Constructing Semi-Directed Level-1 Phylogenetic Networks from Quarnets

Huebler, Sophia; Morris, Rachel; Rusinko, Joseph; Tao, Yifei

doi:10.48550/arxiv.1910.00048

Cited by 3 publications

(4 citation statements)

References 15 publications

(21 reference statements)

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“…[31]) networks. Our results, as well as the ones in [18], provide the first combinatorial results on the semi-directed network topology. The main obstacle, however, was that not all 4-leaf level-1 networks are distinguishable under the considered models.…”

Section: Discussionsupporting

confidence: 64%

Distinguishing level-1 phylogenetic networks on the basis of data generated by Markov processes

Gross¹,

Iersel²,

Janssen³

et al. 2020

Preprint

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Phylogenetic networks can represent evolutionary events that cannot be described by phylogenetic trees. These networks are able to incorporate reticulate evolutionary events such as hybridization, introgression, and lateral gene transfer. Recently, network-based Markov models of DNA sequence evolution have been introduced along with model-based methods for reconstructing phylogenetic networks. For these methods to be consistent, the network parameter needs to be identifiable from data generated under the model. Here, we show that the semi-directed network parameter of a triangle-free, level-1 network model with any fixed number of reticulation vertices is generically identifiable under the Jukes-Cantor, Kimura 2-parameter, or Kimura 3-parameter constraints.

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Section: Discussionsupporting

confidence: 64%

Distinguishing level-1 phylogenetic networks on the basis of data generated by Markov processes

Gross¹,

Iersel²,

Janssen³

et al. 2020

Preprint

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show abstract

“…In this section, the notion of phylogenetic networks and some of their properties will be discussed. We will also present some graph-theoretic terminologies, which are adapted from [9,31,24] and will be used throughout the paper. From now on, we assume that the set X is a finite set corresponding to taxa or a set of species.…”

Section: Preliminaries and Definitionsmentioning

confidence: 99%

“…In [52], the set of triplets, which are the phylogenetic networks on three leaves, is considered. Similarly, the set of quarnets, which are four leaf-networks, is studied in [31] and a set of subnetworks obtained by deleting some edges of the network is considered in [39].…”

Section: Introductionmentioning

confidence: 99%

Distinguishing Level-2 Phylogenetic Networks Using Phylogenetic Invariants

Ardiyansyah¹

2021

Preprint

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In phylogenetics, it is important for the phylogenetic network model parameters to be identifiable so that the evolutionary histories of a group of species can be consistently inferred. However, as the complexity of the phylogenetic network models grows, the identifiability of network models becomes increasingly difficult to analyze. As an attempt to analyze the identifiability of network models, we check whether two networks are distinguishable. In this paper, we specifically study the distinguishability of phylogenetic network models associated with level-2 networks. Using an algebraic approach, namely using discrete Fourier transformation, we present some results on the distinguishability of some level-2 networks, which generalize earlier work on the distinguishability of level-1 networks. In particular, we study simple and semisimple level-2 networks. Simple and semisimple level-2 networks can be thought as generalizations of level-1 sunlet and cycle networks, respectively. Moreover, we also compare the varieties associated with semisimple level-2 and cycle networks.

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“…As opposed 4-leaves trees (quartets), I considered the quarnets, which are leaves networks [5]. Huebler et al constructs level-1 phylogenetic networks from quarnets [6].…”

Section: Introductionmentioning

confidence: 99%

The Structure of Level-2 Semi-directed Binary Phylogenetic Networks

ÖZBALTAN

2023

Cumhuriyet Science Journal

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Phylogenetic trees describe evolution but due to hybridization events, recombination events or lateral gene transfer, it can be represented as a phylogenetic network. In phylogenetic networks, some of the branches of tree combine and create a reticulation node. Level of a network is decided to look at how many nodes in a connected component in a network. In this research, Int this paper, the structure of directed and undirected level-2 networks and how the can be decomposed into level-2 generators is studied..

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Constructing Semi-Directed Level-1 Phylogenetic Networks from Quarnets

Cited by 3 publications

References 15 publications

Distinguishing level-1 phylogenetic networks on the basis of data generated by Markov processes

Distinguishing level-1 phylogenetic networks on the basis of data generated by Markov processes

Distinguishing Level-2 Phylogenetic Networks Using Phylogenetic Invariants

The Structure of Level-2 Semi-directed Binary Phylogenetic Networks

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