Molecular Biology and Evolution, Vol 14, 239-247, Copyright © 1997 by Society for Molecular Biology and Evolution
NC Grassly and EC Holmes
Different regions along nucleotide sequences are often subject to different
evolutionary forces. Recombination will result in regions having different
evolutionary histories, while selection can cause regions to evolve at
different rates. This paper presents a statistical method based on
likelihood for detecting such processes by identifying the regions which do
not fit with a single phylogenetic topology and nucleotide substitution
process along the entire sequence. Subsequent reanalysis of these anomalous
regions may then be possible. The method is tested using simulations, and
its application is demonstrated using the primate psi eta-globin
pseudogene, the V3 region of the envelope gene of HIV-1, and argF sequences
from Neisseria bacteria. Reanalysis of anomalous regions is shown to reveal
possible immune selection in HIV-1 and recombination in Neisseria. A
computer program which implements the method is available.
ORIGINAL ARTICLE
A likelihood method for the detection of selection and recombination using nucleotide sequences
Wellcome Trust Centre for the Epidemiology of Infectious Disease, Department of Zoology, University of Oxford, U.K. nicholas.grassly@zoo.ox.ac.uk
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