Comparative methods with sampling error and within-species variation: Contrasts revisited and revised
Comparative methods with sampling error and within-species variation: Contrasts revisited and revised
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DOI：
10.1086/587525
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发表时间：
2008-06-01
影响因子：
2.9
通讯作者：
Felsenstein, Joseph
中科院分区：
文献类型：
--
作者：
Felsenstein, Joseph
比较方法分析通常假设物种的表型是那些物种的真实手段。在大多数分析中，使用的实际值是中等大小的样本的平均值。对比的协方差既包括进化变化的协方差，也包括种内表型协方差的一小部分，这一部分取决于该物种的样本大小。艾维斯等人。展示了在已知种内表型协方差的情况下如何分析这种情况下的数据。目前的模型允许它们是未知的，并且可以根据数据进行估计。多变量正态统计模型用于有限大小的样本中的多个性状，这些样本来自已知系统发育相关的物种，在通常的布朗运动变化模型下，具有相等的种内表型协方差。每个特征的对比既可以在物种内的个体之间获得，也可以在物种之间获得。可以对所有角色进行每种对比。这些对比度是独立的，每一组对比度都是对不同的人物采取的相同的对比度。集合内的协方差是不相等的，并且取决于未知的真协方差矩阵。推导了一种期望最大化算法，用于对进化变化的协方差和种内表型协方差进行降低的最大似然估计。它可以在PHYLIP程序包的对比程序中找到。计算机模拟表明，当不考虑样本容量的有限性时，协方差是有偏差的，使用本模型可以纠正这种偏差。抽样变异降低了协变在不同性状进化中的推论能力。还讨论了该方法的扩展，以包含来自简单遗传实验的加性遗传协方差的估计。
Comparative methods analyses have usually assumed that the species phenotypes are the true means for those species. In most analyses, the actual values used are means of samples of modest size. The covariances of contrasts then involve both the covariance of evolutionary changes and a fraction of the within-species phenotypic covariance, the fraction depending on the sample size for that species. Ives et al. have shown how to analyze data in this case when the within-species phenotypic covariances are known. The present model allows them to be unknown and to be estimated from the data. A multivariate normal statistical model is used for multiple characters in samples of finite size from species related by a known phylogeny, under the usual Brownian motion model of change and with equal within-species phenotypic covariances. Contrasts in each character can be obtained both between individuals within a species and between species. Each contrast can be taken for all of the characters. These sets of contrasts, each the same contrast taken for different characters, are independent. The within-set covariances are unequal and depend on the unknown true covariance matrices. An expectation-maximization algorithm is derived for making a reduced maximum likelihood estimate of the covariances of evolutionary change and the within-species phenotypic covariances. It is available in the Contrast program of the PHYLIP package. Computer simulations show that the covariances are biased when the finiteness of sample size is not taken into account and that using the present model corrects the bias. Sampling variation reduces the power of inference of covariation in evolution of different characters. An extension of this method to incorporate estimates of additive genetic covariances from a simple genetic experiment is also discussed.