From gene-scale to genome-scale phylogenetics: the data flood in, but the challenges remain.
From gene-scale to genome-scale phylogenetics: the data flood in, but the challenges remain.
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DOI：
10.1007/978-1-59745-581-7_1
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发表时间：
2008
影响因子：
--
通讯作者：
A. Rokas;S. Chatzimanolis
中科院分区：
文献类型：
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作者：
A. Rokas;S. Chatzimanolis
植物遗传学的一个重要目标是能够一致和准确地重建主要器官组之间的分支发生的历史模式。由于单基因和少基因遗传学的分辨率差和不一致性，基因尺度遗传学不足以实现这一目标。越来越多的基因组规模数据的可用性有望克服基因规模遗传学的不足，并以前所未有的准确性揭示所有生物体的谱系挂毯。在这里，我们认为，一个巨大的增加，数据大小单独的，虽然必要的，可能不足以达到预期的准确性有三个原因：（一）存在短茎的生命树，（二）饱和的分子序列中的系统发育信号，和（三）系统发育推断的系统误差的影响。设计策略来改善这些挑战对序列进化的影响，对于目前重建生命之树的努力取得成功至关重要。
An important goal of phylogenetics is to be able to consistently and accurately reconstruct the historical patterns of cladogenesis among major organismic groups. Gene-scale phylogenetics is insufficient to attain this goal owing to the presence of poor resolution and incongruence in single- and few-gene phylogenies. The increasing availability of genomescale amounts of data promises to overcome the insufficiency of gene-scale phylogenetics and uncover the genealogical tapestry uniting all living organisms with unprecedented accuracy. Here, we argue that a vast increase in data size alone—although necessary—may not be sufficient to achieve the desired accuracy for three reasons: (i) the existence of short stems in the tree of life, (ii) the saturation of phylogenetic signal in molecular sequences, and (iii) the effect of systematic error on phylogenetic inference. Devising strategies to ameliorate the effect of such challenges on sequence evolution will be critical to the success of current efforts to reconstruct the tree of life.