Phylogenomics and molecular evolution of polyomaviruses.
Phylogenomics and molecular evolution of polyomaviruses.
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多瘤病毒的系统基因组学和分子进化。
DOI：
10.1007/0-387-32957-9_3
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发表时间：
2006
影响因子：
--
通讯作者：
Viscidi,RaphaelP
中科院分区：
文献类型：
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作者：
Crandall,KeithA;Pérez-Losada,Marcos;Christensen,RyanG;McClellan,DavidA;Viscidi,RaphaelP
在本章中，我们概述了通过标准的系统发育估计方法重建进化关系的基本步骤，以及对更密切相关的序列的网络方法。我们讨论了序列比对、选择进化模型和置信度评估在系统发育推断中的重要性。我们还向读者介绍了用于此类研究的各种软件包。最后，我们通过使用33个多瘤病毒全基因组的数据集来证明这些方法。利用贝叶斯和最大似然方法估计了这些基因组的强大系统发育，并确定了多瘤病毒之间的系统发育关系。此外，使用SV40的总体样本来证明网络方法对密切相关序列的效用。系统发育分析表明，BK病毒、JC病毒和SV40的亲缘关系较近，与小鼠多瘤病毒、猴多瘤病毒和禽多瘤病毒的亲缘关系较远。
We provide in this chapter an overview of the basic steps to reconstruct evolutionary relationships through standard phylogeny estimation approaches as well as network approaches for sequences more closely related. We discuss the importance of sequence alignment, selecting models of evolution, and confidence assessment in phylogenetic inference. We also introduce the reader to a variety of software packages used for such studies. Finally, we demonstrate these approaches throughout using a data set of 33 whole genomes of polyomaviruses. A robust phylogeny of these genomes is estimated and phylogenetic relationships among the polyomaviruses determined using Bayesian and maximum likelihood approaches. Furthermore, population samples of SV40 are used to demonstrate the utility of network approaches for closely related sequences. The phylogenetic analysis suggested a close relationship among the BK viruses, JC viruses, and SV40 with a more distant association with mouse polyomavirus, monkey polymavirus (LPV) and then avian polyomavirus (BFDV).