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Related Concept Videos

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.
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.
Microbial Phylogeny01:28

Microbial Phylogeny

Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Phylogeny01:23

Phylogeny

Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.
Hybrid Zones02:29

Hybrid Zones

Hybrid zones are narrow regions where two closely related species interact, mate, and produce hybrids. Relative to either parent species, hybrids may possess distinct phenotypic or genetic differences that impact their survival and reproductive success. The genetic variances introduced by hybridization influence species diversity and speciation processes within the hybrid zone.

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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

An algorithm for constructing parsimonious hybridization networks with multiple phylogenetic trees.

Yufeng Wu1

  • 1Computer Science and Engineering Department, 371 Fairfield Road, Unit 2155, University of Connecticut Storrs, CT 06269.

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|October 8, 2013
PubMed
Summary

Researchers developed PIRNC, an exact algorithm for reconstructing minimum hybridization networks from gene trees. This method accurately models reticulate evolution without structural assumptions, offering a significant advancement for phylogenetic analysis.

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Area of Science:

  • Computational Biology
  • Phylogenetics
  • Evolutionary Biology

Background:

  • Phylogenetic networks model reticulate evolution, with hybridization networks displaying multiple gene trees.
  • Reconstructing the most parsimonious hybridization network from gene trees is an NP-hard problem.
  • Existing methods often use heuristics or simplifying assumptions.

Purpose of the Study:

  • To develop an exact algorithm for inferring minimum hybridization networks from multiple gene trees.
  • To provide a method that does not rely on structural assumptions.
  • To offer a computationally feasible approach for phylogenetic network reconstruction.

Main Methods:

  • Developed the exact algorithm PIRNC (Phylogenetic Inference of Reticulate Networks using Computation).
  • Implemented PIRNC without making structural assumptions on network topology.
  • Developed a heuristic version, PIRNCH, for complex networks.

Main Results:

  • PIRNC is the first exact algorithm for inferring minimum hybridization networks from multiple gene trees.
  • PIRNC demonstrates reasonable efficiency for datasets with a small number of reticulation events (≤4).
  • PIRNCH generated networks with fewer reticulation events compared to an existing method in simulations.

Conclusions:

  • PIRNC offers an exact and assumption-free approach to phylogenetic network reconstruction.
  • The PIRN software package, including PIRNC and PIRNCH, is available for practical application.
  • These algorithms advance the accurate modeling of reticulate evolution.