Phylogenetic trees and Euclidean embeddings

DOI10.1007/S00285-016-1018-0zbMATH Open1357.92058arXiv1605.01039OpenAlexW2280169270WikidataQ39786091 ScholiaQ39786091MaRDI QIDQ504064FDOQ504064

John A. Rhodes, Mark Layer

Publication date: 25 January 2017

Published in: Journal of Mathematical Biology (Search for Journal in Brave)

Abstract: It was recently observed by de Vienne et al. 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.

Full work available at URL: https://arxiv.org/abs/1605.01039

zbMATH Keywords

multidimensional scalingneighbor joiningdistance methodsphylogenetic trees

Mathematics Subject Classification ID

Applications of graph theory (05C90) Problems related to evolution (92D15) Taxonomy, cladistics, statistics in mathematical biology (92B10) Distance geometry (51K99)

Cites Work

• Title not available (Why is that?)
• Maximum tree: a consistent estimator of the species tree
• Phylogenetic trees and Euclidean embeddings

Cited In (10)

• Information geometry for phylogenetic trees
• Total positivity in multivariate extremes
• Phylogenetic placement problem: a hyperbolic embedding approach
• Encodings of cladograms and labeled trees
• Polyhedral computational geometry for averaging metric phylogenetic trees
• Morphological hierarchies: a unifying framework with new trees
• Closure operations in phylogenetics
• Phylogenetic trees and Euclidean embeddings
• Topological properties of phylogenetic trees in evolutionary models
• A novel approach to phylogenetic trees: d‐Dimensional geometric Steiner trees

Uses Software

• BIONJ
• Phylo-MCOA
• iGLASS

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