Tempo and mode of human and simian T-lymphotropic Virus (HTLV/STLV) evolution revealed by analyses of full-genome sequences

We investigated the tempo and mode of evolution of the primate T-lymphotrop ic viruses (PYLVs). Several different models of nucleotide substitution wer e tested on a general phylogenetic tree obtained using the 20 full-genome H TLV/STLV sequences available. The Likelihood ratio test showed that the Tam ura and Nei model with discrete gamma-distributed rates among sites is the best-fitting substitution model. The heterogeneity of nucleotide substituti on rates along the PTLV genome was further investigated for different genes and at different codon positions (cdp's). Tests of rate constancy showed t hat different PTLV lineages evolve at different rates when first and second cdp's are considered, but the molecular-clock hypothesis holds for some PT LV lineages when the third cdp is used. Negative selection was evident thro ughout the genome. However, in the gp36 region, a small fragment subjected to positive selection was identified using a Monte Carlo simulation based o n a likelihood method. Employing correlations of the virus divergence times with anthropologically documented migrations of their host, a possible tim escale was estimated for each important node of the PTLV tree. The obtained results on these slow-evolving viruses could be used to fill gaps in the h istorical records of some of the host species. In particular, the HTLV-I/ST LV-I history might suggest a simian migration from Asia to Africa not much earlier than 19,500-60,000 years ago.