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Chinese Journal of Oceanology and Limnology 2015年第2期33卷 490-499页

作者：李丽芳马洪钢 AL-RASHEID Khaled A.S. Marine College Shandong University Institute of Evolution & Marine Biodiversity Ocean University of China Zoology Department King Saud University

In this paper, we explore possible conflict between morphological and molecular interpretations of phylogenetic relationships within the well-known peritrichous genus Zoothamnium. On the basis of morphological evidence, for a long time this genus has been believed to be a well-defined monophyletic taxon. Nonetheless, Zoothamnium exhibits higher genetic diversity than the gross morphology of its species. Here, we used all available genetic information for the small subunit of ribosomal RNA （SSU rRNA） and internal transcribed spacer region （ITS1-5.8S-ITS2） for this genus to reconstruct phylogenies for four datasets （SSU rRNA, ITS1, ITS2, and ITS1-5.8S-ITS2） and a combined dataset （SSU rRNA＋ITSI-5.8S- ITS2） using different phylogenetic methods and with consideration of the secondary structure of the genes. Confidence in phylogenetic tree selection was assessed with the approximately unbiased test. The molecular results showed both that Zoothamnium is more likely to be polyphyletic, and morphologically similar genera Zoothamnopsis and Myoschiston were always nested among Zoothamnium species. Accordingly, as with some other groups of ciliates, to understand more fully the correct phylogeny of Zoothamnium there remains a need for additional data from both morphological and molecular studies, covering additional Zoothamnium spp. and members of closely related genera （e.g. Zoothamnopsis, Myoschiston, and Epistylis）.

关键词： peritrichous ciliates Zoothamnium phylogenetic analyses monophyly polyphyly

monophyly of the ring-forming group in Diplopoda(Myriapoda,Arthropoda) based on SSU and LSU ribosomal RNA sequences

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Progress in Natural Science:Materials International 2009年第10期19卷 1297-1303页

作者： Peiyun Conga,b,Xuhua Xiac,Qun Yanga,a State Key Laboratory of Palaeobiology and Strategraphy,Nanjing Institute of Geology and Palaeontology,Chinese Academy of Sciences,Nanjing 210008,China b Yunnan Key Laboratory for Paleobiology,Yunnan University,Kunming 650091,China c Department of Biology,University of Ottawa,Ont.,Canada K1N 6N5 [a]State Key Laboratory of Palaeobiology and Strategraphy Nanjing Institute of Geology and Palaeontology Chinese Academy of Sciences Nanjing 210008 China [b]Yunnan Key Laboratory for Paleobiology Yunnan University Kunming 650091 China [c]Department of Biology University of Ottawa Ont. Canada K1N 6N5

Two controversies exist in the phylogeny of the derived millipedes(Diplopoda).The first is whether millipedes with a fusion ring,including Polydesmida,Spirobolida,Spirostreptida and Julida,form a monophyletic group(the ring-forming group).The second concerns the phylogenetic relationship within the three orders of Juliformia,***,Spirostreptida and *** resolve these phylogenetic controversies,we sequenced 18S and 28S rDNA from six millipede orders and retrieved several homologous sequences from *** results give robust support to the monophyly of the ring-forming group based on maximum parsimony methods,max-imum likelihood methods and Bayesian *** monophyly of the ring-forming group suggests that the fusion of segment sclerites might have occurred only once during millipede evolutionary *** also established a sister-group relationship between Spirobol-ida and Spirostreptida within Juliformia after eliminating a short-branch attraction phenomenon,which is consistent with that from the mitochondrial genome analysis.

关键词： Diplopoda Ring-forming group Ribosomal RNA monophyly Short-branch attraction

Multiple lines of evidence supports the two varieties of Halenia elliptica(Gentianaceae)as two species

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Plant Diversity 2022年第3期44卷 290-299页

作者： Jin-Feng Wu Dong-Rui Jia Rui-Juan Liu Zhi-Li Zhou Lin-Lin Wang Min-Yu Chen Li-Hua Meng Yuan-Wen Duan School of Life Sciences Yunnan Normal UniversityKunming 650092PR China School of Ecology and Environmental Science&Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments Yunnan UniversityKunming 650091PR China Northwest Institute of Plateau Biology Chinese Academy of SciencesXining 810001PR China The Germplasm Bank of Wild Species Institute of Tibetan Plateau Research at KunmingKunming Institute of BotanyChinese Academy of SciencesKunming 650201YunnanPR China Yunnan Lijiang Forest Ecosystem National Observation and Research Station Kunming Institute of BotanyChinese Academy of SciencesLijiang 674100YunnanPR China

Delimiting species requires multiple sources of ***,we delimited two varieties of Halenia elliptica(Gentianaceae)using several lines of evidence,including morphological traits and mating system in a sympatric population,phylogenetic relationships based on nrITS and cpDNA(rpl16)data,and complete chloroplast genome *** analysis of 21 morphological traits clearly separates the two varieties of *** of the flowering process and pollination treatments indicate that *** *** produces seeds via outcrossing,whereas *** *** produces seeds via mixed ***,hand-pollinated hybridization of the two varieties produced no *** of pollinators showed that when bees began a pollination bout on *** *** they preferred to continue pollinating this variety;however,when they began a pollination bout on *** ***,they showed no preference for either *** analysis confirmed the monophyly of ***,which was further divided into two monophyletic clades corresponding to the two varieties.A large number of variants from the chloroplast genomes reflected remarkable genetic dissimilarities between the two varieties of *** recommend that the two varieties of *** should be revised as two species(*** and ***).Our findings indicate that *** varieties may have split into two separate species due to a shift in mating system,changes in flowering phenology and/or post-pollination reproductive isolation.

关键词： Halenia elliptica Flowering phenology Mating system Reproductive isolation monophyly Species delimitation

LVTree Viewer:An Interactive Display for the All-Species Living Tree Incorporating Automatic Comparison with Prokaryotic Systematics

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Genomics, Proteomics & Bioinformatics 2016年第2期14卷 94-102页

作者： Guanghong Zuo Xiaoyang Zhi Zhao Xu Bailin Hao T-Life Research Center Department of PhysicsFudan UniversityShanghai 200433China Yunnan Institute of Microbiology Yunnan UniversityKunming 650091China Thermo Fisher Scientific South San FranciscoCA 94080USA

We describe an interactive viewer for the All-Species Living Tree（LVTree）. The viewer incorporates treeing and lineage information from the ARB-SILVA website. It allows collapsing the tree branches at different taxonomic ranks and expanding the collapsed branches as well, keeping the overall topology of the tree unchanged. It also enables the user to observe the consequence of trial lineage modifications by re-collapsing the tree. The system reports taxon statistics at all ranks automatically after each collapsing and re-collapsing. These features greatly facilitate the comparison of the 16 S rRNA sequence phylogeny with prokaryotic taxonomy in a taxon by taxon *** view of the fact that the present prokaryotic systematics is largely based on 16 S rRNA sequence analysis, the current viewer may help reveal discrepancies between phylogeny and taxonomy. As an application, we show that in the latest release of LVTree, based on 11,939 rRNA sequences, as few as 24 lineage modifications are enough to bring all but two phyla（Proteobacteria and Firmicutes） to monophyletic clusters.

关键词： Archaea and Bacteria 16S rRNA phylogeny monophyly Collapsing and expanding a tree Lineage modifications

Molecular phylogeny of tribe Atraphaxideae(Polygonaceae)evidenced from five cpDNA genes

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Journal of Arid Land 2012年第2期4卷 180-190页

作者： YanXia SUN MingLi ZHANG Key Laboratory of Biogeography and Bioresource in Arid Land Xinjiang Institute of Ecology and Geography Chinese Academy of Sciences Urumqi 830011 China Institute of Botany Chinese Academy of Sciences Beijing 100093 China

Traditionally, Atraphaxis, Calligonum, Pteropyrum and Parapteropyrum are included in the tribe Atraphxideae. Recently, sequence data has revealed that this tribe is not monophyletic. The structure of the tribe was examined by adding more taxa and sequences to clarify the congruence between morphology and molecular phylogeny, the systematic placements of four genera in Polygonaceae, as well as the infra-generic relationships of Atraphaxis and Calligonum within Atraphaxideae. Five chloroplast genes, atpB-rbcL, psbA-trnH, trnL-tmF, psbK-psbl, and rbcL of Atraphaxis, Calligonum, Pteropyrum, and Parapteropyrum were sequenced. The non-monophyly of Atraphaxideae was confirmed. Atraphaxis and Calligonum, respectively, formed a monophyletic group that was well supported. Calligonum is closely related to Pteropyrum; Atraphaxis is sister to Polygonum s. str. and Parapteropyrum is allied with Fagopyrum. Although the morphology suggested the four genera should form a tribe, the molecular data indicated Atraphaxideae was not one monophyletic group. The clades identified within Atraphaxis corresponded well with the current sectional classification based on morphological features. As for Cal- ligonum, Medusa was identified as a non-monophyletic section.

关键词： tribe Atraphaxideae Atraphaxis Calligonum chloroplast genes monophyly

On monospecific genera in prokaryotic taxonomy

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Synthetic and Systems Biotechnology 2017年第3期2卷 226-235页

作者： Guanghong Zuo Bailin Hao T-Life Research Center and Department of Physics Fudan UniversityShanghai 200433China

A monospecific genus contains a single species ever since it was *** formally more than half of the known prokaryotic genera are monospecific,we pick up those which actually raise taxonomic problems by violating monophyly of the taxon within which it *** monophyly as a guiding principle,our arguments are based on simultaneous support from 16S rRNA sequence analysis and whole-genome phylogeny of prokaryotes,as provided by the LVTree Viewer and CVTree Web Server,*** main purpose of this study consists in calling attention to this specific way of global taxonomic ***,we refrain from making formal emendations for the time being.

关键词： Composition Vector Tree 16S rRNA phylogeny Prokaryotic taxonomy Monospecific genera monophyly

Phylogenetic Reconstruction of the Family Acrypteridae (Orthoptera: Acridoidea) Based on Mitochondrial Cytochrome b Gene

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Journal of Genetics and Genomics 2007年第4期34卷 294-306页

作者：霍光明蒋国芳孙正莉刘殿锋张雅林吕林植保资源与病虫害治理教育部重点实验室(西北农林科技大学) 西北农林科技大学昆虫博物馆杨凌712100 南京师范大学生命科学学院江苏省生物资源技术重点实验室南京210097

Sequences from the mitochondrial cytochrome b gene （Cyt b） were determined for 25 species from the superfamily Acridoidae and the homologous sequences of 19 species of grasshoppers were downloaded from the GenBank data library. The purpose was to develop a molecular phylogeny of the Acrypteridae, and to interpret the phylogenetic position of the family within the superfamily Acridoidea. Phylogeny was reconstructed by Maximum-parsimony （MP） and Bayesian criteria using Yunnanites coriacea and Tagasta marginella as outgroups. The alignment length of the fragments was 384 bp after excluding ambiguous sites, including 167 parsimony informative sites. In the fragments, the percentages of A ＋ T and G ＋ C were 70.7% and 29.3%, respectively. The monophyly of Arcypteridae is not supported by phylogenetic trees. Within the Arcypteridae, neither Arcypterinae nor Ceracrinae is supported as a monophyletic group. The current genus Chorthippus is not a monophyletic group, and should be a polyphyletic group. The present results are significantly different from the classification scheme of Arcypteridae, which is based on morphology.

关键词： Caelifera Arcypteridae Cyt b monophyly subfamily

Phylogenetic studies of Chinese labeonine fishes(Teleostei: Cyprinidae)based on the mitochondrial16S rRNA gene

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Progress in Natural Science:Materials International 2005年第3期 21-27页

作者： LI Junbing 1,2 ,WANG Xuzhen 1 ,HE Shunping 1ˇˇ and CHEN Yiyu 1 (1.Institute of Hydrobiology,Chinese Academy of Sciences,Wuhan430072,China 2.Graduate School of the Chinese Academy of Sciences,Beijing100039,China) Institute of Hydrobiology，Chinese Academy of Sciences，Wuhan 430072，China Graduate School of the Chinese Academy of Sciences，Beijing 100039，China Institute of Hydrobiology，Chinese Academy of Sciences，Wuhan 430072，China

The mitochondrial16S ribosomal RNA gene is sequenced from24ingroups taxa,including18species from Labeoninae grouped *** analyses are subjected to neighbor joining,maximum parsimony,maximum likelihood and Bayesian *** analysis indicates that Labeoninae is basically a monophyletic assemblage and can be divided into2major clades:one comprising the genera Cirrhinus,Crossocheilus and Garra;and the other consisting of the genera Labeo,Sinilabeo,Osteochilus,Pseu-doorossocheilus,Parasinilabeo,Ptychidio,Semilabeo,Pseudogyricheilus,Rectori and *** to our present analysis,the features such as the presence of the adhesive disc on the chin and the pharyngeal teeth in2rows used in the traditional taxonomy of Labeoninae provide scarce information for phylogeny of labeonine fishes.

关键词： 16S rRNA Labeoninae monophyly phylogeny Cyprinidae.

Phylogenetic relationships of 18 passerines based on Adenylate Kinase Intron 5 sequences

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Journal of Forestry Research 2008年第3期19卷 239-244页

作者：国会艳于慧鑫白素英马玉堃牡丹江师范学院牡丹江157012 黑龙江大学生命科学学院哈尔滨150080 东北林业大学野生动物资源学院哈尔滨150040

The 18 species of bird studied originally are known to belong to muscicapids, robins and sylviids of passerines, but some dis- putations are always present in their classification systems. In this experiment, phylogenetic relationships of 18 species of passerines were studied using Adenylate Kinase lntron 5 （AKS） sequences and DNA techniques. Through sequences analysis in comparison with each other, phylogenetic tree figures of 18 species of passerines were constructed using Neighbor-Joining （N J） and Maximum-Parsimony （MP） meth- ods . The results showed that sylviids should be listed as an independent family, while robins and flycatchers should be listed into Musci- capidae. Since the phylogenetic relationships between long-tailed tits and old world warblers are closer than that between long-tailed tits and parids, the long-tailed tits should be independent of paridae and be categorized into aegithalidae. Muscicapidae and Paridae are known to be two monophylitic families, but Sylviidae is not a monophyletic group. AK5 sequences had better efficacy in resolving close relationships of interspecies among intrageneric groups.

关键词： molecular phylogeny Adenylate Kinase lntron 5 passeriformes monophyly

A NEW LOACH OF Schistura AND COMMENTS ON THE GENUS

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Zoological Research 1999年第4期20卷 301-305页

作者：陈毅峰中国科学院水生生物研究所武汉430072

Schistura heterognathos Chen,*** described based on specimens from the Nanla River,a tri butary of the Lancangjiang River (upper Mekong River),in Yunnan Province of *** is especially characterized by its abnormal *** jaws are broad,thick and *** upper jaw has no dentoid process and there is a very small or no notch in the lower *** dissociative margins of jaws are *** mouth is broad and transversal,its width approximately equals to snout length and is greater than the interorbital width.

关键词： Schistura New species monophyly Yunnan