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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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Phylogenomics with paralogs.

Marc Hellmuth1, Nicolas Wieseke2, Marcus Lechner3

  • 1Center for Bioinformatics, Saarland University, D-66041 Saarbrücken, Germany; mhellmuth@bioinf.uni-sb.de.

Proceedings of the National Academy of Sciences of the United States of America
|February 4, 2015
PubMed
Summary
This summary is machine-generated.

Phylogenomics can now include gene duplications, not just 1:1 orthologs, by distinguishing paralogs. This approach uses gene duplication information to build accurate species phylogenetic trees, even with horizontal gene transfer.

Keywords:
cographgene treeorthologyparalogyspecies tree

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Area of Science:

  • Evolutionary Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Phylogenomics traditionally requires 1:1 orthologs, excluding gene duplications (paralogs).
  • Paralogs are often removed as noise, potentially losing valuable phylogenetic signals.
  • Recent mathematical phylogenetics advances offer new ways to analyze gene family evolution.

Purpose of the Study:

  • To demonstrate that gene duplications (paralogs) contain significant phylogenetic information.
  • To show that accurate phylogenetic trees can be inferred by distinguishing orthologs from paralogs.
  • To develop methods for incorporating gene duplication events into species tree reconstruction.

Main Methods:

  • Utilizing tree-free orthology estimation.
  • Applying cograph editing to reduce noise and identify event-annotated gene trees.
  • Translating gene tree information into constraints for species tree inference.

Main Results:

  • Gene duplications provide meaningful phylogenetic information when orthologs and paralogs are distinguishable.
  • Cograph editing effectively filters noise, enabling the reconstruction of accurate gene trees.
  • Genome-wide datasets, even with poor individual gene family resolution, yield fully resolved species trees.
  • The method remains robust in the presence of horizontal gene transfer.

Conclusions:

  • The strict exclusion of paralogs in phylogenomics is unnecessary.
  • Incorporating gene duplication events enhances phylogenetic inference accuracy.
  • This approach offers a more inclusive and powerful method for reconstructing evolutionary histories.