Median networks: Speedy construction and greedy reduction, one simulation, and two case studies from human mtDNA
Median networks: Speedy construction and greedy reduction, one simulation, and two case studies from human mtDNA
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DOI：
10.1006/mpev.2000.0792
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发表时间：
2000-07-01
影响因子：
4.1
通讯作者：
Richards, M
中科院分区：
文献类型：
--
作者：
Bandelt, HJ;Macaulay, V;Richards, M
分子数据集具有很少的系统发育信息特征，具有广泛的突变率，例如人类线粒体DNA(MtDNA)的种内控制区序列变异，可以有效地以中间网络的形式进行可视化。在这里，我们提供了手动构建此类网络的逐步指南。我们通过概述一种适用于大数据集的有效的参数化策略贪婪缩减来改进以前实现的算法，这使得重建一些混杂的重复突变成为可能。这还需要一些后处理，这有助于捕获更简约的解决方案。为了简化手工创建的网络，我们描述了一种快速的网络构建方法，基于对处理顺序的仔细规划，为欧亚大陆的人类mtDNA变异量身定做的联合模拟证明了简化的中位网络的有效性，同时强调了所有系统发育方法在这方面面临的臭名昭著的问题。最后，我们结合世界范围的控制区序列数据库和额外的限制性片段长度多态信息，讨论了两个案例研究，涉及人类mtDNA控制区的两个高变区的特征比较。我们的结论是，只有少数攻击第二片段的突变发生在突变频率与第一片段中大多数位点相当的位点上。去掉第二部分中已知的“嘈杂”位置会增强分析效果。(C)2000年学术出版社。
Molecular data sets characterized by few phylogenetically informative characters with a broad spectrum of mutation rates, such as intraspecific control-region sequence variation of human mitochondrial DNA (mtDNA), can be usefully visualized in the form of median networks, Here we provide a step-by-step guide to the construction of such networks by hand, We improve upon a previously implemented algorithm by outlining an efficient parametrized strategy amenable to large data sets, greedy reduction, which makes it possible to reconstruct some of the confounding recurrent mutations. This entails some postprocessing as well, which assists in capturing more parsimonious solutions. To simplify the creation of the resulting network by hand, we describe a speedy approach to network construction, based on a careful planning of the processing order, A coalescent simulation tailored to human mtDNA variation in Eurasia testifies to the usefulness of reduced median networks, while highlighting notorious problems faced by all phylogenetic methods in this context. Finally, we discuss two case studies involving the comparison of characters in the two hypervariable segments of the human mtDNA control region in the light of the worldwide control-region sequence database, as well as additional restriction fragment length polymorphism information. We conclude that only a minority of the mutations that hit the second segment occur at sites that would have a mutation rate comparable to those at most sites in the first segment. Discarding the known "noisy" sites of the second segment enhances the analysis. (C) 2000 Academic Press.