient tea plant trees representing 26 C.sinensis var.assamica populations,plus two of its wild relatives(six and three populations of C.taliensis and C.crassicolumna,respectively)using 16 nuclear microsatellite loci.Results showed that Chinese Assam tea has a relatively high,but comparatively lower gene diversity(H_(S)=0.638)than the wild relative C.crassicolumna(H_S=0.658).Clustering in STRUCTURE indicated that Chinese Assam tea and its two wild relatives formed distinct genetic groups,with considerable interspecific introgression.The Chinese Assam tea accessions clustered into three gene pools,corresponding well with their geographic distribution.However,New Hybrids analysis indicated that 68.48%of ancient Chinese Assam tea plants from Xishuangbanna were genetic intermediates between the Puer and Lincang gene pools.In addition,10%of the ancient Chinese Assam tea individuals were found to be hybrids between Chinese Assam tea and C.taliensis.Our results suggest that Chinese Assam tea was domesticated separately in three gene pools(Puer,Lincang and Xishuangbanna)in the Mekong River valley and that the hybrids were subsequently selected during the domestication process.Although the domestication history of Chinese Assam tea in southwestern Yunnan remains complex,our results will help to identify valuable genetic resources that may be useful in future tea breeding programs.展开更多
Elevation plays a crucial factor in the distribution of plants,as environmental conditions become increasingly harsh at higher elevations.Previous studies have mainly focused on the effects of large-scale elevational ...Elevation plays a crucial factor in the distribution of plants,as environmental conditions become increasingly harsh at higher elevations.Previous studies have mainly focused on the effects of large-scale elevational gradients on plants,with little attention on the impact of smaller-scale gradients.In this study we used 14 microsatellite loci to survey the genetic structure of 332 Juniperus squamata plants along elevation gradient from two sites in the Hengduan Mountains.We found that the genetic structure(single,clonal,mosaic)of J.squamata shrubs is affected by differences in elevational gradients of only 150 m.Shrubs in the mid-elevation plots rarely have a clonal or mosaic structure compared to shrubs in lower-or higher-elevation plots.Human activity can significantly affect genetic structure,as well as reproductive strategy and genetic diversity.Sub-populations at mid-elevations had the highest yield of seed cones,lower levels of asexual reproduction and higher levels of genetic diversity.This may be due to the trade-off between elevational stress and anthropogenic disturbance at mid-elevation since there is greater elevational stress at higher-elevations and greater intensity of anthropogenic disturbance at lower-elevations.Our findings provide new insights into the finer scale genetic structure of alpine shrubs,which may improve the conservation and management of shrublands,a major vegetation type on the Hengduan Mountains and the Qinghai-Tibet Plateau.展开更多
Data gaps and biases are two important issues that affect the quality of biodiversity information and downstream results.Understanding how best to fill existing gaps and account for biases is necessary to improve our ...Data gaps and biases are two important issues that affect the quality of biodiversity information and downstream results.Understanding how best to fill existing gaps and account for biases is necessary to improve our current information most effectively.Two current main approaches for obtaining and improving data include(1)curation of biological collections,and(2)fieldwork.However,the comparative effectiveness of these approaches in improving biodiversity data remains little explored.We used the Flora de Bogota project to study the magnitude of change in species richness,spatial coverage,and sample coverage of plant records based on curation versus fieldwork.The process of curation resulted in a decrease in species richness(synonym and error removal),but it significantly increased the number of records per species.Fieldwork contributed to a slight increase in species richness,via accumulation of new records.Additionally,curation led to increases in spatial coverage,species observed by locality,the number of plant records by species,and localities by species compared to fieldwork.Overall,curationwas more efficient in producing new information compared to fieldwork,mainly because of the large number of records available in herbaria.We recommend intensive curatorial work as the first step in increasing biodiversity data quality and quantity,to identify bias and gaps at the regional scale that can then be targeted with fieldwork.The stepwise strategy would enable fieldwork to be planned more costeffectively given the limited resources for biodiversity exploration and characterization.展开更多
基金supported by the National Key Research and Development Program of China(2023YFF0805800)the Science and Technology Basic Resources Investigation Program(2021FY100200)+2 种基金the Key Basic Research program of Yunnan Province,China(202101BC070003)the Chinese Academy of Sciences President's International Fellowship Initiative(2024PVA0087)supported by the Rural and Environment Science and Analytical Services Division(RESAS)of the Scottish Government.
文摘Over the past century,anthropogenic greenhouse gas emissions have continuously increased global temperature and triggered climate change,significantlyimpacting species distributions and biodiversity patterns.Understanding how climate-driven shifts in species distributions reshape diversity patterns is crucial for formulating effective future conservation strategies.Based on the distribution data of 314 Rhododendron species in China,along with 16 environmental variables,we examined spatial diversity patterns and assessed regional and biome differences in species responses using ensembled species distribution models.Our results indicated that climatic variables significantlyinfluencedspecies distributions,with ongoing climate change expected to concentrate Rhododendron distribution patterns and alter species composition.Regional topography played a critical role in shaping species responses to global warming.In the mountainous areas of southwestern China,species exhibited heightened sensitivity to temperature fluctuations,shifting upward as temperature increased.This region also had a higher proportion of threatened species and showed an overall contraction in primary distribution range.Conversely,in southern China,species were more influencedby precipitation,exhibiting a notable northward shift and expansion in primary distribution areas.Notably,alpine species,occurring in habitats above the treeline,may face severe survival risks due to the high degree of habitat loss and fragmentation.We identifiedseven priority conservation areas,predominantly situated in highly fragmented mountainous regions that were inadequately protected by existing nature reserves.Our findingscontribute to a better understanding of changes in Rhododendron diversity patterns under climate change,providing valuable insights for developing comprehensive,flora-wideconservation plans in China.
基金funded by the following grants:the Natural Environ-ment Research Council-Funded SECO Project(NE/T01279X/1)the Fostering Research&Intra-African Knowledge Transfer Through Mobility&Education(FRAME)Conservation Action Research Network(CARN)through the ASPIRE Grant Programme.
文摘The Miombo ecoregion covers eastern and southern Africa,with variations in plant species composition,structure,and biomass across a broad precipitation gradient.Most studies of woody plant communities focus exclusively on larger overstorey trees(≥5 or≥10cm stem diameter),overlooking the contribution of small trees and shrubs in the understorey,which can comprise a significant portion of total biomass and diversity.Here,we evaluate the contribution of both large overstorey and small understorey woody plants to species diversity and above-ground biomass(AGB),with 17 plots(0.5-1ha)across five sites representing both extremes of rainfall gradient spanning the Miombo ecoregion,in northeast Namibia(500-700mm mean annual precipitation,MAP)and southern Democratic Republic of Congo(DRC)(>1,200mm MAP).Mean AGB per site ranged from 21 to 119Mg·ha^(-1),increasing with rainfall,while the proportional AGB contribution of small trees,saplings,and shrubs decreased.In dry Namibia,small trees,saplings,and shrubs(<5cm DBH)contributed up to 28.2%of total AGB(mean±standard deviation:18.3%±3.4%),whereas in wet DRC,they contributed only up to 2.5%(2.3%±1.4%).Namibian sites,on average,contained a large proportion of woody species diversity exclusively in small trees and shrubs(<5cm DBH),with 55 species representing 59.4%of the total diversity.In contrast,DRC sites had higher overall small woody plant diversity(66 species)but fewer species found exclusively as small individuals(25.2%),with many saplings that grow to larger trees.Understorey composition also differed,with saplings of overstorey trees dominating in DRC,while shrubs dominated in Namibia.Our findings show that woody biomass and diversity in dry woodlands are substantially underestimated when studies focus only on larger trees.This highlights the need to consider all woody vegetation to better understand woody plant diversity and biomass variation.
基金the National Key Research and Development Program of China(2023YFA0915800)the Science and Technology Basic Resources Investigation Program(2021FY100200)+3 种基金the Key Basic Research program of Yunnan Province,China(202101BC070003)the Large-scale Scientific Facilities of the Chinese Academy of Sciences(2017-LSFGBOWS-02)the Chinese Academy of Sciences President's International Fellowship Initiative(2025PD0021)We are grateful to curator of KUN to access the herbarium specimens,and Jiayun Zou,Zhirong Zhang,Jing Yang,Hongtao Li and Chunxia Zeng,for their help with sample collection,laboratory work and data analysis.Molecular experiments and data analysis were performed at the Laboratory of Molecular Biology and iFlora High-Performance Computing Center of Germplasm Bank of Wild Species,Kunming Institute of Botany,CAS.
文摘Deep genome skimming(DGS)has emerged as a promising approach to recover orthologous nuclear genes for large-scale phylogenomic analyses.However,its reliability with low DNA quality and quantity typical of archival specimens,such as herbarium material,remains largely unexplored.We used Rhododendron as a case study to evaluate best practices for DGS in phylogenetic analyses at both deep and shallow scales.We first investigated locus recovery variation with sequencing depth,before evaluating the phylogenetic utility of different sets of loci,including Angiosperms353,target nuclear exons,and extended exon-flanking regions.We found DGS effectively recovered nuclear genes from herbarium specimens,with~15coverage performing similarly to deeper sequencing.The recovery of target exon and flanking regions was improved by using supercontigs as a reference,offering a potential solution to limited sequencing depth.The high-integrity nuclear sequences recovered robust phylogenetic relationships within Rhododendron.Notably,exon-flanking regions showed significant potential for resolving relationships at shallow scales.Genes recovered with taxon-specific references had less missing data than those recovered by Angiosperms353 and generated higher-resolution phylogenetic trees.This study demonstrates the utility of DGS data for obtaining numerous nuclear genes from herbarium specimens for phylogenetic studies,and makes recommendations for best practices regarding sequencing coverage,locus selection,and bioinformatic approaches.
文摘出版于2006年9月的最新版的《国际植物命名法规》,即维也纳法规(Vienna Code),取代了圣路易斯法规(Saint Louis Code)而成为管理植物学(包括藻类学和真菌学)科学命名的唯一有效法规。本文报道了维也纳法规和圣路易斯法规之间的主要区别。这些区别包括两版法规在起始日期、有效发表、合格发表、化石植物、多型真菌、拼写和附录诸方面的不同。
基金supported by BBRSC (Biotechnology and Biological Sciences Research Council,UK),RERAD (Rural and Environment Research and Analysis Directorate,Scotland) and the McIntyre Begonia Research Trust,UK
文摘Leaf development involves many complex genetic interactions,signals between adjacent cells or between more distant tissues and consequent changes in cell fate.This review describes three stages in leaf development where regulation by small RNAs have been used to modulate gene expression patterns.
基金supported by National Natural Science Foundation of China(grants 31971567 and 31622015)Fundamental Research Funds for the Central Universities(YJ201936,SCU2020D003,SCU2021D006,SCU2022D003)。
文摘The strength of phylogeographic breaks can vary among species in the same area despite being subject to the same geological and climate history due to differences in biological traits.Several important phylogeographic breaks exist around the Sichuan Basin in Southwest China but few studies have focused on wind-dispersed plants.Here,we investigated the phylogeographic patterns and the evolutionary history of Populus lasiocarpa,a wind-pollinated and wind-dispersed tree species with a circum-Sichuan Basin distribution in southwest China.We sequenced and analyzed three plastid DNA fragments(ptDNA)and eight nuclear microsatellites(nSSRs)of 265 individuals of P.lasiocarpa from 21 populations spanning the entire distribution range.Distribution patterns based on nSSR data revealed that there are three genetic groups in P.lasiocarpa.This is consistent with the three phylogeographic breaks(Sichuan Basin,the Kaiyong Line and the 105°E line),where the Sichuan basin acts as the main barrier to gene flow between western and eastern groups.However,the distribution pattern based on ptDNA haplotypes poorly matched the phylogeographic breaks,and wind-dispersed seeds may be one of the main contributing factors.Species distribution modelling suggested a larger potential distribution in the last glacial maximum with a severe bottleneck during the last interglacial.A DIYABC model also suggested a population contraction and expansion for both western and eastern lineages.These results indicate that biological traits are likely to affect the evolutionary history of plants,and that nuclear molecular markers,which experience higher levels of gene flow,might be better indicators of phylogeographic breaks.
基金supported by funds from the National Natural Science Foundation of China(31970363,31161140350)the Key Basic Research Program of Yunnan Province,China(202101BC070003)supported by the Scottish Government’s Rural and Environment Science and Analytical Services division。
文摘Chinese Assam tea(Camellia sinensis var.assamica)is an important tea crop with a long history of cultivation in Yunnan,China.Despite its potential value as a genetic resource,its genetic diversity and domestication/breeding history remain unclear.To address this issue,we genotyped 469 ancient tea plant trees representing 26 C.sinensis var.assamica populations,plus two of its wild relatives(six and three populations of C.taliensis and C.crassicolumna,respectively)using 16 nuclear microsatellite loci.Results showed that Chinese Assam tea has a relatively high,but comparatively lower gene diversity(H_(S)=0.638)than the wild relative C.crassicolumna(H_S=0.658).Clustering in STRUCTURE indicated that Chinese Assam tea and its two wild relatives formed distinct genetic groups,with considerable interspecific introgression.The Chinese Assam tea accessions clustered into three gene pools,corresponding well with their geographic distribution.However,New Hybrids analysis indicated that 68.48%of ancient Chinese Assam tea plants from Xishuangbanna were genetic intermediates between the Puer and Lincang gene pools.In addition,10%of the ancient Chinese Assam tea individuals were found to be hybrids between Chinese Assam tea and C.taliensis.Our results suggest that Chinese Assam tea was domesticated separately in three gene pools(Puer,Lincang and Xishuangbanna)in the Mekong River valley and that the hybrids were subsequently selected during the domestication process.Although the domestication history of Chinese Assam tea in southwestern Yunnan remains complex,our results will help to identify valuable genetic resources that may be useful in future tea breeding programs.
基金study was funded by the National Natural Science Foundation of China(grant number:U20A2080,31622015)Sichuan University(Fundamental Research Funds for the Central Universities,SCU2021D006,SCU2020D003).
文摘Elevation plays a crucial factor in the distribution of plants,as environmental conditions become increasingly harsh at higher elevations.Previous studies have mainly focused on the effects of large-scale elevational gradients on plants,with little attention on the impact of smaller-scale gradients.In this study we used 14 microsatellite loci to survey the genetic structure of 332 Juniperus squamata plants along elevation gradient from two sites in the Hengduan Mountains.We found that the genetic structure(single,clonal,mosaic)of J.squamata shrubs is affected by differences in elevational gradients of only 150 m.Shrubs in the mid-elevation plots rarely have a clonal or mosaic structure compared to shrubs in lower-or higher-elevation plots.Human activity can significantly affect genetic structure,as well as reproductive strategy and genetic diversity.Sub-populations at mid-elevations had the highest yield of seed cones,lower levels of asexual reproduction and higher levels of genetic diversity.This may be due to the trade-off between elevational stress and anthropogenic disturbance at mid-elevation since there is greater elevational stress at higher-elevations and greater intensity of anthropogenic disturbance at lower-elevations.Our findings provide new insights into the finer scale genetic structure of alpine shrubs,which may improve the conservation and management of shrublands,a major vegetation type on the Hengduan Mountains and the Qinghai-Tibet Plateau.
基金supported by Colciencias Doctoral funding (727-2015)Universidad del Rosario, through a teaching assistantship and a doctoral grant
文摘Data gaps and biases are two important issues that affect the quality of biodiversity information and downstream results.Understanding how best to fill existing gaps and account for biases is necessary to improve our current information most effectively.Two current main approaches for obtaining and improving data include(1)curation of biological collections,and(2)fieldwork.However,the comparative effectiveness of these approaches in improving biodiversity data remains little explored.We used the Flora de Bogota project to study the magnitude of change in species richness,spatial coverage,and sample coverage of plant records based on curation versus fieldwork.The process of curation resulted in a decrease in species richness(synonym and error removal),but it significantly increased the number of records per species.Fieldwork contributed to a slight increase in species richness,via accumulation of new records.Additionally,curation led to increases in spatial coverage,species observed by locality,the number of plant records by species,and localities by species compared to fieldwork.Overall,curationwas more efficient in producing new information compared to fieldwork,mainly because of the large number of records available in herbaria.We recommend intensive curatorial work as the first step in increasing biodiversity data quality and quantity,to identify bias and gaps at the regional scale that can then be targeted with fieldwork.The stepwise strategy would enable fieldwork to be planned more costeffectively given the limited resources for biodiversity exploration and characterization.
