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Multigene phylogeny and taxonomy of the genus Melanconiella(Diaporthales)

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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Fungal Diversity 2012年第6期57卷 1-44页

作者： Hermann Voglmayr Amy Y.Rossman Lisa A.Castlebury Walter M.Jaklitsch Department of Systematic and Evolutionary Botany Faculty Centre of BiodiversityUniversity of ViennaRennweg 141030WienAustria Systematic Mycology&Microbiology Laboratory USDAAgricultural Research ServiceB010A10300 Baltimore AveBeltsvilleMD 20705USA

molecular phylogenetic analyses of LSU rDNA demonstrate monophyly of the genus Melanconiella,and its status as a genus distinct from Melanconis is confirmed.Data of macro-and microscopic morphology,pure cultures and phylogenetic analyses of partial SSU-ITS-LSU rDNA,tef1 and rpb2 sequences revealed 13 distinct species of Melanconiella,six of which are described as new(M.chrysodiscosporina,M.chrysomelanconium,M.chrysorientalis,M.echinata,M.elegans,M.meridionalis).Melanconiella hyperopta var.orientalis is described as a new variety.Diaporthe carpinicola,D.ellisii,D.flavovirens,D.hyperopta and D.ostryae are formally combined into Melanconiella.The name Melanconiella chrysostroma is excluded from Melanconiella,as it is an obligate synonym of Wuestneia xanthostroma.The type of Melanconiella is confirmed as M.spodiaea.Several species are lecto-and/or epitypified.A key to all treated species ofMelanconiella is provided,and the circumscriptions of the genera Melanconis and Melanconiella are emended.Most Melanconiella species revealed by molecular phylogenetic analyses can be well characterised by a suite of morphological traits including ascospore shape,length and width,colour,absence/presence and shape of appendages and the anamorph.Anamorph-teleomorph connections were confirmed by pure culture and DNA data,revealing the presence of a single melanconium-or discosporina-like anamorph for each species.Colony growth was found to be characteristic of the respective species.Melanconiella is shown to be confined to the host family Betulaceae,and all species are found to be highly host-specific,mostly confined to a single host species.The biodiversity ofMelanconiella was determined to be centred on the genus Carpinus with nine species,five of which have been confirmed on C.betulus.Europe appears to be the geographic centre of Melanconiella biodiversity.

关键词： High diversity Host specificity Melanconidaceae molecular phylogeny New species Pathogen Systematics

phylogeny of Limenitidinae Butterflies (Lepidoptera: Nymphalidae) Inferred from Mitochondrial Cytochrome Oxidase I Gene Sequences

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Agricultural Sciences in China 2011年第4期10卷 566-575页

作者： ZHANG Min CAO Tian-wen ZHONG Yang GUO Ya-ping MA En-bo Research Institute of Applied Biology Shanxi University Taiyuan 030006 P.R.China Institute of Plant Protection Shanxi Academy of Agricultural Sciences Taiyuan 030031 P.R.China School of Life Sciences Fudan University Shanghai 200433 P.R.China

The phylogenetic analyses of the subfamily Limenitidinae are performed based on 1 471 bp of mtDNA cytochrome oxidase subunit I （COI） gene sequence data which were obtained from 21 individuals spanning 9 genera, along with those of 17 species obtained from GenBank, using Apatura iris, Aglais urticae, and Polyura dolon as outgroup species. Although the transitions at the third codon positions of the COI data set were highly saturated, they were still retained for analysis as they contain the majority of the phylogenetic information, and thus, the maximum pasimony （MP） under different weighting schemes and maximum likelihood （ML） trees were reconstructed in this study. The results showed that within this subfamily, the results based on the COI gene sequences are approximately identical to the traditional classification results. However, the clustering of Lexias pardalis and Tanaecia julii within the genus Euthalia as well as the clustering of Phaedyma aspasia within the genus Neptis with weak support are different from that of the current classification scheme made by Chinese scholars. The genus Limenitis is splited into two subclusters in the trees constructed by using MP and ML methods. These results support one of the strongest hypotheses for the tribe relationships within Limenitidinae.

关键词： Nymphalidae Limenitidinae mtDNA molecular phylogeny cytochrome oxidase I gene

phylogeny of Entoloma s.l. subgenus Pouzarella, with descriptions of five new species from China

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Fungal Diversity 2013年第1期58卷 227-243页

作者： Xiao-Lan He Tai-Hui Li Ping-Gen Xi Zi-De Jiang Ya-Heng Shen Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application Guangdong Open Laboratory of Applied MicrobiologyState Key Laboratory of Applied Microbiology(Ministry—Guangdong Province Jointly Breeding Base)South ChinaGuangdong Institute of MicrobiologyGuangzhou 510070China Soil and Fertilizer Institute Sichuan Academy of Agriculture SciencesChengdu 610066China College of Natural Resources and Environment of South China Agricultural University Guangzhou 510642China

Taxonomy and phylogeny of Entoloma s.***.subgenus Pouzarella in China are carried out based on morphological characters and molecular data.Seven species in subg.Pouzarella are recognized in China and a key to these species is provided.Five species,Entoloma changchunense,E.crassicystidiatum,E.furfuraceum,E.subaraneosum and E.tenuissimum,are described as new;a new Chinese record E.dysthaloides is also presented in this paper.Among them,E.crassicystidiatum was discovered from southern China,and the others were found in northeastern China.molecular phylogeny of subg.Pouzarella were conducted based on nLSU,mtSSU and RPB2,and the phylogenetic positions of the five new species are discussed.The placement of subg.Pouzarella in Entoloma s.***.clade is well resolved in all analyses presented here,and the monophyly of subg.Pouzarella is strongly supported by the morphological and molecular phylogeny.The infrageneric classifications in this group were not well recovered in the present study;and further studies based on more samples and gene loci are needed to a better understanding of the infrageneric taxa in subg.Pouzarella in the future.

关键词： Agaricales Entolomataceae New taxa Taxonomy molecular phylogeny

Tibet,the Himalaya,Asian monsoons and biodiversity-In what ways are they related？

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Plant Diversity 2017年第5期39卷 233-244页

作者： Robert A. Spicer Key Laboratory of Tropical Forest Ecology Xishuangbanna Tropical Botanical Garden Chinese Academy of Sciences Menglun Yunnan 666303 PR China School of Environment Earth and Ecosystem Sciences The Open University MK7 6AA UK

Prevailing dogma asserts that the uplift of Tibet, the onset of the Asian monsoon system and high biodiversity in southern Asia are linked, and that all occurred after 23 million years ago in the Neogene.Here, spanning the last 60 million years of Earth history, the geological, climatological and palaeontological evidence for this linkage is reviewed. The principal conclusions are that: 1) A proto-Tibetan highland existed well before the Neogene and that an Andean type topography with surface elevations of at least 4.5 km existed at the start of the Eocene, before final closure of the Tethys Ocean that separated India from Eurasia. 2) The Himalaya were formed not at the start of the India-Eurasia collision, but after much of Tibet had achieved its present elevation. The Himalaya built against a pre-existing proto-Tibetan highland and only projected above the average height of the plateau after approximately 15 Ma. 3)Monsoon climates have existed across southern Asia for the whole of the Cenozoic, and probably for a lot longer, but that they were of the kind generated by seasonal migrations of the Inter-tropical Convergence Zone. 4) The projection of the High Himalaya above the Tibetan Plateau at about 15 Ma coincides with the development of the modern South Asia Monsoon. 5) The East Asia monsoon became established in its present form about the same time as a consequence of topographic changes in northern Tibet and elsewhere in Asia, the loss of moisture sources in the Asian interior and the development of a strong winter Siberian high as global temperatures declined. 6) New radiometric dates of palaeontological finds point to southern Asia's high biodiversity originating in the Paleogene, not the Neogene.

关键词： Tibetan Plateau Himalaya Uplift history Monsoons Biodiversity molecular phylogeny

Evolution and phylogenetic application of the MC1R gene in the Cobitoidea(Teleostei: Cypriniformes)

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Zoological Research 2016年第5期37卷 281-289页

作者： Qiong-Ying TANG Li-Xia SHI Fei LIU Dan YU Huan-Zhang LIU The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences Institute of Hydrobiology Chinese Academy of Sciences Wuhan 430072 China University of Chinese Academy of Sciences Beijing 100049 China

Fish of the superfamily Cobitoidea sensu stricto （namely Ioaches） exhibit extremely high diversity of color patterns, but so far little is known about their evolutionary mechanism. Melanocortin 1 receptor gene （MCIR） plays an important role during the synthesis of melanin and formation of animal body color patterns. In this study, we amplified and sequenced the partial MCIR gene for 44 loach individuals representing 31 species of four families. Phylogenetic analyses yielded a topology congruent with previous studies using multiple nuclear loci, showing that each of the four families was monophyletic with sister relationships of Botiidae＋（Cobitidae＋（Balitoridae＋Nemacheilidae））. Gene evolutionary analyses indicated that MCIR in Ioaches was under purifying selection pressure, with various sites having different dNIds values. Both Botiidae and Cobitidae had lower dN/ds values than those of background lineages, suggesting their evolution might be strongly affected by purifying selection pressure. For Balitoddae and Nemacheilidae, both had larger dNIds values than those of background lineages, suggesting they had a faster evolutionary rate under more relaxed selection pressure. Consequently, we inferred that the relatively stable color patterns in Botiidae and Cobitidae might result from the strong purifying selection pressure on the MC1R gene, whereas the complicated and diverse color patterns in Balitoridae and Nemacheilidae might be associated with the relaxed selection pressure. Given the easy experimental procedure for the partial MCTR gene and its excellent performance in reconstructing phylogeny, we suggest this gene could be used as a good molecular marker for the phylogenetic study of fish species.

关键词： Gene evolution molecular phylogeny Cobitoidea Melanocortin 1 receptor gene

Shaken not stirred: A molecular contribution to the systematics of genus Mugil (Teleostei, Mugilidae)

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Integrative Zoology 2016年第4期11卷 263-281页

作者： Sandra HERAS Ferruccio MALTAGLIATI Maria Victoria FERNÁNDEZ María Inés ROLDÁN Laboratory of Genetic Ichthyology University of GironaGironaSpain Department of Biology University of PisaPisaItaly

With this work we addressed some molecular systematic issues within the Mugil cephalus species complex.Particular attention was paid to the debated situations of:(i)Mugil liza,occurring in partial sympatry with Mugil cephalus in the northwestern Atlantic,and(ii)Mugil platanus,considered by some authors a synonymy of the former species and distributed in the southwestern Atlantic.We sequenced 79 individuals of a 465-bp portion of the mitochondrial control region(CR)from 8 western Atlantic and 2 Mediterranean localities.In addition,all CR sequences available from GenBank for the studied taxa were added to our dataset,for a total of 323 individuals.Overall,229 haplotypes corresponding to 8 divergent monophyletic lineages were detected.Results of phylogenetic analyses were consistent with the occurrence of past speciation events producing the observed lineages.Of these lineages,7 correspond to cryptic species and one is constituted by M.liza and M.platanus.As a matter of fact,these 2 taxa constitute a single lineage within the M.cephalus species complex.However,individuals of M.liza/M.platanus lineage analyzed by means of the 18 mitochondrial markers available in GenBank exhibited a degree of genetic diversity consistent with highly divergent populations.Of the 8 lineages detected,the Mediterraean one(type locality)corresponds to M.cephalus;the lineage M.liza/M.platanus should be named M.liza,under the priority principle,and the left 6 lineages need formal description.

关键词： cryptic species historical demography molecular phylogeny Mugil systematics

Diversifying on the Ark:multiple new endemic lineages of dwarf geckos from the Western Ghats provide insights into the systematics and biogeography of South Asian Cnemaspis(Reptilia:Squamata)

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Zoological Research 2021年第6期42卷 675-691页

作者： Saunak Pal Zeeshan A.Mirza Princia Dsouza Kartik Shanker Bombay Natural History Society MumbaiMaharashtra 400001India Centre for Ecological Sciences Indian Institute of ScienceBengaluruKarnataka 560012India National Centre for Biological Sciences Tata Institute of Fundamental ResearchBengaluruKarnataka 560065India

The highly speciose gekkonid genus Cnemaspis Strauch,1887 is polyphyletic,with three distantly related and geographically isolated clades from Africa,South Asia(SA),and Southeast Asia.At present,there are 85 known species within SA Cnemaspis,although the number continues to increase rapidly with focused surveys and rigorous taxonomic work.Recent studies have provided valuable insights into the diversity and evolutionary history of SA Cnemaspis;however,most of these studies lack sufficient sampling in the Western Ghats(WG),where the genus has its greatest diversity.We addressed this research gap by conducting extensive sampling across the WG and re-examining museum specimens,thus providing a systematic account of various extant Cnemaspis species along with their distribution and natural history.We described 12 new species and a southern WG endemic clade of SA Cnemaspis.Ten of the newly described species are endemic to the forests of the southern WG.We also identified 10 well-supported subclades that can be separated across morphological,geographic,and phylogenetic axes.A time-calibrated phylogeny and ancestral area reconstructions confirmed the Paleocene origin of SA Cnemaspis in the WG and provide insights into its evolutionary history and biogeography.The discovery of multiple endemic and deeply divergent lineages further highlights the evolutionary significance of the WG for lizards.

关键词： Biogeography Cnemaspis Dwarf geckos molecular phylogeny New species Osteology South Asia Systematics Western Ghats

Detection and molecular Characterization of Enteroviruses in Korean Surface Water by Using Integrated Cell Culture Multiplex RT-PCR

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Biomedical and Environmental Sciences 2008年第5期21卷 425-431页

作者： GYUCHEOL LEE CHANHEE LEE CHANSEUNG PARK SANGGI JEONG Water Analysis and Research Center Kwater Division of Life Sciences Chungbuk National University

Objective To identify waterborne enteric viruses in Korean surface water. Methods Integrated cell culture（ICC）multiplex reverse transcription-polymerase chain reaction （RT-PCR） was simultaneously designed to detect coxsackieviruses （CV）, polioviruses （PV）, and reoviruses （RV）. ICC-multiplex RT-PCR and phylogenetic analysis were conducted using 21 total culturable virus assay （TCVA）-positive sample-inoculated cell cultures. Results CV and RV were detected in 9 samples each, and 3 samples were positive for both CV and RV. PV was not detected in any sample. molecular phylogenetic analysis of the VP1 gene sequences revealed that CV types B2 and B4 predominated in Korean surface water, and the nucleotide sequences of CV type B2 were clustered with those of CVs isolated from China and Japan. The results suggested that the evolution of these viruses occurred in a region-specific manner. Conclusion CV and RV are detectable in Korean surface water, with a predominance of CV type B2, and the evolution of CV type B2 occur in a region-specific manner.

关键词： ICC-multiplex RT-PCR Coxsackieviruses molecular phylogeny

Phylogenetic estimation and morphological evolution of Alsineae(Caryophyllaceae)shed new insight into the taxonomic status of the genus Pseudocerastium

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Plant Diversity 2021年第4期43卷 299-307页

作者： Gang Yao Bine Xue Kun Liu Yuling Li Jiuxiang Huang Junwen Zhai College of Forestry and Landscape Architecture South China Agricultural UniversityGuangzhou510642China College of Horticulture and Landscape Architecture Zhongkai University of Agriculture and EngineeringGuangzhou510225GuangdongChina College of Life Sciences Anhui Normal UniversityWuhu241000AnhuiChina College of Landscape Architecture Fujian Agriculture and Forestry UniversityFuzhou350002FujianChina

Pseudocerastium is a monotypic genus in Caryophyllaceae endemic to China.The genus has been widely accepted since it was described in 1998,however its phylogenetic position within Caryophyllaceae has never been studied.In the present study,the whole plastid genome and nuclear ribosomal internal transcribed spacer(ITS)sequences of Pseudocerastium stellarioides was obtained through genome skimming,and the phylogenetic position of the species was studied for the first time.Plastid phylogenomic analysis of Caryophyllaceae revealed that Pseudocerastium is clustered within the tribe Alsineae with strong support.Phylogenetic analyses based on an enlarged taxon sampling of Alsineae using five DNA regions(matK,rbcL,rps16 intron,trnL-F and ITS)revealed that P.stellarioides was nested deeply within Cerastium with strong support.Analyses of morphological character evolution suggest that the ancestral states in Alsineae include three styles and a six-lobed capsule at the apex,while both Cerastium and Pseudocerastium have five styles and ten lobes at the apex of the capsule,further supporting their close relationship.The species Pseudocerastium stellarioides is similar to Cerastium wilsonii in morphology,but differs in having villous indumentum on the lower part of the filaments and compressed globose seeds.Therefore,based on the present molecular and morphological evidence,the generic name Pseudocerastium is reduced here as a new synonym of Cerastium and the species P.stellarioides is transferred to Cerastium as C.jiuhuashanense.

关键词： Alsineae Cerastium Character evolution Genome skimming molecular phylogeny Taxonomy