Spaces of phylogenetic networks from generalized nearest-neighbor interchange operations

Huber, Katharina T., Linz, Simone, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2016) Spaces of phylogenetic networks from generalized nearest-neighbor interchange operations. Journal of Mathematical Biology, 72 (3). pp. 699-725. ISSN 0303-6812

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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 (NNI) 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.

Item Type:	Article
Uncontrolled Keywords:	phylogenetic networks ,spaces of phylogenetic trees,phylogenetic tree metrics ,nearest-neighbor interchange (nni)
Faculty \ School:	Faculty of Science > School of Computing Sciences
UEA Research Groups:	Faculty of Science > Research Groups > Computational Biology > Phylogenetics (former - to 2018) Faculty of Science > Research Groups > Computational Biology Faculty of Science > Research Groups > Computational Biology > Computational biology of RNA (former - to 2018) Faculty of Science > Research Groups > Norwich Epidemiology Centre Faculty of Medicine and Health Sciences > Research Groups > Norwich Epidemiology Centre Faculty of Science > Research Centres > Centre for Ecology, Evolution and Conservation Faculty of Science > Research Groups > Data Science and AI
Depositing User:	Pure Connector
Date Deposited:	19 Oct 2015 10:00
Last Modified:	19 Dec 2024 00:48
URI:	https://ueaeprints.uea.ac.uk/id/eprint/54718
DOI:	10.1007/s00285-015-0899-7

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