New probability matrices for identification of Streptomyces

The character state data obtained for clusters defined in a previous phenetic classification were used to construct two probabilistic matrices for Streptomyces species. These superseded an original published identification matrix by exclusion of other genera and the inclusion of more Streptomyces species. Separate matrices were constructed for major and minor clusters. The minimum number of diagnostic characters for each matrix was selected by computer programs for determination of character separation indices (CHARSEP) and a selection of group diagnostic properties (DIACHAR). The resulting matrices consisted of 26 phena x 50 characters (major clusters) and 28 phena x 39 characters (minor clusters). Cluster overlap (OVERMAT program) was small in both matrices. Identification scores were used to evaluate both matrices. The theoretically best scores for the most typical example of each cluster (MOSTTYP program) were all satisfactory. Input of test data for randomly selected cluster representatives resulted in correct identification with high scores. The major cluster matrix was shown to be practically sound by its application to 35 unknown soil isolates, 77% of which were clearly identified. The minor cluster matrix provides tentative probabilistic identifications as the small number of strains in each cluster reduces its ability to withstand test variation. A diagnostic table for single-membered clusters, constructed using the CHARSEP and DIACHAR programs, was also produced.     

Software for the development and evaluation of probabilistic identification matrices

A number of programs are described for the development and evaluationof probabilistic identification matrices for use with computer-assistedidentification. The program BEST reads an initial matrix ofper cent probabilities for all the binary characters examinedduring a cluster analysis and determines the most useful setof tests for distinguishing taxa in the matrix. Program RESORTcreates from the initial matrix an identification matrix inwhich the order of the tests may be different or the numberof tests reduced. A printed version of a matrix can be producedby MATPRJNT, which creates tables giving the per cent probabilityof a positive test result and the test results presented as‘–’, ‘v’ and ‘+’ dependingon a user-specified threshold. Program IDSC evaluates an identificationmatrix by calculating the best identification score for eachtaxon in the matrix using the expected result for each test.The programs were written in FORTRAN 77 and can be run on anymicrocomputer using the PC/MS-DOS operating system. Received on April 27, 1990; accepted on November 5, 1990     

A probability matrix for the identification of species of Vibrio and related genera

A matrix for the probabilistic identification of species of Vibrio and related genera has been constructed using the data from 1091 strains collected throughout the world and classified. Thirty-eight phenons are included in the matrix, 31 of these represent previously identified species or biovars and seven represent phenons which could not be identified and may represent new species. The identification matrix incorporates 81 characters although a subset of 30 tests can be used to distinguish the 38 phenons from each other. The additional 51 tests were included to assist the identification of some strains for which the initial 30 tests were inadequate. No significant cluster overlap was found at the 5% level and the identification score for the Hypothetical Median Organism of each cluster exceeded 0.9999 in all cases.     

A probability matrix for the identification of species of Vibrio and related genera

A matrix for the probabilistic identification of species of Vibrio and related genera has been constructed using the data from 1091 strains collected throughout the world and classified. Thirty-eight phenons are included in the matrix, 31 of these represent previously identified species or biovars and seven represent phenons which could not be identified and may represent new species. The identification matrix incorporates 81 characters although a subset of 30 tests can be used to distinguish the 38 phenons from each other. The additional 51 tests were included to assist the identification of some strains for which the initial 30 tests were inadequate. No significant cluster overlap was found at the 5% level and the identification score for the Hypothetical Median Organism of each cluster exceeded 0.9999 in all cases.     

Butterflies of the South Pacific

ABSTRACT

Larvae of the invasive mosquito Culex quinquefasciatus Say are morphologically similar to those of the native Culex pervigilans Bergroth, yet distinguishing these species can be hampered by morphological variations in Cx. quinquefasciatus. We present detail about the extent of these variations in an urban population of Cx. quinquefasciatus in Auckland. To aid in identification of this exotic species, we provide images of key diagnostic characters and some observed exceptions to these. Details regarding variation in diagnostic characters for < 3rd instar and 3rd/4th instar larvae are given. Of the nine characters used for identification, three were highly consistent (dorsal papillae, mantle plate, pecten teeth); each observed in > 90% of larvae, although these characters were not always visible. Other characters were less reliable, for instance, the expected position of seta 1a-S in relation to the pecten teeth was observed in < 10% of larvae. Further exploration of regional morphological variation in both Cx. quinquefasciatus and Cx. pervigilans is recommended, ideally with associated molecular characterisation.     

The taxonomic implications of genetic and environmentally induced variations in seaweed morphology

Morphological characters are the most widely used criteria for the discrimination of seaweed taxa. Even so, many examples of extreme phenotypic plasticity are known. Thus, several phycologists have recently initiated studies to evaluate the phenotypic range of taxa under varied conditions as well as to explore the degree of genetic control of individual characters. Several experimental techniques have been employed to enumerate the significance and basis of phenotypic plasticity in seaweeds, including culture studies, detailed seasonal observations of in situ populations, reciprocal transplantation of plants to diverse habitats, statistical analysis of character variations, and evaluation of genetic affinities. Obviously, the taxonomic status of seaweeds should reflect their genetic relationships. Three primary approaches are outlined including electrophoretic studies, quantitative genetic evaluations, and hybridization studies. A detailed summary of these genetic studies, as well as the other experimental field and laboratory techniques, is given in order to critically assess traditional taxonomic criteria and to aid in the search for new ones. An evaluation of the relative merits of morphological and biochemical characters in species delimitations is also outlined. It is suggested that there should be no tacit assumption that biochemical features are in some way more fundamental than morphological ones. Thus, even seemingly trivial morphological features may be of great adaptive value, even though not apparent to the taxonomist. A good taxonomic character is constant, readily observable, and the plant should survive identification. If obscure characters are used to delimit species, strenuous efforts should be made to correlate these characters with more readily observable ones.     

Inferring and testing hypotheses of cladistic character dependence by using character compatibility

The notion that two characters evolve independently is of interest for two reasons. First, theories of biological integration often predict that change in one character requires complementary change in another. Second, character independence is a basic assumption of most phylogenetic inference methods, and dependent characters might confound attempts at phylogenetic inference. Previously proposed tests of correlated character evolution require a model phylogeny and therefore assume that nonphylogenetic correlation has a negligible effect on initial tree construction. This paper develops "tree-free" methods for testing the independence of cladistic characters. These methods can test the character independence model as a hypothesis before phylogeny reconstruction, or can be used simply to test for correlated evolution. We first develop an approach for visualizing suites of correlated characters by using character compatibility. Two characters are compatible if they can be used to construct a tree without homoplasy. The approach is based on the examination of mutual compatibilities between characters. The number of times two characters i and j share compatibility with a third character is calculated, and a pairwise shared compatibility matrix is constructed. From this matrix, an association matrix analogous to a dissimilarity matrix is derived. Eigenvector analyses of this association matrix reveal suites of characters with similar compatibility patterns. A priori character subsets can be tested for significant correlation on these axes. Monte Carlo tests are performed to determine the expected distribution of mutual compatibilities, given various criteria from the original data set. These simulated distributions are then used to test whether the observed amounts of nonphylogenetic correlation in character suites can be attributed to chance alone. We have applied these methods to published morphological data for caecilian amphibians. The analyses corroborate instances of dependent evolution hypothesized by previous workers and also identify novel partitions. Phylogenetic analysis is performed after reducing correlated suites to single characters. The resulting cladogram has greater topological resolution and implies appreciably less change among the remaining characters than does a tree derived from the raw data matrix.     

A probability matrix for the identification of vibrios

A probability matrix for computer-assisted identification of vibrios has been constructed, based on the API 20E system. Data were gathered from 173 strains representing 31 taxa of vibrios and related organisms, from a variety of sources. The matrix was tested internally by four statistical programs. Program OVERMAT tested the separation and program MOSTTYP the discretion and homogeneity of the taxa. Most of the taxa were satisfactory but a few were less so; reasons for this are discussed. Program CHARSEP and program DIACHAR tested the separation and diagnostic values, respectively, of the characters used. The overall test error was 4.5%. The matrix was assessed externally by its performance in the identification of vibrio-like strains isolated from freshwater. Of 243 wild strains, 79.4% were identified with ten taxa, with a Willcox score of greater than or equal to 0.99.     

A frequency matrix for probabilistic identification of some bacilli

A matrix comprising frequencies for positive results for 44 Bacillus taxa for 30 characters has been constructed. The 44 taxa include most of the common species and several clusters of environmental isolates including those described as B. firmus-B. lentus intermediates. The tests, which were chosen for their high diagnostic value, included some of the traditional tests used for identification of bacilli supplemented with a range of sugar fermentations and other characterization tests. The matrix was evaluated by identifying hypothetical median organisms, cluster representatives and a panel of 23 reference strains. All reference strains achieved Willcox probabilities above 0.995. Fifty-eight environmental isolates were also subjected to the 30 tests and identification was attempted. Forty-one strains (70%) achieved a Willcox probability greater than 0.95, which was considered an acceptable identification, and were assigned to 12 taxa. If the SE of taxonomic distance was also considered in the identification score (an acceptable value being less than 7.0), the number of acceptable identifications was reduced to 34 (59%). It was encouraging that bacteria from garden soils identified to the common species such as B. subtilis, B. cereus and B. licheniformis whereas some of the bacteria from an estuarine habitat were identified as species such as B. firmus which are normally identified with that habitat.     

Taxonomic and evolutionary relationships in the genus Vella L. (Cruciferae)

Thirty-two differential characters are numerically analysed for the six existing taxa of the genus Vella L. The closely related monotypic genus Boleum Desv. is also included for comparison. Most of the characters used are morphological, but cariological, ecological and biogeographical aspects have also been studied. The results indicate that four distinct species, one ( V. pseudocytisus L.) with three sub-species, should be distinguished. The new combination V. anremerica (Lit. et Maire) Gómez-Campo (basionym: V. pseudocytisus L. subsp. anremerica Lit. et Maire) and the new name V. pseudocytisus L. subsp. paui Gómez-Campo for V. pseudocytisus L. var. glabrescens Willk., nornen nudum are presented. A key is given to aid identification of these taxa. Their conservation status is also discussed.     

A probability matrix for the identification of vibrios

A probability matrix for computer-assisted identification of vibrios has been constructed, based on the API 20E system. Data were gathered from 173 strains representing 31 taxa of vibrios and related organisms, from a variety of sources. The matrix was tested internally by four statistical programs. Program OVERMAT tested the separation and program MOSTTYP the discretion and homogeneity of the taxa. Most of the taxa were satisfactory but a few were less so; reasons for this are discussed. Program CHARSEP and program DIACHAR tested the separation and diagnostic values, respectively, of the characters used. The overall test error was 4–5%. The matrix was assessed externally by its performance in the identification of vibrio-like strains isolated from freshwater. Of 243 wild strains, 79–4% were identified with ten taxa, with a Willcox score of ζ 0–99.     

An algorithm to find all palindromic sequences in proteins

A palindrome is a set of characters that reads the same forwards and backwards. Since the discovery of palindromic peptide sequences two decades ago, little effort has been made to understand its structural, functional and evolutionary significance. Therefore, in view of this, an algorithm has been developed to identify all perfect palindromes (excluding the palindromic subset and tandem repeats) in a single protein sequence. The proposed algorithm does not impose any restriction on the number of residues to be given in the input sequence. This avant-garde algorithm will aid in the identification of palindromic peptide sequences of varying lengths in a single protein sequence.     

新版DELTA系统在植物分类学中的应用——以羊茅属研究为例

DELTA系统是针对分类学研究开发的综合性多功能软件包。新版DELTA系统在运行环境、程序、指令、界面、操作方式及中文字符处理等重要功能上比旧版本均有较大改进。作为国际分类学数据库数据交换标准,应用该系统可以规范分类学描述,对研究中所有常用性状进行识别和处理,自动生成各个研究对象分类学特征描述并对其进行详尽的相似性和差异性比较,对性状特征和分类单元进行注释和图像示例,将数据转换为数量分类学或分支分类学所需格式以生成树状图,自动生成检索表,建成基于本地和网络的交互式专家辅助鉴定系统等。DELTA系统作为植物分类学研究的常用手段和工具是非常适合及大有帮助的。     

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.     

A review of numerical methods in bacterial identification

Part A of this review describes the particular computer-assisted identification service operated by the NCTC. In Part B, the use of probability matrices is examined, discussing various methods of calculating likelihoods and the problems that arise when calculating these from probability matrices. Part C describes the alternative numerical methods of constructing identification keys and the supplementary methods of selecting best sets of characters to aid identification. Finally, in Part D, the prospects and limitations of numerical methods in bacterial identification are assessed, first with regard to methodology used and then in terms of performance and practical limitations.     

16S mitochondrial sequences associate morphologically dissimilar males and females of the family Phoridae (Diptera)

The genus Phora (Diptera, Phoridae) includes more than 50 species widely distributed in temperate regions of Eurasia and Africa. Taxonomic identification of most species is based upon the morphology of the male hypopygium: hence for many species, including the type species of the genus, females are unknown. We used mitochondrial 16S ribosomal RNA sequences to match males with previously unidentified females from Phora atra , P. stictica , and P. holosericea . We then identified morphological characters that allow identification of females of P. atra and P. stictica without recourse to DNA sequencing. Our results show that small scale sequencing can aid in the development of taxonomic characters for use in the field to identify previously cryptic females. This iterative method of identifying populations genetically followed by re-examination of morphology should allow development of better keys for rapid identification of heretofore cryptic populations of insects. We also found that sequences from individual of P. holosericea from Cambridge, England and Malakhovka, Russia, were more similar to each other than to sequences from a conspecific fly also collected in Cambridge. This result suggests that there is previously un-suspected population structuring in this species.  © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 77 , 267–273.     

THE EFFECT OF ORDERED CHARACTERS ON PHYLOGENETIC RECONSTRUCTION

Abstract Morphological structures are likely to undergo more than a single change during the course of evolution. As a result, multistate characters are common in systematic studies and must be dealt with. Particularly interesting is the question of whether or not multistate characters should be treated as ordered (additive) or unordered (non-additive). In accepting a particular hypothesis of order, numerous others are necessarily rejected. We review some of the criteria often used to order character states and the underlying assumptions inherent in these criteria.
The effects that ordered multistate characters can have on phylogenetic reconstruction are examined using 27 data sets. It has been suggested that hypotheses of character state order are more informative then hypotheses of unorder and may restrict the number of equally parsimonious trees as well as increase tree resolution. Our results indicate that ordered characters can produce more, equal or less equally parsimonious trees and can increase, decrease or have no effect on tree resolution. The effect on tree resolution can be a simple gain in resolution or a dramatic change in sister-taxa relationships. In cases where several outgroups are included in the data matrix, hypotheses of order can change character polarities by altering outgroup topology. Ordered characters result in a different topology from unordered characters only when the hierarchy of the cladogram disagrees with the investigator's a priori hypothesis of order. If the best criterion for assessing character evolution is congruence with other characters, the practice of ordering multistate characters is inappropriate.