Parallel tion in the context of character analysis

For the establishment of polarity of character transformation prior to phylogenetic analysis, various logical and biological criteria are discussed; some are rejected on grounds of liability to systematic error, circularity or unwarranted assumptions aboutParallel tion is used as a non-polar term, with forward and reverse to indicate polarity. A computer program for the detection of parallel tion is described which takes taxa in groups of four. The characters, with two derived: two primitive states or three derived: one primitive state, are listed according to the distribution of states over the four taxa. To each of the 15 phylogenies there corresponds a compatible pair of character patterns. Discordant 2: 2 patterns are unconditionally incompatible (Le Quesne test failure), discordant 3: 1 patterns are incompatible conditional upon correct scoring of polarity. For any putative phylogeny the concordant and discordant characters are identified. In cases of competing alternatives these character sets have to be weighed against one another. Character weighting is discussed; it is argued that it is the individual character transformation which should be weighted, in each direction separately.     

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.     

Slime protein profiling: a non‐invasive tool for species identification in Onychophora (velvet worms)

Onychophorans (velvet worms) use an adhesive, protein‐based slime secretion for prey capture and defence. The glue‐like slime is ejected via a pair of modified limbs and the sticky threads entangle the victim. In this study, we analysed the protein composition of slime in twelve species of Onychophora from different parts of the world, including two species of Peripatidae from Costa Rica and Brazil and ten species of Peripatopsidae from Australia, using sodium dodecyl sulphate polyacrylamide gel electrophoresis. Our results revealed high intraspecific conservation in protein composition of slime in each species studied. In contrast, the protein profiles differ considerably in both number and position of bands between the species. We observed the highest number of differences (in 20 of 33 considered band positions) between a peripatid and a peripatopsid species, whereas the lowest number of differences (in four band positions) occurs between two closely related egg‐laying species. The reconstructed maximum parsimony cladogram based on the electrophoretic characters largely reflects the phylogenetic relationships of the species studied, suggesting that the slime protein profiles contain useful phylogenetic information. Based on our findings, we suggest that the slime protein profiling is a valuable, non‐invasive method for identifying the onychophoran species. Moreover, this method might help to discover potentially new species of Onychophora, given that the ~200 described species most likely underrepresent the actual diversity of the group.     

A discrete method for the identification of parameters of a deterministic epidemic model

We study a problem of identification of the parameters for a deterministic epidemic model of the Kermack-McKendrick type. Particular emphasis is put on the analysis of the conditions of numerical stability of the method of integration used to calculate the solutions of the system of differential equations which describe the model. The numerical method can be regarded as a discrete model which reproduces the basic qualitative properties of the continuous model, which are positivity of the solutions, points of equilibrium, and the “threshold theorem.” This allows us to identify the parameters with good reliability, by means of an iterative procedure to minimize the functional which is the measure of discrepancy between the data observed and the data obtained from the discrete model. The initial estimate of the parameters is obtained by a direct method applied to the discretized system of equations.     

The application of whole-cell protein electrophoresis for the classification and identification of basidiomycetous yeast species

The relationships among 65 basidiomycetous yeast strains were determined by one-dimensional electrophoresis of SDS-solubilized whole-cell proteins. Protein profiles were compared by the Pearson product moment correlation coefficient (r). The strains investigated represented species from the generaCystofilobasidium, Filobasidium, Filobasidiella, Kondoa, Leucosporidium, Mrakia andRhodosporidium. Except for the genusMrakia, all species constituted separate protein electrophoretic clusters. The species of the genusMrakia (M. frigida, M. gelida, M. nivalis andM. stokesii) show highly similar protein patterns, suggesting that these four species may be synonymous. Strains of two varieties ofFilobasidiella neoformans, F. neoformans var.neoformans andF. neoformans var.bacillispora, could not be differentiated by protein electrophoresis.For the delineation of the protein electrophoretic clusters of the yeasts studied, literature data relying on other criteria, such as DNA base composition, carbon source utilization patterns, enzymatic protein electrophoregrams, ubiquinone systems, DNA-DNA homology and rRNA sequence data were used. It was demonstrated that a database of SDS-protein patterns provides a valuable tool for the identification of yeasts.     

The Simulium vernum group (Diptera: Simuliidae) in Europe: multiple character sets for assessing species status

The value of using characters from multiple sources – chromosomes, ecology, gene sequences, and morphology – to evaluate the species status of closely related black flies is demonstrated for three European members of the Simulium vernum group: Simulium crenobium (Knoz, 1961), Simulium juxtacrenobium Bass & Brockhouse, 1990, and Simulium vernum s.s. Macquart, 1826. Simulium juxtacrenobium is a chromosomally, molecularly, and morphologically distinct species that diverged from S. crenobium and S. vernum s.s. about 2 Mya. It is specialized for intermittent streams, is univoltine, and is recorded for the first time from northern Europe, based on collections from Finland and Sweden, representing a range extension of about 1800 km. In contrast, S. crenobium, although confirmed as a distinct species, differs from S. vernum s.s. by only a few larval and chromosomal characters, and by a breeding habitat restricted to mountain spring brooks. Whereas all four character sets independently support the specific distinctness of S. juxtacrenobium and S. vernum s.s., multiple character sets are required to establish the specific validity of S. crenobium.     

A method of deriving subgroups of a population: a study of craniofacial taxonomy

Subgroups within a population are often difficult to discover and describe except by subjective methods. In this study, cluster analysis (numerical taxonomy) methods were used on selected craniofacial measurements obtained from 308 North American White children of both sexes in the age range 6–18 to derive categories of skeletal facial types. Two different cluster analysis approaches were used in conjunction with a separate overall evaluation of facial balance, an independent measure of maxillo-mandibular relationship (AB/FOP), and a traditional classification (Angle). The categories derived rest on corroborative and overlapping evidence from each of those methods. The categories were examined to determine if it is possible to classify a sample by means of cluster analysis, the size and discreteness of each class, how they compare with the Angle classification of the same sample, and the percentage of individuals that may be identified unequivocally by this classification scheme. Five categories were obtained. Labeled Category A — Category E, they show some correspondence to the Angle Classes I, II, and III, but categories A, B, and C appear to be subgroups, heretofore undetected, of Angle Class II. Categories D and E correspond to Angle Classes I and III, respectively. The categories are more realistic and informative than the Angle classes. Each category is reported along with its distinguishing skeletal characteristics.     

A numerical analysis of Sideritis L. (Lamiaceae) from North Africa

REJDALI, MOH, 1992. A numerical analysis of Sideritis L. (Lamiaceae) from North Africa. A numerical analysis is shown to be useful means of discriminating taxa at all levels of the hierarchy in the genus Sideritis. This analysis supports both the separation of the genus into the two sections recognized by Bentham, the three groups of Briquet's treatment and the four groupings as suggested by various lines of evidence presented by Rejdali (1988).     

A new method for identification of protein (sub)families in a set of proteins based on hydropathy distribution in proteins

Structural similarity among proteins is reflected in the distribution of hydropathicity along the amino acids in the protein sequence. Similarities in the hydropathy distributions are obvious for homologous proteins within a protein family. They also were observed for proteins with related structures, even when sequence similarities were undetectable. Here we present a novel method that employs the hydropathy distribution in proteins for identification of (sub)families in a set of (homologous) proteins. We represent proteins as points in a generalized hydropathy space, represented by vectors of specifically defined features. The features are derived from hydropathy of the individual amino acids. Projection of this space onto principal axes reveals groups of proteins with related hydropathy distributions. The groups identified correspond well to families of structurally and functionally related proteins. We found that this method accurately identifies protein families in a set of proteins, or subfamilies in a set of homologous proteins. Our results show that protein families can be identified by the analysis of hydropathy distribution, without the need for sequence alignment.     

A method for the identification of proteins secreted by lactic acid bacteria grown in complex media

Lactic acid bacteria (LAB) are known for their special nutritional requirements, being usually cultured in complex media to achieve optimal growth. In this paper, a protocol based on trichloroacetic acid precipitation of peptides and proteins is presented. The method has been tested on four probiotic LAB strains grown in De Man Rogosa Sharpe (MRS) broth, a complex medium that is often used for the culture of such bacteria. This protocol allowed the detection of 19 proteins after sodium dodecyl sulfate-polyacrylamide gel electrophoresis, 10 of them being successfully identified by tandem MS. Thereafter, the 10 were found to be secreted or surface associated by bioinformatic means. In conclusion, this work supplies a method for the identification of proteins secreted by LAB, allowing discrimination between the proteins present in the MRS and those produced by probiotic LAB.     

国产单叶蔓荆种内变异的数量分类学研究

分析了中国分布单叶蔓荆的种内变异.每个居群随机采取5个以上的完整植株,以16个居群单叶蔓荆作为分类运算单位(operational taxonomic unti,OTU),选取11个有变异的形态学性状和3个品质性状.形态性状以各植株的平均值作为OTUs的原始数据,形成16×14的原始数据矩阵,对矩阵进行聚类分析.根据Q...     

An optimization method for the identification of minimal sets of discriminating gene markers: application to cultivar identification in wheat

A potentially large number of molecular markers are available for identifying genotypes in various species. For wheat, cultivar identity is an important determinant for end-use segregation and for payment of end-point royalties and grower premiums. A number of dominant DNA markers, that give either a positive or negative response, have been developed previously for wheat cultivar identification. This paper gives a method for identifying minimal marker sets for a given cultivar group, for example those grown in a specific geographical zone. It is based on an integer linear programming formulation of the problem, and can find all minimal marker sets for the group if required. The paper then describes the production of two software packages, GGDS and GGIP, that incorporate this methodology. Various practical issues are also discussed. These packages enable the rapid selection of minimal marker sets for the efficient discrimination of any sample set where the marker responses of the samples are known. They are already being used by the Australian wheat industry.     

Stability of classification of filamentous fungi under changes in character coding strategy

The characteristics of a number of filamentous fungal cultures were obtained from two previously published numerical taxonomic studies on Penicillium and Phoma. The coding strategies for some of the physiological and morphological properties employed in the original studies were re-examined and the data was re-coded by combining sets of characters into single ordered multistate characters. The different coding procedures were compared by generating average linkage (UPGMA) dendrograms which were in turn compared by calculating correlation coefficients between the final similarity matrices implied by these dendrograms. The character conversions had no significant effect on the final outcome of the clustering.     

A graphical method for detecting recombination in phylogenetic data sets

Current phylogenetic tree reconstruction methods assume that there is a single underlying tree topology for all sites along the sequence. The presence of mosaic sequences due to recombination violates this assumption and will cause phylogenetic methods to give misleading results due to the imposition of a single tree topology on all sites. The detection of mosaic sequences caused by recombination is therefore an important first step in phylogenetic analysis. A graphical method for the detection of recombination, based on the least squares method of phylogenetic estimation, is presented here. This method locates putative recombination breakpoints by moving a window along the sequence. The performance of the method is assessed by simulation and by its application to a real data set.      

On the leafy nature of lodicules in the genus Triticum (Poaceae)

Lodicules are important organs creating the mating system in grasses, in a range between autogamy in clestogamous flowers and allogamy in chasmogamous flowers. This balance is the main factor determining variation patterns in plant populations. Recognition of variation in lodicule morphology is especially important in wheat, the main crop of the world. For this reason, a broad range of species of wheat was evaluated by means of characters showing the leafy nature of lodicules. The characters were studied under polarizing and epifluorescence microscopes. Development of lodicule stomata is different than that in leaves. Development of stomata and xylem, is distinctly correlated. Other short cells created by epidermal meristemoids are developmentally rather independent of both stomata and xylem. Interrelations between stomata, xylem and morphogenetic traits of the abaxial epidermis of the lodicule are illustrated by pictures and diagrams of numerical analyses, including a non‐metric multidimensional scaling method. Some unthreshable wheats, such as Triticum diccocum, T. ispahanicum and T. spelta, have more leafy lodicules, but intraspecific variation appears in the form of +leafy vs. ?leafy lodicules. Formation of leafy lodicule morphs does not depend on the ploidy level of wheat. An intraspecific mosaic of + or ?leafy lodicules proves a mutational origin of their leafy characters. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 164 , 303–316.     

The phylogenetic significance of flavonoids in Crambe L. (Cruciferae)

A total of 21 flavonoid compounds has been detected in 14 species of Crambe. In general, both the sections of the genus and the species can be distinguished easily by their flavonoid patterns. The members of Crambe sections Crambe and Dendrocrambe seem to be the most primitive with their perennial or rhizocarpous habit. They show a diversity of flavonol glycosides, derived from either kaempferol or quercetin. The presumed presence of proanthocyanidins confers an additional primitive character to Crambe section Dendrocrambe. In contrast, members of Crambe section Leptocrambe show a relatively poor pattern where the quercetin glycosides have disappeared. In the case of C. hispanica and C. abyssinica flavonols are completely absent while two flavones, luteolin and apigenin appear in glycosidic form; these are probably the most evolved Crambe species and exhibit an annual habit. A dendrogram exclusively based on data of the presence or absence of flavonoids has been constructed. It is similar to the one that could have been expected from use of morphological data alone, but it does provide some hints on the possible phylogenetic relationships between the species. Flavonoid evidence also supports the hypothesis on an east-west Mediterranean disjunction within the genus.     

Species separation and identification in the Enchytraeidae (Oligochaeta, Annelida): combining morphology with general protein data

In the Enchytraeidae, species separation and identification is often problematic due to high morphological similarity of closely related species and considerable intraspecific variability of crucial characteristics. Immature specimens are almost undeterminable. To meet these difficulties, this paper recommends the consulting of general protein patterns as exhibited by non-specific silver-staining after isoelectric focusing. A method is presented which allows the successful inclusion of protein data in taxonomic studies and field surveys. Two examples from an investigation on Fridericia field populations show that, with the help of general protein pattern analysis, a clear taxonomic decision on the identity of morphologically aberrant forms and of juvenile specimens as well can be achieved with comparatively little expenditure of time. A combined use of morphological and protein data for taxonomic purposes is suggested.     

淫羊藿属植物的数量分类学研究

通过观测淫羊藿属植物的30个质量性状和15个数量性状,利用聚类分析和主成分分析的方法研究淫羊藿属属下类群的分类关系。结果表明:(1)聚类分析结果将淫羊藿属中国种类划分为大花类群和小花类群,支持Stearn对Sect.Macroceras、Sect.Polyphyllon和Subg.Rhizophyllum的处理,但认为Sect.Epimedium的分类地位尚需进一步探讨。(2)主成分分析结果显示,性状的累积贡献率不是很高,前3个主成分累积贡献率为51.86%,这可能与本属植物演化过程中性状变异的多样化和复杂化相关,但由主成分分析的结果仍可以看出中国种类被划分为大花类群和小花类群。研究认为,花瓣与内萼片长度比、花瓣是否具距、萼片轮数等作为主成分反映的性状对淫羊藿属分类具有重要价值。