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2006
Springer

New Methods for Detecting Lineage-Specific Selection

10 years 11 months ago
New Methods for Detecting Lineage-Specific Selection
Abstract. So far, most methods for identifying sequences under selection based on comparative sequence data have either assumed selectional pressures are the same across all branches of a phylogeny, or have focused on changes in specific lineages of interest. Here, we introduce a more general method that detects sequences that have either come under selection, or begun to drift, on any lineage. The method is based on a phylogenetic hidden Markov model (phylo-HMM), and does not require element boundaries to be determined a priori, making it particularly useful for identifying noncoding sequences. Insertions and deletions (indels) are incorporated into the phylo-HMM by a simple strategy that uses a separately reconstructed "indel history." To evaluate the statistical significance of predictions, we introduce a novel method for computing P-values based on prior and posterior distributions of the number of substitutions that have occurred in the evolution of predicted elements. W...
Adam C. Siepel, Katherine S. Pollard, David Haussl
Added 03 Dec 2009
Updated 03 Dec 2009
Type Conference
Year 2006
Where RECOMB
Authors Adam C. Siepel, Katherine S. Pollard, David Haussler
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