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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.
The separation between the Asian-Austronesian and the African strains was well supported in all analyses (NJ and mpars bootstrap values of This clade further clusters within a large group of STLV-I strains from different simian species and genera originating from Congo, Kenya, Tanzania, and South Africa.
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. In contrast, there appears to have been a more recent introduction of the PTLV-I virus on the African continent, followed by a spread of this virus, leading to different subtypes. 1994, 1997 ); the Central African subtypes HTLV-Ib (Hahn et al. The separate and deep-branching pattern of the Australo- Melanesian HTLV-Ic strains and the Asian STLV-I strains more or less according to host genus probably indicates that these strains have undergone a long, independent evolution in their host over a long period.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.