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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

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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.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

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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...
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A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Maximum likelihood of phylogenetic networks.

Guohua Jin1, Luay Nakhleh, Sagi Snir

  • 1Department of Computer Science, Rice University Houston, TX, USA.

Bioinformatics (Oxford, England)
|August 25, 2006
PubMed
Summary

This study introduces a new framework for detecting and reconstructing horizontal gene transfer (HGT) in bacteria. The developed methods accurately identify HGT events and their locations, crucial for understanding bacterial evolution and antibiotic resistance.

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Area of Science:

  • Computational Biology
  • Evolutionary Biology
  • Genomics

Background:

  • Horizontal gene transfer (HGT) is a significant driver of bacterial genome diversification and antibiotic resistance.
  • Accurate detection and reconstruction of HGT are essential due to its evolutionary importance and impact on human health.

Purpose of the Study:

  • To develop a novel HGT-oriented likelihood framework for phylogeny-based HGT detection and reconstruction.
  • To address the computational complexity of HGT reconstruction problems.

Main Methods:

  • Formulation of likelihood criteria for HGT detection and reconstruction.
  • Development of heuristic algorithms to efficiently solve NP-hard HGT reconstruction problems.
  • Implementation and analysis of heuristics on both biological and synthetic datasets.

Main Results:

  • The proposed framework and heuristics demonstrate high performance in identifying the number of HGT events.
  • Accurate inference of HGT event locations on the species tree was achieved.
  • The methods proved effective on both real-world biological and simulated data.

Conclusions:

  • The developed likelihood framework and heuristics offer an efficient and accurate approach for HGT detection and reconstruction.
  • This work provides valuable tools for studying bacterial evolution and the spread of antibiotic resistance.