Salemi M, Desmyter J, Vandamme A M
Rega Institute for Medical Research, KULeuven, Belgium.
Mol Biol Evol. 2000 Mar;17(3):374-86. doi: 10.1093/oxfordjournals.molbev.a026317.
We investigated the tempo and mode of evolution of the primate T-lymphotropic viruses (PTLVs). Several different models of nucleotide substitution were tested on a general phylogenetic tree obtained using the 20 full-genome HTLV/STLV sequences available. The likelihood ratio test showed that the Tamura and Nei model with discrete gamma-distributed rates among sites is the best-fitting substitution model. The heterogeneity of nucleotide substitution rates along the PTLV genome was further investigated for different genes and at different codon positions (cdp's). Tests of rate constancy showed that different PTLV lineages evolve at different rates when first and second cdp's are considered, but the molecular-clock hypothesis holds for some PTLV lineages when the third cdp is used. Negative selection was evident throughout the genome. However, in the gp46 region, a small fragment subjected to positive selection was identified using a Monte Carlo simulation based on a likelihood method. Employing correlations of the virus divergence times with anthropologically documented migrations of their host, a possible timescale was estimated for each important node of the PTLV tree. The obtained results on these slow-evolving viruses could be used to fill gaps in the historical records of some of the host species. In particular, the HTLV-I/STLV-I history might suggest a simian migration from Asia to Africa not much earlier than 19,500-60,000 years ago.
我们研究了灵长类嗜T淋巴细胞病毒（PTLVs）的进化速度和模式。在使用可得的20个全基因组HTLV/STLV序列构建的一般系统发育树上，测试了几种不同的核苷酸替换模型。似然比检验表明，位点间具有离散伽马分布速率的Tamura和Nei模型是最适合的替换模型。针对不同基因和不同密码子位置（cdp's），进一步研究了PTLV基因组核苷酸替换率的异质性。速率恒定性检验表明，当考虑第一和第二cdp时，不同的PTLV谱系以不同速率进化，但当使用第三cdp时，分子钟假说对某些PTLV谱系成立。整个基因组都存在负选择。然而，在gp46区域，使用基于似然法的蒙特卡罗模拟，鉴定出一个受到正选择的小片段。利用病毒分化时间与宿主经人类学记录的迁徙之间的相关性，估计了PTLV树每个重要节点的可能时间尺度。关于这些进化缓慢的病毒所获得的结果，可用于填补某些宿主物种历史记录中的空白。特别是，HTLV-I/STLV-I的历史可能表明，猿类从亚洲向非洲的迁徙不会早于19,500 - 60,000年前。
