Highly Incomplete Taxa Can Rescue Phylogenetic Analyses from the Negative Impacts of Limited Taxon Sampling
Highly Incomplete Taxa Can Rescue Phylogenetic Analyses from the Negative Impacts of Limited Taxon Sampling
复制标题
DOI：
10.1371/journal.pone.0042925
复制
发表时间：
2012-08
期刊：
影响因子：
3.7
通讯作者：
J. Wiens;Jonathan Tiu
中科院分区：
文献类型：
--
作者：
J. Wiens;Jonathan Tiu
背景系统发育学对生物学的许多领域都是必不可少的，但在某些情况下，系统发育学方法可能会给出不正确的估计。这种类型的一种潜在的常见情况是，采样的分类群很少，而采样的分类群的顶生分枝相对较长。然而，在这种情况下的最佳解决方案(即，采样更多的分类群而不是更多的特征)一直备受争议。这场辩论中的一个普遍假设是，添加的分类群必须是完整的(没有遗漏数据)，以便使分析免受有限分类群采样的负面影响。在这里，我们评估不完整的分类群是否也可以挽救在这些条件下的分析(从经验上检验来自早期模拟研究的预测)。方法/主要发现我们利用了16种具有良好系统发育关系的脊椎动物的DNA序列数据。在每个重复中，我们随机抽样4个物种，估计它们的系统发育(使用贝叶斯、似然和简约方法)，然后评估添加其余12个物种(它们有50%、75%或90%的数据被缺失的数据单元替换)是否可以提高相对于仅分析4个完整分类群的系统发育准确性。我们发现，在那些采样很少的分类群产生不正确估计的情况下，添加50%或75%缺失数据的分类群可以经常(75%的相关重复)挽救贝叶斯和似然分析，恢复原始4个分类群的准确系统发育。即使是数据缺失90%的分类群有时也是有益的。结论添加高度不完全的分类单元可以提高系统发育的准确性，在有限的分类单元采样误导分析的情况下。这些令人惊讶的经验结果证实了那些来自模拟的结果，并表明增加分类群的好处可能会从出人意料的少量数据中获得。这些发现对取样分类群与特征的争论，以及试图解决困难的系统发育问题的研究具有重要的意义。
Background Phylogenies are essential to many areas of biology, but phylogenetic methods may give incorrect estimates under some conditions. A potentially common scenario of this type is when few taxa are sampled and terminal branches for the sampled taxa are relatively long. However, the best solution in such cases (i.e., sampling more taxa versus more characters) has been highly controversial. A widespread assumption in this debate is that added taxa must be complete (no missing data) in order to save analyses from the negative impacts of limited taxon sampling. Here, we evaluate whether incomplete taxa can also rescue analyses under these conditions (empirically testing predictions from an earlier simulation study). Methodology/Principal Findings We utilize DNA sequence data from 16 vertebrate species with well-established phylogenetic relationships. In each replicate, we randomly sample 4 species, estimate their phylogeny (using Bayesian, likelihood, and parsimony methods), and then evaluate whether adding in the remaining 12 species (which have 50, 75, or 90% of their data replaced with missing data cells) can improve phylogenetic accuracy relative to analyzing the 4 complete taxa alone. We find that in those cases where sampling few taxa yields an incorrect estimate, adding taxa with 50% or 75% missing data can frequently (>75% of relevant replicates) rescue Bayesian and likelihood analyses, recovering accurate phylogenies for the original 4 taxa. Even taxa with 90% missing data can sometimes be beneficial. Conclusions We show that adding taxa that are highly incomplete can improve phylogenetic accuracy in cases where analyses are misled by limited taxon sampling. These surprising empirical results confirm those from simulations, and show that the benefits of adding taxa may be obtained with unexpectedly small amounts of data. These findings have important implications for the debate on sampling taxa versus characters, and for studies attempting to resolve difficult phylogenetic problems.