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

DOI10.1007/S00285-011-0450-4MaRDI QIDQ455729zbMATH OpenOpenAlexWikidataFDO

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)

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

zbMATH Keywords

lassophylogenetic treetree metrictree reconstructioncord of a lasso

Mathematics Subject Classification ID

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

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.

Recommendations

• Lassoing and corralling rooted phylogenetic trees
• Tree reconstruction from triplet cover distances
• Distinguished minimal topological lassos
• Reconstructing trees from subtree weights.
• Encoding phylogenetic trees in terms of weighted quartets

Cites work

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

Cited in

(16)

• Characterizing phylogenetically decisive taxon coverage
• A matroid associated with a phylogenetic tree
• 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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