MBE Advance Access published online on May 30, 2003
Molecular Biology and Evolution, doi:10.1093/molbev/msg149
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2003; all rights reserved
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1 Bioinformatics Research Center (BiRC), Department of Genetics and Ecology, The Institute of Biological Sciences, University of Aarhus, Building 550, Ny Munkegade, 8000 Århus C, Denmark
* To whom correspondence should be addressed. E-mail: forsberg{at}stats.ox.ac.uk.
Parasites sometimes expand their host range by acquiring a new host species. Following a host change event, the selective regime acting on a given parasite gene may change due to host-specific adaptive alterations of protein functionality or host-specific immune-mediated selection. We present a codon-based model that attempts to include these effects by allowing the position-specific substitution process to change in conjunction with a host change event. Following maximum-likelihood parameter estimation, we employ an empirical Bayesian procedure to identify candidate sites, potentially involved in host-specific adaptation. We discuss the applicability of the model to the more general problem of ascertaining whether the selective regime differs between two groups of related organisms. The utility of the model is illustrated on a dataset of nucleoprotein sequences from the influenza A virus obtained from avian and human hosts. Key Words:
host-specific adaptation, Influenza evolution, codon model
© 2003 Society for Molecular Biology and Evolution
Original Articles
A Codon-Based Model of Host-Specific Selection in Parasites, with an Application to the Influenza A Virus
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