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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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中国科学院东亚植物... [73]
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昆明植物所硕博研究... [15]
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李德铢 [25]
Sun Hang [20]
彭华 [11]
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向春雷 [8]
邓涛 [7]
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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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Fund of the National Natural Science Foundation of China","jscount":"1","jsurl":"/simple-search?field1=all&rpp=10&accurate=false&advanced=false&sort_by=2&isNonaffiliated=false&search_type=-1&query1=infrageneric%2Bphylogenetic%2Bresolution&order=desc&&fq=dc.project.title_filter%3AUnited%5C+Fund%5C+of%5C+the%5C+National%5C+Natural%5C+Science%5C+Foundation%5C+of%5C+China"},{"jsname":"Yunnan Natural Science Foundation[U1136602]","jscount":"1","jsurl":"/simple-search?field1=all&rpp=10&accurate=false&advanced=false&sort_by=2&isNonaffiliated=false&search_type=-1&query1=infrageneric%2Bphylogenetic%2Bresolution&order=desc&&fq=dc.project.title_filter%3AYunnan%5C+Natural%5C+Science%5C+Foundation%5C%5BU1136602%5C%5D"},{"jsname":"lastIndexed","jscount":"2023-09-22"}],"Funding Project","dc.project.title_filter")'>
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Testing genome skimming for species discrimination in the large and taxonomically difficult genus Rhododendron
期刊论文
MOLECULAR ECOLOGY RESOURCES, 2022, 卷号: 22, 期号: 1, 页码: 404-414
Authors:
Fu,Chao-Nan
;
Mo,Zhi-Qiong
;
Yang,Jun-Bo
;
Cai,Jie
;
Ye,Lin-Jiang
;
Zou,Jia-Yun
;
Qin,Han-Tao
;
Zheng,Wei
;
Hollingsworth,Peter M.
;
Li,De-Zhu
;
Gao,Lian-Ming
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Himalaya-Hengduan Mountains
infrageneric phylogenetic resolution
next generation DNA barcoding
Rhododendron
species discrimination
PHYLOGENETIC-RELATIONSHIPS
SECTIONAL RELATIONSHIPS
CHLOROPLAST GENOME
DNA BARCODES
ERICACEAE
HYBRIDIZATION
YUNNAN
DIVERSITY
PATTERNS
AGASTUM
Phylogenetic Analysis Based on Chloroplast and Nuclear DNA Sequences and a Revised Infrageneric Classification
期刊论文
ACTA PHYTOTAXONOMICA ET GEOBOTANICA, 2021, 卷号: 72, 期号: 3, 页码: 179-204
Authors:
Watanabe,Seita T.
;
Hayashi,Kazuhiko
;
Arakawa,Katsuro
;
Fuse,Shizuka
;
Nagamasu,Hidetoshi
;
Ikeda,Hiroshi
;
Kuyama,Atsushi
;
Suksathan,Piyakaset
;
Poopath,Manop
;
Pooma,Rachun
;
Yang,Yong-Ping
;
Tamura,Minoru N.
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monocotyledons
new infrageneric classification
phylog-eny
tepal morphology
MOLECULAR PHYLOGENY
NONCODING REGIONS
UNIVERSAL PRIMERS
LILIUM
SPACER
LILIACEAE
AMPLIFICATION
NOMOCHARIS
DISPERSAL
LILIALES
An updated tribal classification of Lamiaceae based on plastome phylogenomics
期刊论文
BMC BIOLOGY, 2021, 卷号: 19, 期号: 1, 页码: 2
Authors:
Zhao,Fei
;
Chen,Ya-Ping
;
Salmaki,Yasaman
;
Drew,Bryan T.
;
Wilson,Trevor C.
;
Scheen,Anne-Cathrine
;
Celep,Ferhat
;
Braeuchler,Christian
;
Bendiksby,Mika
;
Wang,Qiang
;
Min,Dao-Zhang
;
Peng,Hua
;
Olmstead,Richard G.
;
Li,Bo
;
Xiang,Chun-Lei
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Lamiaceae
Lamioideae
Mints
Phylogenomics
Tribal relationships
COMPLETE CHLOROPLAST GENOME
HAWAIIAN ENDEMIC MINTS
MOLECULAR PHYLOGENY
POLLEN MORPHOLOGY
CLERODENDRUM LAMIACEAE
LAMIOIDEAE LAMIACEAE
STACHYDEAE LAMIACEAE
CHARACTER EVOLUTION
STAMINAL EVOLUTION
PERICARP STRUCTURE
Plastome phylogenomics of Cephalotaxus (Cephalotaxaceae) and allied genera
期刊论文
ANNALS OF BOTANY, 2021, 卷号: 127, 期号: 5, 页码: 697-708
Authors:
Ji,Yunheng
;
Liu,Changkun
;
Landis,Jacob B.
;
Deng,Min
;
Chen,Jiahui
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Gymnosperm
Cephalotaxaceae
Taxaceae
phylogeny
molecular dating
taxonomic delineation
recent speciation
QUANTITATIVE RECONSTRUCTION
PHYLOGENETIC-RELATIONSHIPS
EVOLUTIONARY HISTORY
MOLECULAR PHYLOGENY
SOUTHWEST CHINA
TAXACEAE
FLORA
CHLOROPLAST
SEQUENCE
CLIMATE
Delimiting species in Basidiomycota: a review
期刊论文
FUNGAL DIVERSITY, 2021, 卷号: 109, 期号: 1, 页码: 181-237
Authors:
Cao,Bin
;
Haelewaters,Danny
;
Schoutteten,Nathan
;
Begerow,Dominik
;
Boekhout,Teun
;
Giachini,Admir J.
;
Gorjon,Sergio P.
;
Gunde-Cimerman,Nina
;
Hyde,Kevin D.
;
Kemler,Martin
;
Li,Guo-Jie
;
Liu,Dong-Mei
;
Liu,Xin-Zhan
;
Nuytinck,Jorinde
;
Papp,Viktor
;
Savchenko,Anton
;
Savchenko,Kyryll
;
Tedersoo,Leho
;
Theelen,Bart
;
Thines,Marco
;
Tomsovsky,Michal
;
Toome-Heller,Merje
;
Uron,Judith P.
;
Verbeken,Annemieke
;
Vizzini,Alfredo
;
Yurkov,Andrey M.
;
Zamora,Juan Carlos
;
Zhao,Rui-Lin
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Biological species concept
Morphological species concept
Phylogenetic species concept
Taxonomy
INTERNAL TRANSCRIBED SPACER
FRAGMENT-LENGTH-POLYMORPHISMS
FLIGHT MASS-SPECTROMETRY
RUST FUNGI PUCCINIALES
NUCLEAR RIBOSOMAL DNA
MOLECULAR PHYLOGENETIC-RELATIONSHIPS
HEBELOMA-CRUSTULINIFORME COMPLEX
ASSESSING NATURAL RELATIONSHIPS
DESORPTION IONIZATION-TIME
MULTIPLE GENE GENEALOGIES
Leveraging plastomes for comparative analysis and phylogenomic inference within Scutellarioideae (Lamiaceae)
期刊论文
PLOS ONE, 2020
Authors:
Zhao, Fei
;
Li, Bo
;
Drew, Bryan T.
;
Chen, Ya-Ping
;
Wang, Qiang
;
Yu, Wen-Bin
;
Liu, En-De
;
Salmaki, Yasaman
;
Peng, Hua
;
Xiang, Chun-Lei
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A global plastid phylogeny of the fern genus Asplenium (Aspleniaceae)
期刊论文
CLADISTICS, 2020
Authors:
Xu, Ke-Wang
;
Zhang, Liang
;
Rothfels, Carl J.
;
Smith, Alan R.
;
Viane, Ronald
;
Lorence, David
;
Wood, Kenneth R.
;
Chen, Cheng-Wei
;
Knapp, Ralf
;
Zhou, Lin
;
Ngan Thi Lu
;
Zhou, Xin-Mao
;
Wei, Hong-Jin
;
Fan, Qiang
;
Chen, Su-Fang
;
Cicuzza, Daniele
;
Gao, Xin-Fen
;
Liao, Wen-Bo
;
Zhang, Li-Bing
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Comparative analysis of complete plastid genome reveals powerful barcode regions for identifying wood of Dalbergia odorifera and D. tonkinensis (Leguminosae)
期刊论文
JOURNAL OF SYSTEMATICS AND EVOLUTION, 2020
Authors:
Qin, Ming
;
Zhu, Cheng-Jie
;
Yang, Jun-Bo
;
Vatanparast, Mohammad
;
Schley, Rowan
;
Lai, Qiang
;
Zhang, Dan-Yan
;
Tu, Tie-Yao
;
Klitgard, Bente B.
;
Li, Shi-Jin
;
Zhang, Dian-Xiang
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Complete plastomes of 17 species of maples (Sapindaceae: Acer): comparative analyses and phylogenomic implications
期刊论文
PLANT SYSTEMATICS AND EVOLUTION, 2020
Authors:
Wang, Wencai
;
Chen, Siyun
;
Zhang, Xianzhi
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Plastome Evolution in Dolomiaea (Asteraceae, Cardueae) Using Phylogenomic and Comparative Analyses
期刊论文
FRONTIERS IN PLANT SCIENCE, 2020
Authors:
Shen, Jun
;
Zhang, Xu
;
Landis, Jacob B.
;
Zhang, Huajie
;
Deng, Tao
;
Sun, Hang
;
Wang, Hengchang
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