Phylogenetic trees and Euclidean embeddings
Phylogenetic trees and Euclidean embeddings
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DOI：
10.1007/s00285-016-1018-0
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发表时间：
2017-01-01
影响因子：
1.9
通讯作者：
Rhodes, John A.
中科院分区：
文献类型：
--
作者：
Layer, Mark;Rhodes, John A.
最近由de Vienne等人（Syst Biol 60（6）：826-832，2011）观察到，系统发生树上的分类群之间的距离的简单平方根变换允许将分类群嵌入到欧几里得空间中。虽然这是基于一个扩散模型的连续字符演变沿着树的理由，在这里，我们给它提供了一个直接和基本的解释，提供了大量的额外的见解。我们使用这种嵌入来重新解释NJ和BIONJ树构建算法之间的差异，提供这种嵌入如何反映数据中的树结构的一个例子。
It was recently observed by de Vienne et al. (Syst Biol 60(6):826-832, 2011) that a simple square root transformation of distances between taxa on a phylogenetic tree allowed for an embedding of the taxa into Euclidean space. While the justification for this was based on a diffusion model of continuous character evolution along the tree, here we give a direct and elementary explanation for it that provides substantial additional insight. We use this embedding to reinterpret the differences between the NJ and BIONJ tree building algorithms, providing one illustration of how this embedding reflects tree structures in data.