1. Generation of Binary Tree-Child phylogenetic networks
- Author
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Gabriel Cardona, Joan Carles Pons, Celine Scornavacca, University of the Balearic Islands (UIB), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Research of GC and JCP has been partially supported by the Spanish Ministry of Science, Innovation and Universities (http://www.ciencia.gob.es/), Spanish State Research Agency (http://www.ciencia.gob.es/portal/site/MICINN/aei) and European Regional Development Fund (https://ec.europa.eu/regional_policy/es/funding/erdf/) projects DPI2015-67082-P and PGC2018-096956-B-C43. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.', Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)
- Subjects
0301 basic medicine ,filogenia ,Leaves ,Theoretical computer science ,Computer science ,Speciation ,Binary number ,Plant Science ,Upper and lower bounds ,Database and Informatics Methods ,0302 clinical medicine ,Biology (General) ,Phylogeny ,Data Management ,biología computacional ,Sequence ,Binary tree ,Ecology ,Phylogenetic tree ,Directed Graphs ,Plant Anatomy ,Applied Mathematics ,Simulation and Modeling ,Phylogenetic Analysis ,Directed graph ,[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] ,Reticulate evolution ,Phylogenetics ,Computational Theory and Mathematics ,Modeling and Simulation ,Physical Sciences ,Sequence Analysis ,Network Analysis ,Algorithms ,Research Article ,simulación por ordenador ,Computer and Information Sciences ,Evolutionary Processes ,QH301-705.5 ,Bioinformatics ,Research and Analysis Methods ,Set (abstract data type) ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,algoritmos ,Genetics ,Computer Simulation ,Evolutionary Systematics ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Taxonomy ,Evolutionary Biology ,Computational Biology ,Biology and Life Sciences ,030104 developmental biology ,Graph Theory ,030217 neurology & neurosurgery ,Mathematics - Abstract
Phylogenetic networks generalize phylogenetic trees by allowing the modelization of events of reticulate evolution. Among the different kinds of phylogenetic networks that have been proposed in the literature, the subclass of binary tree-child networks is one of the most studied ones. However, very little is known about the combinatorial structure of these networks. In this paper we address the problem of generating all possible binary tree-child (BTC) networks with a given number of leaves in an efficient way via reduction/augmentation operations that extend and generalize analogous operations for phylogenetic trees, and are biologically relevant. Since our solution is recursive, this also provides us with a recurrence relation giving an upper bound on the number of such networks. We also show how the operations introduced in this paper can be employed to extend the evolutive history of a set of sequences, represented by a BTC network, to include a new sequence. An implementation in python of the algorithms described in this paper, along with some computational experiments, can be downloaded from https://github.com/bielcardona/TCGenerators., Research of GC and JCP has been partially supported by the Spanish Ministry of Science, Innovation and Universities (http://www.ciencia.gob.es/) and European Regional Development Fund (https://ec.europa.eu/regional_policy/es/funding/erdf/) projects DPI2015-67082-P and PGC2018-096956-B-C43. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
- Published
- 2019