Walsh David A, Sharma Adrian K
Department of Biochemistry and Molecular Biology, Dalhousie University, Nova Scotia, Canada.
Methods Mol Biol. 2009;502:131-68. doi: 10.1007/978-1-60327-565-1_9.
A common approach for investigating evolutionary relationships between genes and organisms is to compare extant DNA or protein sequences and infer an evolutionary tree. This methodology is known as molecular phylogenetics and may be the most informative means for exploring phage evolution, since there are few morphological features that can be used to differentiate between these tiny biological entities. In addition, phage genomes can be mosaic, meaning different genes or genomic regions can exhibit conflicting evolutionary histories due to lateral gene transfer or homologous recombination between different phage genomes. Molecular phylogenetics can be used to identify and study such genome mosaicism. This chapter provides a general introduction to the theory and methodology used to reconstruct phylogenetic relationships from molecular data. Also included is a discussion on how the evolutionary history of different genes within the same set of genomes can be compared, using a collection of T4-type phage genomes as an example. A compilation of programs and packages that are available for conducting phylogenetic analyses is supplied as an accompanying appendix.
研究基因与生物体之间进化关系的一种常见方法是比较现存的DNA或蛋白质序列，并推断出进化树。这种方法被称为分子系统发育学，它可能是探索噬菌体进化最具信息量的手段，因为几乎没有形态特征可用于区分这些微小的生物实体。此外，噬菌体基因组可能是镶嵌的，这意味着由于不同噬菌体基因组之间的横向基因转移或同源重组，不同的基因或基因组区域可能呈现出相互冲突的进化历史。分子系统发育学可用于识别和研究这种基因组镶嵌现象。本章对用于从分子数据重建系统发育关系的理论和方法进行了一般性介绍。还讨论了如何以一组T4型噬菌体基因组为例，比较同一基因组集合中不同基因的进化历史。附录中提供了可用于进行系统发育分析的程序和软件包汇编。
