The taxonomic value of male Coccoidea (Homoptera) with an evaluation of some numerical techniques

The taxonomic value of characters provided by male Coccoidea is reviewed in relation to traditional classifications based on the female. Numerical methods based largely on principal component analysis are applied to the classification of some Diaspididae and the various techniques are compared and evaluated.     

Information theory and character selection in the numerical taxonomy of some male Diaspididae (Hemiptera: Coccoidea)

Abstract. Data on twenty-six species of male Diaspididae, two of them dimorphic, are analysed in relation to the information content and other quantitative attributes of the characters used to construct analysis. It is shown that simple information theory and the use of other numerical criteria enable one to select a relatively small number of characters which effectively reproduce the salient features of referednce classification based on the entire set of available characters. The conclusion are discussed in relation to views on characters weighting and the stability of numeriocal classificatins.     

木耳栽培种质资源的数量分类研究

在木耳栽培种质资源农艺性状调查的基础上,应用数量分类学中的Q型聚类分析法对20个木耳菌株进行分类研究,并对14个农艺性状进行R型聚类分析和主成分分析。结果表明：Q型聚类将20个木耳菌株在欧氏距离6.29处依据子实体朵型性状分为簇生型菌株和菊花型菌株两大类群,菊花型类群在欧式距离4.79处依据生育期性状的原基发生类型划分为分散型和集中型两个亚群;R型聚类表明菌丝体性状（1个）、生育期性状（2个）、子实体性状（8个）等11个农艺性状间相关性较强;主成分分析中,发现子实体背面皱褶、耳片数、原基发生时间、子实体朵型、干耳背面颜色等5个性状是14个农艺性状的第1主成分,贡献率高达62.26%,把第1主成分命名为朵型-生育期构成因子,作为种质评价的指标。     

Graph theory, tionary trees and classification

Many methods have been used for analysing information about organisms in order to understand tionary relationships and/or to determine classifications. The reationship between some of these methods is illustrated for the character state matrix, incompatibility and similarity matrices, minimal unrooted and rooted trees, and tionary classifications. Existing methods of determining the shortest possible tree are described. In addition a new method of building a minimal tree is introduced which starts with the largest possible subset (clique) of characters that is compatible for all pairs of characters. The remaining characters are ranked in order of their increasing number of incompatibilities. These characters are added singly, a tree constructed and then tested for minimality by previously described methods for partitioning characters into subsets. The procedure is repeated at least until the tree can no longer be proved minimal. The relationship between trees and tionary and phylogenetic classifications has been neglected but three methods are metioned and a new criterion suggested. It is suggested that graph theory, rather than statistics, is better suited for the primary analysis of comparative data.     

Evaluating the stability of the classification of community data

We propose a method for a posteriori evaluation of classification stability which compares the classification of sites in the original data set (a matrix of species by sites) with classifications of subsets of its sites created by without‐replacement bootstrap resampling. Site assignments to clusters of the original classification and to clusters of the classification of each subset are compared using Goodman‐Kruskal's lambda index. Many resampled subsets are classified and the mean of lambda values calculated for the classifications of these subsets is used as an estimation of classification stability. Furthermore, the mean of the lambda values based on different resampled subsets, calculated for each site of the data set separately, can be used as a measure of the influence of particular sites on classification stability. This method was tested on several artificial data sets classified by commonly used clustering methods and on a real data set of forest vegetation plots. Its strength lies in the ability to distinguish classifications which reflect robust patterns of community differentiation from unstable classifications of more continuous patterns. In addition, it can identify sites within each cluster which have a transitional species composition with respect to other clusters.     

Intraspecific variation in Licuala glabra Griff. (Palmae) in Peninsular Malaysia– a morphometric analysis

We studied vegetative and reproductive characters of 74 herbarium specimens of Licuala glabra Griff. (Palmae) collected from 22 localities throughout Peninsular Malaysia. To test the null hypothesis that there are no distinct groups within the species, cluster analysis (nearest neighbour), principal coordinates and principal components analyses were performed on the set of 43 qualitative and quantitative characters. The results obtained suggested that: (1) there are three infraspeciflc groups within the species, viz., the two published varieties glabra and selangorensis as well as a possible third novel taxon; (2) there is clustering of individuals corresponding to their geographic localities; (3) clusters generated using only reproductive characters indicate a biogeographic distribution of populations correlated with the mountain ranges in the peninsula.     

A taxonomic revision of Limacoccus Bondar with a cladistic analysis of its relationships with other scale insects (Hemiptera: Coccoidea)

The scale insect genus Limacoccus and its four palm pest species are revised and all instars with sexual dimorphism are described and illustrated. A key to Limacoccus species is provided. The unique life-history of this genus with construction of a protective tunnel by the second-instar female is described. A cladistic analysis of Limacoccus and eleven representative species of Diaspididae, Halimococcidae, Phoenicococcidae and Beesoniidae, was undertaken using fifty-four traditional and new characters from first and second instars and adult females. Character polarity was determined by outgroup comparison with Margarodidae, Pseudococcidae, Eriococcidae and Asterolecaniidae as outgroups. Nine most parsimonious trees were found. Analysis of the eleven terminal taxa of the strict consensus tree using Phoenicococcidae, Halimococcidae and Diaspididae as outgroups produced one parsimonious tree. As result of this analysis, Limacoccus is believed to be a monophyletic group of characterized by seven autapomorphies and is assigned to the family Beesoniidae fam.rev. The redefined family is divided into two tribes: Beesoniini stat.nov. with genera Beesonia and Mangalorea and Limacocciini stat.nov. with the genus Limacoccus. The Beesoniidae are here regarded as a sister group of Phoenicococcidae.     

Clines: character number and the multivariate analysis of simple patterns of geographic variation

The stability of a clinal pattern geographic variation in relation to character number was investigated by the random selection of real characters. The characters used were selected from a set of 18 significant characters, drawn from four different character systems, and had a low within-group correlation. Principal component/coordinate analysis was used to elucidate the main pattern of geographic variation and the first principal coordinate was plotted against a geographical transect to illustrate this pattern. The existence of 'clinal' or 'monotically clinal' variation was assessed by the rank correlation between geographic position and coordinate score and the congruence between patterns of geographic variation was assessed by the correlation between the first principal coordinates of the appropriate analyses.
Two procedural models were used: A, the congruence between completely independent character sets based on 1–9 characters, and B, congruence between the 'total' analysis and those analyses based on 1–16 characters. The frequency of the types of pattern of geographic variation shown by these Model B analyses was also determined. Congruence is asymptotic in relation to character number and is described by various mathematical models, depending upon parameter and procedure. A broad pattern of clinal variation occurred in all analyses based on six or more characters and appears to be a stable feature of the racial affinities that is unlikely to be influenced by character choice. The details of the clinal pattern cannot be shown to be stable and may be influenced by the choice of character. This study had several findings in common with a previous study of categorical variation, e.g. the approximately hyperbolic relationship between character number and congruence in Model B, which may prove to be generally true in comparable situations.     

A multivariate comparison between three NW. European populations ofArtemisia norvegica (Asteraceae) by means of chemometric and morphometric data

Specimens from Scotland, S. and C. Norway were grown in the botanical garden of Bergen, Norway. Some of the Scottish specimens came from a meristem tissue culture. The specimens were compared by a principal component analysis of lipids and related compounds, and of morphological characters from leaves and flowers. The populations differed from each other, but some overlap was found in leaf characters. The results are discussed in relation to distribution and immigration history, and it is argued that the differences among the populations may have evolved in postglacial time.     

Proteomic signatures: amino acid and oligopeptide compositions differentiate among phyla

Availability of complete genome sequences allows in-depth comparison of single-residue and oligopeptide compositions of the corresponding proteomes. We have used principal component analysis (PCA) to study the landscape of compositional motifs across more than 70 genera from all three superkingdoms. Unexpectedly, the first two principal components clearly differentiate archaea, eubacteria, and eukaryota from each other. In particular, we contrast compositional patterns typical of the three superkingdoms and characterize differences between species and phyla, as well as among patterns shared by all compositional proteomic signatures. These species-specific patterns may even extend to subsets of the entire proteome, such as proteins pertaining to individual yeast chromosomes. We identify factors that affect compositional signatures, such as living habitat, and detect strong eukaryotic preference for homopeptides and palindromic tripeptides. We further detect oligopeptides that are either universally over- or underabundant across the whole proteomic landscape, as well as oligopeptides whose over- or underabundance is phylum- or species-specific. Finally, we report that species composition signatures preserve evolutionary memory, providing a new method to compare phylogenetic relationships among species that avoids problems of sequence alignment and ortholog detection.     

基于表型性状的孔雀草种质遗传多样性分析

为了了解孔雀草种质间的亲缘关系,提高孔雀草种质的利用效率,从18个形态特征对40份孔雀草种质进行了遗传变异分析、主成分分析及聚类分析。结果表明,孔雀草表型多样性丰富,种质间表型性状变异程度高,变异系数(CV值)范围3.92%~46.25%,以花朵数最大,其次是冠幅和株高;Shannon-Weaver多样性指数则以叶片性状及花性状较高,平均2.0以上。国内种质比国外种质多样性更丰富。通过主成分分析,筛选出对总体方差累计贡献率达78.949%的4个主成分,并筛选出综合性状表现良好的种质10份。参试的40份种质在欧氏距离阈值为7.29处可分为两大类,一类植株生长势较强包含2份种质(水星黄色和橙色);其余38份种质为一类,在欧氏距离阈值为6.0处,又以花色差异可进一步划分为2个类群,说明生长势及花色可作为孔雀草种质依据表型性状分类的重要指标。     

检索表的矛盾分析及其实践意义(综述)

通过对生物检索表结构的分析,认为检索表的根本矛盾是标本具有的个性性状与检索表使用的共性性状的矛盾。单道检索表的主要矛盾是检索表对性状的有条件使用与单个标本性状有限性之间的矛盾,因而单道检索表未能很好地解决其基本矛盾,使得其应用范围和使用效果受到诸多影响。多道检索表的主要矛盾是性状数据库内性状的有限性与物种具有的个性性状的无限性之间的矛盾,不存在个性与共性的矛盾,即解决了根本矛盾问题,便于检索应用。     

Principal component analysis as an alternative treatment for morphometric characters: phylogeny of caseids as a case study

In a recent study, the phylogeny of Caseidae (a herbivorous family of Palaeozoic synapsids belonging to the paraphyletic grade known as pelycosaurs) was analysed with a dataset employing more than three hundred continuous morphological characters in an effort to follow the principles of total evidence. Continuous characters are a source of great debate, with disagreements surrounding their suitability for and treatment in phylogenetic analysis. A number of shortcomings were identified in the handling of continuous characters in this study of caseids, including the use of gap weighting to discretize the characters and potential issues with redundancy and character non‐independence. Therefore, an alternative treatment for these characters is suggested here. First, rather than using gap weighting, the continuous characters were analysed in the program TNT, in which the raw values can be treated as continuous rather than discrete. Second, prior to the phylogenetic analysis, the continuous characters were subjected to a log‐ratio principal component analysis, and then the principal components were included in the character matrix rather than the raw ratios. Analysing the original data in TNT produced little difference in the results, but using the principal components as continuous characters resulted in alternative positions for Caseopsis agilis, Ennatosaurus tecton and Caseoides sanangeloensis. The differences are judged to be due to the reduced redundancy of the characters, the smaller number of principal components not overwhelming the discrete characters and the use of a scaling method which allows principal components with a higher variance to have a greater influence on the analysis. The positions of highly fragmentary fossils depended heavily on the method used to treat the missing characters in the principal component analysis, and so the method proposed here is not recommended for analysing very incomplete taxa.     

Analysis of characters and classification based on information theory in the species of the Greater Antilles of the fern familiy Gleicheniaceae

We define a set of characters for the study of the fern family Gleicheniaceae. These characters have no ordered states. We establish a classification, through a divisive strategy, on the basis of these characters applied to the species occurring in the Greater Antilles. We used a technique based on information theory. A computational program was implemented to obtain this classification. With the same technique a procedure is used in order to compare a set of classifications reached under a different set of characters. The results obtained under three classifications on the family of this study are shown.     

云南医学革螨数值分类研究

以云南省57种医学革螨作为分类单元,以形态特征为主列出60项分类性状特征来探讨云南省医学革螨不同属和种的亲缘关系。运用SPSS 11.5 统计软件中的系统聚类分析和主成分分析,对57种医学革螨进行了数值分类分析。结果显示：57种医学革螨划分为厉螨科（La elapidae）、寄螨科（Parasitidae）、皮刺螨科（Dermanyssidae）、赫刺螨科（Hirstionyssidae）和裂胸螨科（Aceosejidae）5个类群。赫刺螨属和棘刺螨属从厉螨科中分离出来另立为赫刺螨科,柏氏禽刺螨归入了皮刺螨科而不是巨刺螨科。分类结果与传统形态分类结果基本一致,因而认为数值分类能比较客观地反映医学革螨各分类阶元的分类地位与亲缘关系。     

Fifty years of character compatibility concepts at work

In the mid 19th century,systematic biologists realized that observable similarities and differences among a group of related species could be the basis for hypotheses about the evolutionary relationships among the species and their ancestors.Such hypotheses Can be expressed as characters.A character is comprised of two or more character states of species considered to be similar with respect to a basis for comparison.The states of a character may also be arranged into a character state tree to hypothesize speciation events associated with changes from one character state to another.In the mid 20th century.some systematists realized that sometimes paxrs of characters(or character state trees)could be incompatible as hypotheses,i.e.,they could not both be true.Through the 1950s,'60s and'70s,tests for,and ways to resolve,incompatibilities were used to estimate an ancestor relation based on mutually compatible characters.An estimate was often shown as a diagram connecting ancestors to their immediate descendants(not quite correctly)called a phylogenetic tree.More recently,other applications of compatibility concepts have been developed,including:identify characters that appear to be random in the context of their data set;combine estimates of ancestor relations for subsets of taxa in a larger collection into a single estimate(a so-called supertree)for the whole collection;and interpret geographic patterns in an evolutionary context.     

Morphometric Identification of Queens,Workers and Intermediates in In Vitro Reared Honey Bees (Apis mellifera)

In vitro rearing is an important and useful tool for honey bee (Apis mellifera L.) studies. However, it often results in intercastes between queens and workers, which are normally are not seen in hive-reared bees, except when larvae older than three days are grafted for queen rearing. Morphological classification (queen versus worker or intercastes) of bees produced by this method can be subjective and generally depends on size differences. Here, we propose an alternative method for caste classification of female honey bees reared in vitro, based on weight at emergence, ovariole number, spermatheca size and size and shape, and features of the head, mandible and basitarsus. Morphological measurements were made with both traditional morphometric and geometric morphometrics techniques. The classifications were performed by principal component analysis, using naturally developed queens and workers as controls. First, the analysis included all the characters. Subsequently, a new analysis was made without the information about ovariole number and spermatheca size. Geometric morphometrics was less dependent on ovariole number and spermatheca information for caste and intercaste identification. This is useful, since acquiring information concerning these reproductive structures requires time-consuming dissection and they are not accessible when abdomens have been removed for molecular assays or in dried specimens. Additionally, geometric morphometrics divided intercastes into more discrete phenotype subsets. We conclude that morphometric geometrics are superior to traditional morphometrics techniques for identification and classification of honey bee castes and intermediates.     

紫花苜蓿复合体(Medicago sativa complex)叶片形态特征及数量分类研究

运用比较形态学和比较解剖学方法,使用扫描电镜和光学显微镜对紫花苜蓿复合体(Medicago sativa complex)6个分类群的叶片形态特征和叶片解剖结构进行了观察和比较,并以15个叶片表征形态性状为基础,采用聚类分析法(UPGMA)和主成分分析方法(PCA)对6个分类群进行了数量分类研究.观察结果表明:各分类群叶片的上、下表皮多为不规则形细胞;垂周壁呈深浅不一的波状;气孔器为不规则型,具有蜡质气孔盖,气孔密度有一定差异.6个分类群的叶片均为薄纸质型,厚度130～170 μm,表皮细胞切面近圆形或近长方形;栅栏组织细胞1～2层,厚度41～68 μm,细胞排列紧密;海绵组织厚度32～75 μm,细胞排列疏松;不同分类群叶片的组织疏松度和组织紧缩度有一定的差异,大花苜蓿(M. trautvetterii Sumnev. )叶片的组织疏松度最高,紫花苜蓿叶片的组织紧缩度最高.UPGMA结果显示:在结合线1.53处可将6个分类群划分为2支,其中,黄花苜蓿(M. falcata L. )独立为一支,其余5个分类群聚成另一支;在结合线1.18处,第2支又被分成2个亚支,其中一个亚支包含紫花苜蓿和天山苜蓿(M. tianschanica Vassilcz. ),另一个亚支则包含西锡金苜蓿(M. schischkinii Sumnev. )、座垫苜蓿(M. rivularis Vassilcz. )和大花苜蓿.PCA结果表明:对紫花苜蓿复合体而言,叶片表皮细胞形状、垂周壁式样、轴性分化特征、组织疏松度和气孔密度等特征具有较好的分类价值;基于主成分分析的Q分布图与聚类分析结果也具有较高的一致性.根据本研究结果及前人的研究结果,认为国产的紫花苜蓿复合体应包含3个分类群,即紫花苜蓿、黄花苜蓿及多变苜蓿(M. varia Martyn).此外,西锡金苜蓿、座垫苜蓿、天山苜蓿和大花苜蓿等杂交后代分类群的性状分化不稳定,应属于多变苜蓿的同种异名植物.     

中国原产石蒜属植物的数量分类和主成分分析

应用数量分类学方法对中国原产石蒜属13种2变种的35个性状进行Q、R聚类分析和主成分分析,探讨国产石蒜属植物种间的亲缘关系,并对分类性状进行评价。研究结果显示,Q型聚类可分为2个大类和8小类,安徽石蒜与长筒石蒜的亲缘关系很近,认为将其作为长筒石蒜的变种更为合适,同时支持玫瑰石蒜、红蓝石蒜、乳白石蒜、江苏石蒜、稻草石蒜的杂交起源观点。R型聚类可分为7个组;经主成分分析,35个性状可综合为5个主成分,其累积贡献率达82.55%,根据这5个主成分与性状间的相关性,选出影响比较大的16个性状,其中鳞茎形状、花被片宽和雄蕊长/花被片长的比值最为重要,可作为大类群划分的依据,而花被片是否具条纹、花丝颜色、花色、花葶粗、幼叶尖端及边缘颜色、种子有无等可作为物种划分的重要依据。