Training materials for different categories of users

Agricultural and Food Policy, Environmental Economics and Policy, Farm Management, Land Economics/Use, Production Economics, Teaching/Communication/Extension/Profession,

A Composite Genome Approach to Identify Phylogenetically Informative Data from Next-Generation Sequencing

We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps of de novo whole genome assembly, genome-genome alignment, and annotation. For simulations SISRS is able to identify large numbers of loci containing variable sites with phylogenetic signal. For genomic data from apes, SISRS identified thousands of variable sites, from which we produced an accurate phylogeny. Finally, we used SISRS to identify phylogenetic markers that we used to estimate the phylogeny of placental mammals. We recovered phylogenies from multiple datasets that were consistent with previous conflicting estimates of the relationships among mammals. SISRS is open source and freely available at https://github.com/rachelss/SISRS.Comment: 12 pages plus36 figures, 1 supplementary table, 3 supplementary figure

Evolutionary simulations to detect functional lineage-specific genes

Motivation: Supporting the functionality of recent duplicate gene copies is usually difficult, owing to high sequence similarity between duplicate counterparts and shallow phylogenies, which hamper both the statistical and experimental inference. Results: We developed an integrated evolutionary approach to identify functional duplicate gene copies and other lineage-specific genes. By repeatedly simulating neutral evolution, our method estimates the probability that an ORF was selectively conserved and is therefore likely to represent a bona fide coding region. In parallel, our method tests whether the accumulation of non-synonymous substitutions reveals signatures of selective constraint. We show that our approach has high power to identify functional lineage-specific genes using simulated and real data. For example, a coding region of average length (∼1400 bp), restricted to hominoids, can be predicted to be functional in ∼94-100% of cases. Notably, the method may support functionality for instances where classical selection tests based on the ratio of non-synonymous to synonymous substitutions fail to reveal signatures of selection. Our method is available as an automated tool, ReEVOLVER, which will also be useful to systematically detect functional lineage-specific genes of closely related species on a large scale. Availability: ReEVOLVER is available at . Contact: [email protected] Supplementary Data: Supplementary Data are available at Bioinformatics onlin

SSOR preconditioning in simulations of the QCD Schr\"odinger functional

We report on a parallelized implementation of SSOR preconditioning for O(a) improved lattice QCD with Schr\"odinger functional boundary conditions. Numerical simulations in the quenched approximation at parameters in the light quark mass region demonstrate that a performance gain of a factor $\sim$ 1.5 over even-odd preconditioning can be achieved.Comment: 15 pages, latex2e, 4 Postscript figures, uses packages elsart and epsfi