Rodrigo A G, Mullins J I
Department of Microbiology, University of Washington, Seattle 98195-7740, USA.
AIDS Res Hum Retroviruses. 1996 Dec 10;12(18):1681-5. doi: 10.1089/aid.1996.12.1681.
Human immunodeficiency virus (HIV) envelope genes are highly variable between and often within individuals. Part of this variability is thought to be the result of immune-mediated positive selection for sequence diversity. To measure positive selection it has become customary in HIV research to calculate the ratio of the proportions of synonymous (ds) and nonsynonymous (dn) substitutions per potential synonymous or nonsynonymous site, respectively. However, another measure that can be used is the difference between ds and dn, delta d. We show, by example, that using the ratio, ds/dn, or the difference, delta d, may lead us to different conclusions regarding the existence of positive selection pressure. We conclude by noting that until we understand the processes that mediate nucleotide variation in a host selective environment, inferences based on summary statistics characterizing types of nucleotide substitutions should be made with caution.
人类免疫缺陷病毒（HIV）包膜基因在个体之间以及个体内部通常具有高度变异性。这种变异性的一部分被认为是免疫介导的序列多样性正向选择的结果。为了衡量正向选择，在HIV研究中，习惯上分别计算每个潜在同义或非同义位点的同义（ds）和非同义（dn）替换比例的比值。然而，另一种可用的衡量方法是ds和dn之间的差异，即Δd。我们通过实例表明，使用比值ds/dn或差异Δd，可能会使我们在正向选择压力的存在问题上得出不同的结论。我们最后指出，在我们了解宿主选择环境中介导核苷酸变异的过程之前，基于表征核苷酸替换类型的汇总统计数据进行的推断应谨慎进行。
