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

Towards an optimal sampling strategy for assessing genetic variation within and among white clover (Trifolium repens L.) cultivars using AFLP

Cost reduction in plant breeding and conservation programs depends largely on correctly defining the minimal sample size required for the trustworthy assessment of intra- and inter-cultivar genetic variation. White clover, an important pasture legume, was chosen for studying this aspect. In clonal plants, such as the aforementioned, an appropriate sampling scheme eliminates the redundant analysis of identical genotypes. The aim was to define an optimal sampling strategy, i.e., the minimum sample size and appropriate sampling scheme for white clover cultivars, by using AFLP data (283 loci) from three popular types. A grid-based sampling scheme, with an interplant distance of at least 40 cm, was sufficient to avoid any excess in replicates. Simulations revealed that the number of samples substantially influenced genetic diversity parameters. When using less than 15 per cultivar, the expected heterozygosity (He) and Shannon diversity index (I) were greatly underestimated, whereas with 20, more than 95% of total intra-cultivar genetic variation was covered. Based on AMOVA, a 20-cultivar sample was apparently sufficient to accurately quantify individual genetic structuring. The recommended sampling strategy facilitates the efficient characterization of diversity in white clover, for both conservation and exploitation

Acute spinal rigidity

In each section of this chapter, relevant case histories from the literature illustrating structural, inflammatory or paraneoplastic causes of spinal rigidity are discussed to highlight the presenting and diagnostic features. Such cases are rare, and the importance of imaging cannot be overemphasised in cases of segmental rigidity where a spinal origin is supsected. Modern imaging techniques permit detailed anatomical examination of the spinal cord, making such diagnoses much simpler than in the past.P.D. Thompso

Population genetic structuring in a rare tropical plant:\ud Idiospermum australiense (Diels) S.T. Blake

Idiospermum australiense (Diels) S.T. Blake is considered to be one of the few remaining species of an ancient assemblage to have survived the attrition ofAustralian tropical rain forest during historically drier periods. This monotypic species is currently restricted to two very wet lowland rain forest locations in Australia’s wet tropical World Heritage Area that are thought to have provided refuge for humid-adapted taxa during the last glacial maximum. Two dominant (RAPD and ISSR) molecular marker sets were employed to investigate whether the genetic structure of Idiospermum could be attributed to its restriction to these quite disjunct localities. The results reveal that neither its restriction to purported\ud Pleistocene refugia nor the geographic distance between\ud populations could fully explain the distribution of variation in the Idiospermum data set, with evidence to suggest that potentially deeper time events have played a role in population structuring and the distribution of diversity. Although there is sufficient evidence in the data to suggest that gene dispersal is quite limited in the species, further investigation is still needed to yield more informative detail on additional factors, such as breeding and germination strategies and their potential influence over population structuring and diversity levels within each population and refugium