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. 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.Due to the small number of strains in some of the investigated groups, these data on selective pressure should be taken with caution. If you do not see its contents the file may be temporarily unavailable at the journal website or you do not have a PDF plug-in installed and enabled in your browser. Vandamme 0 1 0 me, Rega Institute for Medical Research, Kotholieke Universiteit Leu- ven , Minderbroedersstraat 10, B-3000 Leuven , Belgium 1 Rega Institute for Medical Research, Kotholieke Universiteit Leuven , Leuven , Belgium To investigate the origin of the African PTLV-I virus, we phylogenetically analyzed the available HTLV-I and STLV-I strains. 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.for HTLV-Id 1 STLV-IAF04931, L46624, L46644, L46645, L76414, Y19060, Y19061.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.Molecular-Clock Analysis The molecular-clock hypothesis, assuming a constant rate of evolution, was tested on the LTR-env data set in Puzzle, version 4.0 (Strimmer and von Haeseler 1997), as previously described (Van Dooren et al. The most appropriate substitution model for HTLV-I, the Tamura-Nei substitution model with a gamma distributed rate heterogeneity (Salemi, Desmyter, and Vandamme 2000), was used.Test for Purifying Versus Positive Selection 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.Alternatively, you can download the file locally and open with any standalone PDF reader: https://mbe.oxfordjournals.org/content/18/4/661pdf S. We also attempted to date the presumed interspecies transmissions that resulted in the African HTLV-I subtypes. HTLV-I clusters are interspersed with STLVI 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.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 env third-codon-position sequences. Considering the evolutionary inferences, based on these phylogenetic studies, several transmission events between primate genera (Macaca and Papio, Cercopithecus and Papio) and primate families (human and simian, Cercopithecus and Pan troglodytes) (Koralnik et al. In this study, we succeeded in estimating a time frame for the origin of the African HTLV-I subtypes and of the presumed interspecies transmissions that most probably occurred at the origin of these subtypes based on the currently known HTLV-I and STLV-I sequences.
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.All other Central African human strains clustered between and together with African simian strains in four different human subtypes. tree with PAML using a variant of the Tamura-Nei model allowing for different parameters in the LTR and env revealed no statistical difference in the estimates of the branch lengths (data not shown).In addition, several simian clades had no human representative. 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.