Two new graphical methods for mapping trait evolution on phylogenies
Two new graphical methods for mapping trait evolution on phylogenies
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DOI：
10.1111/2041-210x.12066
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发表时间：
2013-08-01
影响因子：
6.6
通讯作者：
Revell, Liam J.
中科院分区：
文献类型：
--
作者：
Revell, Liam J.
1.现代系统发育比较生物学使用来自物种之间的关系的数据（系统发育）结合表型性状的比较信息来绘制关于进化过去的基于模型的统计推断。近年来，用于进化推理的遗传学方法已成为有机进化研究的中心。在这里，我提出了两种不同的图形方法来可视化树上的表型进化。方法1是一种新的方法，用于绘制后验密度的随机映射字符的历史上的一个二元（两个状态）的表型性状的单基因。方法2是一个密切相关的技术，使用祖先的字符估计可视化的历史字符状态的连续性状沿着树枝的树。方法2的一个缺点是，通过沿着树的分支沿着映射祖先状态的点估计，我们有效地忽略了与连续性状的祖先性状估计相关的不确定性。为了缓解这个问题，我提出了一种新的方法来可视化祖先状态的不确定性，使用一种类型的投影到形态空间的树称为“traitgram。'4.所有这些方法在总结关于祖先性格重建的复杂比较推理方面都应该证明是有用的。它们在免费提供和开源的R & D遗传学软件包phytools中实现。'
1. Modern phylogenetic comparative biology uses data from the relationships between species (phylogeny) combined with comparative information for phenotypic traits to draw model-based statistical inferences about the evolutionary past. Recent years have seen phylogeny methods for evolutionary inference become central in the study of organic evolution.2. Here, I present two different graphical methods for visualizing phenotypic evolution on the tree. Method 1 is a new approach for plotting the posterior density of stochastically mapped character histories for a binary (two-state) phenotypic trait on a phylogeny. Method 2 is a closely related technique that uses ancestral character estimation to visualize historical character states for a continuous trait along the branches of a tree.3. One shortcoming of Method 2 is that by mapping the point estimates of ancestral states along the branches of the tree, we have effectively ignored the uncertainty associated with ancestral character estimation of continuous traits. To alleviate this issue, I propose a new method for visualizing ancestral state uncertainty using a type of projection of the tree into morphospace called a 'traitgram.'4. All of these approaches should prove useful in summarizing complex comparative inferences about ancestral character reconstruction. They are implemented in the freely available and open-source R phylogenetics package 'phytools.'