Evsey Kosman

Similarity coefficients for molecular markers in studies of genetic relationships between individuals for haploid, diploid, and polyploid species

Determining true genetic dissimilarity between individuals is an important and decisive point for clustering and analysing diversity within and among populations, because different dissimilarity indices may yield conflicting outcomes. We show that there are no acceptable universal approaches to assessing the dissimilarity between individuals with molecular markers. Different measures are relevant to dominant and codominant DNA markers depending on the ploidy of organisms. The Dice coefficient is the suitable measure for haploids with codominant markers and it can be applied directly to (0,1)‐vectors representing banding profiles of individuals. None of the common measures, Dice, Jaccard, simple mismatch coefficient (or the squared Euclidean distance), is appropriate for diploids with codominant markers. By transforming multiallelic banding patterns at each locus into the corresponding homozygous or heterozygous states, a new measure of dissimilarity within locus was developed and expanded to assess dissimilarity between multilocus states of two individuals by averaging across all codominant loci tested. There is no rigorous well‐founded solution in the case of dominant markers. The simple mismatch coefficient is the most suitable measure of dissimilarity between banding patterns of closely related haploid forms. For distantly related haploid individuals, the Jaccard dissimilarity is recommended. In general, no suitable method for measuring genetic dissimilarity between diploids with dominant markers can be proposed. Banding patterns of diploids with dominant markers and polyploids with codominant markers represent individuals’ phenotypes rather than genotypes. All dissimilarity measures proposed and developed herein are metrics.

Emergency Room Visits of Asthmatic Children, Relation to Air Pollution, Weather, and Airborne Allergens

BACKGROUND The worldwide increase in the incidence, prevalence, and severity of asthma may suggest that environmental factors play a role in these epidemiologic changes. OBJECTIVE To examine the correlations between air pollutants, weather conditions, airborne allergens, and the incidence of emergency room (ER) visits of children with acute asthma attacks. DESIGN One-year prospective study. Data of daily concentration of air pollutants, weather conditions, and selective airborne allergens were collected and compared with the number of ER visits of asthmatic children. SUBJECTS 1076 asthmatic children (aged 1 to 18 years) who presented at the Pediatric ER between January 1 and December 31, 1993. RESULTS Correlations between fluctuations in ER visits of asthmatic children and various environmental parameters were more relevant for weekly than for daily values. Emergency room visits correlated positively with concentrations of NOx, SO2 and with high barometric pressure; and negatively with O3 concentration and minimal and maximal temperature. There were no significant correlations with concentrations of particulates, humidity, or airborne pollen and spores. An exceptionally high incidence of ER visits of asthmatic children was observed during September. This peak coincided with the beginning of the school year and the Jewish holidays. The correlations between ER visits and the environmental factors increased significantly when the September peak was excluded, revealing that 61% of the variance in ER visits was explained by NOx, SO2, and 03 concentrations, 46% by weather parameters, 66% by NOx, SO2 and barometric pressure, and 69% by the combination of air pollutants and weather parameters. CONCLUSION The major factors found to be associated with ER visits of asthmatic children were high NOx, high SO2, and high barometric pressure. Negative correlation was found between ER visits of asthmatic children and ozone concentrations. The particularly high number of ER visits at the beginning of the school year and the Jewish holidays was probably associated with an increase in the number of viral infections and/or emotional stress.

Virulence and Diversity of Blumeria graminis f. sp. hordei in Israel and in the Czech Republic

Three hundred and nine isolates were obtained from three natural populations of Blumeria graminis f. sp. hordei occurring on wild barley (Hordeum vulgare subsp. spontaneum) at two locations in Israel during 1997 and 1999. Their virulence frequency was determined on 32 differential lines. No isolate was virulent on the differential lines possessing the genes Mla13, mlo, Mlf1, and Mli, and conversely no isolate was avirulent on the differential lines possessing the genes MlRu2, MlLa, Mlh, Mla8, Mla25, and Mlj. The frequencies of isolates overcoming the genes Mlg, Mla7, and Mla27 were 0 to 16% at individual locations; frequencies of isolates overcoming the genes Mla9, Mla17, and Mla18 ranged from 37 to 78%, and frequencies of virulences to genes Mla1, Mla3, Mla6, Mlp1, Mlat, Mla12, Mlra, Mlk1, Mla19, Mla20, Mla26, Mla28, Mla29, Mla30, Mla32, and mlt1 were 79 to 99%. Based on examination of 376 isolates collected in the same years from the Czech Republic, these populations differed greatly from the Israeli ones. The Czech populations showed greater diversity of virulence and lower mean virulence complexity than the Israeli populations. Diversity in the Israeli populations differed also among clusters of niches at the same location.

Physiologic Specialization of Puccinia triticina on Wheat in the United States in 2001

Collections of Puccinia triticina were obtained from rust-infected wheat leaves by cooperators throughout the United States and from surveys of wheat fields and nurseries in the Great Plains, Ohio Valley, Gulf Coast, California, Pacific Northwest, and Atlantic Coast States in order to determine the virulence of the wheat leaf rust fungus in 2001. Single uredinial isolates (477 in total) were derived from the wheat leaf rust collections and tested for virulence phenotype on lines of Thatcher wheat that are near-isogenic for leaf rust resistance genes Lr1, Lr2a, Lr2c, Lr3, Lr9, Lr16, Lr24, Lr26, Lr3ka, Lr11, Lr17, Lr30, LrB, Lr10, Lr14a, and Lr18. The isolates also were tested for virulence on adult plants with leaf rust resistance genes Lr12, Lr13, Lr22a, Lr22b, Lr34, Lr35, and Lr37. In the United States in 2001, 44 virulence phenotypes of P. triticina were found. Virulence phenotype MBDS, which is virulent to resistance gene Lr17, was the most common phenotype in the United States. MBDS was found in the Southeast, Great Plains, and Ohio Valley regions. Virulence phenotype THBJ, which is virulent to Lr16 and Lr26, was the second most common phenotype, and occurred almost exclusively in the north-central Great Plains region. Phenotype MCDS, which is virulent to Lr17 and Lr26, was the third most common phenotype and was found primarily in the Southeast, Ohio Valley, and Great Plains regions. The Southeast and Ohio Valley regions differed from the Great Plains region for predominant virulence phenotypes, which indicate that populations of P. triticina in those areas are not closely connected. The northern and southern areas of the Great Plains region differed for phenotypes with virulence to Lr16; however, the two areas had other phenotypes in common. Virulence to the adult plant resistance genes Lr35 and Lr37 was detected for the first time in North America in the MBDS, MCJS, and MCDS phenotypes.

Measuring diversity: from individuals to populations

Making inferences about variation within and among various operational units may depend on the ability of a selected approach to diversity analysis to utilize correctly all information available in the raw data. Frequency-based genotypic and gene diversity parameters, methods of ‘true diversity’ and functional diversity, as well as two types of dissimilarity based approaches (by means of averaging pairwise dissimilarities, and solution of the assignment problem) are comprehensively discussed. The dissimilarity based approaches need a suitable assessment of dissimilarity between individual operational units (individuals, communities, populations, clusters, functions, phylogenetic trees etc.). Many commonly used diversity parameters can be derived in terms of the average based measures. The assignment based methods are able to address some limitations and shortcomings of the commonly used measures of population diversity, and they are preferable in the case of possible association between traits. They are always mathematically valid, whereas validity of the average based methods depends on the selected dissimilarity measure. The dissimilarity based methods actually assess functional diversity in the space of the selected traits, and they allow measuring complex diversity and assessment of total γ-diversity as the sum of the independent components of α- and β-diversity with descriptors of different types. The dissimilarity based method for diversity analysis can be consistently employed together with other approaches to data analysis (e.g. clustering). In particular, they may provide valid diversity estimates and replace Nei’s diversity measures, which are often inconsistently used with binary molecular marker data.

Clustering of allergenic pollen on the basis of skin responses of atopic patients by matrix analysis

The responses of 148 atopic patients to some 43 different extracts of allergenic pollen were tested by prick tests. The measure of dissimilarity was introduced and calculated for all pairs of allergens. The investigated allergens were clustered into groups, according to their unbiased greatest similarity, by a matrix‐structuring method. Results indicate that subgroups of allergens can be distinguished even within groups of closely related pollen allergens that were believed to be fully cross‐reactive. A few cases are demonstrated for various varieties of olives, pecans, date palms, and turf grasses and for some wild chenopods and amaranths. The usefulness of the suggested solution for allergy research and for clinical practice is discussed.

Decomposing functional diversity

Summary 1.One aspect of biodiversity, functional diversity, reflects the functional role of species within a community as measured by species characteristics. We present a new metric, functional trait dispersion, based on the concept of species distinctiveness measured as the distance among species in the multidimensional space defined by trait values. This metric can be decomposed into components of species richness, functional evenness and mean dispersion, and into parts that measure diversity within and among subgroups. 2.Using an appropriate distance measure, mean dispersion (M′) is calculated as the average distance among all possible pairs of species. Functional evenness [qE(T)] is derived from Hill diversity based on the proportional distances between pairs of species and species richness (S). Functional trait dispersion [qD(TM)] is then computed as 1 + (S-1) × qE(T) × M′. It has a range of [1,S] and measures the effective number of functionally-distinct species for a given level of species dispersion. 3.Using constructed data, we demonstrate that qD(TM) captures appropriate ecological properties such that a community with greater species richness, greater dispersal in trait space, or greater mean dispersion has greater functional diversity. Functional trait dispersion can also provide measures of within-community dispersion and the effective number of functionally-distinctive compartments (groups of communities with similar functional structure). Using empirical data of bats along an elevational gradient in Peru, we demonstrate that functional trait dispersion and its components provide insights about gradients of biodiversity. 4.Functional trait dispersion comports to reasonable criteria for a metric of functional diversity and can be decomposed in a variety of ways that facilitate understanding of patterns of variation. Other metrics of functional diversity neither integrate all three diversity components, nor can many be decomposed into variation within and among subgroups. Because functional trait dispersion measures properties of distance and the effective number of functionally-distinct species, it can be used in conjunction with other biodiversity metrics that are based on species identity, abundance or phylogenetic relatedness to inform management and the preservation of biodiversity. This article is protected by copyright. All rights reserved.

Virulence and diversity of Puccinia striiformis f. sp. tritici in Ethiopia

Stripe rust of wheat (Triticum spp.), caused by Puccinia striiformis f. sp. tritici, is an important disease in Ethiopia. To investigate the population structure of the pathogen, 107 single-pustule isolates were collected from four regions (northern, central, southern, and southeastern Ethiopia) and tested on 24 differential genotypes with known resistance genes. The isolates were classified into 39 pathotypes. All isolates were virulent on Yr7 and avirulent on Yr1, Yr5, Yr15, and YrSp. Virulence complexity of the isolates ranged from 7 to 16, with a mean of 11.72. No common pathotype was shared by these regional collections. Distribution of pathotypes within the regions was quite even, whereas the richness of populations varied considerably between 1.78 (the central region) and 2.96 (the southeastern region). The genotypic, gene, and genetic diversities within populations were characterized using the Simpson, Nei, and Kosman indices. Significant differences among the regional populations were detected for both gene and genetic diversity within populations, whereas the genotypic diversity was rather stable. The lowest and highest diversities of wheat stripe rust occurred in the southern and northern regions, respectively. Genetic variation in the population structure of the pathogen observed in different geographical areas might indicate that unique wheat cultivars should be developed and released for production on a regional basis.

Genetic Variation and Virulence on Lr26 in Puccinia triticina

ABSTRACT The genetic relationships between isolates of Puccinia triticina virulent on wheat with the Lr26 resistance gene were studied. The diversity within and between isolates of P. triticina from Israel, Europe, and the United States was determined by virulence on near-isogenic Thatcher lines and by random amplified polymorphic DNA. According to the molecular markers, isolates that were virulent on Lr26 had diversity levels similar to those of Lr26 nonpathogenic isolates. Distances between subpopulations of isolates virulent and avirulent on Lr26 varied and were unrelated to the Lr26 virulence phenotype. Cluster analysis suggested four groups, three of which were closely associated with the geographical origin of the isolates-Israel, the United States, and Europe. All four groups included both Lr26 virulent and avirulent pathotypes. The results showed that Lr26 virulent rust pathotypes are as genetically dissimilar as the rest of the population. The cluster analysis showed that the rust population in Israel includes at least two different subpopulations, both of which contain Lr26 virulent and Lr26 avirulent isolates.

Diversity of fungal endophytes in recent and ancient wheat ancestors Triticum dicoccoides and Aegilops sharonensis

Endophytes have profound impacts on plants, including beneficial effects on agriculturally important traits. We hypothesized that endophytes in wild plants include beneficial endophytes that are absent or underrepresented in domesticated crops. In this work, we studied the structure of endophyte communities in wheat-related grasses, Triticum dicoccoides and Aegilops sharonensis, and compared it to an endophyte community from wheat (T. aeastivum). Endophytes were isolated by cultivation and by cultivation-independent methods. In total, 514 intergenic spacer region sequences from single cultures were analyzed. Categorization at 97% sequence similarity resulted in 67 operational taxonomic units (OTUs) that were evenly distributed between the different plant species. A narrow core community of Alternaria spp. was found in all samples, but each plant species also contained a significant portion of unique endophytes. The cultivation-independent analysis identified a larger number of OTUs than the cultivation method, half of which were singletons or doubletons. For OTUs with a relative abundance >0.5%, similar numbers were obtained by both methods. Collectively, our data show that wild grass relatives of wheat contain a wealth of taxonomically diverse fungal endophytes that are not found in modern wheat, some of which belong to taxa with known beneficial effects.