Why the phylogenetic regression appears robust to tree misspecification.
Why the phylogenetic regression appears robust to tree misspecification.
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为什么系统发育回归对树错误指定表现出稳健。
DOI：
10.1093/sysbio/syq098
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发表时间：
2011
影响因子：
6.5
通讯作者：
Stone,EricA
中科院分区：
文献类型：
--
作者：
Stone,EricA
系统发育比较方法使用进化关系的估计，明确建模种间数据的协方差结构。通过解释共同祖先，可以研究两个或多个性状之间的共同进化，作为对彼此或环境变量的反应，而不会因血统而混淆相似性。由于真正的亲缘关系是不可知的，必须使用估计值，这给系统发育比较分析引入了一个难以量化的误差来源。这份手稿的目的是阐明如何通过比较分析传播树错误规范。我专注于系统发育的布朗运动模型下的进化回归，并考虑局部系统发育扰动的回归拟合的效果。出于Felsenstein的独立对比的方法，我推导出一个矩阵平方根的系统发育协方差矩阵，有一个明显的系统发育的解释。我用这个结果将扰动系统发育回归模型转换成一个普通的线性回归，其中一个可解释的点受到影响。这个公式的简单性允许的数据和遗传学的贡献被解开时，研究树的错误指定的影响。因此，我发现，分支长度错误可以很容易地解释在子树之间的对比度分数的重新加权。分析考虑到这一点和其他扰动有助于解释为什么系统发育回归似乎一般是强大的树误指定，我能够确定的条件下，回归可能不会产生强大的结果。我讨论了为什么软polytomies不满足这些有问题的条件，导致的结论是，未解决的分叉应该只有适度的回归拟合的影响。
The phylogenetic comparative method uses estimates of evolutionary relationships to explicitly model the covariance structure of interspecific data. By accounting for common ancestry, the coevolution between 2 or more traits, as a response to one another or to environmental variables, can be studied without confounding similarities due to identity by descent. Because the true phylogeny is unknowable, an estimate must be used, introducing a source of error into phylogenetic comparative analysis that can be difficult to quantify. This manuscript aims to elucidate how tree misspecification is propagated through a comparative analysis. I focus on the phylogenetic regression under a Brownian motion model of evolution and consider the effect of local phylogenetic perturbations on the regression fit. Motivated by Felsenstein's method of independent contrasts, I derive a matrix square root of the phylogenetic covariance matrix that has an obvious phylogenetic interpretation. I use this result to transform the perturbed phylogenetic regression model into an ordinary linear regression in which one interpretable point has been affected. The simplicity of this formulation allows the contributions of data and phylogeny to be disentangled when studying the effect of tree misspecification. Consequentially, I find that branch length misspecification can be easily explained in terms of the reweighting of contrast scores between subtrees. An analytical consideration of this and other perturbations helps to explain why the phylogenetic regression appears generally to be robust to tree misspecification, and I am able to identify conditions under which the regression may not yield robust results. I discuss why soft polytomies do not meet these problematic conditions, leading to the conclusion that unresolved bifurcations should have only modest effects on the regression fit.
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