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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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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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Phylogenetic Trees03:21

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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.
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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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A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Using phylogenetic profiles to predict functional relationships.

Matteo Pellegrini1

  • 1Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA. matteop@mcdb.ucla.edu

Methods in Molecular Biology (Clifton, N.J.)
|December 7, 2011
PubMed
Summary
This summary is machine-generated.

Phylogenetic profiling compares gene family evolution to infer functional relationships. This method aids in understanding gene function, particularly for protein-coding genes, by identifying coupled evolutionary patterns.

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Genomics

Background:

  • Phylogenetic profiling compares phylogenetic data across gene families to identify coupled evolution.
  • This technique assumes that correlated evolution between gene families suggests a functional relationship.
  • It is primarily applied to protein-coding genes to infer their cellular roles.

Purpose of the Study:

  • To explore the concept and applications of phylogenetic profiling in computational biology.
  • To review various implementations and methodologies of phylogenetic profiling.
  • To highlight available software and databases for performing phylogenetic profiling analysis.

Main Methods:

  • Construction of phylogenetic trees or related data structures for gene families.
  • Comparison of phylogenetic profiles (e.g., binary vectors) across different gene families.
  • Analysis of coevolution patterns of protein families on phylogenetic trees.

Main Results:

  • Identified dozens of implementations of phylogenetic profiling developed over the last decade.
  • Demonstrated the range of methods from simple binary vectors to complex coevolution models.
  • Highlighted the utility of phylogenetic profiling in inferring functional relationships between genes.

Conclusions:

  • Phylogenetic profiling is a powerful approach for inferring functional linkages between genes based on evolutionary patterns.
  • The technique can predict functional coupling, such as involvement in protein complexes or biochemical pathways.
  • Numerous tools and databases exist to facilitate the application of phylogenetic profiling in biological research.