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Related Concept Videos

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...
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...
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...
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,...
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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Updated: Jun 6, 2026

Enumeration of Neural Stem Cells Using Clonal Assays
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Enumeration of Neural Stem Cells Using Clonal Assays

Published on: October 4, 2016

Are node-based and stem-based clades equivalent? Insights from graph theory.

Jeremy Martin1, David Blackburn, E O Wiley

  • 1University of Kansas; University of Kansas Biodiversity Institute and The University of Kansas.

Plos Currents
|March 2, 2012
PubMed
Summary
This summary is machine-generated.

This study clarifies the biological meaning of stem-based and node-based phylogenetic trees, showing they contain identical information but differ in evolutionary concept representation. Proper naming conventions must align with the tree type to avoid logical inconsistencies in systematics.

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Area of Science:

  • Systematics and evolutionary biology
  • Mathematical modeling in biology
  • Phylogenetic analysis

Background:

  • The interpretation of mathematical models for phylogenetic relationships can be unclear.
  • Systematists and evolutionary biologists widely use "tree-thinking" but may misunderstand different tree representations.

Purpose of the Study:

  • To compare and clarify the biological meaning of stem-based and node-based phylogenetic trees.
  • To provide an algorithm for translating between stem-based and node-based tree models.
  • To establish clear guidelines for naming clades based on tree type.

Main Methods:

  • Comparison of two discrete mathematical models: stem-based and node-based trees.
  • Development of a translation algorithm between the two tree types.
  • Analysis of how evolutionary concepts like monophyly are represented in each model.

Main Results:

  • Stem-based and node-based trees carry identical information and have similar biological interpretations.
  • A simple algorithm facilitates translation between stem-based and node-based tree representations.
  • Monophyly is represented differently in stem-based versus node-based trees, necessitating distinct naming conventions.

Conclusions:

  • Clarifying the mathematical representation of phylogenetic trees is crucial for accurate biological interpretation.
  • Consistent application of stem-based or node-based naming conventions with their respective tree types is essential.
  • Misapplication of naming conventions can lead to logical inconsistencies in phylogenetic systematics.