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Related Concept Videos

Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

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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.
In contrast, regions which code...
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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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Gene Duplication and Divergence02:37

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The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
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In a population that is not at Hardy-Weinberg equilibrium, the frequency of alleles changes over time. Therefore, any deviations from the five conditions of Hardy-Weinberg equilibrium can alter the genetic variation of a given population. Conditions that change the genetic variability of a population include mutations, natural selection, non-random mating, gene flow, and genetic drift (small population size).
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Related Experiment Video

Updated: Mar 16, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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Efficient Gene Tree Correction Guided by Genome Evolution.

Emmanuel Noutahi1, Magali Semeria2, Manuel Lafond1

  • 1Département d'Informatique (DIRO), Université de Montréal, H3C3J7 Montréal, Canada.

Plos One
|August 12, 2016
PubMed
Summary
This summary is machine-generated.

ProfileNJ improves gene tree accuracy by integrating species tree and genomic data, resolving weakly supported branches. This method enables genome-wide analysis of gene duplication and loss patterns in eukaryotes.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Phylogenetics

Background:

  • Gene tree inference from sequence alignments often yields uncertain branches.
  • Genomic context and species tree information can resolve these uncertainties.
  • Existing integrative methods are computationally intensive for large-scale genomic databases.

Purpose of the Study:

  • To develop an efficient method for correcting weakly supported gene tree branches.
  • To apply this method to large genomic databases for improved phylogenetic analysis.
  • To enable genome-wide studies of gene duplication and loss patterns.

Main Methods:

  • ProfileNJ method integrates gene tree, species tree, and distance matrix information.
  • The method corrects weakly supported branches in gene trees.
  • Low running time allows application to large databases like Ensembl Compara.

Main Results:

  • ProfileNJ provides a more plausible set of gene trees for the Ensembl Compara database.
  • Genome-wide analysis of gene duplication and loss patterns across 63 eukaryote species was performed.
  • Ancestral gene content and order were predicted for all ancestors in the phylogeny.

Conclusions:

  • ProfileNJ offers an efficient and effective approach for gene tree refinement.
  • The method facilitates large-scale genomic analyses of evolutionary processes.
  • RefineTree web interface and ProfileNJ code are available for broader use.