Phylogenomic inferences from reference-mapped and de novo assembled short-read sequence data using RADseq sequencing of California white oaks (Quercus subgenus Quercus)

The emergence of next generation sequencing has increased by several orders of magnitude the amount of data available for phylogenetics. Reduced representation approaches, such as restriction-site associated DNA sequencing (RADseq), have proven useful for phylogenetic studies of non-model species at a wide range of phylogenetic depths. However, analysis of these datasets is not uniform and we know little about the potential benefits and drawbacks of de novo assembly versus assembly by mapping to a reference genome. Using RADseq data for 83 oak samples representing 16 Quercus taxa , we identified variants via three pipelines: mapping sequence reads to a recently published draft genome of Quercus lobata, and de novo assembly under two sets of locus filters. For each pipeline, we inferred the maximum likelihood phylogeny. All pipelines produced similar trees, with minor shifts in relationships within well-supported clades, despite the fact that they yielded different numbers of loci (68K â 111K loci) and different degrees of overlap with the reference genome. We conclude that both the reference-aligned and de novo assembly pipelines yield reliable results, and that advantages and disadvantages of these approaches pertain mainly to downstream uses of RADseq data, not to phylogenetic inference per se.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Teaching high performance computing to undergraduate faculty and undergraduate students

A growing proportion of Science, Technology, Engineering & Mathematics (STEM) research is increasingly dependent on Cyberinfrastructure (CI). CI has experienced rapid progress in enabling technologies - hardware, storage, networking, middleware, tools, libraries - but much slower improvements in workforce development. Currently, CI consumers tend to lag substantially behind CI capabilities. This paper de-scribes a series of linked efforts to address the gap between the workforce and the technology. Copyright 2010 ACM

Comparing Apples With Oranges: Evaluating Twelve Paradigms Of Agency

We report on a study in which twelve different paradigms were used to implement agents acting in an environment which borrows elements from artificial life and multi-player strategy games. In choosing the paradigms we strived to maintain a balance between high level, logic based approaches to low level, physics oriented models; between imperative programming, declarative approaches and learning from basics as well as between anthropomorphic or biologically inspired models on one hand and pragmatic, performance oriented approaches on the other. Instead of strictly numerical comparisons (which can be applied to certain pairs of paradigms, but might be meaningless for others), we had chosen to view each paradigm as a methodology, and compare the design, development and debugging process of implementing the agents in the given paradigm. We found that software engineering techniques could be easily applied to some approaches, while they appeared basically meaningless for other ones. The performance of some agents were easy to predict from the start of the development, for other ones, impossible. The effort required to achieve certain functionality varied widely between the different paradigms. Although far from providing a definitive verdict on the benefits of the different paradigms, our study provided a good insight into what type of conceptual, technical or organizational problems would a development team face depending on their choice of agent paradigm. © Springer-Verlag Berlin Heidelberg 2007

Genomic landscape of the global oak phylogeny

The tree of life is highly reticulate, with the history of population divergence emerging from populations of gene phylogenies that reflect histories of introgression, lineage sorting and divergence. In this study, we investigate global patterns of oak diversity and test the hypothesis that there are regions of the oak genome that are broadly informative about phylogeny.We utilize fossil data and restriction-site associated DNA sequencing (RAD-seq) for 632 individuals representing nearly 250 Quercus species to infer a time-calibrated phylogeny of the world's oaks. We use a reversible-jump Markov chain Monte Carlo method to reconstruct shifts in lineage diversification rates, accounting for among-clade sampling biases. We then map the > 20 000 RAD-seq loci back to an annotated oak genome and investigate genomic distribution of introgression and phylogenetic support across the phylogeny.Oak lineages have diversified among geographic regions, followed by ecological divergence within regions, in the Americas and Eurasia. Roughly 60% of oak diversity traces back to four clades that experienced increases in net diversification, probably in response to climatic transitions or ecological opportunity.The strong support for the phylogeny contrasts with high genomic heterogeneity in phylogenetic signal and introgression. Oaks are phylogenomic mosaics, and their diversity may in fact depend on the gene flow that shapes the oak genome