ZPS: visualization of recent adaptive evolution of proteins.
ZPS: visualization of recent adaptive evolution of proteins.
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DOI：
10.1186/1471-2105-8-187
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发表时间：
2007-06-07
影响因子：
3
通讯作者：
Sokurenko EV
中科院分区：
文献类型：
--
作者：
Chattopadhyay S;Dykhuizen DE;Sokurenko EV
在最近的短期选择下检测蛋白质的适应性氨基酸变化对于研究微生物病原体或任何其他生物物种的微进化过程的研究人员来说非常感兴趣。然而，此类点突变在遗传多样性单倍型中的独立发生使得很难通过使用传统的分子进化分析来检测选择足迹。最近开发的区域系统发育（ZP）已被证明是识别短期正选择足迹的有用分析工具。 ZP 将蛋白质编码基因分为进化长期（具有沉默多样性）和短期（无沉默多样性）类别或区域，然后进行统计分析以检测短期区域中正选择的迹象。然而，成功地广泛应用 ZP 来分析大型单倍型数据集需要相对劳动密集型的计算过程的自动化。在这里，我们介绍了区域系统发育软件 (ZPS)，该应用程序描述了任何给定蛋白质编码基因座的同义（沉默）和非同义（替换）性质的单核苷酸多态性 (SNP) 沿着 DNA 树分支的分布。基于此信息，ZPS 将具有沉默变异性的蛋白质变体单倍型（主要区域）与最近通过氨基酸变化从主要区域变体进化而来的蛋白质变体单倍型（外部区域）分开。对两个区域之间的突变热点频率和单倍型多样性的进一步比较分析可以确定外部区域单倍型是否在正选择下出现。作为一种可视化工具，ZPS 描绘了 DNA 树中的蛋白质树，指示基于最大似然的 DNA 树的分支上同义和非同义变化的最简约数量，以及有关同质性、回复和结构突变热点的信息。通过区带分化，ZPS 允许通过选择有利的结构突变来检测最近的适应性进化，即使这些突变赋予的优势相对短期（如“源-库”进化动力学的情况，这可能代表微生物毒力进化的主要模式）。
Detection of adaptive amino acid changes in proteins under recent short-term selection is of great interest for researchers studying microevolutionary processes in microbial pathogens or any other biological species. However, independent occurrence of such point mutations within genetically diverse haplotypes makes it difficult to detect the selection footprint by using traditional molecular evolutionary analyses. The recently developed Zonal Phylogeny (ZP) has been shown to be a useful analytic tool for identifying the footprints of short-term positive selection. ZP separates protein-encoding genes into evolutionarily long-term (with silent diversity) and short-term (without silent diversity) categories, or zones, followed by statistical analysis to detect signs of positive selection in the short-term zone. However, successful broad application of ZP for analysis of large haplotype datasets requires automation of the relatively labor-intensive computational process. Here we present Zonal Phylogeny Software (ZPS), an application that describes the distribution of single nucleotide polymorphisms (SNPs) of synonymous (silent) and non-synonymous (replacement) nature along branches of the DNA tree for any given protein-coding gene locus. Based on this information, ZPS separates the protein variant haplotypes with silent variability (Primary zone) from those that have recently evolved from the Primary zone variants by amino acid changes (External zone). Further comparative analysis of mutational hot-spot frequencies and haplotype diversity between the two zones allows determination of whether the External zone haplotypes emerged under positive selection. As a visualization tool, ZPS depicts the protein tree in a DNA tree, indicating the most parsimonious numbers of synonymous and non-synonymous changes along the branches of a maximum-likelihood based DNA tree, along with information on homoplasy, reversion and structural mutation hot-spots. Through zonal differentiation, ZPS allows detection of recent adaptive evolution via selection of advantageous structural mutations, even when the advantage conferred by such mutations is relatively short-term (as in the case of "source-sink" evolutionary dynamics, which may represent a major mode of virulence evolution in microbes).
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影响因子：
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作者：
Voight BF;Kudaravalli S;Wen X;Pritchard JK
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影响因子：
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作者：
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通讯作者：
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