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Phylogeny01:23

Phylogeny

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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.
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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.
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Statically indeterminate problems are those where statics alone can not determine the internal forces or reactions. Consider a structure comprising two cylindrical rods made of steel and brass. These rods are joined at point B and restrained by rigid supports at points A and C. Now, the reactions at points A and C and the deflection at point B are to be determined. This rod structure is classified as statically indeterminate as the structure has more supports than are necessary for maintaining...
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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...
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Updated: Mar 28, 2026

A Practical Guide to Phylogenetics for Nonexperts
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Cophylogenetic Reconciliation with ILP.

Nicolas Wieseke, Tom Hartmann, Matthias Bernt

    IEEE/ACM Transactions on Computational Biology and Bioinformatics
    |December 17, 2015
    PubMed
    Summary

    CoRe-ILP is a new integer linear programming (ILP) method for host-parasite cophylogenetic reconciliation. It optimizes time consistency and prioritizes cospeciation events, outperforming other reconciliation tools.

    Area of Science:

    • Computational Biology
    • Bioinformatics
    • Evolutionary Biology

    Background:

    • Cophylogenetic reconciliation aims to understand the coevolutionary history of hosts and their parasites.
    • Existing methods often rely on predefined event costs or simplified models.
    • Incorporating phylogenetic branch lengths can refine reconciliation accuracy.

    Purpose of the Study:

    • To introduce CoRe-ILP, an integer linear programming (ILP) approach for time-consistent cophylogenetic host-parasite reconciliation.
    • To develop a model that prioritizes cospeciation and minimizes host switching events without explicit cost assignments.
    • To leverage phylogenetic branch lengths for improved ancestral interaction inference.

    Main Methods:

    • Integer linear programming (ILP) formulation for cophylogenetic reconciliation.

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  • A simplified event model prioritizing cospeciation and minimizing host switching.
  • Integration of phylogenetic branch lengths to filter ancestral interactions.
  • Implementation using IBM ILOG CPLEX Optimizer 12.6.

    • Main Results:

    • CoRe-ILP successfully utilizes phylogenetic branch length information for reconciliation.
    • The method demonstrates strong performance on both biological and simulated datasets.
    • CoRe-ILP results show competitive or superior outcomes compared to established tools like Jane 4, Treemap 3b, NOTUNG 2.8 Beta, and Ranger-DTL.

    Conclusions:

    • CoRe-ILP offers an effective and accurate approach to time-consistent cophylogenetic host-parasite reconciliation.
    • The integration of branch lengths enhances the biological relevance of reconciliation outcomes.
    • CoRe-ILP provides a valuable, freely available tool for evolutionary biology research.