`Lassoing' a phylogenetic tree. I: Basic properties, shellings, and covers

DOI10.1007/S00285-011-0450-4zbMATH Open1251.05030arXiv1102.0309OpenAlexW1995427389WikidataQ51550376 ScholiaQ51550376MaRDI QIDQ455729FDOQ455729

Authors: Andreas W. M. Dress, Katharina T. Huber, Mike Steel 

Publication date: 22 October 2012

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

Abstract: A classical result, fundamental to evolutionary biology, states that an edge-weighted tree $T$ with leaf set $X$, positive edge weights, and no vertices of degree 2 can be uniquely reconstructed from the set of leaf-to-leaf distances between any two elements of $X$. In biology, $X$ corresponds to a set of taxa (e.g. extant species), the tree $T$ describes their phylogenetic relationships, the edges correspond to earlier species evolving for a time until splitting in two or more species by some speciation/bifurcation event, and their length corresponds to the genetic change accumulating over that time in such a species. In this paper, we investigate which subsets of $$ suffice to determine (`lasso') a tree from the leaf-to-leaf distances induced by that tree. The question is particularly topical since reliable estimates of genetic distance - even (if not in particular) by modern mass-sequencing methods - are, in general, available only for certain combinations of taxa.

Full work available at URL: https://arxiv.org/abs/1102.0309

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zbMATH Keywords

lassophylogenetic treetree metrictree reconstructioncord of a lasso

Mathematics Subject Classification ID

Problems related to evolution (92D15) Trees (05C05)

Cites Work

• Tree structures for proximity data
• Constructing rooted supertrees using distances
• The complexity of reconstructing trees from qualitative characters and subtrees
• A robust model for finding optimal evolutionary tree
• Basic phylogenetic combinatorics.
• The performance of neighbor-joining methods of phylogenetic reconstruction
• Patching up \(X\)-trees
• On the extension of a partial metric to a tree metric
• An Optimal Diagonal Tree Code
• \(X\)-trees and weighted quartet systems
• The triangles method to build \(X\)-trees from incomplete distance matrices
• A Hall-type theorem for triplet set systems based on medians in trees
• Encoding phylogenetic trees in terms of weighted quartets

Cited In (16)

• A matroid associated with a phylogenetic tree
• Characterizing phylogenetically decisive taxon coverage
• Tree reconstruction from triplet cover distances
• Completion of tree metrics and rank 2 matrices
• On dissimilarity vectors of general weighted trees
• Do tree split probabilities determine the branch lengths?
• Combinatorial properties of triplet covers for binary trees
• Minimum triplet covers of binary phylogenetic \(X\)-trees
• Reconstructing trees from subtree weights.
• Cyclic permutations and evolutionary trees
• Phylogenetic diversity over an abelian group
• Distinguished minimal topological lassos
• Dynamic Ising model: reconstruction of evolutionary trees
• Recovering a tree from the lengths of subtrees spanned by a randomly chosen sequence of leaves
• Lassoing and corralling rooted phylogenetic trees
• On the weights of simple paths in weighted complete graphs

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