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Related Concept Videos

Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
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Block Diagram Reduction01:22

Block Diagram Reduction

The process of deriving the transfer function of a control system often involves reducing its block diagram to a single block. This simplification can be achieved through a series of strategic operations, including relocating branch points and comparators. These operations preserve the overall function of the system while allowing for easier manipulation and combination of blocks.
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Phylogenetic Trees03:21

Phylogenetic Trees

Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...
Phylogenetic Trees03:21

Phylogenetic Trees

Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...
Survival Tree01:19

Survival Tree

Survival trees are a non-parametric method used in survival analysis to model the relationship between a set of covariates and the time until an event of interest occurs, often referred to as the "time-to-event" or "survival time." This method is particularly useful when dealing with censored data, where the event has not occurred for some individuals by the end of the study period, or when the exact time of the event is unknown.
 Building a Survival Tree
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Restricted trees: simplifying networks with bottlenecks.

Stephen J Willson1

  • 1Department of Mathematics, Iowa State University, Ames, IA 50011, USA. swillson@iastate.edu

Bulletin of Mathematical Biology
|March 2, 2011
PubMed
Summary

This study introduces a method to simplify complex phylogenetic networks into a "restricted tree." This process ensures fundamental evolutionary relationships are preserved in a more understandable format.

Area of Science:

  • Phylogenetics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Phylogenetic networks model complex evolutionary histories, including hybridizations and lateral gene transfers.
  • Simplifying these networks into trees is crucial for understanding fundamental relationships.
  • Existing methods for network simplification lack uniformity and clear definitions.

Purpose of the Study:

  • To present a uniform and well-defined procedure for deriving a species tree from a phylogenetic network.
  • To introduce the concept of a "restricted" connected surjective digraph (CSD) map for network simplification.
  • To define and construct the "restricted tree" of a given phylogenetic network.

Main Methods:

  • Defining a "restricted" set of vertices in a phylogenetic network as a bottleneck.

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  • Introducing a "restricted" connected surjective digraph (CSD) map between networks.
  • Developing a uniform procedure to generate a restricted tree from any given phylogenetic network.

    • Main Results:

    • A uniform procedure is established to yield a well-defined tree, termed the "restricted tree," from a phylogenetic network.
    • A restricted CSD map is demonstrated to exist from the original network to its restricted tree.
    • Key evolutionary relationships present in the tree are proven to be conserved within the original network.

    Conclusions:

    • The "restricted tree" provides a simplified yet accurate representation of fundamental evolutionary relationships from complex phylogenetic networks.
    • The introduced methodology offers a standardized approach to phylogenetic network simplification.
    • This work facilitates a clearer understanding of evolutionary histories in the presence of reticulate evolution.