Use of secondary data in numerical taxonomy of the genus Erwinia

Incorporating Hierarchical Characters into Phylogenetic Analysis

Popular optimality criteria for phylogenetic trees focus on sequences of characters that are applicable to all the taxa. As studies grow in breadth, it can be the case that some characters are applicable for a portion of the taxa and inapplicable for others. Past work has explored the limitations of treating inapplicable characters as missing data, noting that this strategy may favor trees where interval nodes are assigned impossible states, where the arrangement of taxa within subclades is unduly influenced by variation in distant parts of the tree, and/or where taxa that otherwise share most primary characters are grouped distantly. Approaches that avoid the first two problems have recently been proposed. Here, we propose an alternative approach which avoids all three problems. We focus on data matrices that use reductive coding of traits, that is, explicitly incorporate the innate hierarchy induced by inapplicability, and as such our approach extend to hierarchical characters, in general. In the spirit of maximum parsimony, the proposed criterion seeks the phylogenetic tree with the minimal changes across any tree branch, but where changes are defined in terms of dissimilarity metrics that weigh the affects of inapplicable characters. The approach can accommodate binary, multistate, ordered, unordered, and polymorphic characters. We give a polynomial-time algorithm, inspired by Fitch's algorithm, to score trees under a family of dissimilarity metrics, and prove its correctness. We show that the resulting optimality criteria is computationally hard, by reduction to the NP-hardness of the maximum parsimony optimality criteria. We demonstrate our approach using synthetic and empirical data sets and compare the results with other recently proposed methods for choosing optimal phylogenetic trees when the data includes hierarchical characters.

A new family of dissimilarity metrics for discrete character matrices that include inapplicable characters and its importance for disparity studies

The use of discrete character data for disparity analyses has become more popular, partially due to the recognition that character data describe variation at large taxonomic scales, as well as the increasing availability of both character matrices co-opted from phylogenetic analysis and software tools. As taxonomic scope increases, the need to describe variation leads to some characters that may describe traits not found across all the taxa. In such situations, it is common practice to treat inapplicable characters as missing data when calculating dissimilarity matrices for disparity studies. For commonly used dissimilarity metrics like Wills's GED and Gower's coefficient, this can lead to the reranking of pairwise dissimilarities, resulting in taxa that share more primary character states being assigned larger dissimilarity values than taxa that share fewer. We introduce a family of metrics that proportionally weight primary characters according to the secondary characters that describe them, effectively eliminating this problem, and compare their performance to common dissimilarity metrics and previously proposed weighting schemes. When applied to empirical datasets, we confirm that choice of dissimilarity metric frequently affects the rank order of pairwise distances, differentially influencing downstream macroevolutionary inferences.

Deoxyribonucleic acid relatedness among species of Erwinia and between Erwinia species and other enterobacteria

Relatedness in species of Erwinia was assessed by determining the extent of reassociation in heterologous deoxyribonucleic acid preparations. Thermal elution chromatography on hydroxyapatite was used to separate reassociated nucleotide sequences from nonreassociated sequences and to determine the thermal stability of related nucleotide sequences. An apparent 15% core of relatedness is present between fire blight, soft-rot, and "atypical" Erwinia species. All Erwinia species showed low to moderate reaction with representative enteric bacteria.

Unusual fermentative, gram-negative bacilli isolated from clinical specimens. I. Characterization of Erwinia strains of the "lathyri-herbicola group"

Five strains of gram-negative, yellow chromogenic bacilli were recovered from clinical specimens which fit the characteristics of the "lathyri-herbicola group" within the genus Erwinia. The strains were facultatively anaerobic, fermentative, anaerogenic bacilli with peritrichous flagella which grew at 37 C, reduced nitrate to nitrite, and failed to produce oxidase, pectinase, arginine dihydrolase, and decarboxylases for lysine and ornithine. Aggregations of bacteria (symplasmata) were observed in the syneresis water of slant cultures, and analogous granular aggregates and biconvex, spindle-shaped bodies developed in colonies on plate cultures. Awareness of these characteristics should result in more frequent identification of Erwinia species from human sources.

Factors affecting reproducibility of numerical classifications

Results obtained with reference organisms which had been included in each of three different investigations were compared. Positions of the reference organisms in diagrams based on highest-link numerical groupings varied with the composition of the microbial samples studied, but significant correlations were found between the results of different investigations. Correlations between the overall groupings obtained in different studies were often better than the correlations between actual similarity values computed between specific pairs of organisms. Similarity values based on different sets of features showed significant correlations, regardless of the kinds of features involved or of the number of features (above a minimum of about 40). Correlations between values based on totally different features were nearly as good as those between values based on similar features which had been determined by different investigators.

Selection of characters for an Adansonian analysis of mycobacterial taxonomy

Tests which are most frequently employed to provide characters for numerical analysis of bacterial taxonomy provide little differentiation among the slow-growing members of the genus Mycobacterium. A special scheme was proposed to deal with this problem. Characters were based, to some extent, on quantitative reactions to tests, and were defined, for each test, in terms of natural clustering behavior of a large collection of assorted strains. Inter- and intrataxon analyses were based on comparisons of reaction patterns with tentative hypothetical median strain patterns. This permitted the analysis of larger numbers of cultures than can be practically studied in a conventional n x n table.

Classification of enterobacteria based on overall similarity

Krieg, R. E. (Iowa State University, Ames), and W. R. Lockhart. Classification of enterobacteria based on overall similarity. J. Bacteriol. 92:1275-1280. 1966.-A numerical study was made of 53 organisms, representing 12 genera of the family Enterobacteriaceae and 4 members of the genus Aeromonas. A total of 105 features was determined for each culture. Matching coefficients were computed, and the organisms were sorted into phenetic groups by use of the "highest-link" criterion. The genera Enterobacter (Aerobacter), Escherichia, Citrobacter, Arizona, Shigella, and Salmonella formed a single, large cluster with little or no evidence of subdivisions into tribes or genera. Paracolobactrum and Klebsiella were joined to the large group as subclusters. Members of the genera Erwinia and Serratia formed separate, distinct clusters related to the large group at a lower level of similarity. At a still lower level were appended Aeromonas, Proteus, Providencia, and some individual species from other genera. These organisms were no more closely related to one another than to the larger group.