Polytomies and phylogenetically independent contrasts:: Examination of the bounded degrees of freedom approach
Polytomies and phylogenetically independent contrasts:: Examination of the bounded degrees of freedom approach
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DOI：
10.1080/106351599260139
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发表时间：
1999-09-01
影响因子：
6.5
通讯作者：
Díaz-Uriarte, R
中科院分区：
文献类型：
--
作者：
Garland, T;Díaz-Uriarte, R
我们研究了软多分割术对Felsenstein（1985; Am. 125：1-15）用于估计双变量相关性的遗传独立对比方法。我们特别测试了Purvis和加兰（1993;系统生物学42：569-575）建议的边界自由度的适当性。我们模拟了布朗运动（假设独立的对比）和其他八个模型上的五个系统发育树的二元字符进化。对于非布朗运动模拟，分支长度标准化的充分性用简单的诊断来检查（加兰等人，1992; Syst.Biol.41：18-32），并如所示应用转化。令人惊讶的是，当使用布朗运动以外的模型时，软多分裂对I型错误率的影响往往可以忽略不计。总体而言，不考虑进化模型，自由度适当限制假设检验，并获得相关系数的无偏估计。我们的研究结果，沿着与以前的模拟研究，表明独立的对比可以可靠地适用于真实的数据，即使与系统发育的不确定性。
We examined the effect of soft polytomies on the performance (Type I error rate and bias) of Felsenstein's (1985; Am. Nat. 125:1-15) method of phylogenetically independent contrasts for estimating a bivariate correlation. We specifically tested the adequacy of bounding degrees of freedom, as suggested by Purvis and Garland (1993; Syst. Biol. 42:569-575). We simulated bivariate character evolution under Brownian motion (assumed by independent contrasts) and eight other models on five phylogenetic trees. For non-Brownian motion simulations, the adequacy of branch-length standardization was checked with a simple diagnostic (Garland et al., 1992; Syst. Biol. 41: 18-32), and transformations were applied as indicated. Surprisingly soft polytomies tended to have negligible effects on Type I error rates when models other than Brownian motion were used. Overall, and irrespective of evolutionary model, degrees of freedom were appropriately bounded for hypothesis testing, and unbiased estimates of the correlation coefficient were obtained. Our results, along with those of previous simulation studies, suggest that independent contrasts can reliably be applied to real data, even with phylogenetic uncertainty.