Phylogeny,character evolution,and classification of Selaginellaceae(lycophytes)

Selaginella is the largest and most taxonomically complex genus in lycophytes.The fact that over 750 species are currently treated in a single genus makes Selaginellales/Selaginellaceae unique in pteridophytes.Here we assembled a dataset of six existing and newly sampled plastid and nuclear loci with a total of 684 accessions(74%increase of the earlier largest sampling)representing ca.300 species to infer a new phylogeny.The evolution of 10 morphological characters is studied in the new phylogenetic context.Our major results include:(1)the nuclear and plastid phylogenies are congruent with each other and combined analysis well resolved and strongly supported the relationships of all but two major clades;(2)the Sinensis group is resolved as sister to S.subg.Pulviniella with strong support in two of the three analyses;(3)most morphological characters are highly homoplasious but some characters alone or combinations of characters well define the major clades in the family;and(4)an infrafamilial classification of Selaginellaceae is proposed and the currently defined Selaginella s.l.is split into seven subfamilies(corresponding to the current six subgenera t the Sinensis group)and 19 genera(the major diagnosable clades)with nine new species-poor genera.We support the conservation of Selaginella with a new type,S.flabellata,to minimize nomenclatural instability.We provide a key to subfamilies and genera,images illustrating their morphology,their morphological and geographical synopses,a list of constituent species,and necessary new combinations.This new classification will hopefully facilitate communication,promote further studies,and help conservation.

Nudivirus Genomics: Diversity and Classification

Nudiviruses represent a diverse group of arthropod specific, rod-shaped and dsDNA viruses. Due to similarities in pathology and morphology to members of the family Baculoviridae, they have been previously classified as the so-called “non-occluded” baculoviruses. However, presently they are taxonomically orphaned and are not assigned to any virus family because of the lack of genetic relatedness to Baculoviridae,. Here, we report on recent progress in the genomic analysis of Heliothis zea nudivirus 1 (HzNV-1), Oryctes rhinoceros nudivirus (OrNV), Gryllus bimaculatus nudivirus (GbNV) and Heliotis zea nudivirus 2 (HzNV-2). Gene content comparison and phylogenetic analyses indicated that the viruses share 15 core genes with baculoviruses and form a monophyletic sister group to them. Consequences of the genetic relationship are discussed for the classification of nudiviruses.

Species diversity,taxonomy and phylogeny of Polyporaceae(Basidiomycota)in China

Polyporaceae is one of the most important families of Basidiomycota.Investigations on the species diversity,taxonomy and phylogeny of Polyporaceae in China are carried out.So far 217 species belonging to 42 genera are reported from China.Two new genera:Amylosporia gen.nov.and Murinicarpus gen.nov.,twelve new species:Coriolopsis dendriformis sp.nov.,C.hainanensis sp.nov.,Funalia cystidiata sp.nov.,Haploporus microsporus sp.nov.,Perenniporia citrinoalba sp.nov.,P.yinggelingensis sp.nov.,Picipes hainanensis sp.nov.,P.jiajinensis sp.nov.,P.pseudovarius sp.nov.,Trametes duplexa sp.nov.,T.ellipsoidea sp.nov.and T.stiptica sp.nov.,and six new combinations,Amylosporia hattorii comb.nov.,Hornodermoporus latissimus comb.nov.,Murinicarpus subadustus comb.nov.,Picipes pumilus comb.nov.,Vanderbylia delavayi comb.nov.and Vanderbylia robiniophila comb.nov.,are proposed.All the species are described based on the Chinese collections.Keys to genera of Polyporaceae occurring in China and keys to species of each genus are provided.This monograph provides a revised classification of Polyporaceae in China according to the modern taxonomy.The phylogeny of Polyporaceae from China are reconstructed based on DNA sequences of multiple loci including the internal transcribed spacer(ITS)regions,the large subunit nuclear ribosomal RNA gene(nLSU),the small subunit nuclear ribosomal RNA gene(nSSU),the small subunit mitochondrial rRNA gene sequences(mtSSU),the translation elongation factor 1-αgene(TEF1),theβ-tubulin gene(TBB1),the RNA polymerase II largest subunit(RPB1)and second largest subunit(RPB2)genes.In addition,full morphological descriptions,illustrations,color photographs,taxonomic notes,ecology and all the available sequences of Polyporaceae species found from China are provided.

水生肉食亚目(Hydradephaga)系统发育学研究简论

水生肉食亚目(Hydradephaga)属于鞘翅目Coleoptera,是一类具有水生习性的食肉性真正水生甲虫(True water beetles)。在真正水生甲虫的系统分类中存在三种假说,一种是肉食亚目(Adephaga)位于该系统的基部,一种是多食亚目(Polyphaga)位于该系统基部,第三种是藻食亚目(Myxophaga)位于该系统基部。最近研究结果更多倾向第一种假说。目前水生肉食亚目大约有5 500个种,200多个属,含8个科。水生肉食亚目的科间水平系统发育关系虽被广泛研究,但观点仍不统一。有代表意义的有三个假说,一是豉甲科(Gyrinidae)位于系统基部,接下来是龙虱科(Dytiscidae)、两栖甲科(Amphizoidae)、水甲科(Hygrobiidae)、小粒龙虱科(Noteridae)与沼梭科(Haliplidae);二是沼梭科位于系统的基部;三是豉甲科位于系统的基部,接下来是沼梭科和龙虱总科(Dytiscoidea),其中龙虱总科由两栖甲科、水甲科、龙虱科、小粒龙虱科组成。目前根据形态学的分类,并结合分子系统学研究方法,第三种假说更符合水生肉食亚目的系统分类,也支持了水生肉食亚目作为一个单系,其祖先来自陆生的假说。

Towards a natural classification of Botryosphaeriales

The type specimens of Auerswaldia,Auerswaldiella,Barriopsis,Botryosphaeria,Leptoguignardia,Melanops,Neodeightonia,Phaeobotryon,Phaeobotryosphaeria,Phyllachorella,Pyrenostigme,Saccharata,Sivanesania,Spencermartinsia and Vestergrenia were examined and fresh specimens of Botryosphaeriales were collected from Thailand.This material is used to provide a systematic treatment of Botryosphaeriales based on morphology and phylogeny.Two new genera,Botryobambusa and Cophinforma are introduced and comparedwith existing genera.Four species newto science,Auerswaldia dothiorella,A.lignicola,Botryosphaeria fusispora and Phaeobotryosphaeria eucalypti,are also described and justified.We accept 29 genera in Botryosphaeriales,with Macrovalsaria being newly placed.In the phylogenetic tree,the 114 strains of Botyrosphaeriales included in the analysis cluster into two major clades with 80%,96%and 1.00(MP,ML and BY)support,with Clade A containing the family type of Botryosphaeriaceae,and Clade B containing Phyllosticta,Saccharata and Melanops species.This group may represent Phyllostictaceae.In Clade A the taxa analyzed cluster in eight sub-clades(Clades A1-8).Clade A1 comprises three distinct subclusters corresponding to the genera Diplodia(Diplodia Clade),Neodeightonia(Neodeightonia Clade)and Lasiodiplodia(Lasiodiplodia Clade).Clade A2 clusters into three groups representing Phaeobotryosphaeria(100%),Phaeobotryon(100%)and Barriopsis(94%).Clade A3 incorporates 17 strains that cluster into three well-supported genera(Dothiorella(86%),Spencermartinsia(100%)and Auerswaldia(63%);the position of Macrophomina is not stable.Clade A4 is a single lineage(100%)representing the new genus Botryobambusa.Clade A5 is a wellsupported subclade incorporating Neofussicoccum.Clade A6 represents the type species of Botryosphaeria,three other Botryosphaeria species and two other genera,Neoscytalidium and Cophinforma gen.nov.Clade A7 comprises two Pseudofusicoccum species and Clade A8 has two Aplosporella species.These sub-clades may eventually require separate families but this requires analysis of a much larger dataset.Our data advances the understanding of Botryosphaeriales,there is,however,still much research to be carried out with resolution of families and genera,linkage of sexual and asexual morphs and differentiation of cryptic species.

Towards a natural classification and backbone tree for Graphostromataceae,Hypoxylaceae,Lopadostomataceae and Xylariaceae

Species and generic recognition in the order Xylariales has been uncertain due to lack of molecular data from authentic cultures,as well as overlapping morphological characteristics.In this study,we revise the families Graphostromataceae,Hypoxylaceae,Lopadostomataceae and Xylariaceae in Xylariales.Our study is based on DNA sequence data derived from living cultures of fresh isolates,data from GenBank and morphological observation of type and worldwide herbarium specimens.We also collected new specimens from Germany,Italy and Thailand.Combined analyses of ITS,LSU,RPB2 and b-tubulin sequence data were used to reconstruct the molecular phylogeny of the above families.Generic and familiar boundaries between these families are revised and presented in an updated combined phylogenetic tree.We accept six genera in Graphostromataceae,19 genera in Hypoxylaceae,four in Lopadostomataceae and 37 genera in Xylariaceae.Five genera previously treated in Xylariaceae are placed in Amphisphaeriales genera incertae sedis and seven genera are placed in Xylariales genera incertae sedis.Two genera are placed in Sordariomycetes genera incertae sedis,while four genera are placed as Xylariomycetidae genera incertae sedis.Three genera are considered as doubtful.Barrmaelia and Cannonia,presently included in Xylariaceae are transferred to Diatrypaceae and Coniochaetales respectively,based on their morphology and phylogeny.Areolospora and Myconeesia are excluded from Xylariaceae and synonymized with Phaeosporis and Anthostomella respectively.Updated descriptions and illustrations are provided for all taxa with notes provided on each genus.Excluded and doubtful genera are listed with notes on their taxonomy and phylogeny.Taxonomic keys are provided for all revised families with morphological details for genera within the families.

One stop shopⅢ:taxonomic update with molecular phylogeny for important phytopathogenic genera:51–75(2019)

This is a continuation of a series focused on providing a stable platform for the taxonomy of phytopathogenic fungi and organisms.This paper focuses on 25 phytopathogenic genera:Alternaria,Capnodium,Chaetothyrina,Cytospora,Cyphellophora,Cyttaria,Dactylonectria,Diplodia,Dothiorella,Entoleuca,Eutiarosporella,Fusarium,Ilyonectria,Lasiodiplodia,Macrophomina,Medeolaria,Neonectria,Neopestalotiopsis,Pestalotiopsis,Plasmopara,Pseudopestalotiopsis,Rosellinia,Sphaeropsis,Stagonosporopsis and Verticillium.Each genus is provided with a taxonomic background,distribution,hosts,disease symptoms,and updated backbone trees.A new database(Onestopshopfungi)is established to enhance the current understanding of plant pathogenic genera among plant pathologists.

苹果属种、杂交种及品种之间关系的AFLP分析

用AFLP技术,对72个苹果属植物样本(34个种、变种、杂交种及38个品种)进行遗传多样性分析。在64对AFLP引物中选出6对引物进行扩增,得到有效谱带1692条,其中多态谱带1547条,多态谱带比率为91.4%。对72个样品的试验数据进行聚类分析,它们的相似系数为0.54～0.82。在相似系数0.60处参试材料被分为4大类,即佛罗伦萨苹果(Malusflorentina)为一类;绿苹果组(Sect.Choromeles)和多胜苹果组(Sect.Docyniopsis)分别各聚一类;花楸组(Sect.Sorbomalus)、脱萼组(Sect.Gymnomeles)和苹果组(Sect.Malus)聚为一类,所有苹果品种和观赏海棠品种全聚在原产亚洲的花楸组、脱萼组及苹果组中。亚洲原产的苹果属植物对于苹果及观赏海棠品种的发展起重要作用。根据试验结果及文献资料,支持将佛罗伦萨苹果组(Sect.Florentinae ChengM.H.)成立单种组;建议将原属花楸组植物除佛罗伦萨苹果外,全部并入苹果组;取消脱萼组,将其组内的植物全部并入苹果组。

乳白蚁属Coptotermes(Isoptera:Rhinotermitidae)检疫分子鉴定研究进展

白蚁是一类受到世界广泛关注的重要社会性昆虫,对人类生活、经济以及生态环境等有很大的影响,特别是乳白蚁属Coptotermes众多种类危害尤为严重。乳白蚁常随木质包装或原木远距离传播异地建群,其为害隐蔽、潜伏期长,一旦爆发则为害严重且难防治,因其种类多、形态趋同,同一巢群中有龄期不一的虫态和多种生物型,可用分类特征少,造成形态分类困难、人为分类现象普遍。近年来分子生物学技术的日益发展,使得白蚁的分类鉴定更加快速、灵敏和可靠,系统发育分析研究更为深入全面,遗传进化方面取得大量研究成果。本文对基于生物信息学的乳白蚁属检疫分类鉴定和系统发育研究方法进行了介绍和评述,并对DNA技术在乳白蚁属分类和进化研究中的应用进行了讨论。

DNA条形码技术在鲻科鱼类鉴定中的应用

本研究选用DNA条形码的通用基因片段,采用特异性扩增测序及与GenBank已有序列结合分析的方法,进行了鲻科（Mugilidae）6属17种鱼类的COI基因片段的序列比较、分子树构建和系统进化研究。研究表明,在所得的17种鲻科鱼类共有的555bp COI基因片段中平均GC含量为46.9%。其中,第二密码子位点含量最高（49.8%~56.2%）,平均54.9%;第一密码子变化范围最大（31.9%~48.6%）,平均42.9%;第三密码子差别不显著（42.5%~43.4%）,平均42.7%。依据Kimura-2-parameter模型（K2P）,17种鲻科鱼类种内遗传距离的平均值为0.004 5,种间遗传距离为0.191,是种内遗传距离的42倍。在分子系统树上,所有物种均呈单系,5属为独立分支,只有隶属于梭属（Liza）的尖头梭（Liza tade）与莫鲻属（Moolgarda）聚类,表现出与传统形态学分类不一致的结果。本研究结果验证了线粒体COI基因作为DNA条形码对鲻科鱼类进行物种鉴定的有效性,可用于辅助探讨鲻科科下属、种分类阶元系统发育问题。

RNA二级结构在微生物系统发育分析上的应用

RNA二级结构用于微生物分类和系统发育分析在近年来逐渐受到注意并发展起来。文章就此方面的发展做了简要综述,其中对在系统发育分析上的应用部分作了较重点介绍。

榕树-传粉者共生体系的协同进化与系统学研究进展及展望

榕树_传粉者共生体系是目前植物与昆虫协同进化研究中的典型模式之一。国内外已经开展了大量的相关研究 ,从不同方面探讨了其特殊的一一对应的共生关系。榕树_传粉者的专一性互惠共生关系中蕴含了与系统发育有关的多因子协同进化的机理 ,因此 ,进行系统发育研究将有助于更好地揭示榕树_传粉者的协同进化历史和理解二者的专一性互惠共生关系。本文简单地介绍了目前榕树及其传粉者共生体系的研究状况之后 ,论述了榕树_传粉者协同进化的系统发育分子生物学研究成果。同时针对国际上在榕属植物的传统的系统与分类研究中存在的一些分歧及榕树传粉者亚科分类不匹配等问题 ,回顾了榕属的分类研究进展及其与传粉者的关系。最后 ,结合我国榕树与传粉者共生体系的研究状况对我国榕属的重新分类和系统发育研究作了展望。

触角感器特征应用于昆虫分类的研究进展

触角是昆虫重要的感觉器官,触角感器对昆虫感受外界环境、实现信息交流具有重要意义。不同种类昆虫的触角感器形态、结构、分布、数量等特征存在差异,可以作为昆虫分类的依据。本文综述了应用触角感器特征鉴定昆虫种类、订正分类地位、讨论昆虫系统发育关系的研究进展,为依据昆虫超微结构进行分类提供科学依据。

中国鼠兔亚属(Subgenus Ochotona)种系发生的探讨

本文对鼠兔亚属主要产于国内的14种,进行了严格的支序系统分析。通过对这14种形态特征分析、对比,找出了22个具有种系发生意义的性状,并用国内学者尚未采用的格局分支论的组分分析,重建了它们的种间分支亲缘关系。根据分支图及国内已有的化石和地史资料,对该亚属的演化作了初步探讨。

盔甲鱼亚纲(无颌类)的系统发育关系(英文)

基于对53个形态学特征的讨论,首次开展了无颌类儒甲鱼亚纲的简约性分析,获得了3 个最简约的分支图,其步长为126,一致性指数为0．508,保留指数为0．801。在此基础上,修订了盔甲鱼亚纲的分类。研究结果表明,志留纪兰多维列世至温洛克世的汉阳鱼类、修水鱼类和大庸鱼类属于盔甲鱼亚纲的基干类群。在其余盔甲鱼类中,识别出3个大的单系类群, 分别是真盔甲鱼目、多鳃鱼目和华南鱼目。在盔甲鱼亚纲中,头甲背窗的起源至少发生了两次,一次在多鳃鱼目支系中,另一次在华南鱼目支系中。基于背窗特征而建立的大窗鱼类并不是一个单系类群。盔甲鱼类的年代分布指示该类群的两次辐射演化,分别是兰多维列世特列奇期基干盔甲鱼类和真盔甲鱼目的辐射演化,和早泥盆世洛霍考夫期多鳃鱼目和华南鱼目的辐射演化。

龙胆属的系统发育分析(英文)

本文运用支序分类的原理和方法,对龙胆科龙胆属的属下等级进行了重新归类和系统发育分析。龙胆属是一个单系群,以3项近裔共性为归类依据。性状分析作了性状同源性分析和性状极性分析。性状极化主要以外类群比较、性状相关性及染色体资料为依据,其它方法,如生物重演律原则、地理递进原则以及孢粉形态等也被结合使用。分析结果,双蝴蝶属和蔓龙胆属被选择为外类群,71个性状被选择作为建立数据矩阵的基本资料。使用PAUP程序对矩阵进行了运算,得到4个最简约的谱系分支图,它们均具一致性系数0.637,支序长度为160步,f-比值范围为0.179～0.189,其中具最低f-比值的图被选作为类群归类和讨论亲缘关系的基础。在支序图上龙胆属归为15个组;其中5个组又划分为系,共包括23个系,其余组为单型组,故共有33个属下类群。一个严格的一致性谱系分支图总结了所有的一致点,从而支持了支序分析的结果。

高维空间点覆盖方法在物种计算机自动分类中的应用

长期以来物种的分类主要依靠形态学方法,难以形成计算机自动分类.本文提出了一种基于高维空间几何分析的序列对比方法,并应用该方法对9个嗜肝病毒科病毒和14个花椰菜花叶病毒科病毒做出了进化树,结果完全符合国际病毒学命名委员会公布的病毒分类标准.在此基础上,本文探索性的提出了一种基于仿生模式识别的物种自动分类方法,并应用该方法对嗜肝病毒科病毒和花椰菜花叶病毒科病毒做了自动分类,正确分类率分别达到100%和94%.

新疆马鹿群体的系统发育

为探讨新疆马鹿系统发生关系及分类地位,对塔里木马鹿、阿尔泰马鹿、天山马鹿共3个亚种38个个体的Cyt b全序列(1 140 bp)扩增、测序,分析了碱基组成和变异以及核苷酸序列差异,并以黇鹿(Fallowdeer,Cervus dama Linnaeus)为外群,分别采用邻接法(NJ)和最大简约法(MP)构建了系统发育树。结果显示:突变转换/颠换比值较高(R=25.665),Cyt b基因密码子碱基使用具有偏倚性;塔里木马鹿与阿尔泰马鹿、天山马鹿遗传距离较远;塔里木马鹿与天山马鹿有部分单倍型与其他亚种聚为一类。因此认为塔里木马鹿与阿尔泰马鹿、天山马鹿属于不同的类群;塔里木马鹿与天山马鹿都受到外种入侵,疑为引种杂交所致。

乳白蚁属Coptotermes分子分类研究进展

乳白蚁Coptotermes是危害林木和建筑的重要社会性昆虫,常随木质包装或原木远距离传播到异地建群,其为害隐蔽、潜伏期长,一旦爆发则为害严重且难防治。因其种类多、形态趋同,同一巢群中有龄期不一的虫态,可用分类特征少,造成形态分类困难、人为分类现象普遍。本文综述了世界乳白蚁属分子分类状况,阐述了近年来分子生物技术应用于乳白蚁属分类的研究进展,以期为基于分子手段对乳白蚁属种类修订及系统发育分析提供支持。

土白蚁属Odontotermes分子研究进展

土白蚁(Odontotermes)是一类高等培菌白蚁,对维持自然生态系统平衡有重要作用,但其对农林作物、堤坝水库和木结构建筑构成严重危害,已引起人们广泛关注。随着分子技术和基因组学的发展,分子生物学手段已逐渐应用于白蚁研究中,由此推动了土白蚁属生物学各个方面的深入研究。总结土白蚁属传统形态分类的不足,比较分子生物技术白蚁分类鉴定中的优势,展示目前在土白蚁属分子分类的研究状况。追溯土白蚁属的起源,分析印度与中国土白蚁属的关系,回顾大白蚁亚科的系统发育,详述土白蚁属系统发育,探讨土白蚁属与地白蚁属的分类地位,归纳土白蚁属与共生真菌及其他共生物间的协同进化关系。旨在加深对全球土白蚁属的深刻理解,探究土白蚁属分子研究的方向,展望新技术在土白蚁分子研究中的应用。