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DNA barcoding:species delimitation in tree peonies

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Science china(Life sciences) 2009年第6期52卷 568-578页

作者： ZHANG JinMei1,2,WANG JianXiu1,2,XIA Tao1,2 & zhou ShiLiang1 1state key laboratory of systematic and evolutionary botany,institute of botany,the chinese academy of sciences,beijing 100093,china 2Graduate School of the chinese academy of sciences,beijing 100039,china 1. state key laboratory of systematic and evolutionary botany Institute of Botany the Chinese Academy of Sciences Beijing 100093 China 2. Graduate School of the chinese academy of sciences Beijing 100039 China

Delimitations of species are crucial for correct and precise identification of *** "spe-cies" is more a subjective than an objective concept in taxonomic practice due to difficulties in revealing patterns of infra-or inter-specific *** phylogenetic studies at the population level solve this problem and lay a sound foundation for DNA *** this paper we exemplify the necessity of adopting a phylogenetic concept of species in DNA barcoding for tree peonies(Paeonia ***).We used 40 samples representing all known populations of rare and endangered species and several populations of widely distributed tree *** currently recognized species and major variants have been included in this *** chloroplast gene fragments,***,rps16-trnQ,trnL-F and trnS-G(a total of 5040 characters,96 variable and 69 parsimony-informative characters) and one variable and single-copy nuclear GPAT gene fragment(2093?2197 bp,279 variable and 148 parsi-mony-informative characters) were used to construct phylogenetic relationships among the *** evolutionary lineages revealed by the nuclear gene and the chloroplast genes are inconsistent with the current circumscriptions of ***,***,***,and *** based on *** inconsistencies come from(1) significant chloroplast gene divergence but little nuclear GPAT gene divergence among population systems of *** + ***,and(2) well-diverged nuclear GPAT gene but little chloroplast gene divergence between *** and *** incongruence of the phylogenies based on the chloroplast genes and the nuclear GPAT gene is probably due to the chloro-plast capture event in evolutionary history,as no reproductive barriers exist to prevent inter-specific *** also evaluated the suitability of these genes for use as DNA barcodes for tree *** variability of chloroplast genes among well-defined species or population systems of a specie

关键词： DNA barcoding evolution Paeonia phylogeny species concept

Molecular identification of species in Prunus sect. Persica (Rosaceae), with emphasis on evaluation of candidate barcodes for plants

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Journal of systematics and Evolution 2011年第2期49卷 138-145页

作者： 1,2 Xu QUAN 1 Shi-Liang zhou 1 (state key laboratory of systematic and evolutionary botany, institute of botany, chinese academy of sciences, beijing 100093, china) 2 (Graduate School of the chinese academy of sciences, beijing 100049, china) (state key laboratory of systematic and evolutionary botany Institute of Botany Chinese Academy of Sciences Beijing 100093 China) (Graduate School of the chinese academy of sciences Beijing 100049 China) *Correspondence: Shi-Liang zhou *Correspondence: Author for correspondence. E-mail: slzhou@*** Tel.: 86-10-62836503 Fax: 86-10-62590843.

Species of Prunus L. sect. Persica are not only important fruit trees, but also popular ornamental and medicinal plants. Correct identification of seedlings, barks, or fruit kernels is sometimes required, but no reliable morphological characters are available. Nowadays, the technique of DNA barcoding has the potential to meet such requirements. In this study, we evaluated the suitability of 11 DNA loci (atpB-rbcL, trnH-psbA, trnL-F, trnS-G, atpF-H, rbcL, matK, rpoB, rpoC1, nad1, and internal transcribed spacer [ITS]) as candidate DNA barcodes for peaches, using samples from 38 populations, covering all the species in sect. Persica. On the whole, the primers worked well in this group and sequencing difficulties were met only in the case of ITS locus. Five loci (rbcL, matK, rpoB, rpoC, and nad1) have very low variation rates, whereas atpB-rbcL, atpF-H, trnH-psbA, trnL-F and trnS-G show more variability. The most variable loci, atpB-rbcL and trnH-psbA, can distinguish three of the five species. Two two-locus combinations, atpB-rbcL+trnL-F and atpB-rbcL+atpF-H, can resolve all five species. We also find that identification powers of the loci are method-dependent. The NeighborNet method shows higher species identification power than maximum parsimony, neighbor joining, and unweighted pair group method with arithmetic mean methods.

关键词： atpB-rbcL DNA barcode Prunus sect. Persica trnL-F.

Paleogene integrative stratigraphy,biotas,and paleogeographical evolution of the Qinghai-Tibetan Plateau and its surrounding areas

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Science china Earth sciences 2024年第4期67卷 1290-1325页

作者： Jia LIU Ai SONG Lin DING Tao SU zhekun zhou CAS key laboratory of Tropical Forest Ecology Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesMengla 666303China state key laboratory of Palaeobiology and Stratigraphy Nanjing Institute of Geology and PalaeontologyChinese Academy of SciencesNanjing 210008China institute of Paleontology Yunnan UniversityKunming 650500China state key laboratory of Tibetan Plateau Earth System Environment and Resources(TPESER)Institute of Tibetan Plateau ResearchChinese Academy of SciencesBeijing 100101China

The Paleogene is a crucial period when terrestrial and marine ecosystems recovered from major disruptions and gradually approached their modern *** the Qinghai-Tibetan Plateau and its surrounding regions,the Paleogene also represents a significant phase of tectonic evolution in the Qinghai-Tibetan Plateau-Himalaya orogeny,reorganization of Asian climates,and evolution of *** to limitations in research conditions and understanding,there are still many controversies regarding stratigraphic divisions in the Qinghai-Tibetan Plateau and its surrounding *** recent years,extensive studies on sedimentary petrology,magnetostratigraphy,and isotope dating have been conducted in the *** fossils have been discovered and reported,contributing to a more systematic understanding of *** studies have laid a solid foundation for the comprehensive investigation of the stratigraphy,biotas and paleogeographic evolution of the Qinghai-Tibetan Plateau and its surrounding regions during the *** this paper,we integrate recent research on fossils,isotopic dating,magnetostratigraphy,and geochemistry to refine the stratigraphic divisions and correlation framework of different tectonic units in the region,building upon previous *** the Second Tibetan Plateau Scientific Expedition and Research,the knowledge of Paleogene floras has gradually *** paper discusses the biostratigraphic significance of extinct and newly appeared taxa based on the latest dating results of these plant *** new understanding of fossil species such as the“Eucalyptus”and Arecaceae establishes connections between the Paleogene flora of the Qinghai-Tibetan region and the biotas of Gondwana,specifically Oceania and South *** evolutionary history of key taxa near the Yarlung Zangbo suture zone indicates that the collision between the Indian and Eurasian plates occurred approximately 65-54 *** reconstructions,based o

关键词： Qinghai-Tibetan Plateau Fossils Biostratigraphy Paleoenvironment Paleogeography Paleogene

New universal matK primers for DNA barcoding angiosperms

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Journal of systematics and Evolution 2011年第3期49卷 176-181页

作者： 1,2Jing YU 1Jian-Hua XUE 1Shi-Liang zhou* 1(state key laboratory of systematic and evolutionary botany,institute of botany,chinese academy of sciences,beijing 100093,china) 2(Graduate University of the chinese academy of sciences,beijing 100049,china) (state key laboratory of systematic and evolutionary botany Institute of Botany Chinese Academy of Sciences Beijing 100093 China) (Graduate University of the chinese academy of sciences Beijing 100049 China) *Correspondence: Shi-Liang zhou *Correspondence: ?Author for correspondence. E-mail: slzhou@*** Tel.: 86-10-6283-6503 Fax: 86-10-6259-0843.

The chloroplast maturase K gene(matK) is one of the most variable coding genes of angiosperms and has been suggested to be a "barcode" for land ***,matK exhibits low amplification and sequencing rates due to low universality of currently available primers and mononucleotide *** resolve these technical problems,we evaluated the entire matK region to find a region of 600-800 bp that is highly variable,represents the best of all matK regions with priming sites conservative enough to design universal primers,and avoids the mononucleotide *** careful evaluation,a region in the middle was chosen and a pair of primers named matK472F and matK1248R was designed to amplify and sequence the matK fragment of approximately 776 *** region encompasses the most variable sites,represents the entire matK region best,and also exhibits high amplification rates and quality of *** universality of this primer pair was tested using 58 species from 47 families of angiosperm *** primers showed a strong amplification(93.1%) and sequencing(92.6%) successes in the species *** propose that the new primers will solve,in part,the problems encountered when using matK and promote the adoption of matK as a DNA barcode for angiosperms.

关键词： angiosperm DNA barcoding matK primer.

How complicated and interesting taxonomy is?—Implications from the phylogenetic positions of Penkimia and Ascocentrum(Orchidaceae:Vandeae,Aeridinae)

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How complicated and interesting taxonomy is?—Implications f...

Plant DNA barcoding in china

后植物志时代的系统与进化植物学——2011年全国系统与进化植物学暨第十届青年学术研讨会

作者： Xiaoguo Xiang,Xiaohua Jin~*,Hailang zhou,Weitao Jin,yangjun Lai (Herbarium & state key laboratory of systematic and evolutionary botany,chinese academy of sciences, beijing 100093,china)

The orchid subtribe,Aeridinae,is notorious for its taxonomic confusion due to both convergence and divcrgence in floral and vegetative *** generic delimitation of Holcoglossum-Vanda alliance is one of taxonomic"black-boxes". Aim to understand the systematic positions of Penkimia and Ascocentrum,two little known genera of Holcoglossum-Vanda alliance,we employed nuclear ITS and extensive sampling including 55 species of

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Journal of systematics and Evolution 2011年第03期49卷 165-168页

作者： 1De-Zhu LI 2Jian-Quan LIU 3Zhi-Duan CHEN 1Hong WANG 4Xue-Jun GE 3Shi-Liang zhou 1Lian-Ming GAO 5Cheng-Xin FU 6Shi-Lin CHEN 1(Plant Germplasm and Genomics Centre,Germplasm Bank of Wild Species in Southwest china key laboratory of Biodiversity and Biogeography,Kunming institute of botany,chinese academy of sciences,Kunming 650204,china) 2(key laboratory of Arid and Grassland Ecology,College of Life sciences,Lanzhou University,Lanzhou 730000,china) 3(state key laboratory of systematic and evolutionary botany,institute of botany,chinese academy of sciences,beijing 100093,china) 4(key laboratory of Plant Resources Conservation and Sustainable Utilization,South china Botanical Garden,chinese academy of sciences,Guangzhou 510650,china) 5(key laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education,College of Life sciences,Zhejiang University,Hangzhou 310058,china) 6(institute of Medicinal Plant Development,chinese academy of Medical sciences,Peking Union Medical College,beijing 100193,china) (Plant Germplasm and Genomics Centre Germplasm Bank of Wild Species in Southwest China key laboratory of Biodiversity and Biogeography Kunming Institute of Botany Chinese Academy of Sciences Kunming 650204 China) (key laboratory of Arid and Grassland Ecology College of Life Sciences Lanzhou University Lanzhou 730000 China) (state key laboratory of systematic and evolutionary botany Institute of Botany Chinese Academy of Sciences Beijing 100093 China) (key laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical Garden Chinese Academy of Sciences Guangzhou 510650 China) (key laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education College of Life Sciences Zhejiang University Hangzhou 310058 China) (institute of Medicinal Plant Development Chinese Academy of Medical Sciences Peking Union Medical College Beijing 100193 China) *Correspondence: De-Zhu LI *Correspondence: ?Author for correspondence. E-mail: dzl@*** Tel.: 86-871-5223503 Fax: 86-871-5217791.

Identification is the keystone of biology(Bell, 1986).However,to biologists and students of biology, the total numbers of species that must be identified far outnumber the names commonly used in English,chinese,or oth... 详细信息

关键词： DNA Plant DNA barcoding in china matK

Tibetan Plateau: An evolutionary junction for the history of modern biodiversity

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Science china Earth sciences 2020年第2期63卷 172-187页

作者： Tao DENG Feixiang WU zhekun zhou Tao SU key laboratory of Vertebrate Evolution and Human Origins Institute of Vertebrate Paleontology and PaleoanthropologyChinese Academy of SciencesBeijing 100044China CAS Center for Excellence in Life and Paleoenvironment Beijing 100044China University of chinese academy of sciences Beijing 100049China key laboratory of Tropical Forest Ecology Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesXishuangbanna 666303China

Holding particular biological resources,the Tibetan Plateau is a unique geologic-geographic-biotic interactively unite and hence play an important role in the global biodiversity *** Tibetan Plateau has undergone vigorous environmental changes since the Cenozoic,and played roles switching from"a paradise of tropical animals and plants"to"the cradle of Ice Age mammalian fauna".Recent significant paleontological discoveries have refined a big picture of the evolutionary history of biodiversity on that plateau against the backdrop of major environmental changes,and paved the way for the assessment of its far-reaching impact upon the biota around the plateau and even in more remote ***,based on the newly reported fossils from the Tibetan Plateau which include diverse animals and plants,we present a general review of the changing biodiversity on the Tibetan Plateau and its influence in a global *** define the Tibetan Plateau as a junction station of the history of modern biodiversity,whose performance can be categorized in the following three patterns:(1)Local origination of endemism;(2)Local origination and"Out of Tibet";(3)Intercontinental dispersal via *** first pattern is exemplified by the snow carps,the major component of the freshwater fish fauna on the plateau,whose temporal distribution pattern of the fossil schizothoracines approximately mirrors the spatial distribution pattern of their living *** ascent with modification,their history reflects the biological responses to the stepwise uplift of the Tibetan *** second pattern is represented by the dispersal history of some mammals since the Pliocene and some *** ancestors of some Ice Age mammals,e.g.,the wholly rhino,Arctic fox,and argali sheep first originated and evolved in the uplifted and frozen Tibet during the Pliocene,and then migrated toward the Arctic regions or even the North American continent at beginning of the Ice Age;the ancestor of panthe

关键词： Tibetan Plateau Cenozoic Biodiversity Evolution Plants Fish Mammals

Late Eocene sclerophyllous oak from Markam Basin, Tibet, and its biogeographic implications

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Science china Earth sciences 2021年第11期64卷 1969-1981页

作者： Linlin CHEN Weiyudong DENG Tao SU Shufeng LI zhekun zhou key laboratory of Tropical Forest Ecology Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesMengla 666303China key laboratory of Biodiversity and Biogeography Kunming Institute of BotanyChinese Academy of SciencesKunming 650204China University of chinese academy of sciences Beijing 100049China Center of Plant Ecology Core Botanical GardensChinese Academy of SciencesMengla 666303China

Sclerophyllous evergreen broad-leaved forests,mainly made up of sclerophyllous oak,Quercus section Heterobalanus(Øerst.)Menitsky,Fagaceae,represent the most typical forest type in the Hengduan *** distribution pattern is closely related to the growth and formation of the Qinghai-Tibetan Plateau(QTP).The oldest fossil record of Quercus *** so far discovered is from the middle Miocene of the Gazhacun Formation in Namling County,southern ***,our recent discovery of leaf fossils from the upper Eocene of Lawula Formation in Markam Basin,southeastern Tibet,illustrates that their origin is nearly 20 Myr older than previously *** integrating the results from geometric morphometrics,geographical range expansion,and ecological niche shifts of this section in what is now the QTP and the Hengduan Mountains,we infer that the leaves of Quercus *** were already adapted to cool and dry conditions in some local regions no later than in the late ***,with the growth of the QTP and late Cenozoic global cooling,the expansion of cooler and drier habitats benefited the spread and development of this section and their leaves exhibited morphological stasis through stabilizing *** on published fossil records and recent discoveries,we argue that Quercus *** appeared in the subtropical evergreen and deciduous broad-leaved mixed forests of the southeastern margin of what is now the QTP no later than in the late *** taxa spread westwards along the Gangdese Mountains and later the Himalaya,and others spread eastwards and southeastwards,gradually becoming a dominant group of species in the Hengduan *** dispersal route is contrary to the previous“northwards hypothesis”of this section,and further supports the hypothesis of an East Asian origin for Quercus section Ilex Loudon.

关键词： Quercus section Heterobalanus Cenozoic Qinghai-Tibetan Plateau Geometric Morphometrics Morphological evolutionary Stasis Biogeography

Phylogenetic relationships and divergence times of the family Araucariaceae based on the DNA sequences of eight genes

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chinese Science Bulletin 2009年第15期54卷 2648-2655页

作者： LIU Nian ZHU yong WEI ZongXian CHEN Jie WANG QingBiao JIAN ShuGuang zhou DangWei SHI Jing yang yong ZHONG yang Ministry of Education key laboratory for Biodiversity Science and Ecological Engineering School of Life Sciences Fudan University Shanghai 200433 China Lushan Botanical Garden Chinese Academy of Sciences Lushan 332900 China Shanghai Center for Bioinformation Technology Shanghai 200235 China South china Botanical Garden Chinese Academy of Sciences Guangzhou 510650 China Northwest institute of Plateau Biology Chinese Academy of Sciences Xining 810001 China laboratory of systematic and evolutionary botany Institute of Botany Chinese Academy of Sciences Beijing 100093 China

Araucariaceae is one of the most primitive families of the living conifers, and its phylogenetic rela-tionships and divergence times are critically important issues. The DNA sequences of 8 genes, i.e., nuclear ribosomal 18S and 26S rRNA, chloroplast 16S rRNA, rbcL, matK and rps4, and mitochondrial coxI and atp1, obtained from this study and GenBank were used for constructing the molecular phylogenetic trees of Araucariaceae, indicating that the phylogenetic relationships among the three genera of this family should be ((Wollemia, Agathis), Araucaria). On the basis of the fossil calibrations of Wol-lemia and the two tribes Araucaria and Eutacta of the genus Araucaria, the divergence time of Arauca-riaceae was estimated to be (308 ± 53) million years ago, that is, the origin of the family was in the Late Carboniferous rather than Triassic as a traditional view. With the same gene combination, the diver-gence times of the genera Araucaria and Agathis were (246 ± 47) and (61 ± 15) Ma, respectively. Statistical analyses on the phylogenetic trees generated by using different genes and comparisons of the divergence times estimated by using those genes suggested that the chloroplast matK and rps4 genes are most suitable for investigating the phylogenetic relationships and divergence times of the family Araucariaceae.

关键词：系统发育关系 DNA序列南洋杉基因基础分歧家庭