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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

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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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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...
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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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Survival Tree

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A Practical Guide to Phylogenetics for Nonexperts
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Probability Steiner trees and maximum parsimony in phylogenetic analysis.

J F Weng1, I Mareels, D A Thomas

  • 1Department of Mechanical Engineering, The University of Melbourne, Melbourne, VIC 3010, Australia. jfweng@unimelb.edu.au

Journal of Mathematical Biology
|June 28, 2011
PubMed
Summary

This study introduces a probability representation model for phylogenetic trees (PTs), offering a novel approach to evolutionary pathway analysis. The new model provides plausible alternative ancestral states and branch lengths compared to the classical maximum parsimony method.

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Area of Science:

  • Computational Biology
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Phylogenetic tree (PT) construction is crucial for understanding evolutionary relationships.
  • The maximum parsimony (MP) method is a widely used approach for inferring PTs based on observable sequence changes.
  • Non-uniqueness in evolutionary pathways within the MP method necessitates alternative modeling strategies.

Purpose of the Study:

  • To introduce and investigate a novel probability representation model for phylogenetic trees.
  • To construct probability phylogenetic trees (PPTs) using a parsimony criterion.
  • To compare the PPT approach with the classical MP method in terms of inferred evolutionary pathways.

Main Methods:

  • Developed a probability representation model where nodes in a PT are represented by probability distributions of nucleotide or amino acid states.
  • Modeled the PT at each site as a probability Steiner tree in a high-dimensional vector space.
  • Constructed PPTs using the parsimony criterion and compared them with trees derived from the classical MP method.

Main Results:

  • The optimal topology and total tree length of PPTs are consistent with those from the classical MP method for a given input set.
  • Inferred ancestral states and branch lengths differ between the PPT and classical MP methods.
  • The PPT approach yields plausible alternative evolutionary inferences.

Conclusions:

  • The probability representation model offers a valuable alternative for phylogenetic inference, particularly when dealing with non-unique evolutionary pathways.
  • This new model provides a more nuanced understanding of evolutionary history by incorporating probabilistic states.
  • Further research can explore the broader applications and implications of probability phylogenetic trees in evolutionary studies.