Lassoing and corralling rooted phylogenetic trees

DOI10.1007/S11538-013-9815-8zbMATH1308.92075OpenAlexW3103995024WikidataQ51265135MaRDI QIDQ376433FDOQ376433

Authors Katharina T. Huber, Andrei-Alin Popescu

Publication date 5 November 2013

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

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

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)

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.

Recommendations

• Distinguished minimal topological lassos
• `Lassoing' a phylogenetic tree. I: Basic properties, shellings, and covers
• Tree reconstruction from triplet cover distances
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Cites work

• scientific article; zbMATH DE number 1865935 (Why is no real title available?)
• scientific article; zbMATH DE number 2203240 (Why is no real title available?)
• Basic phylogenetic combinatorics.
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• Recognizing treelike \(k\)-dissimilarities
• Reconstructing trees from subtree weights.
• \(n\)-semimetrics
• \(n\)-way metrics
• `Lassoing' a phylogenetic tree. I: Basic properties, shellings, and covers

Cited in

(4)

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

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