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A Composite Genome Approach to Identify Phylogenetically Informative Data from Next-Generation Sequencing
"... A high quality dataset for phylogenetic analysis contains a maximum amount of information regarding evolutionary relationships and a minimal amount of noise. We have developed a novel approach for rapidly obtaining such data directly from next-generation sequencing reads without a reference genome. ..."
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A high quality dataset for phylogenetic analysis contains a maximum amount of information regarding evolutionary relationships and a minimal amount of noise. We have developed a novel approach for rapidly obtaining such data directly from next-generation sequencing reads without a reference genome. Using this approach, which we call SISRS (for Site Identification from Short Read Sequences), we avoid the time consuming steps of de novo assembly, genome-genome alignment, and annotation to identify potential phylogenetic markers. SISRS identifies data that are informative at specified taxonomic levels, eliminating homoplasious data that could cause error in phylogenetic estimates. For simulations, SISRS was able to identify large numbers of variable sites as long as the data contained phylogenetic signal. Over 97 % of these sites were true variants that allow the accurate recovery of the simulation tree. For empirical data from apes, SISRS identified thousands of variable sites, which resulted in an accurate estimate of the phylogeny. An easy-to-use software implementation of SISRS is available at
RH: IMPACTS OF TERRACES Impacts of terraces on phylogenetic inference
, 2014
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"... D ow nloaded from 2 Abstract: We describe new methods for characterizing gene tree discordance in phylogenomic datasets, which screen for deviations from neutral expectations, summarize variation in statistical support among gene trees, and allow comparison of the patterns of discordance induced by ..."
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D ow nloaded from 2 Abstract: We describe new methods for characterizing gene tree discordance in phylogenomic datasets, which screen for deviations from neutral expectations, summarize variation in statistical support among gene trees, and allow comparison of the patterns of discordance induced by various analysis choices. Using an exceptionally complete set of genome sequences for the short arm of chromosome 3 in Oryza (rice) species, we applied these methods to identify the causes and consequences of differing patterns of discordance in the sets of gene trees inferred using a panel of 20 distinct analysis pipelines. We found that discordance patterns were strongly affected by aspects of data selection, alignment, and alignment masking. Unusual patterns of discordance evident when using certain pipelines were reduced or eliminated by using alternative pipelines, suggesting that they were the product of methodological biases rather than evolutionary processes. In some cases, once such biases were eliminated, evolutionary processes such as
