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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...
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,...
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...
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Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...

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Updated: Jun 14, 2026

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things).

Liam J Revell1,2

  • 1Department of Biology, University of Massachusetts Boston, Boston, MA, USA.

Peerj
|January 9, 2024
PubMed
Summary
This summary is machine-generated.

The phytools R package offers a comprehensive suite of tools for phylogenetic comparative analysis, aiding researchers in trait evolution and diversification studies. This software facilitates diverse phylogenetic biology research with numerous functions and updated workflows.

Keywords:
Computational biologyPhylogenetic comparative methodsPhylogeny

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Area of Science:

  • Evolutionary Biology
  • Computational Biology
  • Bioinformatics

Background:

  • Phylogenetic comparative methods utilize phylogenetic trees for secondary inferences on trait evolution, diversification, biogeography, and community ecology.
  • The phytools R package has become a key research tool in phylogenetic comparative analysis over the last decade.
  • phytools is a widely used R library with hundreds of functions for various phylogenetic biology tasks.

Purpose of the Study:

  • To describe significant features and recent updates of the phytools R package.
  • To illustrate popular workflows within the phytools computational software.
  • To highlight the utility of phytools in phylogenetic comparative analysis.

Main Methods:

  • Utilizing the phytools R package for phylogenetic comparative analyses.
  • Implementing functions for fitting models of trait evolution.
  • Applying methods for reconstructing ancestral states and studying diversification on trees.
  • Employing visualization tools for phylogenies and comparative data.

Main Results:

  • phytools provides extensive functionality for diverse phylogenetic biology research.
  • The package includes methods for trait evolution, ancestral state reconstruction, and diversification analysis.
  • Recent updates enhance the package's capabilities and usability for researchers.

Conclusions:

  • phytools is an essential and evolving R package for phylogenetic comparative methods.
  • The software supports a wide array of analyses in evolutionary biology and related fields.
  • Continued development of phytools benefits the broader scientific community in phylogenetic research.