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Most of these HTLV-I strains are phylogenetically indistinguishable from STLV-I strains.
Evolutionary data are transformed, or, more precisely, “canonically decomposed,” into a sum of “weakly compatible splits” and then represented by a so-called splits graph.
Since transitions occur much more often than transversions, transitions should increase faster than transversions.
In the case of substitution saturation, when multiple substitutions have occurred at each site, the phylogenetic signal is essentially lost and its effect is detectable because transversions gradually outnumber transitions.
Interspecies transmissions, most probably simian to human, must have occurred around that time and probably continued later. The Gen Bank accession numbers for the phylogenetic analysis were AF035542–AF035545, AF045928, D00294, J02029, L02534, L36905, L42250, L46624, L46627, L46628, L46630, L46641, L46645, L76414, M94195, U03122, U03124, U03126–U03132, U03134, U03142, U03146– U03152, U03154, U03157–U03160, U56855, U94516, X88882, Y13348, Y16486, Y16492, Y17021–Y17023, Y19058–Y19061, Z28966, and Z46900.
When the synonymous and nonsynonymous substitution ratios were compared, it was clear that purifying selection was the driving force for PTLV-I evolution in the The human and simian T-cell lymphotropic viruses type I (HTLV-I and STLV-I, respectively) share numerous epidemiological, molecular, phylogenetic, and geographical features and are therefore referred to as primate T-cell lymphotropic viruses type I (PTLV-I). The program Splits Tree, version 2.3f (Huson 1998 ), was used to generate splits graphs for the LTR- (third-codon-position) data set composed for the molecular-clock analysis.
We also attempted to date the presumed interspecies transmissions that resulted in the African HTLV-I subtypes. Since African STLV-I strains have been found to cluster tightly with African HTLV-I subtypes, except for HTLV- Ia, we were able to investigate the possible selective pressure due to intra- and interspecies transmission using synonymous versus nonsynonymous substitution ratios.The topologies of the phylogenetic trees generated by three different methods (NJ, mpars, and ML) were very similar, although the internal branching pattern within some well-defined clusters remained ambiguous.Figures 1 and 2 show the NJ tree of the LTR and regions, respectively, with bootstrap support for the NJ and mpars trees noted on the branches.Molecular-clock analysis was performed using the Tamura-Nei substitution model and gamma distributed rate heterogeneity based on the maximum-likelihood topology of the combined long-terminal-repeat and third-codon-position sequences. Phylogenetic trees were generated from the multiple alignments (made in Geneworks 2.5.1, Oxford Molecular Systems, United Kingdom) of the long-terminal- repeat (LTR) and regions separately, using neighbor- joining (NJ), maximum-parsimony (mpars), and maximum-likelihood (ML) (under the Tamura-Nei substitution model) methods implemented in the software package PAUP*, version 4.0b4a (Swofford 1998 ).Since the molecular clock was not rejected and no evidence for saturation was found, a constant rate of evolution at these positions for all 33 HTLV-I and STLV-I strains was reasonably assumed. PTLV-I has been associated with both malignant lymphoma and leukemia in humans (Yoshida, Miyoshi, and Hinuma 1982 ) and nonhuman primates (Miyoshi et al. The transition/transversion ratios used were scored using Puzzle, version 4.0 (Strimmer and von Haeseler 1997 ): 4.44 for the LTR alignment and 5.57 for the analysis.
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Since the cosmopolitan HTLV-Ia and the Central African HTLV-Ib are well-established subtypes with good phylogenetic support (Liu et al. All available strains of the other African HTLV-I subtypes (21 HTLV-I strains in total) were also included.