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We inferred a maximum likelihood phylogeny for the primate simplex viruses using this g B data set (fig. Again, the phylogenetic relationships among the primate simplex viruses were well supported (approximate likelihood ratio test [a LRT] = 1.0). These findings suggest that t MRCAs obtained using a standard model are likely biased.

For example, humans are frequently infected by a macaque simplex virus (MHV-1, formerly known as B virus) (Elmore and Eberle 2008), resulting in severe illness, though human-to-human transmission is exceptionally rare (Centers for Disease Control and Prevention 1987). In the case of human herpes simplex viruses, molecular sequence dating could be used to identify which divergence event (i.e., HSV-1/Ch HV or HSV-2/Ch HV) corresponds to the speciation between around 6 Ma (Kumar et al. Previous dating analysis accompanying the discovery of Ch HV used pairwise genetic distance regression analysis to suggest that HSV-2 was the result of codivergence 6 Ma and that HSV-1 originated from an orangutan cross-species transmission event (fig. In contrast, our selection-informed model suggests a new explanation for the origin of human herpes simplex viruses, in which HSV-2 was acquired by an extinct species from an ancestor of modern chimpanzees.Because codon-substitution models that explicitly include variation in the strength of natural selection cannot be readily implemented in BEAST or similar packages, we employed a penalized likelihood framework (r8s) (Sanderson 2003) to apply a molecular clock using branch lengths previously estimated using BSREL.We calibrated the molecular clock using the same four internal node ages used in the BMCMC analysis.Herpesviruses have been infecting and codiverging with their vertebrate hosts for hundreds of millions of years.The primate simplex viruses exemplify this pattern of virus–host codivergence, at a minimum, as far back as the most recent common ancestor of New World monkeys, Old World monkeys, and apes.

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