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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...
Molecular Models02:00

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
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...
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...
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,...

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A Practical Guide to Phylogenetics for Nonexperts
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A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

A model for phylogenetic inference using structural and chemical covariates.

S Tavaré1, D C Adams, O Fedrigo

  • 1Departments of Biological Sciences, Mathematics and Preventative Medicine, University of Southern California, Los Angeles, CA 90089, USA.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
|March 27, 2001
PubMed
Summary

DNA base pair evolution is not uniform. Nucleotide sites cluster into five distinct groups based on codon position and degeneracy, impacting models of molecular evolution.

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Area of Science:

  • Molecular Evolution
  • Genomics
  • Bioinformatics

Background:

  • Evolutionary change in DNA sequences is typically modeled assuming homogeneity.
  • Understanding variation in evolutionary rates across different nucleotide sites is crucial for accurate phylogenetic inference.

Purpose of the Study:

  • To investigate if evolutionary change in DNA sequence data is homogeneous across different classes of base pairs.
  • To identify distinct classes of nucleotide sites that exhibit differential evolutionary behavior.

Main Methods:

  • Obtained DNA sequences for eight protein-coding mitochondrial genes from 38 vertebrate taxa.
  • Classified nucleotide sites by codon position, genetic code degeneracy, and hydrophobicity.
  • Estimated evolutionary transition matrices using parsimony on a phylogenetic tree and analyzed with canonical variates analysis.

Main Results:

  • Identified five distinct clusters of transition matrices, primarily defined by codon position and degeneracy.
  • This clustering pattern was consistent across all investigated mitochondrial genes.
  • A stochastic model incorporating covariates significantly explained more sequence variation than simpler models.

Conclusions:

  • Confirms that different classes of base pairs evolve at different rates.
  • Suggests that incorporating covariate information into models of sequence evolution can improve accuracy.
  • Highlights a common underlying process in the molecular evolution of the mitochondrial genome.