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molecular phylogeny,biogeography and character evolution of the montane genus Incarvillea Juss.(Bignoniaceae)

Plant Diversity 2021年第1期43卷 1-14页

作者： Santosh Kumar Rana Dong Luo Hum Kala Rana Shaotian Chen Hang Sun CAS Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunming 650201China University of the Chinese Academy of Sciences Beijing 100049China College of Pharmaceutical Science Yunnan University of Chinese MedicineKunming 650500China

The complex orogeny of the Himalaya and the Qinghai-Tibet Plateau(QTP)fosters habitat fragmentation that drives morphological differentiation of mountain plant species.Consequently,determining phylogenetic relationships between plant subgenera using morphological characters is unreliable.Therefore,we used both molecular phylogeny and historical biogeographic analysis to infer the ancestral states of several vegetative and reproductive characters of the montane genus Incarvillea.We determined the taxonomic position of the genus Incarvillea within its family and inferred the biogeographical origin of taxa through Bayesian inference(BI),maximum likelihood(ML)and maximum parsimony(MP)analyses using three molecular data sets(trnL-trnF sequences,nr ITS sequences,and a data set of combined sequences)derived from 81%of the total species of the genus Incarvillea.Within the genus-level phylogenetic framework,we examined the character evolution of 10 key morphological characters,and inferred the ancestral area and biogeographical history of the genus.Our analyses revealed that the genus Incarvillea is monophyletic and originated in Central Asia during mid-Oligocene ca.29.42 Ma.The earliest diverging lineages were subsequently split into theWestern Himalaya and Sino-Himalaya during the early Miocene ca.21.12 Ma.These lineages resulted in five re-circumscribed subgenera(Amphicome,Olgaea,Niedzwedzkia,Incarvillea,and Pteroscleris).Moreover,character mapping revealed the ancestral character states of the genus Incarvillea(e.g.,suffruticose habit,cylindrical capsule shape,subligneous capsule texture,absence of capsule wing,and loculicidal capsule dehiscence)that are retained at the earliest diverging ancestral nodes across the genus.Our phylogenetic tree of the genus Incarvillea differs from previously proposed phylogenies,thereby recommending the placement of the subgenus Niedzwedzkia close to the subgenus Incarvillea and maintaining two main divergent lineages.

关键词： Biodiversity hotspots Biogeography Incarvillea molecular phylogeny Phytools Stochastic character mapping

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molecular phylogeny of Pamphagidae （Acridoidea, Orthoptera） from China based on mitochondrial cytochrome oxidase II sequences

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Insect Science 2011年第2期18卷 234-244页

作者： Dao-Chuan Zhang Hong-Yan Han Hong Yin Xin-Jiang Li Zhan Yin Xiang-Chu Yin College of Life Sciences Hebei University Baoding Hebei Province College of Plant Protection Shandong Agncultural University Taian Shandong Province China

Phylogenetic relationships of Pamphagidae were examined using cytochrome oxidase subunit II （COIl） mtDNA sequences （684 bp）. Twenty-seven species of Acridoidea from 20 genera were sequenced to obtain mtDNA data, along with four species from the GenBank nucleotide database. The purpose of this study was analyzing the phylogenetic relationships among subfamilies within Pamphagidae and interpreting the phylogenetic position of this family within the Acridoidea superfamily. Phylogenetic trees were reconstructed using neighbor-joining （NJ）, maximurn parsimony （MP） and Bayesian inference （BI） methods. The 684 bp analyzed fragment included 126 parsimony informative sites. Sequences diverged 1.0%-11.1% between genera within subfamilies, and 8.8%-12.3% between subfamilies. Amino acid sequence diverged 0-6.1% between genera within subfamilies, and 0.4%-7.5% between subfamilies. Our phylogenetic trees revealed the monophyly of Pamphagidae and three distinct major groups within this family. Moreover, several well supported and stable clades were found in Pamphagidae. The global clustering results were similar to that obtained through classical morphological classification： Prionotropisinae, Thrinchinae and Pamphaginae were monophyletic groups. However, the current genus Filchnerella （Prionotropisinae） was not a monophyletic group and the genus Asiotmethis （Prionotropisinae） was a sister group of the genus Thrinchus （Thrinchinae）. Further molec- ular and morphological studies are required to clarify the phylogenetic relationships of the genera Filchnerella and Asiotmethis.

关键词： Acridoidea cytochrome oxidase II gene molecular phylogeny mtDNA,Pamphagidae subfamily

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molecular phylogeny of Osmanthus(Oleaceae) based on non-coding chloroplast and nuclear ribosomal internal transcribed spacer regions

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Journal of Systematics and Evolution 2010年第6期48卷 482-489页

作者： 1,2Wang-Jun YUAN 1Wei-Rui ZHANG 1Yuan-Ji HAN 1Mei-Fang DONG 1Fu-De SHANG 1(College of Life Sciences,Henan University,Kaifeng 475004,China) 2(Institute of Chinese Materia Medica,Henan University,Kaifeng 475004,China) (College of Life Sciences Henan University Kaifeng 475004 China) (Institute of Chinese Materia Medica Henan University Kaifeng 475004 China)

The phylogenetic relationships of Osmanthus Lour.were investigated using the nuclear ribosomal internal transcribed spacer(ITS) regions and non-coding chloroplast regions(psbA-trnH,trnL-F).The two datasets support the conclusion that Osmanthus is polyphyletic,with some species of the subtribe Oleinae nested within Osmanthus.Osmanthus didymopetalus P.S.Green is nested within the clade formed by species of section Osmanthus in two trees.Osmanthus attenuatus P.S.Green,O.yunnanensis P.S.Green,and O.gracilinervis R.L.Lu of traditional section Osmanthus are clearly divergent from other accessions,and do not form a monophyletic group with other Osmanthus accessions.Osmanthus marginatus Hemsl.is embedded in the clade formed by species of section Osmanthus in the ITS tree.In cpDNA trees all species of section Osmanthus are placed in the large clade and all species of section Leiolea formed a group.The taxonomic incongruence among trees for ITS and cpDNA indicate hybridization,as introgression may have occurred among some species of sections Osmanthus and Leiolea.phylogeny of Osmanthus is discussed in light of molecular and morphological data,and a revised infrageneric classification with three sections(Leiolea,Siphosmanthu,and Osmanthus) is presented.The section Linocieroides is abandoned and united with section Osmanthus.

关键词： ITS molecular phylogeny Osmanthus psbA-trnH trnL-F.

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phylogeny and Geographical Derivation of Genus Hildenbrandia Based on Morphological and molecular Evidence

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Journal of Ocean University of China 2023年第6期22卷 1649-1659页

作者： NAN Fangru ZHAO Huiying LI Juan LIU Xudong LIU Qi LV Junping FENG Jia XIE Shulian School of Life Science Shanxi UniversityTaiyuan 030006China

The marine and freshwater Hildenbrandia samples were collected from diverse locations of China and Japan,and mor-phological characterization and molecular phylogenetic analysis were conducted on these samples.Morphological measurements of freshwater specimens were consistent with the results of H.jigongshanensis,whereas cell dimensions of marine specimens were slightly larger than those of widely distributed H.rubra and H.crouanii.Phylogenetic trees based on rbcL,psbA and UPA sequences were consistent.Freshwater specimens collected in this study formed an independent clade with H.jigongshanensis supported by high values.Species attribution was confirmed further by the similar ITS2 secondary structures among the samples of H.jigongshan-ensis.It was found that the intraspecific divergence of rbcL gene in H.jigongshanensis was smaller than other two freshwater species H.rivularis and H.angolensis.Phylogenetic trees showed that marine specimens in this study grouped together with H.rubra samples of North America,and were different with the H.rubra samples of Europe.Combining the comparison results of CBC numbers in ITS2 secondary structure,we propose the marine samples collected in this study to be a new species Hildenbrandia qingdaoensis sp.nov.The separation of the marine and freshwater specimens was supported by the rbcL,UPA and psbA phylogeny as well as ITS2 se-condary structure inference.Biogeographical reconstruction showed the ancestor of freshwater Hildenbrandia might derive from South America and dispersed from North America to Europe and then to Asian countries,which needs to be verified further with more sam-ples and molecular evidences from South America.

关键词： Hildenbrandia morphology molecular phylogeny ITS secondary structure biogeography

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DNA barcoding of genus Toxoptera Koch （Hemiptera： Aphididae） Identification and molecular phylogeny inferred from mitochondrial COl sequences

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Insect Science 2009年第6期16卷 475-484页

作者： Jian-Feng Wang Ge-Xia Qiao Institute of Zoology Chinese Academy of Sciences Beijing College of Biological and Environmental Engineering Shenyang University Shenyang China

Identification of aphid species is always difficult due to the shortage of easily distinguishable morphological characters. Aphid genus Toxoptera consists of species with similar morphology and similar to Aphis in most morphological characters except the stridulatory apparatus. DNA barcodes with 1 145 bp sequences of partial mitoehondrial cytochrome-coxidase I （COI） genes were used for accurate identification of Toxoptera. Results indicated mean intraspecific sequence divergences were 1.33%, whereas mean interspecific divergences were greater at 8.29% （0.13% and 7.79% if T. aurantii 3 and T. aurantii 4 are cryptic species）. Sixteen samples were distinguished to four species correctly by COI barcodes, which implied that DNA barcoding was successful in discrimination of aphid species with similar morphology. Phylogenetic relationships among species of this genus were tested based on this portion of COI sequences. Four species of Toxoptera assembled a clade with low support in maximum-parsimony （MP） analysis, maximumlikelihood （ML） analysis and Bayesian phylogenetic trees, the genus Toxoptera was not monophyletic, and there were two sister groups, such as T. citricidus and T. victoriae, and two clades of T. aurantii which probably presented cryptic species in the genus.

关键词： Aphididae barcoding citrus aphid COI molecular phylogeny Toxoptera

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Genetic Diversity of MHC Gene and molecular phylogeny in Wanbei Cattle

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Animal Husbandry and Feed Science 2011年第2期3卷 1-2,17页

作者： WEI Lei DU Yong-cai WANG Yu-min Suzhou Vocational and Technological College Suzhou 234000 China

[Objective] To investigate the genetic diversity, molecular phylogeny and origination in Wanbei cattle. [Methedl Blood samples were collected from 50 Wanbei cattle and 14 local cattle breeds. According to the bovine MHC gene sequence, one pair of primers was designed and used for PCR amplification. The sequences of amplified MHC genes were aligned to detect MHC haplotypes and nucleotide polyrnorphisms. A phy- Iogenetic tree based on the MHC gene was also constructed. [Result] A total of 24 polymorphic loci covering 7.86% of the entire length of the se- quences and seven MHC haplotypes were detected. Among these polymorphic loci, there were 18 transitions, 1 tranversions and 5 transition / tran- version. The difference in nucleotide sequence was 0.26% -4.53% between the haplotypes. The nucleotide diversity （π value） and haplotype di- versity （H） were 0.012 - 0.019 and 0.602 - 0.617, respectively. [ Conclusion ] Wanbei cattle do not have rich MHC genetic diversity. They have closer aenetic relationship with Luxi cattle, and both are within the same sister group.

关键词： Wanbei cattle MHC gene Genetic diversity molecular phylogeny

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Characterization and molecular phylogeny of coxsackievirus A16 strains associated with hand,foot,and mouth disease epidemics in Hubei province of China,in 2010 and 2011

Characterization and molecular phylogeny of coxsackievirus A...

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2012全国临床微生物与感染免疫学术研讨会

作者： Liu Wanhong~1,Dong Lanlan~1,Shi Yingying~1,Liu Yongjuan~1,Zhou Bingfei~1,Fu Chong~1,He Xiaohua~(1,2) 1.School of Basic Medical Sciences,Wuhan University 2.Wuhan Center for Medical Treatment

Coxsackievirus A16(CA16),a RNA virus of the family Picornaviridae,is cocirculating with Human enterovirus 71(HEV71) to cause hand,foot,and mouth disease(HFMD) worldwide.To clarify the characterization and molecular phylogeny of CA16 strains associated with HFMD epidemics in Hubei province of China, throat swab specimens from 205 cases were collected during 2010-2011.78 specimens were collected from April to May,2010 and 127 specimens were collected from April to August,2011.Reverse transcriptase-polymerase chain reaction(PCR) followed by sequencing and phylogenetic analysis served to detect enterovirus and determine subtype.Enterovirus was found in 29.48%(23/78) and 29.92%(38/127) of cases and coxsackievirus A16 in 7.69%(6/78) and 11.02%(14/127) of laboratory-confirmed cases in 2010 and 2011,respectively.Phylogenetic analysis of the sequence of the VPl region of isolates indicated that most of the Hubei strains belong to the C1 subgenotype except one strain from Enshi city belongs to C3.This finding suggests that C1 is a major subgenotype of CA16 that caused HFMD in Hubei province and additional surveilance of epidemiology and monitoring of disease severity should be continued.

关键词： Coxsackievirus A16 HFMD molecular phylogeny VP1

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Plant Pharmacophylogeny:Review and Future Directions

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Chinese Journal of Integrative Medicine 2022年第6期28卷 567-574页

作者： GONG Xue YANG Min HE Chun-nian BI Ya-qiong ZHANG Chun-hong LI Min-hui XIAO Pei-gen Department of Pharmacy Baotou Medical CollegeBaotouInner Mongolia Autonomous Region014040China Institute of Medicinal Plant Development Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100193China Pharmaceutical Laboratory Inner Mongolia Institute of Traditional Chinese MedicineHohhot010020China Guangxi Botanical Garden of Medicinal Plants Nanning530000China Inner Mongolia Key Laboratory of Characteristic Geoherbs Resources Protection and Utilization Baotou Medical CollegeBaotouInner Mongolia Autonomous Region014040China

Medicinal plants have provided numerous medicinal active ingredients for thousands of years and these ingredients have been used in Chinese medicine(CM)and traditional pharmacologies worldwide.Recently,the exploitation and utilisation of medicinal plant resources has increased significantly.The results of the studies have led to the identification of many active components,such as steroidal alkaloids,saponins,terpenoids,and glycosides,in various medicinal plants with different evolutionary levels.Moreover,research on the chemical classification,molecular phylogeny,and pharmacological activity of medicinal plants is increasing in popularity.Pharmacophylogeny is an interdisciplinary topic that studies the correlation between plant phylogeny,chemical composition,and curative effects(pharmacological activity and the traditional curative effect)of medicinal plants.In addition,it provides the basic tools to enable research and development of CM resources.This literature review,based on the genetic relationship between phytogroup and species,highlights the formation process,research content,applications,and future directions of pharmacophylogeny.

关键词： pharmacophylogeny phytogroup molecular phylogeny chemical composition curative effect

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A revision of Dryopteris sect.Diclisodon(Dryopteridaceae)based on morphological and molecular evidence with description of a new species

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Plant Diversity 2022年第2期44卷 181-190页

作者： Zheng-Yu Zuo Ting Zhao Xin-Yu Du Yun Xiong Jin-Mei Lu De-Zhu Li Germplasm Bank of Wild Species Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnan650201China Kunming College of Life Science University of Chinese Academy of SciencesKunmingYunnan650201China Gongshan Bureau of the Gaoligongshan National Nature Reserve GongshanYunnan673500China

Dryopteris sect.Diclisodon is a small section of ferns with about 12 species mainly distributed in East Asia.Here,we carried out morphological and phylogenetic analyses of this section.A new species from southwest China,D.gaoligongensis,is described and illustrated.Dryopteris gaoligongensis resembles D.indonesiana and D.sparsa,but differs by having a creeping rhizome and large 4-pinnate fronds.We also show that D.glabrior Ching&Z.Y.Liu is a distinct species;however,because it is a later homonym of D.glabrior Copel.,it should be renamed D.renchangiana.We conclude that a species previously known as D.nitidula,also an illegitimate homonym,should be recognized with a new name,D.sinonepalensis.We resolve the phylogenetic position of D.yoroii as sister to other sampled species of D.sect Diclisodon.Our phylogenetic analyses confirm the distinctiveness of D.gaoligongensis,D.renchangiana,and D.sinonepalensis.A key to species of D.sect Diclisodon in China is provided.

关键词： Dryopteris gaotigongensis Dryopteris renchangiana Dryopteris sect.Nephrocystis Dryopteris sinonepalensis molecular phylogeny Nomenclatural novelties

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Taxonomy of Two New Peritrich Ciliates(Protozoa:Ciliophora)from Inland Saltwaters of China

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Journal of Ocean University of China 2024年第3期23卷 811-821页

作者： YU Ying ZHANG Yong LIANG Ziyao LI Jiqiu LIN Xiaofeng Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems Fujian Provincial Key Laboratory of Coastal Ecology and Environmental StudiesCollege of the Environment and EcologyXiamen UniversityXiamen 361102China School of Life Science South China Normal UniversityGuangzhou 510631China State Key Laboratory of Marine Environmental Science Xiamen UniversityXiamen 361102China

The inland saltwater lakes harbor exceptional biodiversity.Here,two new species of solitary sessile peritrich ciliates were isolated from Qinghai Lake,the largest inland saltwater lake in China.Their morphology,ciliature,silverline system,and molecular phylogeny were investigated based on live observation,silver staining,and analysis of the small subunit ribosomal DNA(SSU rDNA).Vorticella paraglobosa sp.***.is characterized mainly by its obconical or elongate bell-shaped zooid,C-shaped macronucleus,single ventrally located contractile vacuole,two-rowed infundibular polykinety 3,and 28-38 silverlines between peristome and aboral tro-chal band and 10-15 between aboral trochal band and scopula.Vorticella cotyliformis sp.***.differs from its congeners mainly by its double-layered peristomial lip,cup-shaped zooid,J-shaped macronucleus,single ventrally positioned contractile vacuole,three-rowed infundibular polykinety 3,and 70-85 silverlines between peristome and aboral trochal band and 21-25 between aboral trochal band and scopula.The SSU rDNA sequences of the two new species were obtained,and the subsequent molecular phylogenetic analysis supported their taxonomic classification.

关键词： molecular phylogeny morphology new species Qinghai Lake taxonomy

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