All that Glisters is not Galled

@article{Rossell2009AllTG,
  title={All that Glisters is not Galled},
  author={Francesc Rossell{\'o} and Gabriel Valiente},
  journal={Mathematical biosciences},
  year={2009},
  volume={221 1},
  pages={
          54-9
        }
}

Figures from this paper

Comparison of Galled Trees

To which extent several distance measures for the comparison of evolutionary networks are metrics for galled trees, and hence, when they can be safely used to evaluate galled tree reconstruction methods are established.

Uprooted Phylogenetic Networks

It is shown that not only can a so-called (uprooted) 1-nested network N be obtained from the Buneman graph associated with the split system $$Sigma (N)$$Σ(N) induced on the set of leaves of N but also that that graph is, in a well-defined sense, optimal.

Identifying Species Network Features from Gene Tree Quartets Under the Coalescent Model

  • H. Baños
  • Computer Science
    Bulletin of mathematical biology
  • 2019
It is shown that many topological features of level-1 species networks are identifiable from the distribution of the gene tree quartets under the network multi-species coalescent model, a step toward justifying the inference of such networks.

Identifying Species Network Features from Gene Tree Quartets Under the Coalescent Model

  • H. Baños
  • Computer Science
    Bulletin of Mathematical Biology
  • 2018
It is shown that many topological features of level-1 species networks are identifiable from the distribution of the gene tree quartets under the network multi-species coalescent model, a step toward justifying the inference of such networks.

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

It is shown 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-parameters constraints.

Two Results on Distances for Phylogenetic Networks

We establish two new results on distances for phylogenetic networks. First, that Nakhleh’s metric for reduced networks [15] is a metric on the class of semibinary tree-sibling networks, being thus

Phylogenetic consensus networks: Computing a consensus of 1-nested phylogenetic networks

The approach builds on a previous result by Roselló et al. that describes an encoding for any 1-nested phylogenetic network in terms of a collection of ordered pairs of subsets of X and uses this characterization to compute a consensus network in O(t|X| + |X|) time.

Spaces of phylogenetic networks from generalized nearest-neighbor interchange operations

This paper considers spaces of phylogenetic networks defined by some novel local operations that are modeled on the well-studied nearest-neighbor interchange operations on phylogenetic trees, 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.

Spaces of phylogenetic networks from generalized nearest-neighbor interchange operations

This paper considers spaces of phylogenetic networks defined by some novel local operations that are modeled on the well-studied nearest-neighbor interchange operations on phylogenetic trees, 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.

NANUQ: a method for inferring species networks from gene trees under the coalescent model

A new algorithm for statistical inference of a level-1 species network under the network multispecies coalescent model is proposed, from data consisting of gene tree topologies, and the theoretical justification for it is provided.

References

SHOWING 1-10 OF 27 REFERENCES

Beyond Galled Trees - Decomposition and Computation of Galled Networks

A Decomposition Theorem is proved for galled networks, in which reticulations are not necessarily independent, but may overlap in a tree-like manner, and a fixed-parameter-tractable algorithm for computing such networks from trees or binary sequences is presented.

Reconstructing Reticulate Evolution in SpeciesTheory and Practice

Two new methods for reconstructing reticulate evolution of species due to events such as horizontal transfer or hybrid speciation are presented, based upon extensions of Wayne Maddison's approach in his seminal 1997 paper.

Reconstructing reticulate evolution in species: theory and practice

We present new methods for reconstructing reticulate evolution of species due to events such as horizontal transfer or hybrid speciation; both methods are based upon extensions of Wayne Maddison's

The Fine Structure of Galls in Phylogenetic Networks

The main contribution here is to show how structure in the phylogenetic network is reflected in the structure of an efficiently-computable graph, called the conflict graph, both for purposes of insight into phylogenetic networks and to speed up parts of the previous algorithm.

A Decomposition Theory for Phylogenetic Networks and Incompatible Characters

The conjecture from Gusfield and Bansal (2005) is disproved in general, the answer to the conjecture is yes in several natural special cases, and the proof is constructive and leads to a polynomial-time algorithm to find the unique underlying maximal tree structure.

Unicyclic networks: compatibility and enumeration

  • C. SempleM. Steel
  • Biology
    IEEE/ACM Transactions on Computational Biology and Bioinformatics
  • 2006
This work characterize when a set of binary phylogenetic trees is displayed by a unicyclic network in terms of tree rearrangement operations, which leads to a triple-wise compatibility theorem and a simple, fast algorithm to determine 1-cycle compatibility.

Constructing Level-2 Phylogenetic Networks from Triplets

It is shown that, assuming density, it is tractable to construct plausible evolutionary histories from input triplets even when such histories are heavily nontree-like, which further strengthens the case for the use of triplet-based methods in the construction of phylogenetic networks.

Efficient reconstruction of phylogenetic networks with constrained recombination

This paper considers the problem of determining whether the sequences can be derived on a phylogenetic network where the recombination cycles are node disjoint, and develops an efficient algorithm that is guaranteed to be both a necessary and sufficient test for the existence of a galled-tree for the data.

Perfect phylogenetic networks with recombination

It is shown that the problem of finding a perfect phylogenetic network with the minimum number of recombination events is NP-hard; an efficient polynomial time algorithm is presented for an interesting restricted version of the problem.

Optimal, Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination

It is proved that if there is a galled-tree, then the one produced by the algorithm minimizes the number of recombinations over all phylogenetic networks for the data, even allowing multiple-crossover recombinations.