衣藻属的系统发育分析——基于形态状和nrDNA ITS序列

通过实验分析莱茵衣藻（Ｃｈｌａｍｙｄｏｍｏｎａｓ ｒｅｉｎｈａｒｄｔｉｉ）１个种和互连网获得藻属１５个种及丝藻属１个种（Ｕｌｏｔｈｒｉｘ ｚｏｎａｔａ）,共１７个种的ｎｒＤＮＡ ＩＴＳ序列,并以Ｕ．ｚｏｎａｔａ为外类群,采用计算机分析软件包对其进行分析及构建分子系统发育树图。同时以１２个传统分类性状,对此１６种衣藻构建数据矩阵;以Ｕ．ｚｏｎａｔａ动孢子的相应性状为外类群原妈性状,用Ｗａｇｎｅｒｉｆ     

基于ITS序列探讨忍冬属的系统发育关系

以七子花(Heptacodium miconioides)为外类群,运用MEGA软件对20种忍冬属植物进行系统发育分析,采用邻接法(NJ)和最大简约法(MP)构建系统发育树,从分子系统学角度探讨忍冬属下的亲缘关系.结果表明:(1)在NJ和MP系统树中,没有形成系统树的基部分支,忍冬亚属(Subg.Chamaecerasus)和轮花亚属(Subg.Lonicera)没有形成姐妹群关系.(2)在各系统树中,囊管组内的各种没有聚为一支,故认为对囊管组的划分应进一步探讨.(3)忍冬属ITS区(ITS1+ITS2)的信息位点达到11.0%,信息位点比较丰富,证明ITS序列可以为解决忍冬属植物的系统发育问题提供较强的证据.     

基于ITS序列对中国簇毛黄耆亚属（黄耆属）系统学问题的初步研究

测定了簇毛黄耆亚属（Pogonophace)4组8种和外类群Caragana roborovskyi的ITS序列,从GenBank中调出相关12属47种的ITS序列,组成数据距阵,应用PAUP程序中的最大简约法构建了系统发育树状图。扁荚组（Sect.Sesbanella)与亚属其余类群在系统树上处于不同的分支,亲缘关系较远这个亚属不是一个单系类群;膨果组（Sect.Bibracteola)。背扁组（Sect.Phyllolobium)和袋果组（Sect.Trichostylus)作为一个单系类群能得到ITS序列的支持,但与分组以及膨果组下系的划分都得不到ITS序列分析的支持。     

中国库蚊属四十个种(亚种)的分子系统发育关系研究(双翅目:蚊科)

【目的】对在中国有分布的库蚊属Culex种(亚种)的COⅠ序列和ITS2序列进行测序,构建和讨论这些种(亚种)的分子系统发育关系。【方法】测定了库蚊属20个种(亚种)的COⅠ和ITS2序列,并从NCBI数据库中下载了库蚊属另外20个种(亚种)的COⅠ和3个种(亚种)的ITS2序列。对库蚊属40个种(亚种)的COⅠ序列和其中23个种(亚种)的ITS2序列进行碱基构成、种间遗传距离和饱和度分析,并对COⅠ+ITS2序列进行ILD(incongruence length difference)检验。分别使用2种分子数据集(COⅠ和ITS2)的核苷酸序列,用最大似然法(ML)、贝叶斯法(BI)、邻接法(NJ)和最大简约法(MP)推断这些种的系统发育关系。通过Kishino-Hasegawa(KH)和ShimodairaHasegawa(SH)检验评估这4种系统树间的差异,确定最为合理的系统发育树。【结果】本研究新测序获得20种(亚种)的COⅠ和ITS2序列的长度范围分别为625~685 bp和300~559 bp。COⅠ和ITS2序列在库蚊属成对蚊种间的遗传距离分别是0.002~0.198和0.006~1.807。库蚊属23个种(亚种)的COⅠ+ITS2序列的ILD检验结果显示,数据集具有不相容性,因此COⅠ+ITS2序列不适用于这些种(亚种)的系统发育研究。经KH和SH检验显示,4种系统发育树中,基于COⅠ序列构建的BI树最为合理,而基于ITS2序列构建的MP树最为合理。基于COⅠ核苷酸序列所构建的BI树显示,除幼小库蚊Cx.infantulus和短须库蚊Cx.brevipalpis外,各亚属间成员聚类结果与传统的形态学归类结果吻合;路蚊亚属Lutiza和包蚊亚属Barraudius都归入库蚊亚属Culex内;梅蚊亚属Maillotia和新库蚊亚属Nexoculex聚为一支;库状蚊亚属Culiciomyia、真黑蚊亚属Eumelanomyia和簇角蚊亚属Lophoceramyia均显示为单系。基于ITS2序列所构建的MP树显示,各亚属间和种(亚种)间关系混乱。【结论】重建的分子系统发育树表明库蚊亚属不是一个单系群。在重建库蚊属系统发育关系时,相较于ITS2和COⅠ+ITS2,COⅠ是更为理想的分子标记。本研究构建的分子系统发育关系为中国库蚊属中各亚属和各种(亚种)之间的亲缘关系的研究奠定了基础。     

基于ITS序列对中国簇毛黄耆亚属(黄耆属)系统学问题的初步研究

测定了簇毛黄耆亚属(Pogonophace)4组8种和外类群Caragana roborovskyi的ITS序列,从GenBank中调出相关12属47种的ITS序列,组成数据距阵,应用PAUP程序中的最大简约法构建了系统发育树状图.扁荚组(Sect. Sesbanella)与亚属其余类群在系统树上处于不同的分支,亲缘关系较远,这个亚属不是一个单系类群;膨果组(Sect. Bibracteola),背扁组(Sect. Phyllolobium)和袋果组(Sect. Trichostylus)作为一个单系类群能得到ITS序列的支持,但与鱼鳔槐亚族比与黄耆属其他类群的关系更近; Astragatus complanatus和A. tribulifolius可能为一对替代种;亚属下的分组以及膨果组下系的划分都得不到ITS序列分析的支持.     

基于nrDNA ITS 和 ETS序列对樟科黄肉楠属（Actinodaphne)的系统学研究

应用nrDNA ITS和ETS序列探讨了樟科Lauraceae黄肉楠属Actinodaphne的系统演化关系。对得到的3个序列矩阵(ITS、ETS和ITS/ETS), 采用MP (maximum parsimony), ML (maximum likelihood)和Bayesian 3种分析方法进行了系统发育分析。结果显示, 本文选的黄肉楠属Actinodaphne物种与所选的月桂族中的外类群靠近并混和在一起, 进一步证实了本属为一个复系类群。结合对传统的形态学性状的重新认识, 认为花序类型特征可能是重新界定黄肉楠属的最重要的性状, 具有相同花序类型的物种可能具有相同的起源。然而, 由于取样数量相对较少以及对矩阵的单独分析存在一定的差异, 还需更详细的研究来验证本文对黄肉楠属系统演化关系的假设, 并进一步更精确地重建本属的系统发育关系。     

基于ITS与 trn L-F序列探讨槭树科的系统发育

报道了槭树科41种(其中槭属39种)植物的 trn L-F和ITS序列(其中部分种的ITS序列为重新测定),以期通过分子手段对槭树科内部尤其是复杂的槭属的系统发育关系进行重建.以无患子科和七叶树科为外类群,基于对57个种单独的ITS序列(包括从GenBank下载的16种的序列)、41种 trn L-F序列及41种两者序列的联合数据,分别采用最大简约法(Maximum Parsimony Method)和邻接法(Neighbor-Joining Method)对槭树科的系统发育进行了分析.结果显示,整个槭树科为一单系类群;金钱槭位于槭树科的基部;但由于云南金钱槭( Dipteronia dyerana )聚在了槭属内部,认为金钱槭属和槭属均可能是非单系类群;槭属内组间关系的支持率普遍较低,但多数组的组内关系得到了较好的支持.将两个片段结合比单独的ITS或 trn L-F分析能更好地解决槭属内部的系统关系,其中sect.Palmata 和sect.Microcarpa ,sect.Platanoidea 、sect.Lithocarpa 和sect.Macrophylla ,sect.Integrifolia 、sect.Trifoliata 和sect.Pentaphylla ,以及sect.Acer 、sect.Goniocarpa 和sect.Saccharina (sensu Ogata)的组间亲缘关系得到了一定的支持,但对其中部分组的划分可能应做进一步调整.重新评价了徐廷志系统中对sect.Rubra 和sect.Saccharodendron 的处理.     

中国淡水胭脂藻属植物形态及分子系统发育分析

以云南省玉溪市和河南省焦作市新采集的2株淡水胭脂藻标本为材料, 对其进行形态特征观察和分子系统发育分析, 联合我国已报道的其他胭脂藻序列信息, 构建该属植物可靠的系统发育关系。根据其现代地理分布模式, 对胭脂藻属进行了祖先地理起源重建。基于rbcL、psbA和UPA序列, 利用贝叶斯法、最大似然法和邻接法构建的系统发育树高度一致, 研究中的标本与鸡公山胭脂藻H. jigongshanensis聚合为一个独立分支, 并得到了很高的支持率, 根据分子生物学证据, 将其鉴定为鸡公山胭脂藻。通过研究中所采集2株鸡公山胭脂藻的形态特征比较, 发现传统的形态分类特征包括藻体高度和细胞直径, 在不同的环境条件下是可变的, 不适合作为胭脂藻属植物种类鉴定的依据。对于胭脂藻属这一形态结构较为简单的类群, 必须借助分子生物学证据和系统发育分析手段对其进行种类鉴定和系统发育分析。分子系统发育分析结果表明, 中国特有种鸡公山胭脂藻H. jigongshanensis形成单系类群, 其与日本胭脂藻H. japananense亲缘关系较近, 所有淡水胭脂藻种类形成一个独立的聚类群, 与海洋种类遗传差异较大。祖先地理重建的分析结果表明, 淡水胭脂藻的祖先起源地位于北美洲, 然后逐渐向东加勒比海区域、拉丁美洲和欧亚大陆扩散, 形成现代地理分布模式。胭脂藻属独特的种类地理分布特点, 可能与其较为古老的起源时间和漫长的进化历史相关, 同时淡水胭脂藻在北美洲区域起源时间较早, 进化历史漫长, 遗传多样性大, 这与该地理区域分布的种类H. angolensis为多系类群是相一致的。     

基于ITS序列探讨金线草的系统学位置

金线草的系统位置一直存在争议,该试验以Triplaris weigeltiana为外类群,采用最大简约法对金线草及其近缘类群的ITS序列进行了系统发育分析.结果表明:(1)金线草和蓼属的春蓼组、刺蓼组形成三个并列的分支,因此,金线草没有必要独立成属,分子证据支持金线草成立为组;(2)金线草和春蓼组、刺蓼组植物聚在一起,...     

中国东北地区壳囊孢属真菌分类和系统发育研究

对采自中国东北地区不同寄主植物上的壳囊孢属真菌标本进行了形态学观察,依据其子实体顶盘、腔室、分生孢子以及子囊壳、子囊、子囊孢子的形态特征,并结合其培养性状等划分为5个形态学类群;利用ITS序列分析构建了系统发育树,结果显示这5个类群的划分均得到了分子证据的支持。腔室特征、孔口数量、中柱以及黑色基线的有无、分生孢子大小等可作为壳囊孢属分类的主要依据。     

五味子科的系统发育:核糖体DNA ITS区序列证据

The Schisandraceae is one of the most important taxa for understanding the origin and evolution of primitive angiosperms due to its basal position in the recent cladograms of the angiosperm based both on several gene sequences and on morphological characters, but phylogenetic relationships within the family are still unresolved. The sequences of nrDNA ITS region of 15 species representing four sections of Schisandra Michx., two sections of Kadsura Kaempf. ex Juss. and one outgroup, Illicium fargesii Finet et Gagnep., were used to reconstruct the phylogeny of Schisandraceae. Fourteen most parsimonious trees (Length=259, CI=0.934 and RI=0.889) were obtained from the analysis with I．fargesii as the outgroup. In the consensus tree, the genus Schisandra was found to be divided into three clades. Sect. Pleiostema formed a clade together with sect. Maximowiczia, sect. Sphaerostema was weakly supported to be the sister group of a clade comprising S. bicolor var. tuberculata and Kadsura species. In particular, S. bicolor var. tuberculata, a species of sect. Schisandra, was nested within Kadsura. It seems from this result and the morphological characters that Schisandra might not be a monophyletic group. According to the present molecular phylogeny, both elongated hypocarpium and deciduous habit originated independently at least twice in the Schisandraceae, and therefore, the value of the present morphological characters used in the classification of the family Schisandraceae should be reevaluated.     

Molecular phylogeny of selected Old World Astragalus (Fabaceae): incongruence among chloroplast trnL-F, ndhF and nuclear ribosomal DNA ITS sequences

This study reports maximum parsimony and Bayesian phylogenetic analyses of selected Old World Astragalus using two chloroplast fragments including trnL-F and ndhF and the nuclear ribosomal internal transcribed spacer (nrDNA ITS). A total of 52 taxa including 34 euploid Old World and New World Astragalus , one aneuploid species from the Neo-Astragalus clade as a representative and 14 other Astragalean taxa, plus Cheseneya astragalina and two species of Caragana as outgroups were analyzed for both trnL-F and nrDNA ITS regions. ndhF was analyzed in 30 taxa and the same number for the combination of these three datasets were examined. In general, the trnL-F dataset and the ndhF and nrDNA ITS datasets generated more or less the same clades within Astragalus . However, in the trnL-F and ndhF phylogenies, Astragalus species are not gathered in a single clade, the so-called Astragalus s.s., as indicated by the nrDNA ITS tree. Visual inspection of these three phylogenies revealed that they were inconsistent regarding the position and relationships of Astragalus hemsleyi , A. ophiocarpus , A. annularis–A. epiglottis / Astragalus pelecinus, A. echinatus and A. arizonicus . Incongruence length difference test suggested that the trnL-F , ndhF and nrDNA ITS datasets were incongruent. In spite of this, phylogenetic analyses of the combined datasets as one unit or as three partitions generated trees that were topologically similar as a mix of the cpDNA and the nrDNA ITS trees. However, the combined dataset provided more resolved and statistically supported clades. The recently described A. memoriosus appeared closely related to A. stocksii (both from sect. Caraganella ) based on both trnL-F and nrDNA ITS sequences.     

基于形态特征和ITS序列对7个鹅膏菌属菌株的分类鉴定

以采自浙江省丽水地区的7个鹅膏菌属菌株作为研究材料,在基于形态特征进行初步鉴定的基础上,对7种鹅膏菌的rDNAITS区段进行克隆测序和序列特征比较分析。进一步对ITS序列进行核酸序列数据库GenBank同源性检索比对,将从GenBank检索获得的9个最相似物种的ITS序列连同7种鹅膏菌的ITS序列一起作系统发育分析。结果表明:基于ITS序列对f6、f9和f493个菌株的分子鉴定支持了基于形态特征的鉴定结果,对f5的分子鉴定不支持形态鉴定的结果,f8为鹅膏菌属内某种,f66为鹅膏菌属内某种,并与Amanitafulva,A.atrofusca,A.orientifulva3种鹅膏菌的亲缘关系较近,f7与另外6种鹅膏菌的亲缘关系相差甚远。研究结果提示基于分子水平上的ITS序列分析不能单方面作为大型真菌分类鉴定的可靠依据,可以作为基于传统形态学分类鉴定的辅助参考依据。     

Morphological and molecular phylogenetics in the genus Leptopilina (Hymenoptera: Cynipoidea: Eucoilidae)

We have conducted cladistic analyses of the genus Leptopilina , a group of Drosophila parasitoids studied intensively by (behavioural) ecologists. Twenty-three morphological characters were scored in ten Leptopilina and two outgroup species. At the same time, DNA sequences for the second ribosomal internal transcribed spacer (ITS2) were gathered for eight Leptopilina and one outgroup species. Both data sets yielded phylogenetic trees which were largely compatible. A 'total evidence' analysis resulted in a single tree that provides a relatively robust phylogenetic reconstruction of the group, which may serve as a basis for historically interpreting the distribution of ecological and behavioural traits.     

Species-specific molecular signature of Commiphora species of Saudi Arabia inferred from internal transcribed spacer sequences of nuclear ribosomal DNA

The deciduous habit and tendency to produce flowers prior to developing leaves, and a predominantly dioecious system of breeding in the genus Commiphora leads to difficulties in its taxonomic identification at species level. The characteristics of easy amplification by universal primer, shorter length and higher discrimination power at the species level makes the internal transcribed spacer (ITS) sequence of nuclear ribosomal DNA (nrDNA) to a smart gene for generating species-specific phylogenetic inferences in most of the plants groups. The present study deals the ITS sequence of nrDNA based molecular genotyping of seven species of the genus Commiphora of Saudi Arabia. The molecular phylogenetic analysis of ITS sequences of nrDNA of Commiphora species distributed in Saudi Arabia reveals the the occurrence of C. madagascariens in Saudi Arabia.     

Genotypic and phenotypic diversity of cyanobacteria assigned to the genus <Emphasis Type="Italic">Phormidium</Emphasis> (Oscillatoriales) from different habitats and geographical sites

In this study, 30 strains of filamentous, non-heterocystous cyanobacteria from different habitats and different geographical regions assigned to diverse oscillatorian genera but here collectively referred to as members of the Phormidium group have been characterized using a polyphasic approach by comparing phenotypic and molecular characteristics. The phenotypic analysis dealt with cell and filament morphology, ultrastructure, phycoerythrin content, and complementary chromatic adaptation. The molecular phylogenetic analyses were based on sequences of the 16S rRNA gene and the adjacent intergenic transcribed spacer (ITS). The sequences were located on multiple branches of the inferred cyanobacterial 16S rRNA tree. For some, but not all, strains with identical 16S rDNA sequences, a higher level of discrimination was achieved by analyses of the less conserved ITS sequences. As shown for other cyanobacteria, no correlation was found between position of the strains in the phylogenetic tree and their geographic origin. Genetically similar strains originated from distant sites while other strains isolated from the same sampling site were in different phylogenetic clusters. Also the presence of phycoerythrin was not correlated with the strains’ position in the phylogenetic trees. In contrast, there was some correlation among inferred phylogenetic relationship, original environmental habitat, and morphology. Closely related strains came from similar ecosystems and shared the same morphological and ultrastructural features. Nevertheless, structural properties are insufficient in themselves for identification at the genus or species level since some phylogenetically distant members also showed similar morphological traits. Our results reconfirm that the Phormidium group is not phylogenetically coherent and requires revision.     

Genetic evidence for host specificity in the hemi-parasitic Viscum album L. (Viscaceae)

Nuclear ribosomal DNA (nrDNA) ITS sequences and partial sequences of three non-coding chloroplast DNA (cpDNA) introns and spacers were used to assess genetic variation within and among three presumed host races of the hemi-parasite Viscum album L. Currently, identification of host races occurs via the host trees, and morphological differences are minute at best. cpDNA and nrDNA ITS sequences revealed little sequence variation, but the variation found consistently supported the distinction of three host races. cpDNA and ITS sequences were not incongruent, as assessed by the incongruence length difference test. A combined analysis supported the sister group relationship between mistletoes from deciduous trees and fir.     

Molecular phylogenetics and delimitation of species in Cortinarius section Calochroi (Basidiomycota, Agaricales) in Europe

Cortinarius is the most species rich genus of mushroom forming fungi with an estimated 2000 spp. worldwide. However, species delimitation within the genus is often controversial. This is particularly true in the section Calochroi (incl. section Fulvi), where the number of accepted taxa in Europe ranges between c.60 and c.170 according to different taxonomic schools. Here, we evaluated species delimitation within this taxonomically difficult group of species and estimated their phylogenetic relationships. Species were delimited by phylogenetic inference and by comparison of ITS sequence data in combination with morphological characters. A total of 421 ITS sequences were analyzed, including data from 53 type specimens. The phylogenetic relationships of the identified species were estimated by analyzing ITS data in combination with sequence data from the two largest subunits of RNA polymerase II (RPB1 and RPB2). Seventy-nine species were identified, which are believed to constitute the bulk of the diversity of this group in Europe. The delimitation of species based on ITS sequences is more consistent with a conservative morphological species concept for most groups. ITS sequence data from 30 of the 53 types were identical to other taxa, and most of these can be readily treated as synonyms. This emphasizes the importance of critical analysis of collections before describing new taxa. The phylogenetic separation of species was, in general, unambiguous and there is considerable potential for using ITS sequence data as a barcode for the group. A high level of homoplasy and phenotypic plasticity was observed for morphological and ecological characters. Whereas most species and several minor lineages can be recognized by morphological and ecological character states, these same states are poor indicators at higher levels.     

MOLECULAR AND MORPHOMETRIC DATA PINPOINT SPECIES BOUNDARIES IN HALIMEDA SECTION RHIPSALIS (BRYOPSIDALES,CHLOROPHYTA)1

Molecular systematic studies have changed the face of algal taxonomy. Particularly at the species level, molecular phylogenetic research has revealed the inaccuracy of morphology‐based taxonomy: Cryptic and pseudo‐cryptic species were shown to exist within many morphologically conceived species. This study focused on section Rhipsalis of the green algal genus Halimeda. This section was known to contain cryptic diversity and to comprise species with overlapping morphological boundaries. In the present study, species diversity within the section and identity of individual specimens were assessed using ITS1–5.8S–ITS2 (nrDNA) and rps3 (cpDNA) sequence data. The sequences grouped in a number of clear‐cut genotypic clusters that were considered species. The same specimens were subjected to morphometric analysis of external morphological and anatomical structures. Morphological differences between the genotypic cluster species were assessed using discriminant analysis. It was shown that significant morphological differences exist between genetically delineated species and that allocation of specimens to species on the basis of morphometric variables is nearly perfect. Anatomical characters yielded better results than external morphological characters. Two approaches were offered to allow future morphological identifications: a probabilistic approach based on classification functions of discriminant analyses and the classical approach of an identification key.     

Phylogenetic relationships of Steinernema Travassos, 1927 (Nematoda: Cephalobina: Steinernematidae) based on nuclear, mitochondrial and morphological data

Entomopathogenic nematodes of the genus Steinernema are lethal parasites of insects that are used as biological control agents of several lepidopteran, dipteran and coleopteran pests. Phylogenetic relationships among 25 Steinernema species were estimated using nucleotide sequences from three genes and 22 morphological characters. Parsimony analysis of 28S (LSU) sequences yielded a well-resolved phylogenetic hypothesis with reliable bootstrap support for 13 clades. Parsimony analysis of mitochondrial DNA sequences (12S rDNA and cox 1 genes) yielded phylogenetic trees with a lower consistency index than for LSU sequences, and with fewer reliably supported clades. Combined phylogenetic analysis of the 3-gene dataset by parsimony and Bayesian methods yielded well-resolved and highly similar trees. Bayesian posterior probabilities were high for most clades; bootstrap (parsimony) support was reliable for approximately half of the internal nodes. Parsimony analysis of the morphological dataset yielded a poorly resolved tree, whereas total evidence analysis (molecular plus morphological data) yielded a phylogenetic hypothesis consistent with, but less resolved than trees inferred from combined molecular data. Parsimony mapping of morphological characters on the 3-gene trees showed that most structural features of steinernematids are highly homoplastic. The distribution of nematode foraging strategies on these trees predicts that S. hermaphroditum, S. diaprepesi and S. longicaudum (US isolate) have cruise forager behaviours.