Literature DB >> 29478083

Recovering normal networks from shortest inter-taxa distance information.

Magnus Bordewich1, Katharina T Huber2, Vincent Moulton2, Charles Semple3.   

Abstract

Phylogenetic networks are a type of leaf-labelled, acyclic, directed graph used by biologists to represent the evolutionary history of species whose past includes reticulation events. A phylogenetic network is tree-child if each non-leaf vertex is the parent of a tree vertex or a leaf. Up to a certain equivalence, it has been recently shown that, under two different types of weightings, edge-weighted tree-child networks are determined by their collection of distances between each pair of taxa. However, the size of these collections can be exponential in the size of the taxa set. In this paper, we show that, if we have no "shortcuts", that is, the networks are normal, the same results are obtained with only a quadratic number of inter-taxa distances by using the shortest distance between each pair of taxa. The proofs are constructive and give cubic-time algorithms in the size of the taxa sets for building such weighted networks.

Entities:  

Keywords:  Distance matrix; Normal network; Tree–child network

Mesh:

Year:  2018        PMID: 29478083     DOI: 10.1007/s00285-018-1218-x

Source DB:  PubMed          Journal:  J Math Biol        ISSN: 0303-6812            Impact factor:   2.259


  9 in total

1.  Determining phylogenetic networks from inter-taxa distances.

Authors:  Magnus Bordewich; Charles Semple
Journal:  J Math Biol       Date:  2015-12-14       Impact factor: 2.259

2.  Hybrids in real time.

Authors:  Mihaela Baroni; Charles Semple; Mike Steel
Journal:  Syst Biol       Date:  2006-02       Impact factor: 15.683

3.  Reconstructing an ultrametric galled phylogenetic network from a distance matrix.

Authors:  Ho-Leung Chan; Jesper Jansson; Tak-Wah Lam; Siu-Ming Yiu
Journal:  J Bioinform Comput Biol       Date:  2006-08       Impact factor: 1.122

4.  Unique determination of some homoplasies at hybridization events.

Authors:  Stephen J Willson
Journal:  Bull Math Biol       Date:  2007-02-23       Impact factor: 1.758

5.  Reconstruction of some hybrid phylogenetic networks with homoplasies from distances.

Authors:  Stephen J Willson
Journal:  Bull Math Biol       Date:  2007-06-08       Impact factor: 1.758

6.  Properties of normal phylogenetic networks.

Authors:  Stephen J Willson
Journal:  Bull Math Biol       Date:  2009-09-30       Impact factor: 1.758

7.  Comparison of tree-child phylogenetic networks.

Authors:  Gabriel Cardona; Francesc Rosselló; Gabriel Valiente
Journal:  IEEE/ACM Trans Comput Biol Bioinform       Date:  2009 Oct-Dec       Impact factor: 3.710

8.  The neighbor-joining method: a new method for reconstructing phylogenetic trees.

Authors:  N Saitou; M Nei
Journal:  Mol Biol Evol       Date:  1987-07       Impact factor: 16.240

9.  Tree-average distances on certain phylogenetic networks have their weights uniquely determined.

Authors:  Stephen J Willson
Journal:  Algorithms Mol Biol       Date:  2012-05-15       Impact factor: 1.405

  9 in total

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