Department of Biology, 401 Widtsoe Building, Brigham Young University, Provo, UT 84602-5181, USA.
Mol Phylogenet Evol. 2012 Feb;62(2):777-92. doi: 10.1016/j.ympev.2011.11.019. Epub 2011 Nov 27.
Molecular phylogenetics has revolutionized the study of not only evolution but also disparate fields such as genomics, bioinformatics, epidemiology, ecology, microbiology, molecular biology and biochemistry. Particularly significant are its achievements in population genetics as a result of the development of coalescent theory, which have contributed to more accurate model-based parameter estimation and explicit hypothesis testing. The study of the evolution of many microorganisms, and HIV in particular, have benefited from these new methodologies. HIV is well suited for such sophisticated population analyses because of its large population sizes, short generation times, high substitution rates and relatively small genomes. All these factors make HIV an ideal and fascinating model to study molecular evolution in real time. Here we review the significant advances made in HIV evolution through the application of phylogenetic approaches. We first examine the relative roles of mutation and recombination on the molecular evolution of HIV and its adaptive response to drug therapy and tissue allocation. We then review some of the fundamental questions in HIV evolution in relation to its origin and diversification and describe some of the insights gained using phylogenies. Finally, we show how phylogenetic analysis has advanced our knowledge of HIV dynamics (i.e., phylodynamics).
分子系统发生学不仅彻底改变了进化的研究，还对基因组学、生物信息学、流行病学、生态学、微生物学、分子生物学和生物化学等不同领域产生了深远影响。由于合并理论的发展，它在群体遗传学方面取得了特别重要的成就，这有助于更准确的基于模型的参数估计和明确的假设检验。这些新方法促进了许多微生物，特别是 HIV 的进化研究。由于 HIV 具有庞大的种群数量、较短的世代时间、高替换率和相对较小的基因组，因此非常适合进行这种复杂的群体分析。所有这些因素使得 HIV 成为实时研究分子进化的理想而引人入胜的模型。在这里，我们通过应用系统发生方法来回顾 HIV 进化方面的重大进展。我们首先研究了突变和重组在 HIV 的分子进化及其对药物治疗和组织分配的适应性反应中的相对作用。然后，我们回顾了与 HIV 起源和多样化相关的一些 HIV 进化的基本问题，并描述了使用系统发育树获得的一些见解。最后，我们展示了系统发生分析如何提高我们对 HIV 动力学（即系统发生动力学）的认识。
