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Related Concept Videos

Microbial Phylogeny01:28

Microbial Phylogeny

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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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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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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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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.
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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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Phylogeny Building for Structural Phylogenomic Research.

Arshan Nasir1, Gustavo Caetano-Anollés2

  • 1Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA. arshan.nasir@gmail.com.

Methods in Molecular Biology (Clifton, N.J.)
|April 29, 2026
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Summary
This summary is machine-generated.

Structure-based phylogenomic analysis offers advantages over traditional methods for studying organism and virus evolution. This protocol enhances evolutionary insights, especially with AI-driven protein structure prediction.

Keywords:
HMMPhylogeneticsProtein structurePythonSCOPSUPERFAMILYStructural domainTree of Life

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Area of Science:

  • Molecular Biology
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Traditional phylogenies often struggle with complex genomic data, fast-evolving organisms, and accurately representing evolutionary events.
  • Protein structure information provides a robust alternative for phylogenetic analysis, offering improved resolution and handling of evolutionary complexities.
  • Recent advancements in AI-driven protein structure prediction necessitate updated phylogenomic analysis protocols.

Purpose of the Study:

  • To present a generic, adaptable protocol for phylogenomic analysis using molecular structure data.
  • To highlight the advantages of structure-based phylogenies in resolving evolutionary relationships.
  • To provide a timely resource for molecular biologists in the era of AI-driven structure prediction.

Main Methods:

  • Utilizing protein structure information to construct phylogenetic trees.
  • Developing a generic protocol applicable to various molecular structures and characteristics.
  • Illustrating the protocol with viral protein structures.

Main Results:

  • Structure-based phylogenies offer enhanced resolution of basal branches compared to traditional methods.
  • These trees provide a more realistic depiction of evolutionary events like gene duplication and horizontal gene transfer.
  • The protocol demonstrates reduced susceptibility to sequence alignment artifacts.

Conclusions:

  • The presented protocol offers a valuable, adaptable tool for molecular biologists to enrich their phylogenetic analyses.
  • Structure-based phylogenomics is particularly beneficial for studying fast-evolving organisms and viruses.
  • This approach complements traditional methods and leverages advancements in AI for structure prediction.