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中国科学院昆明植物研究所知识管理系统
Knowledge Management System of Kunming Institute of Botany,CAS
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GST, P < 0.05) were exhibited by this species. The SAMOVA revealed seven diverging groups of related chlorotypes, six of them had distinct nonoverlapping geographical ranges: one in the northeast comprising 10 populations, a second with a southeast distribution comprising 22 populations, and the remaning four groups comprising 15 populations located in the west part of the species’ range along different river valleys. The genetic clustering of populations into three regions was also supported by analysis of molecular variance, which showed that most genetic variation (82.43%) was found among these three regions. Two clusters were distinguished by both phylogenetic analysis and genealogical analysis of chlorotypes, one consisting of chlorotypes from the western region and the second consisting of those from the eastern region. Significant genetic differences between the two regions might be attributed to vicariance and restricted gene flow, and this vicariance could be explained by the physical environmental heterogeneity on each side of the Tanaka-Kaiyong Line. Following the uplift of the Tibetan Plateau, the reorganization of the major river drainages was primarily caused by river separation and capture events. These historical events could change the distribution of S. davidii from fragmented to continuous (Upper/Lower Jinshajiang and Yalongjiang/Daduhe), and from continuous to fragmented (Nujiang and Jinshajiang/Honghe). However, spatial and temporal patterns of phylogeographic divergence are strongly associated with historical disjunction rather than modern drainage connections. Moreover, the following north-south split in the eastern region and effective isolation with their genetic diversity were essentially modelled by genetic drift. The higher chlorotype richness and genetic divergence for populations in western region compared with other two regions suggests that there were multipe refugia or in situ survival of S. davidii in the Himalayan-Hengduan Mountain region. Fixation of chlorotypes in the northeastern region and near fixation in the southeastern region suggest a recent colonization of these areas. We further found that this species underwent past range expansion around 37-303 thousand years ago (kya). The southeastern populations likely experienced a demographic expansion via unidirectional gene flow along rivers, while northeastern populations underwent a more northward expansion, both from initial populations (s) (21, 22, 23) preserved on eastern refugia (Jinshajiang). This process might have been accompanied with a series of founder effects or bottlenecks making populations genetically impoverished. 3. Phylogeographic analysisbased on nuclear sequence，We sequenced the nuclear (ncpGS) region in all populations sampled, recovering 23 nuclear haplotypes. Compared to cpDNA, both NST (0.470) and GST (0.338) were relatively lower, but NST was also significantly larger than GST. 37.10% of the total variation was distributed among regions which was much lower than that shown by chlorotypes. Thus, more extensive distribution of nuclear haplotypes was exhibited across the geographical range instead of the strong population subdivision observed in chlorotypes. Similarly to the chloroplast data, we found that genetic differentiation of nDNA was positively correlated with the geographical distance, but the increase in the geographical distance between populations did not increase the genetic differentiation of nDNA as rapidly as that of cpDNA. These contrasting levels between the chloroplast and nuclear genomes of S. davidii are likely due to limited gene flow of cpDNA by seeds vs. the extensive gene flow of nDNA by wind-mediated pollen in the population history. We also determined from nuclear markers that haplotype diversity was reduced in the southeastern and northeastern regions due to the loss of rare haplotypes in western region. This reduction of gene diversity is also a signature of founder events or recent bottleneck during post-glacial colonization. However, nuclear diversity within populations remains high. This provides evidence that regionally pollen flow might be sufficiently high to blur the genetic identity of founder populations over a reasonably large spatial scale.3. Relationships among three varieties，The phylogenetic analysis identified two phylogroups of chlorotypes, corresponding to S. davidii var. davidii and var. chuansinesis. The former was distinguished by the abscence of predonminant nuclear haplotype H1 of the latter. The monophyletic group of chlorotypes in var. davidii and var. liangshanesis showed their relatively close relationship. And their genetic divergence from the third variety appears to be relative to their slight morphological difference in leaf size and the divergent environmental niche spaces they occupy. Thus, the observed differences in morphological characters between var. chuansinesis and other two varieties can be explained by the seed dispersal limitation illustrated above (as inferred by geographical separation) and by environmental heterogeneity (as inferred by precipitation or elevation) or by a combination of both. After all, the geological changes, drainage reorganization, and floristic differences following the Himalayan uplift have been suggested to affect the genetic structure of S. davidii. These results provide new insights into the phylogeographic pattern of plants in China. In addition, the unique population genetic structure found in S. davidii has provided important insights into the evolutionary history of this species. The genetic profile uncovered in this study is also critical for its conservation management. Our study has uncovered the existence of at least two ‘evolutionary significant units’ independent units within S. davidii, corresponding to var. davidii from eastern region and var. chuansinensis from western region. The conservation efforts should first focus on most western populations and on the southeastern ones exhibiting high levels of genetic diversity, while the genetically homogeneous northeastern populations located in the degraded Loess Plateau should require much greater conservation 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temperate woody bamboos are a morphologically diverse group with a complicated taxonomy. The Arundinaria group has an East Asia-North America disjunct distribution, which is one of those with complex taxonomy in the temperate woody bamboos. In this study, the phylogeny of the temperate woody bamboos was reconstructed based on eight non-coding regions of the chloroplast genome and nuclear gene GBSSI using large sample set (124 species in 24 genera) with an emphasis on the Arundinaria group. The monophyly of the temperate woody bamboos was resolved in all phylogenies. Ten major lineages were obtained in the chloroplast phylogeny with unresolved relationships among them; the recovered phylogeny is strongly incongruent with the classifications based on morphology at both subtribal and generic ranks; some subclades that are related to the geographic distribution were obtained in those lineages. Five lineages in the GBSSI gene phylogeny were recovered as the same in the chloroplast phylogeny, and the other lineages were incongruent with chloroplast phylogeny in some ways. The reticulate evolution caused by hybridization, introgression and lineage sorting may be an explanation for the molecular phylogenetic incongruence. Based on the facts of diverse morphology, broad distribution and molecular phylogeny, we inferred that the major clades and species within most of the clades of the temperate woody bamboos were originated during several rapid adaptive radiations. Ten putative hybrids were discussed based on molecular phylogenies, morphology and distribution. The micromorphology of the leaf epidermis under SEM (scanning electron microscope) was observed and divided into nine types; the micromorphology can provide some evidence for the bamboo taxonomy and inference of putative hybrids. Additionally, taxonomic revisions were presented for some species based on field observation and herbarium work.","jscount":"1","jsurl":"/simple-search?field1=all&rpp=10&accurate=false&advanced=false&sort_by=2&isNonaffiliated=false&search_type=-1&query1=Ndhf&order=desc&&fq=dc.project.title_filter%3AThe%5C+temperate%5C+woody%5C+bamboos%5C+are%5C+a%5C+morphologically%5C+diverse%5C+group%5C+with%5C+a%5C+complicated%5C+taxonomy.%5C+The%5C+Arundinaria%5C+group%5C+has%5C+an%5C+East%5C+Asia%5C-North%5C+America%5C+disjunct%5C+distribution%2C%5C+which%5C+is%5C+one%5C+of%5C+those%5C+with%5C+complex%5C+taxonomy%5C+in%5C+the%5C+temperate%5C+woody%5C+bamboos.%5C+In%5C+this%5C+study%2C%5C+the%5C+phylogeny%5C+of%5C+the%5C+temperate%5C+woody%5C+bamboos%5C+was%5C+reconstructed%5C+based%5C+on%5C+eight%5C+non%5C-coding%5C+regions%5C+of%5C+the%5C+chloroplast%5C+genome%5C+and%5C+nuclear%5C+gene%5C+GBSSI%5C+using%5C+large%5C+sample%5C+set%5C+%5C%28124%5C+species%5C+in%5C+24%5C+genera%5C%29%5C+with%5C+an%5C+emphasis%5C+on%5C+the%5C+Arundinaria%5C+group.%5C+The%5C+monophyly%5C+of%5C+the%5C+temperate%5C+woody%5C+bamboos%5C+was%5C+resolved%5C+in%5C+all%5C+phylogenies.%5C+Ten%5C+major%5C+lineages%5C+were%5C+obtained%5C+in%5C+the%5C+chloroplast%5C+phylogeny%5C+with%5C+unresolved%5C+relationships%5C+among%5C+them%5C%3B%5C+the%5C+recovered%5C+phylogeny%5C+is%5C+strongly%5C+incongruent%5C+with%5C+the%5C+classifications%5C+based%5C+on%5C+morphology%5C+at%5C+both%5C+subtribal%5C+and%5C+generic%5C+ranks%5C%3B%5C+some%5C+subclades%5C+that%5C+are%5C+related%5C+to%5C+the%5C+geographic%5C+distribution%5C+were%5C+obtained%5C+in%5C+those%5C+lineages.%5C+Five%5C+lineages%5C+in%5C+the%5C+GBSSI%5C+gene%5C+phylogeny%5C+were%5C+recovered%5C+as%5C+the%5C+same%5C+in%5C+the%5C+chloroplast%5C+phylogeny%2C%5C+and%5C+the%5C+other%5C+lineages%5C+were%5C+incongruent%5C+with%5C+chloroplast%5C+phylogeny%5C+in%5C+some%5C+ways.%5C+The%5C+reticulate%5C+evolution%5C+caused%5C+by%5C+hybridization%2C%5C+introgression%5C+and%5C+lineage%5C+sorting%5C+may%5C+be%5C+an%5C+explanation%5C+for%5C+the%5C+molecular%5C+phylogenetic%5C+incongruence.%5C+Based%5C+on%5C+the%5C+facts%5C+of%5C+diverse%5C+morphology%2C%5C+broad%5C+distribution%5C+and%5C+molecular%5C+phylogeny%2C%5C+we%5C+inferred%5C+that%5C+the%5C+major%5C+clades%5C+and%5C+species%5C+within%5C+most%5C+of%5C+the%5C+clades%5C+of%5C+the%5C+temperate%5C+woody%5C+bamboos%5C+were%5C+originated%5C+during%5C+several%5C+rapid%5C+adaptive%5C+radiations.%5C+Ten%5C+putative%5C+hybrids%5C+were%5C+discussed%5C+based%5C+on%5C+molecular%5C+phylogenies%2C%5C+morphology%5C+and%5C+distribution.%5C+The%5C+micromorphology%5C+of%5C+the%5C+leaf%5C+epidermis%5C+under%5C+SEM%5C+%5C%28scanning%5C+electron%5C+microscope%5C%29%5C+was%5C+observed%5C+and%5C+divided%5C+into%5C+nine%5C+types%5C%3B%5C+the%5C+micromorphology%5C+can%5C+provide%5C+some%5C+evidence%5C+for%5C+the%5C+bamboo%5C+taxonomy%5C+and%5C+inference%5C+of%5C+putative%5C+hybrids.%5C+Additionally%2C%5C+taxonomic%5C+revisions%5C+were%5C+presented%5C+for%5C+some%5C+species%5C+based%5C+on%5C+field%5C+observation%5C+and%5C+herbarium%5C+work."},{"jsname":"lastIndexed","jscount":"2025-06-04"}],"资助项目","dc.project.title_filter")'>
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Systematics and Biogeography of Aralia L. (Araliaceae):Revision of Aralia Sects. Aralia, Humiles, Nanae, andSciadodendron
期刊论文
出版物, 3111, 卷号: 57, 期号: 0, 页码: 1-172
作者:
Jun Wen
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浏览/下载：473/8
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提交时间：2017/07/24
Aralia
Aralia Sect. Aralia
Aralia Sect. Dimorphanthus
Aralia Sect. Humiles
Aralia Sect. Nanae
Aralia Sect. pentapanax
Aralia Sect. Sciadodendron
Biogeography
Araliaceae
Systematics
Comparative chloroplast genome analyses of diverse Phoebe (Lauraceae) species endemic to China provide insight into their phylogeographical origin
期刊论文
PEERJ, 2023, 卷号: 11, 页码: e14573
作者:
Shi,Wenbo
;
Song,Weicai
;
Chen,Zimeng
;
Cai,Haohong
;
Gong,Qin
;
Liu,Jin
;
Shi,Chao
;
Wang,Shuo
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Adobe PDF(1788Kb)
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浏览/下载：162/44
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提交时间：2024/07/17
Phoebe
Chloroplast genome
Comparative analysis
Phylogeny
Phylogeographical origin
Conservation
POLYMORPHISM ANALYSIS
SEQUENCE
DNA
ANNOTATION
REGION
TOOLS
Resurrection of Tectaria cadieri from T. ingens (Tectariaceae) Based on Morphological and Molecular Data
期刊论文
SYSTEMATIC BOTANY, 2023, 卷号: 48, 期号: 2, 页码: 192-199
作者:
Li,Shu-Han
;
Zuo,Zheng-Yu
;
Dong,Shi-Yong
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Adobe PDF(32494Kb)
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浏览/下载：173/28
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提交时间：2024/07/17
Fern
Indochina
phylogeny
species identification
PHYLOGENY
EVOLUTION
Complete chloroplast genomes of four Atalantia (Rutaceae) species: insights into comparative analysis, phylogenetic relationships, and divergence time estimation
期刊论文
PLANT SYSTEMATICS AND EVOLUTION, 2023, 卷号: 309, 期号: 5, 页码: 31
作者:
Shi,Wenbo
;
Song,Weicai
;
Zhao,Yuqi
;
Shi,Chao
;
Wang,Shuo
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浏览/下载：175/23
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提交时间：2024/05/09
Atalantia
Chloroplast genome
Comparative analysis
Divergence times
Molecular markers
Phylogeny
ACETYL-COA CARBOXYLASE
CITRUS
SEQUENCE
AURANTIOIDEAE
EVOLUTION
DIVERSITY
FOSSIL
DNA
BIOGEOGRAPHY
RADIATIONS
Chloroplast genome characteristics and phylogeny of the sinodielsia clade (apiaceae: apioideae)
期刊论文
BMC PLANT BIOLOGY, 2023, 卷号: 23, 期号: 1, 页码: 284
作者:
Weng,Long
;
Jiang,Yunhui
;
Wang,Yong
;
Zhang,Xuemei
;
Zhou,Ping
;
Wu,Mei
;
Li,Hongzhe
;
Sun,Hang
;
Chen,Shaotian
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Adobe PDF(8740Kb)
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浏览/下载：181/17
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提交时间：2024/05/09
Sinodielsia clade
Systematics
Cp genome
Highly variable region
Apioideae
SUBFAMILY APIOIDEAE
SEQUENCE
NRDNA
ANGIOSPERMS
ANGELICA
Characteristics of plastid genomes in the genus Ceratostigma inhabiting arid habitats in China and their phylogenomic implications
期刊论文
BMC PLANT BIOLOGY, 2023, 卷号: 23, 期号: 1, 页码: 303
作者:
Zhao,Yu-Juan
;
Liu,Jian
;
Yin,Gen-Shen
;
Gong,Xun
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浏览/下载：232/54
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提交时间：2024/05/09
Ceratostigma
Plastid genome
Comparative analysis
Interspecific relationship
Plumbaginaceae
COMPLETE CHLOROPLAST GENOME
MEKONG-SALWEEN DIVIDE
LIMONIUM-SINENSE
INVERTED REPEAT
SEQUENCE
EVOLUTION
DNA
PLUMBAGINACEAE
CONSEQUENCES
DIVERSITY
叶绿体全基因组序列在香薷属（唇 形科）系统发育中的应用
学位论文
: 中国科学院大学, 2022
作者:
孙增朋
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浏览/下载：183/1
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提交时间：2024/05/14
香薷属
Elsholtzia
叶绿体基因组
Plastomes
系统发育重建
Phylogenetic reconstruction
生物地理学
Biogeography
高变区
Highly variable region
Phylogenomic and comparative analyses of Coffeeae alliance (Rubiaceae): deep insights into phylogenetic relationships and plastome evolution
期刊论文
BMC PLANT BIOLOGY, 2022, 卷号: 22, 期号: 1, 页码: 88
作者:
Amenu, Sara Getachew
;
Wei, Neng
;
Wu, Lei
;
Oyebanji, Oyetola
;
Hu, Guangwan
;
Zhou, Yadong
;
Wang, Qingfeng
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浏览/下载：139/14
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提交时间：2024/04/30
Coffeeae alliance
Phylogenomic
Plastome
Plastome structural variations (PSVs)
Rubiaceae
COMPLETE CHLOROPLAST GENOME
CODON USAGE BIAS
INVERTED REPEAT
SEQUENCE
ALIGNMENT
GENE
SUBFAMILIES
CONTRACTION
ANGIOSPERMS
EXPANSION
Plastome characteristics and species identification of Chinese medicinal wintergreens (Gaultheria, Ericaceae)
期刊论文
PLANT DIVERSITY, 2022, 卷号: 44, 期号: 6, 页码: 519-529
作者:
Xu, Yan-Ling
;
Shen, Hao-Hua
;
Du, Xin-Yu
;
Lu, Lu
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浏览/下载：178/44
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提交时间：2024/04/30
DNA barcodes
Gene duplication
Plastome
Repeat sequences
Structural variation
CHLOROPLAST GENOME
PHYLOGENETIC ANALYSIS
INVERTED REPEAT
EVOLUTION
SEQUENCE
DNA
SOFTWARE
INSIGHTS
REARRANGEMENTS
ORGANIZATION
Comparative Analysis the Complete Chloroplast Genomes of Nine Musa Species: Genomic Features, Comparative Analysis, and Phylogenetic Implications
期刊论文
FRONTIERS IN PLANT SCIENCE, 2022, 卷号: 13, 页码: 832884
作者:
Song, Weicai
;
Ji, Chuxuan
;
Chen, Zimeng
;
Cai, Haohong
;
Wu, Xiaomeng
;
Shi, Chao
;
Wang, Shuo
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Adobe PDF(7732Kb)
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浏览/下载：119/6
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提交时间：2024/08/21
Musa
chloroplast genome
genetic structure
comparative analysis
phylogenetic analysis
interspecific relationships
BANANA
SEQUENCE
GENES
DNA
WASTE
ANGIOSPERMS
ANNOTATION
EVOLUTION
REMOVAL
PLANTS
