Kelsey C R, Crandall K A, Voevodin A F
Department of Zoology, Brigham Young University, Provo, Utah 84602-5255, USA.
Mol Phylogenet Evol. 1999 Nov;13(2):336-47. doi: 10.1006/mpev.1999.0663.
Using nucleotide sequences from three genomic regions of the human and simian T-cell lymphotropic virus type I (HTLV-I/STLV-I)-consisting of 69 sequences from a 140-bp segment of the pol region, 98 sequences from a 503-bp segment of the LTR, and 154 sequences from a 386-bp segment of the env region-we tested two hypotheses concerning the geographic origin and evolution of STLV-I and HTLV-I. First, we tested the assumption of equal rates of evolution along STLV-I and HTLV-I lineages using a likelihood ratio test to ascertain whether current levels of genomic diversity can be used to determine ancestry. We demonstrated that unequal rates of evolution along HTLV-I and STLV-I lineages have occurred throughout evolutionary time, thus calling into question the use of pairwise distances to assign ancestry. Second, we constructed phylogenetic trees using multiple phylogenetic techniques to test for the geographic origin of STLV-I and HTLV-I. Using the principle of likelihood, we chose a statistically justified model of evolution for each data set. We demonstrated the utility of the likelihood ratio test to determine which model of evolution should be chosen for phylogenetic analyses, revealing that using different models of evolution produces conflicting results, and neither the hypothesis of an African origin nor the hypothesis of an Asian origin can be rejected statistically. Our best estimates of phylogenetic relationships, however, support an African origin of PTLV for each gene region.
利用来自人类和猴T细胞嗜淋巴细胞病毒I型（HTLV-I/STLV-I）三个基因组区域的核苷酸序列——包括来自pol区域140 bp片段的69个序列、来自LTR 503 bp片段的98个序列以及来自env区域386 bp片段的154个序列——我们检验了关于STLV-I和HTLV-I地理起源及进化的两个假设。首先，我们使用似然比检验来确定当前基因组多样性水平是否可用于确定谱系，以此检验沿着STLV-I和HTLV-I谱系进化速率相等的假设。我们证明，在整个进化过程中，HTLV-I和STLV-I谱系的进化速率并不相等，因此对使用成对距离来确定谱系提出了质疑。其次，我们使用多种系统发育技术构建系统发育树，以检验STLV-I和HTLV-I的地理起源。根据似然原理，我们为每个数据集选择了一个统计学上合理的进化模型。我们证明了似然比检验在确定系统发育分析应选用哪种进化模型方面的效用，结果表明使用不同的进化模型会产生相互矛盾的结果，而且非洲起源假说和亚洲起源假说在统计学上都不能被拒绝。然而，我们对系统发育关系的最佳估计支持每个基因区域的PTLV起源于非洲。
