No substitute for real data: A cautionary note on the use of phylogenies from birth–death polytomy resolvers for downstream comparative analyses
No substitute for real data: A cautionary note on the use of phylogenies from birth–death polytomy resolvers for downstream comparative analyses
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DOI：
10.1111/evo.12817
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发表时间：
2015-12
期刊：
影响因子：
3.3
通讯作者：
D. Rabosky
中科院分区：
文献类型：
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作者：
D. Rabosky
系统发育的统计估计总是与不确定性相关，而适应这种不确定性是现代系统发育比较分析的重要组成部分。生死多分解析器是一种解释系统发育不确定性的方法，该方法仅使用分类信息将缺失（未采样）的分类群放置到系统发育树上。最近对鸟类和哺乳动物的研究已经使用这种方法来生成在物种水平上完整的系统发育树的伪后分布，即使在许多物种的遗传数据缺失的情况下也是如此。许多研究人员已使用这些系统发育分布进行下游进化分析，其中涉及对表型进化、地理和群落组装的推断。我证明，使用以这种方式构建的系统发育对于许多涉及性状的问题是不合适的。由于物种是根据性状值随机放置在树上的，因此出生-死亡多态解析器打破了性状系统发育结构的自然模式。基于这些树的推论是可预测的，并且通常在取决于性状系统发育结构的潜在（真实）模式的方向上存在极大偏差。我使用全球鸟类系统发育的例子来说明连续性状和离散性状这一现象的严重性。
The statistical estimation of phylogenies is always associated with uncertainty, and accommodating this uncertainty is an important component of modern phylogenetic comparative analysis. The birth–death polytomy resolver is a method of accounting for phylogenetic uncertainty that places missing (unsampled) taxa onto phylogenetic trees, using taxonomic information alone. Recent studies of birds and mammals have used this approach to generate pseudoposterior distributions of phylogenetic trees that are complete at the species level, even in the absence of genetic data for many species. Many researchers have used these distributions of phylogenies for downstream evolutionary analyses that involve inferences on phenotypic evolution, geography, and community assembly. I demonstrate that the use of phylogenies constructed in this fashion is inappropriate for many questions involving traits. Because species are placed on trees at random with respect to trait values, the birth–death polytomy resolver breaks down natural patterns of trait phylogenetic structure. Inferences based on these trees are predictably and often drastically biased in a direction that depends on the underlying (true) pattern of phylogenetic structure in traits. I illustrate the severity of the phenomenon for both continuous and discrete traits using examples from a global bird phylogeny.