Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent
Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent
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DOI：
10.1016/j.tpb.2014.12.005
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发表时间：
2015-03-01
影响因子：
1.4
通讯作者：
Steel, Mike
中科院分区：
文献类型：
--
作者：
Roch, Sebastien;Steel, Mike
从基因组数据重建物种树面临着双重障碍。首先，描述每个基因进化的（基因）树可能与物种树不同，例如，由于不完整的谱系排序。第二，在每个基因树的叶子处的比对的基因序列仅提供基因树的拓扑的不完美估计。在本说明中，我们正式证明，一个基本的统计问题出现，如果试图避免占这两个过程，并直接通过级联方法分析遗传数据。更确切地说，我们表明，在多物种合并与标准的网站替代模型，最大似然估计序列数据，已连接跨基因和不正确的假设下，所有网站都独立地发展和相同的固定树是一个统计不一致的估计物种树。我们的结果为Kubatko和Degnan（2007）等人描述的模拟结果提供了正式的证明，并补充了DeGlorgio和Degnan（2010）以及Chifman和Kubtako（2014）的最新理论结果。(C)2014爱思唯尔公司All rights reserved.
The reconstruction of a species tree from genomic data faces a double hurdle. First, the (gene) tree describing the evolution of each gene may differ from the species tree, for instance, due to incomplete lineage sorting. Second, the aligned genetic sequences at the leaves of each gene tree provide merely an imperfect estimate of the topology of the gene tree. In this note, we demonstrate formally that a basic statistical problem arises if one tries to avoid accounting for these two processes and analyses the genetic data directly via a concatenation approach. More precisely, we show that, under the multispecies coalescent with a standard site substitution model, maximum likelihood estimation on sequence data that has been concatenated across genes and performed under the incorrect assumption that all sites have evolved independently and identically on a fixed tree is a statistically inconsistent estimator of the species tree. Our results provide a formal justification of simulation results described of Kubatko and Degnan (2007) and others, and complements recent theoretical results by DeGlorgio and Degnan (2010) and Chifman and Kubtako (2014). (C) 2014 Elsevier Inc. All rights reserved.