Evolutionary Phylogenetic Networks: Models and Issues

Nakhleh, Luay

doi:10.1007/978-0-387-09760-2_7

Cited by 92 publications

(88 citation statements)

References 111 publications

(123 reference statements)

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“…While these criteria have their shortcomings for model selection, the question of how to account for phylogenetic network complexity is still wide open and no methods exist for addressing it systematically [10].…”

Section: Introductionmentioning

confidence: 99%

The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection

2012

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Gene tree topologies have proven a powerful data source for various tasks, including species tree inference and species delimitation. Consequently, methods for computing probabilities of gene trees within species trees have been developed and widely used in probabilistic inference frameworks. All these methods assume an underlying multispecies coalescent model. However, when reticulate evolutionary events such as hybridization occur, these methods are inadequate, as they do not account for such events. Methods that account for both hybridization and deep coalescence in computing the probability of a gene tree topology currently exist for very limited cases. However, no such methods exist for general cases, owing primarily to the fact that it is currently unknown how to compute the probability of a gene tree topology within the branches of a phylogenetic network. Here we present a novel method for computing the probability of gene tree topologies on phylogenetic networks and demonstrate its application to the inference of hybridization in the presence of incomplete lineage sorting. We reanalyze a Saccharomyces species data set for which multiple analyses had converged on a species tree candidate. Using our method, though, we show that an evolutionary hypothesis involving hybridization in this group has better support than one of strict divergence. A similar reanalysis on a group of three Drosophila species shows that the data is consistent with hybridization. Further, using extensive simulation studies, we demonstrate the power of gene tree topologies at obtaining accurate estimates of branch lengths and hybridization probabilities of a given phylogenetic network. Finally, we discuss identifiability issues with detecting hybridization, particularly in cases that involve extinction or incomplete sampling of taxa.

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Section: Introductionmentioning

confidence: 99%

The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection

2012

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“…One popular methodology is to construct phylogenetic networks by merging sets of trees according to some optimality criterion [18,24]. For example, in the Hybridization Number (HN) problem we are given a set of rooted phylogenetic trees as input and we are required to topologically embed them into a network N = (V, E) such that the reticulation number r (N ) = |E| − (|V | − 1) is minimized; the minimum value thus obtained is known as the hybridization number of the input trees.…”

Section: Introductionmentioning

confidence: 99%

On Unrooted and Root-Uncertain Variants of Several Well-Known Phylogenetic Network Problems

et al. 2017

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The hybridization number problem requires us to embed a set of binary rooted phylogenetic trees into a binary rooted phylogenetic network such that the number of nodes with indegree two is minimized. However, from a biological point of view accurately inferring the root location in a phylogenetic tree is notoriously difficult and poor root placement can artificially inflate the hybridization number. To this end we study a number of relaxed variants of this problem. We start by showing that the fundamental problem of determining whether an unrooted phylogenetic network displays (i.e. embeds) an unrooted phylogenetic tree, is NP-hard. On the positive side we show that this problem is FPT in reticulation number. In the rooted case the corresponding FPT result is trivial, but here we require more subtle argumentation. Next we show that the hybridization number problem for unrooted networks (when given B Georgios 123Algorithmica two unrooted trees) is equivalent to the problem of computing the tree bisection and reconnect distance of the two unrooted trees. In the third part of the paper we consider the "root uncertain" variant of hybridization number. Here we are free to choose the root location in each of a set of unrooted input trees such that the hybridization number of the resulting rooted trees is minimized. On the negative side we show that this problem is APX-hard. On the positive side, we show that the problem is FPT in the hybridization number, via kernelization, for any number of input trees.

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“…7,8 Genomic segments evolve in a species network model just as they do in species tree models, except that for some lineages, several alternative paths to the common ancestor are possible.…”

Section: Introductionmentioning

confidence: 99%

Simulation-Based Evaluation of Hybridization Network Reconstruction Methods in the Presence of Incomplete Lineage Sorting

Kamneva

Rosenberg

2017

Evol Bioinform Online

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Hybridization events generate reticulate species relationships, giving rise to species networks rather than species trees. We report a comparative study of consensus, maximum parsimony, and maximum likelihood methods of species network reconstruction using gene trees simulated assuming a known species history. We evaluate the role of the divergence time between species involved in a hybridization event, the relative contributions of the hybridizing species, and the error in gene tree estimation. When gene tree discordance is mostly due to hybridization and not due to incomplete lineage sorting (ILS), most of the methods can detect even highly skewed hybridization events between highly divergent species. For recent divergences between hybridizing species, when the influence of ILS is sufficiently high, likelihood methods outperform parsimony and consensus methods, which erroneously identify extra hybridizations. The more sophisticated likelihood methods, however, are affected by gene tree errors to a greater extent than are consensus and parsimony.

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Evolutionary Phylogenetic Networks: Models and Issues

Cited by 92 publications

References 111 publications

The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection

The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection

On Unrooted and Root-Uncertain Variants of Several Well-Known Phylogenetic Network Problems

Simulation-Based Evaluation of Hybridization Network Reconstruction Methods in the Presence of Incomplete Lineage Sorting

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