Phylogenetic trees and Euclidean embeddings

详细信息    查看全文

• 作者：Mark Layer ; John A. Rhodes
• 关键词：Phylogenetic trees ; Distance methods ; Multidimensional scaling ; Neighbor joining
• 刊名：Journal of Mathematical Biology
• 出版年：2017
• 出版时间：January 2017
• 年：2017
• 卷：74
• 期：1-2
• 页码：99-111
• 全文大小：
• 刊物类别：Mathematics and Statistics
• 刊物主题：Mathematical and Computational Biology; Applications of Mathematics;
• 出版者：Springer Berlin Heidelberg
• ISSN：1432-1416
• 卷排序：74

文摘

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.