The node-density effect is an artifact of phylogeny reconstruction that can cause branch lengths to be underestimated in areas of the tree with fewer taxa. Webster, Payne, and Pagel (2003, Science 301:478) introduced a statistical procedure (the "delta" test) to detect this artifact, and here we report the results of computer simulations that examine the test's performance. In a sample of 50,000 random data sets, we find that the delta test detects the artifact in 94.4% of cases in which it is present. When the artifact is not present (n = 10,000 simulated data sets) the test showed a type I error rate of approximately 1.69%, incorrectly reporting the artifact in 169 data sets. Three measures of tree shape or "balance" failed to predict the size of the node-density effect. This may reflect the relative homogeneity of our randomly generated topologies, but emphasizes that nearly any topology can suffer from the artifact, the effect not being confined only to highly unevenly sampled or otherwise imbalanced trees. The ability to screen phylogenies for the node-density artifact is important for phylogenetic inference and for researchers using phylogenetic trees to infer evolutionary processes, including their use in molecular clock dating.

中文翻译：

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检测系统发育重建中的节点密度伪影

节点密度效应是系统发育重建的人工产物，它可能导致树中分类群较少的区域的分支长度被低估。Webster、Payne 和 Pagel (2003, Science 301:478) 引入了一种统计程序（“delta”测试）来检测这种伪影，在这里我们报告了检查测试性能的计算机模拟结果。在 50,000 个随机数据集的样本中，我们发现 delta 测试在 94.4% 的情况下检测到了工件。当伪影不存在时（n = 10,000 个模拟数据集），测试显示 I 类错误率约为 1.69%，在 169 个数据集中错误地报告了伪影。树形或“平衡”的三个度量未能预测节点密度效应的大小。这可能反映了我们随机生成的拓扑的相对同质性，但强调几乎任何拓扑都可能受到伪影的影响，这种影响不仅限于高度不均匀采样或其他不平衡的树。筛选节点密度伪影的系统发育的能力对于系统发育推断和使用系统发育树来推断进化过程的研究人员很重要，包括它们在分子钟年代测定中的使用。