Diversity Arrays Technology (DArT) for Pan-Genomic Evolutionary Studies of Non-Model Organisms

Background: High-throughput tools for pan-genomic study, especially the DNA microarray platform, have sparked a remarkable increase in data production and enabled a shift in the scale at which biological investigation is possible. The use of microarrays to examine evolutionary relationships and processes, however, is predominantly restricted to model or near-model organisms. Methodology/Principal Findings: This study explores the utility of Diversity Arrays Technology (DArT) in evolutionary studies of non-model organisms. DArT is a hybridization-based genotyping method that uses microarray technology to identify and type DNA polymorphism. Theoretically applicable to any organism (even one for which no prior genetic data are available), DArT has not yet been explored in exclusively wild sample sets, nor extensively examined in a phylogenetic framework. DArT recovered 1349 markers of largely low copy-number loci in two lineages of seed-free land plants: the diploid fern Asplenium viride and the haploid moss Garovaglia elegans. Direct sequencing of 148 of these DArT markers identified 30 putative loci including four routinely sequenced for evolutionary studies in plants. Phylogenetic analyses of DArT genotypes reveal phylogeographic and substrate specificity patterns in A. viride, a lack of phylogeographic pattern in Australian G. elegans, and additive variation in hybrid or mixed samples. Conclusions/Significance: These results enable methodological recommendations including procedures for detecting and analysing DArT markers tailored specifically to evolutionary investigations and practical factors informing the decision to use DArT, and raise evolutionary hypotheses concerning substrate specificity and biogeographic patterns. Thus DArT is a demonstrably valuable addition to the set of existing molecular approaches used to infer biological phenomena such as adaptive radiations, population dynamics, hybridization, introgression, ecological differentiation and phylogeography

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Phylogenetic Analysis of 5 Medically Important Candida Species As Deduced On the Basis of Small Ribosomal-subunit Rna Sequences

The classification of species belonging to the genus Candida Berkhout is problematic. Therefore, we have determined the small ribosomal subunit RNA (srRNA) sequences of the type strains of three human pathogenic Candida species; Candida krusei, C. lusitaniae and C. tropicalis. The srRNA sequences were aligned with published eukaryotic srRNA sequences and evolutionary trees were inferred using a matrix optimization method. An evolutionary tree comprising all available eukaryotic srRNA sequences, including two other pathogenic Candida species, C. albicans and C. glabrata, showed that the yeasts diverage rather late in the course of eukaryote evolution, namely at the same depth as green plants, ciliates and some smaller taxa. The cluster of the higher fungi consists of 10 ascomycetes and ascomycete-like species with the first branches leading to Neurospora crassa, Pneumocystis carinii, Candida lusitaniae and C. krusei, in that order. Next there is a dichotomous divergence leading to a group consisting of Torulaspora delbrueckii, Saccharomyces cerevisiae, C. glabrata and Kluyveromyces lactis and a smaller group comprising C. tropicalis and C. albicans. The divergence pattern obtained on the basis of srRNA sequence data is also compared to various other chemotaxonomic data

Spaced antenna analysis of atmospheric radar backscatter model data

A simple computer model of atmospheric radar backscatter is used to investigate and compare various spaced antenna (SA) techniques, including the full correlation analysis (FCA) and a number of imaging interferometry techniques. The results illustrate that the FCA true velocity proves to be an excellent estimate of the model input velocity for all magnitudes of model turbulent motions. On the other hand, the interferometric velocities increase as the magnitude of the turbulent motions are increased, providing a poor estimate of the model input velocity for large turbulent motion magnitudes. Maps illustrating the interferometry‐estimated scattering positions superimposed upon the actual model scatterer positions reveal the estimated positions to be inaccurate. The estimated positions are shown to approach the zenith as the magnitude of the turbulent motions increases, confirming the volume scatter derived suggestions of Briggs (1995). Furthermore, the estimated positions have a preferred azimuth angle agreeing with volume scatter derived suggestions. The effects of receiver noise upon the interferometric techniques are investigated, revealing an effect analogous to the FCA triangle size effect whereby the estimated velocity decreases with increasing noise level. The effects of the thresholds used to preclude individual Doppler frequencies from the analyses are illustrated. The results are in excellent agreement with the experimental results obtained in a number of different studies. Copyright 1995 by the American Geophysical Union