20 research outputs found
Algorithms for Visualizing Phylogenetic Networks
We study the problem of visualizing phylogenetic networks, which are
extensions of the Tree of Life in biology. We use a space filling visualization
method, called DAGmaps, in order to obtain clear visualizations using limited
space. In this paper, we restrict our attention to galled trees and galled
networks and present linear time algorithms for visualizing them as DAGmaps.Comment: Appears in the Proceedings of the 24th International Symposium on
Graph Drawing and Network Visualization (GD 2016
Level-k Phylogenetic Network can be Constructed from a Dense Triplet Set in Polynomial Time
Given a dense triplet set , there arise two interesting
questions: Does there exists any phylogenetic network consistent with
? And if so, can we find an effective algorithm to construct one?
For cases of networks of levels or 1 or 2, these questions were answered
with effective polynomial algorithms. For higher levels , partial answers
were recently obtained with an time algorithm for
simple networks. In this paper we give a complete answer to the general case.
The main idea is to use a special property of SN-sets in a level-k network. As
a consequence, we can also find the level-k network with the minimum number of
reticulations in polynomial time
Constructing the Simplest Possible Phylogenetic Network from Triplets,
A phylogenetic network is a directed acyclic graph that visualises
an evolutionary history containing so-called reticulations such
as recombinations, hybridisations or lateral gene transfers. Here we consider
the construction of a simplest possible phylogenetic network consistent
with an input set T, where T contains at least one phylogenetic
tree on three leaves (a triplet) for each combination of three taxa. To
quantify the complexity of a network we consider both the total number
of reticulations and the number of reticulations per biconnected component,
called the level of the network. We give polynomial-time algorithms
for constructing a level-1 respectively a level-2 network that contains a
minimum number of reticulations and is consistent with T (if such a
network exists). In addition, we show that if T is precisely equal to the
set of triplets consistent with some network, then we can construct such
a network, which minimises both the level and the total number of reticulations,
in time O(|T|^{k+1}), if k is a fixed upper bound on the level
When two trees go to war
Rooted phylogenetic networks are often constructed by combining trees,
clusters, triplets or characters into a single network that in some
well-defined sense simultaneously represents them all. We review these four
models and investigate how they are related. In general, the model chosen
influences the minimum number of reticulation events required. However, when
one obtains the input data from two binary trees, we show that the minimum
number of reticulations is independent of the model. The number of
reticulations necessary to represent the trees, triplets, clusters (in the
softwired sense) and characters (with unrestricted multiple crossover
recombination) are all equal. Furthermore, we show that these results also hold
when not the number of reticulations but the level of the constructed network
is minimised. We use these unification results to settle several complexity
questions that have been open in the field for some time. We also give explicit
examples to show that already for data obtained from three binary trees the
models begin to diverge
Phylogenetic Networks Do not Need to Be Complex: Using Fewer Reticulations to Represent Conflicting Clusters
Phylogenetic trees are widely used to display estimates of how groups of
species evolved. Each phylogenetic tree can be seen as a collection of
clusters, subgroups of the species that evolved from a common ancestor. When
phylogenetic trees are obtained for several data sets (e.g. for different
genes), then their clusters are often contradicting. Consequently, the set of
all clusters of such a data set cannot be combined into a single phylogenetic
tree. Phylogenetic networks are a generalization of phylogenetic trees that can
be used to display more complex evolutionary histories, including reticulate
events such as hybridizations, recombinations and horizontal gene transfers.
Here we present the new CASS algorithm that can combine any set of clusters
into a phylogenetic network. We show that the networks constructed by CASS are
usually simpler than networks constructed by other available methods. Moreover,
we show that CASS is guaranteed to produce a network with at most two
reticulations per biconnected component, whenever such a network exists. We
have implemented CASS and integrated it in the freely available Dendroscope
software
Kernelizations for the hybridization number problem on multiple nonbinary trees
Given a finite set , a collection of rooted phylogenetic
trees on and an integer , the Hybridization Number problem asks if there
exists a phylogenetic network on that displays all trees from
and has reticulation number at most . We show two kernelization algorithms
for Hybridization Number, with kernel sizes and
respectively, with the number of input trees and their maximum
outdegree. Experiments on simulated data demonstrate the practical relevance of
these kernelization algorithms. In addition, we present an -time
algorithm, with and some computable function of
Spaces of phylogenetic networks from generalized nearest-neighbor interchange operations
Phylogenetic networks are a generalization of evolutionary or phylogenetic trees that are used to represent the evolution of species which have undergone reticulate evolution. In this paper we consider spaces of such networks defined by some novel local operations that we introduce for converting one phylogenetic network into another. These operations are modeled on the well-studied nearest-neighbor interchange (NNI) operations on phylogenetic trees, and lead to natural generalizations of the tree spaces that have been previously associated to such operations. We present several results on spaces of some relatively simple networks, called level-1 networks, including the size of the neighborhood of a fixed network, and bounds on the diameter of the metric defined by taking the smallest number of operations required to convert one network into another.We expect that our results will be useful in the development of methods for systematically searching for optimal phylogenetic networks using, for example, likelihood and Bayesian approaches
Constructing level-2 phylogenetic networks from triplets
Jansson and Sung showed that, given a dense set of input triplets T
(representing hypotheses about the local evolutionary relationships of triplets
of species), it is possible to determine in polynomial time whether there
exists a level-1 network consistent with T, and if so to construct such a
network. They also showed that, unlike in the case of trees (i.e. level-0
networks), the problem becomes NP-hard when the input is non-dense. Here we
further extend this work by showing that, when the set of input triplets is
dense, the problem is even polynomial-time solvable for the construction of
level-2 networks. This shows that, assuming density, it is tractable to
construct plausible evolutionary histories from input triplets even when such
histories are heavily non-tree like. This further strengthens the case for the
use of triplet-based methods in the construction of phylogenetic networks. We
also show that, in the non-dense case, the level-2 problem remains NP-hard