Forest-based networks

Huber, K. T., Moulton, V. ORCID: and Scholz, G. E. (2022) Forest-based networks. Bulletin of Mathematical Biology, 84. ISSN 0092-8240

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In evolutionary studies it is common to use phylogenetic trees to represent the evolutionary history of a set of species. However, in case the transfer of genes or other genetic information between the species or their ancestors has occurred in the past, a tree may not provide a complete picture of their history. In such cases tree-based phylogenetic networks can provide a useful, more refined representation of the species' evolution. Such a network is essentially a phylogenetic tree with some arcs added between the tree's edges so as to represent reticulate events such as gene transfer, hybridization, and recombination. Even so, this model does not permit the direct representation of evolutionary scenarios where reticulate events have taken place between different subfamilies or lineages of species. To represent such scenarios, in this paper we introduce the notion of a forest-based network, that is, a collection of leaf- disjoint phylogenetic trees on a set of species with arcs added between the edges of distinct trees within the collection. Forest-based networks include the recently introduced class of overlaid species forests which can be used to model introgression. As we shall see, even though the definition of forest-based networks is closely related to that of tree-based networks, they lead to new mathematical theory which complements that of tree-based networks. As well as studying the relationship of forest-based networks with other classes of phylogenetic networks, such as tree-child networks and universal tree-based networks, we present some characterizations of some special classes of forest-based networks. We expect that our results will be useful for developing new models and algorithms to understand reticulate evolution, such as introgression and gene transfer between species.

Item Type: Article
Uncontrolled Keywords: phylogenetic network,lateral gene transfer,orest-based network,tree-based network,phylogenetic network,lateral gene transfer,forest-based network,tree-based network,agricultural and biological sciences(all),environmental science(all),mathematics(all),biochemistry, genetics and molecular biology(all),neuroscience(all),pharmacology,computational theory and mathematics,immunology ,/dk/atira/pure/subjectarea/asjc/1100
Faculty \ School: Faculty of Science > School of Computing Sciences
UEA Research Groups: Faculty of Science > Research Groups > Computational Biology
Faculty of Science > Research Groups > Norwich Epidemiology Centre
Faculty of Medicine and Health Sciences > Research Groups > Norwich Epidemiology Centre
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Depositing User: LivePure Connector
Date Deposited: 06 Sep 2022 11:49
Last Modified: 19 Apr 2023 01:09
DOI: 10.1007/s11538-022-01081-9


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