Positive Darwinian Selection at Single Amino Acid Sites Conferring Plant Virus Resistance |
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Authors: | J R Cavatorta A E Savage I Yeam S M Gray M M Jahn |
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Institution: | (1) Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA;(2) Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA;(3) United States Department of Agriculture-Agricultural Research Station (USDA-ARS), Department of Plant Pathology, Cornell University, Ithaca, NY, USA;(4) College of Agricultural and Life Sciences, University of Wisconsin, Madison, WI, USA |
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Abstract: | Explicit evaluation of the accuracy and power of maximum likelihood and Bayesian methods for detecting site-specific positive
Darwinian selection presents a challenge because selective consequences of single amino acid changes are generally unknown.
We exploited extensive molecular and functional characterization of amino acid substitutions in the plant gene eIF4E to evaluate the performance of these methods in detecting site-specific positive selection. We documented for the first time
a molecular signature of positive selection within a recessive resistance gene in plants. We then used two statistical platforms,
Phylogenetic Analysis Using Maximum Likelihood and Hypothesis Testing Using Phylogenies (HyPhy), to look for site-specific
positive selection. Their relative power and accuracy are assessed by comparing the sites they identify as being positively
selected with those of resistance-determining amino acids. Our results indicate that although both methods are surprisingly
accurate in their identification of resistance sites, HyPhy appears to more accurately identify biologically significant amino
acids using our data set.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.
J. R. Cavatorta and A. E. Savage have contributed equally to this work. |
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Keywords: | Disease resistance eIF4E Positive selection |
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