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Evaluation of an Improved Branch Site Likelihood Method for Detecting Positive Selection at the Molecular Level Jianzhi Zhang Rasmus Nielsen and Ziheng Yang Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor Centre for Bioinformatics University of Copenhagen Denmark Department of Biology University College London London United Kingdom Detecting positive Darwinian selection at the DNA sequence level has been a subject of considerable interest However positive selection is difficult to detect because it often operates episodically on a few amino acid sites and the signal may be masked by negative selection Several methods have been developed to test positive selection that acts on given branches branch methods or on a subset of sites site methods Recently Yang Z and R Nielsen 2002 Codon substitution models for detecting molecular adaptation at individual sites along specific lineages Mol Biol Evol 19 908 917 developed likelihood ratio tests LRTs based on branch site models to detect positive selection that affects a small number of sites along prespecified lineages However computer simulations suggested that the tests were sensitive to the model assumptions and were unable to distinguish between relaxation of selective constraint and positive selection Zhang J 2004 Frequent false detection of positive selection by the likelihood method with branch site models Mol Biol Evol 21 1332 1339 Here we describe a modified branch site model and use it to construct two LRTs called branch site tests 1 and 2 We applied the new tests to reanalyze several real data sets and used computer simulation to examine the performance of the two tests by examining their false positive rate power and robustness We found that test 1 was unable to distinguish relaxed constraint from positive selection affecting the lineages of interest while test 2 had acceptable falsepositive rates and appeared robust against violations of model assumptions As test 2 is a direct



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