Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA
Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA
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DOI：
10.1016/j.ympev.2004.06.015
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发表时间：
2004-11-01
影响因子：
4.1
通讯作者：
Swofford, DL
中科院分区：
文献类型：
--
作者：
Anderson, FE;Swofford, DL
虽然长分支吸引(LBA)经常被认为是异常系统发育分组的原因，但涉及真实序列数据的LBA例子很少。我们通过分析133个后生动物的18S rDNA序列的亚样本，发现了几个可能的LBA病例。在一个例子中，来自两个轮虫、一个鞭毛虫和一个多毛目环节动物的序列的最大简约分析导致了对由两个长枝分类群(一个轮虫和鞭毛虫)组成的树的强烈支持。对相同序列的最大似然分析为生物上更合理的“单株轮虫”树提供了强有力的支持。通过增加分类单元采样来分解有问题的亚样本的长分支的尝试减少了，但没有消除LBA问题。为了比较最大似然法、等权简约法和另外两种简约法的性能，对50个序列的子集的所有四位组进行了详尽的分析；这些方法在恢复树的失败率上确实有很大的不同，这些方法与已建立的、但高度未解决的系统发育一致。使用模拟进行的功率分析表明，最大简约的一些不正确的推断是由于统计上的不一致，并且当对某些四重奏的中心分支长度的估计非常低时，即使有大量数据，最大似然分析也很难恢复公认的系统发育。这些例子表明，LBA问题可能发生在真实的数据集中，它们提供了一个机会来调查不正确推断的原因。(C)2004 Elsevier Inc.保留所有权利。
Although long-branch attraction (LBA) is frequently cited as the cause of anomalous phylogenetic groupings, few examples of LBA involving real sequence data are known. We have found several cases of probable LBA by analyzing subsamples from an alignment of 18S rDNA sequences for 133 metazoans. In one example, maximum parsimony analysis of sequences from two rotifers, a ctenophore, and a polychaete annelid resulted in strong support for a tree grouping two "long-branch taxa" (a rotifer and the ctenophore). Maximum-likelihood analysis of the same sequences yielded strong support for a more biologically reasonable "rotifer monophyly" tree. Attempts to break up long branches for problematic subsamples through increased taxon sampling reduced, but did not eliminate, LBA problems. Exhaustive analyses of all quartets for a subset of 50 sequences were performed in order to compare the performance of maximum likelihood, equal-weights parsimony, and two additional variants of parsimony; these methods do differ substantially in their rates of failure to recover trees consistent with well established, but highly unresolved phylogenies. Power analyses using simulations suggest that some incorrect inferences by maximum parsimony are due to statistical inconsistency and that when estimates of central branch lengths for certain quartets are very low, maximum-likelihood analyses have difficulty recovering accepted phylogenies even with large amounts of data. These examples demonstrate that LBA problems can occur in real data sets, and they provide an opportunity to investigate causes of incorrect inferences. (C) 2004 Elsevier Inc. All rights reserved.