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Copyright 2003 by the Genetics Society of America Effect of Recombination on the Accuracy of the Likelihood Method for Detecting
 

Summary: Copyright 2003 by the Genetics Society of America
Effect of Recombination on the Accuracy of the Likelihood Method for Detecting
Positive Selection at Amino Acid Sites
Maria Anisimova,*,,1
Rasmus Nielsen
and Ziheng Yang*
*Department of Biology, University College London, London WC1E 6BT, United Kingdom,
Center for Mathematics and Physics in the Life
Sciences and Experimental Biology (CoMPLEX), University College London, London WC1E 6BT, United Kingdom and
Department of
Biometrics, Cornell University, Ithaca, New York 14853-7801
Manuscript received July 30, 2002
Accepted for publication March 31, 2003
ABSTRACT
Maximum-likelihood methods based on models of codon substitution accounting for heterogeneous
selective pressures across sites have proved to be powerful in detecting positive selection in protein-coding
DNA sequences. Those methods are phylogeny based and do not account for the effects of recombination.
When recombination occurs, such as in population data, no unique tree topology can describe the
evolutionary history of the whole sequence. This violation of assumptions raises serious concerns about
the likelihood method for detecting positive selection. Here we use computer simulation to evaluate the

  

Source: Anisimova, Maria - Institute of Scientific Computing, Eidgenössische Technische Hochschule Zürich (ETHZ)
Yang, Ziheng - Department of Genetics, Evolution and Environment, University College London

 

Collections: Biology and Medicine; Environmental Sciences and Ecology