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Virtually all Old World monkey species from the Cercopithecinae subfamily (Macaca, Cercopithecus, Papio, Mandrillus, Cercocebus and Erythrocebus) and from the Pongidae family () harbor STLV-I (Lee et al. The split decomposition method is a transformation-based approach.

HTLV-I clusters are interspersed with STLV- I strains from different species, suggesting that species and genus barriers have been repeatedly crossed, at least once for each human subtype (Vandamme, Salemi, and Desmyter 1998 ). 1998 ; Vandamme, Salemi, and Desmyter 1998 ) must have occurred in the past and are likely still ongoing.

However, when the LTR data set was combined with only the third codon position (3rdcp) of the gp21 revealed no statistical difference in the estimates of the branch lengths (data not shown).

When the latter data set was tested for substitution saturation using Dambe (Xia 2000 ), it was clear that no saturation could be observed when transitions and transversions were plotted versus evolutionary distance (fig. The plot shows that transitions and transversions increase linearly with increasing divergence between different PTLV strains.

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.

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Transitions and transversions are then scored after applying Kimura's two-parameter method to correct for multiple hits.The presence of purifying selection is assumed when the -test.The strains used were as follows: for HTLV-Ia— D00294, J02029, L03561, L33265, L36905, L46596, L46597, L46600–L46603, L46608, L46610, L46615, L48560, L48561, M67490, M86840, M93098, U03134, UO3136, U03153, U03154, U81865, U81866, X88879– X88881, Y16488, Y16490–Y16497, Z28964; for HTLV-Ib STLV-I—L26586, L46613, L46614, L46616, L46618–L46623, L46626, L46627, L46630, L46631, L46637, L46642, L46643, L46646, L48558, L48559, L76415, M67514, U03124, U03139, U03141, U03142, U03147, UO3148, X88882, X88884, X88885, Y17023. According to previously published phylogenetic data, the HTLV-I strains can be classified into six different subtypes: the cosmopolitan HTLV-Ia subtype (Miura et al. The only clear separation within the trees inferred from these sequences is found between the African (including the cosmopolitan subtype HTLV-Ia) PTLV-I strains and the Asian-Austronesian strains.

1998 ); and the Australo-Melanesian subtype HTLV-Ic (Gessain et al. In every genetic region studied, STLV-I and HTLV-I strains from the same geographic origin show a closer phylogenetic relationship than do PTLV-I strains from the same primate species.

ML trees generated in PAUP*, version 4.0b4a (Swofford 1998 ), were used in PAML, version 3.0 (Yang 1997 ), to reconstruct the ancestral sequences at the internal nodes of the tree with Base ML.

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