A LIKELIHOOD METHOD FOR THE DETECTION OF SELECTION AND RECOMBINATION USING NUCLEOTIDE-SEQUENCES

Different regions along nucleotide sequences are often subject to diff erent evolutionary forces. Recombination will result in regions having different evolutionary histories, while selection can cause regions t o evolve at different rates. This paper presents a statistical method based on likelihood for detecting such processes by identifying the re gions which do not fit with a single phylogenetic topology and nucleot ide substitution process along the entire sequence. Subsequent reanaly sis of these anomalous regions may then be possible. The method is tes ted using simulations, and its application is demonstrated using the p rimate psi eta-globin pseudogene, the V3 region of the envelope gene o f HIV-1, and argF sequences from Neisseria bacteria. Reanalysis of ano malous regions is shown to reveal possible immune selection in HIV-1 a nd recombination in Neisseria. A computer program which implements the method is available.