Spaces of phylogenetic networks from generalized nearest-neighbor interchange operations.

Katharina T Huber, Simone Linz, Vincent Moulton, Taoyang Wu
Author Information
  1. Katharina T Huber: School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK. katharina.huber@cmp.uea.ac.uk.
  2. Simone Linz: Department of Computer Science, University of Auckland, Auckland, New Zealand. s.linz@auckland.ac.nz.
  3. Vincent Moulton: School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK. vincent.moulton@cmp.uea.ac.uk.
  4. Taoyang Wu: School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK. taoyang.wu@gmail.com.

Abstract

Phylogenetic networks are a generalization of evolutionary or phylogenetic trees that are used to represent the evolution of species which have undergone reticulate evolution. In this paper we consider spaces of such networks defined by some novel local operations that we introduce for converting one phylogenetic network into another. These operations are modeled on the well-studied nearest-neighbor interchange operations on phylogenetic trees, and lead to natural generalizations of the tree spaces that have been previously associated to such operations. We present several results on spaces of some relatively simple networks, called level-1 networks, including the size of the neighborhood of a fixed network, and bounds on the diameter of the metric defined by taking the smallest number of operations required to convert one network into another. We expect that our results will be useful in the development of methods for systematically searching for optimal phylogenetic networks using, for example, likelihood and Bayesian approaches.

Keywords

References

  1. J Bioinform Comput Biol. 2012 Aug;10(4):1250004 [PMID: 22809417]
  2. IEEE/ACM Trans Comput Biol Bioinform. 2013 Jul-Aug;10(4):1076-9 [PMID: 24334399]
  3. J Math Biol. 2012 Jul;65(1):157-80 [PMID: 21755321]
  4. IEEE/ACM Trans Comput Biol Bioinform. 2011 Mar-Apr;8(2):410-27 [PMID: 20660951]
  5. IEEE/ACM Trans Comput Biol Bioinform. 2011 May-Jun;8(3):635-49 [PMID: 21393651]
  6. Mol Biol Evol. 2007 Jan;24(1):324-37 [PMID: 17068107]
  7. IEEE/ACM Trans Comput Biol Bioinform. 2006 Jan-Mar;3(1):84-91 [PMID: 17048395]
  8. Bull Math Biol. 2014 Oct;76(10):2517-41 [PMID: 25234337]
  9. J Theor Biol. 1973 Mar;38(3):423-57 [PMID: 4632522]
  10. Math Biosci. 2009 Sep;221(1):54-9 [PMID: 19576908]
  11. Proc Natl Acad Sci U S A. 2014 Nov 18;111(46):16448-53 [PMID: 25368173]
  12. IEEE/ACM Trans Comput Biol Bioinform. 2013 May-Jun;10(3):721-8 [PMID: 24091404]
  13. IEEE/ACM Trans Comput Biol Bioinform. 2010 Apr-Jun;7(2):218-22 [PMID: 20431142]
  14. Bioinformatics. 2006 Nov 1;22(21):2604-11 [PMID: 16928736]
  15. J Math Biol. 2005 Aug;51(2):171-82 [PMID: 15868201]
  16. IEEE/ACM Trans Comput Biol Bioinform. 2009 Oct-Dec;6(4):552-69 [PMID: 19875855]
  17. Mol Biol Evol. 2000 Jun;17(6):875-81 [PMID: 10833193]
  18. J Theor Biol. 1996 Oct 21;182(4):463-7 [PMID: 8944893]

MeSH Term

Algorithms
Bayes Theorem
Biological Evolution
Computational Biology
Likelihood Functions
Mathematical Concepts
Models, Biological
Phylogeny

Word Cloud

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