Intragenic recombination and selection analyses were performed in DNA sequences of human alpha-papillomavirus. Recombination was estimated and the corresponding breakpoints obtained by re-analyzing data grouped by phylogenetic and epidemiological criteria, using different alignment methods. Diversifying or positive selection has been scarcely studied in these viruses probably due to the high divergence rates. We have applied maximum likelihood, empirical Bayesian and maximum parsimony methods to detect the presence of positive selection. Within the HPV 16 type, significant positive selection was detected at the time of the separation of the African 1 and African 2 branches from the other populations. At the inter-type level, positive selection can be traced in some codons of the gene L2 of the high and low risk groups. These results indicate that positive selection could have been important in the evolution of HPV both at inter- and intra-type levels.
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