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Related Concept Videos

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.
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.
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...
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.
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...

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Related Experiment Video

Updated: May 27, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Characterizing the phylogenetic tree-search problem.

Daniel Money1, Simon Whelan

  • 1Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK.

Systematic Biology
|November 15, 2011
PubMed
Summary
This summary is machine-generated.

Maximum likelihood tree-search in phylogenetics is complex. This study reveals heuristics like subtree-pruning-and-regrafting perform well, while nearest-neighbor-interchange is less effective for finding optimal phylogenetic trees.

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Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

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Related Experiment Videos

Last Updated: May 27, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

A Practical Guide to Phylogenetics for Nonexperts
12:00

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Published on: February 5, 2014

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Area of Science:

  • Computational Biology
  • Phylogenetics
  • Bioinformatics

Background:

  • Phylogenetic trees are crucial for understanding evolutionary relationships and genome annotation.
  • Finding the optimal phylogenetic tree is an NP-hard problem, requiring heuristic search algorithms.
  • Limited understanding exists regarding tree-search characteristics and their interaction with statistical inference.

Purpose of the Study:

  • To examine maximum likelihood tree-search performance on diverse, real genome-scale datasets.
  • To investigate the characteristics and interactions of tree-search algorithms in phylogenetics.
  • To identify trends that can inform the development of improved tree-search heuristics.

Main Methods:

  • Analyzed all possible trees for 106 genes in an eight-taxa yeast dataset.
  • Applied and compared different tree-search algorithms (nearest-neighbor-interchange, subtree-pruning-and-regrafting).
  • Extended analysis to larger genome-scale and disparate datasets for benchmarking.

Main Results:

  • The best (maximum likelihood) tree often exhibits the shortest branch lengths.
  • Tree-search heuristics show a weak tendency to recover the optimal tree.
  • Genes with higher information content tend to present fewer local optima during tree-search.
  • Subtree-pruning-and-regrafting consistently performs well, nearing the best tree, unlike nearest-neighbor-interchange.
  • Implementation details, including parameter optimization timing, significantly impact tree-search outcomes.

Conclusions:

  • Heuristic performance in phylogenetic tree-search varies significantly by algorithm.
  • Subtree-pruning-and-regrafting is a more reliable heuristic for finding optimal trees.
  • Optimizing tree-search strategies, potentially by combining methods, is key for accurate phylogenetic inference.