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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,...
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.
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...
Basic Plant Anatomy: Roots, Stems, and Leaves02:27

Basic Plant Anatomy: Roots, Stems, and Leaves

The primary organs of vascular plants are roots, stems, and leaves, but these structures can be highly variable, adapted for the specific needs and environment of different plant species.

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Related Experiment Video

Updated: May 22, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Rooting gene trees without outgroups: EP rooting.

Janet S Sinsheimer, Roderick J A Little, James A Lake

    Genome Biology and Evolution
    |May 18, 2012
    PubMed
    Summary
    This summary is machine-generated.

    This study introduces new evolutionary parsimony (EP) methods to root gene trees directly from sequence data, even without outgroups or gene paralogs. These algorithms enable rooted phylogenetic analysis, advancing evolutionary biology research.

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    Published on: May 2, 2018

    Area of Science:

    • Evolutionary Biology
    • Molecular Evolution
    • Bioinformatics

    Background:

    • Phylogenetic trees are crucial for understanding evolutionary relationships.
    • Determining the root of a phylogenetic tree is essential for many evolutionary questions.
    • Current methods for rooting gene trees often rely on outgroups or gene paralogs, which are not always available.

    Purpose of the Study:

    • To develop novel algorithms for rooting gene trees directly from gene and genomic sequences.
    • To provide methods for phylogenetic analysis in the absence of outgroups and gene paralogs.
    • To extend the principles of evolutionary parsimony (EP) for tree rooting.

    Main Methods:

    • Explicitly enumerated linear invariants containing rooting information based on evolutionary parsimony (EP).
    • Derived algorithms for rooting gene trees using sequence data.
    • Extended EP rooting invariants for three-taxon trees and provided rules for more taxa.
    • Applied the method to 18S ribosomal DNA sequences to root the animal phylogeny.

    Main Results:

    • Developed new EP linear rooting invariants that allow direct rooting of gene trees from sequence data.
    • Successfully rooted phylogenetic trees without the need for outgroups or gene paralogs.
    • Demonstrated the method's efficacy on short sequences and in the absence of paralogs.
    • The rooted animal phylogeny is consistent with current scientific consensus.

    Conclusions:

    • The new EP rooting invariants provide a powerful tool for phylogenetic analysis when outgroups or paralogs are unavailable.
    • This method facilitates the determination of rooted trees directly from gene and genomic sequences.
    • The approach advances the study of evolutionary relationships, particularly for ancient divergences.