Lassoing and corralling rooted phylogenetic trees

DOI10.1007/S11538-013-9815-8zbMATH Open1308.92075arXiv1208.5594OpenAlexW3103995024WikidataQ51265135 ScholiaQ51265135MaRDI QIDQ376433FDOQ376433

Authors: Katharina T. Huber, Andrei-Alin Popescu 

Publication date: 5 November 2013

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

Abstract: The construction of a dendogram on a set of individuals is a key component of a genomewide association study. However even with modern sequencing technologies the distances on the individuals required for the construction of such a structure may not always be reliable making it tempting to exclude them from an analysis. This, in turn, results in an input set for dendogram construction that consists of only partial distance information which raises the following fundamental question. For what subset of its leaf set can we reconstruct uniquely the dendogram from the distances that it induces on that subset. By formalizing a dendogram in terms of an edge-weighted, rooted phylogenetic tree on a pre-given finite set X with |X|>2 whose edge-weighting is equidistant and a set of partial distances on X in terms of a set L of 2-subsets of X, we investigate this problem in terms of when such a tree is lassoed, that is, uniquely determined by the elements in L. For this we consider four different formalizations of the idea of "uniquely determining" giving rise to four distinct types of lassos. We present characterizations for all of them in terms of the child-edge graphs of the interior vertices of such a tree. Our characterizations imply in particular that in case the tree in question is binary then all four types of lasso must coincide.

Full work available at URL: https://arxiv.org/abs/1208.5594

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zbMATH Keywords

lassocorralincomplete taxon coveragepartial distancerooted phylogenetic tree

Mathematics Subject Classification ID

Applications of graph theory (05C90) Genetics and epigenetics (92D10) Problems related to evolution (92D15)

Cites Work

• Title not available (Why is that?)
• \(n\)-semimetrics
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• Title not available (Why is that?)
• Characterizing phylogenetically decisive taxon coverage
• `Lassoing' a phylogenetic tree. I: Basic properties, shellings, and covers

Cited In (4)

• A matroid associated with a phylogenetic tree
• Nonbifurcating Phylogenetic Tree Inference via the Adaptive LASSO
• Distinguished minimal topological lassos
• `Lassoing' a phylogenetic tree. I: Basic properties, shellings, and covers

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