Do Triplets Have Enough Information to Construct the Multi-Labeled Phylogenetic Tree?

Hassanzadeh, Reza; Eslahchi, Changiz; Sung, Wing-Kin

doi:10.1371/journal.pone.0103622

Cited by 2 publications

(3 citation statements)

References 28 publications

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“…Following [13], we call a MUL-tree on three leaves a MUL-triplet. So for example for Y = (suppressing resulting degree two vertices and, if this has rendered the root of M a vertex of degree one, identifying that root with its unique child) such that M and τ are isomorphic, it is easy to check that the MUL-triplet (M, µ) constructed in the previous example is displayed by the left MUL-tree depicted in Figure 5(i) where we represent each leaf by its label.…”

Section: Some Remarks About Reconstructing Stable Phylogenetic Networkmentioning

confidence: 99%

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Phylogenetic networks that are their own fold-ups

Huber

2020

Advances in Applied Mathematics

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Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted directed acyclic graphs whose leaves are labelled by, for example, species. A number of mathematically interesting classes of phylogenetic networks are known. These include the biologically relevant class of stable phylogenetic networks whose members are defined via certain "fold-up" and "un-fold" operations that link them with concepts arising within the theory of, for example, graph fibrations. Despite this exciting link, the structural complexity of stable phylogenetic networks is still relatively poorly understood.Employing the popular tree-based, reticulation-visible, and tree-child properties which allow one to gauge this complexity in one way or another, we provide novel characterizations for when a stable phylogenetic network satisfies either one of these three properties.

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Section: Some Remarks About Reconstructing Stable Phylogenetic Networkmentioning

confidence: 99%

“…Following [13], we call a MUL-tree on three leaves a MUL-triplet. So for example for Y = {1, 2}, the MUL-tree (M, µ) with leaf set {a, b, c} and lca M (a, b) strictly below lca M (a, c) and µ(1) = {a, c} and µ(2) = {b} is a MUL-triplet on Y .…”

Section: Some Remarks About Reconstructing Stable Phylogenetic Networkmentioning

confidence: 99%

Phylogenetic networks that are their own fold-ups

Huber

2020

Advances in Applied Mathematics

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“…In Section 7 we show that for every event-labeled gene tree T , there always exists a TreeNetreconciliation map from T to some species network N. To prove this result we employ the concept of so-called MUL-trees [6,7,23,29,31,40,47]. Our proof essentially relies on first defining a reconciliation map between an event-labeled tree and a multiple-labeled tree, or MUL-tree.…”

Section: Introductionmentioning

confidence: 99%

Reconciling event-labeled gene trees with MUL-trees and species networks

2019

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Phylogenomics commonly aims to construct evolutionary trees from genomic sequence information. One way to approach this problem is to first estimate event-labeled gene trees (i.e., rooted trees whose non-leaf vertices are labeled by speciation or gene duplication events), and to then look for a species tree which can be reconciled with this tree through a reconciliation map between the trees. In practice, however, it can happen that there is no such map from a given event-labeled tree to any species tree. An important situation where this might arise is where the species evolution is better represented by a network instead of a tree. In this paper, we therefore consider the problem of reconciling event-labeled trees with species networks. In particular, we prove that any event-labeled gene tree can be reconciled with some network and that, under certain mild assumptions on the gene tree, the network can even be assumed to be multi-arc free. To prove this result, we show that we can always reconcile the gene tree with some multi-labeled (MUL-)tree, which can then be "folded up" to produce the desired reconciliation and network. In addition, we study the interplay between reconciliation maps from event-labeled gene trees to MUL-trees and networks. Our results could be useful for understanding how genomes have evolved after undergoing complex evolutionary events such as polyploidy.

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Do Triplets Have Enough Information to Construct the Multi-Labeled Phylogenetic Tree?

Cited by 2 publications

References 28 publications

Phylogenetic networks that are their own fold-ups

Phylogenetic networks that are their own fold-ups

Reconciling event-labeled gene trees with MUL-trees and species networks

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