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The statistical significance of the difference between KA and KS is calculated using a paired t-test.The strains used were as follows: for HTLV-Ia D00294, J02029, L03561, L33265, L36905, L46596, L46597, L46600L46603, L46608, L46610, L46615, L48560, L48561, M67490, M86840, M93098, U03134, UO3136, U03153, U03154, U81865, U81866, X88879 X88881, Y16488, Y16490 Y16497, Z28964; for HTLV-Ib 1 STLV-IL26586, L46613, L46614, L46616, L46618L46623, L46626, L46627, L46630, L46631, L46637, L46642, L46643, L46646, L48558, L48559, L76415, M67514, U03124, U03139, U03141, U03142, U03147, UO3148, X88882, X88884, X88885, Y17023.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.For ideal data, this is a tree, whereas less ideal data will give rise to a treelike network that can be interpreted as possible evidence for different and conflicting phylogenies.
Phylogenetic analysis of the LTR region was performed on a 510-nt fragment and separately on a 522nt fragment of the gp21 of the env region using all available known EMBL/Gen Bank database STLV-I strain sequences (33 strains for LTR and 45 strains for env). 1997), only a few strains of each subtype, representing the highest divergence within these subtypes, were chosen to illustrate their relationship to the simian strains.
Using the available strains, the HTLV-If subtype appears to have emerged within the last 3,000 years, and the HTLV-Ia, HTLV-Ib, HTLV-Id, and HTLV-Ie subtypes appear to have diverged between 21,100 and 5,300 years ago. 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 env analysis.
Interspecies transmissions, most probably simian to human, must have occurred around that time and probably continued later. To test the robustness of the NJ and mpars tree topologies, 1,000 bootstrap replicates were performed.
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 env gene, irrespective of the host species. The Gen Bank accession numbers for the LTR phylogenetic analysis were AF012728AF012730, AF035538AF035541, AF045929, AF045931 AF045933, AF054627, AF061438, AF061441, AF061837, AF061838, AF061840, AF061847 AF061849, D00294, D23693, D23694, J02029, L02534, L36905, L47128, L58023, L60024, L60026, L75787, L76032, L76033, L76306, L76307, L76309, L76310, L76312, M33063, M33064, M92845, U12806, U12807, U86376, Y13347, Y16475, Y16481, Y17014, Y17016, Y17017, Z32527, and Z46900.
Due to the small number of strains in some of the investigated groups, these data on selective pressure should be taken with caution. The Gen Bank accession numbers for the env phylogenetic analysis were AF035542AF035545, AF045928, D00294, J02029, L02534, L36905, L42250, L46624, L46627, L46628, L46630, L46641, L46645, L76414, M94195, U03122, U03124, U03126U03132, U03134, U03142, U03146 U03152, U03154, U03157U03160, U56855, U94516, X88882, Y13348, Y16486, Y16492, Y17021Y17023, Y19058Y19061, Z28966, and Z46900.