Hybridization in Nonbinary Trees
Simone Linz,Charles Semple +1 more
TL;DR: It is shown that the NP-hard problem of calculating the minimum number of reticulation events for two (arbitrary) rooted phylogenetic trees parameterized by this minimum number is fixed-parameter tractable.
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Abstract: Reticulate evolution - the umbrella term for processes like hybridization, horizontal gene transfer, and recombination - plays an important role in the history of life of many species. Although the occurrence of such events is widely accepted, approaches to calculate the extent to which reticulation has influenced evolution are relatively rare. In this paper, we show that the NP-hard problem of calculating the minimum number of reticulation events for two (arbitrary) rooted phylogenetic trees parameterized by this minimum number is fixed-parameter tractable.
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Citations
Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks.
TL;DR: Dendroscope 3 is a new program for working with rooted phylogenetic trees and networks that provides a number of methods for drawing and comparingRoot phylogenetic networks, and for computing them from rooted trees.
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Phylogenetic networks do not need to be complex
TL;DR: In this article, the authors present the new Cass algorithm that can combine any set of clusters into a phylogenetic network, which is guaranteed to produce a network with at most two reticulations per biconnected component whenever such a network exists.
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Phylogenetic Networks Do not Need to Be Complex: Using Fewer Reticulations to Represent Conflicting Clusters
TL;DR: The new Cass algorithm is presented, which is a generalization of phylogenetic trees that can combine any set of clusters into a phylogenetic network, and it is shown that the networks constructed by Cass are usually simpler than Networks constructed by other available methods.
51
•Posted Content
Fixed-Parameter and Approximation Algorithms for Maximum Agreement Forests
TL;DR: Efficient fixed-parameter and approximation algorithms for the NP-hard problem of computing a maximum agreement forest (MAF) of a pair of multifurcating (nonbinary) rooted trees are presented.
Parameterized and approximation algorithms for maximum agreement forest in multifurcating trees
TL;DR: This work studies parameterized algorithms and approximation algorithms for the maximum agreement forest problem, which, for two given leaf-labeled trees, is to find a maximum forest that is a subgraph of both trees, giving the first constant-ratio approximation algorithm for general trees.
37
References
Hybridization as an invasion of the genome
TL;DR: This work surveys studies of natural interspecific hybridization in plants and a variety of animals to show that limited invasions of the genome are widespread, with potentially important consequences in evolutionary biology, speciation, biodiversity, and conservation.
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Computing the minimum number of hybridization events for a consistent evolutionary history
Magnus Bordewich,Charles Semple +1 more
TL;DR: The main results of this paper show that computing this smallest number of hybridization events required to explain a given (input) set of data in a single (hybrid) phylogeny is APX- hard, and thus NP-hard, in the case the input is a collection of phylogenetic trees on sets of present-day species.
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Hybrids in Real Time
TL;DR: A simple result is presented to show that, despite the presence of Reticulation, there is always a well-defined underlying tree that corresponds to those parts of life that do not have a history of reticulation.
Phylogenetic relationships and biogeography of Ranunculus and allied genera (Ranunculaceae) in the Mediterranean region and in the European Alpine System
TL;DR: The results from this study suggest that the split of allied genera from Ranunculus s.l.s. occurred during the Eocene and Oligocene, and a hypothesis of an origin of alpine buttercups from lowland ancestors of the same geographical region is supported.
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