The Space of Tree-Based Phylogenetic Networks

Fischer, Mareike; Francis, Andrew R.

doi:10.1007/s11538-020-00744-9

Cited by 3 publications

(3 citation statements)

References 18 publications

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“…In this paper we prove that the space of rooted tree-based networks is connected under rNNI moves. This is the rooted analogue of the result of Fischer and Francis [4] showing the connectedness of (unrooted) tree-based networks under NNI moves. We also show that the space is connected under the recently introduced tail -moves [11].…”

Section: Introductionsupporting

confidence: 64%

Rooted NNI moves on tree-based phylogenetic networks

Erdős,

Francis,

Mezei

2020

Preprint

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Section: Introductionsupporting

confidence: 64%

Rooted NNI moves on tree-based phylogenetic networks

Erdős,

Francis,

Mezei

2020

Preprint

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“…There are also several results concerning the relationship between tree-based networks and other special classes of phylogenetic networks, as well as structural results on spaces of tree-based networks (see e.g. [2], [21,Corollary 10.18]). For a brief review of tree-based networks see [21,Section 10.4.2] (i) (ii) Recently, overlaid species forests were introduced [18], which are closely related to tree-based networks (see also [8]).…”

Section: Introductionmentioning

confidence: 99%

Forest-based networks

Huber¹,

Moulton²,

E.³

2022

Preprint

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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. Even so, this model does not permit the 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 phylogenetic 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 are 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 gene transfer between collections of bacteria that live in different environments.

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“…In addition, efficient algorithms have been presented for deciding whether or not a phylogenetic network is tree-based [see, e.g., Francis and Steel (2015) and Jetten and van Iersel (2018)]. There are also several results concerning the relationship between tree-based networks and other special classes of phylogenetic networks, as well as structural results on spaces of tree-based networks [see, e.g., Fischer andFrancis (2020), Steel (2016), Corollary 10.18]. For a brief review of tree-based networks, see (Steel 2016, Section 10.4.2) In this paper, we introduce a new class of networks called forest-based networks.…”

Section: Introductionmentioning

confidence: 99%

Forest-Based Networks

Huber

Moulton

2022

Bull Math Biol

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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.

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The Space of Tree-Based Phylogenetic Networks

Cited by 3 publications

References 18 publications

Rooted NNI moves on tree-based phylogenetic networks

Rooted NNI moves on tree-based phylogenetic networks

Forest-based networks

Forest-Based Networks

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