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Related Experiment Videos

The human phylome.

Jaime Huerta-Cepas1, Hernán Dopazo, Joaquín Dopazo

  • 1Bioinformatics Department, Centro de Investigación Príncipe Felipe, Autopista del Saler, 46013 Valencia, Spain.

Genome Biology
|June 15, 2007
PubMed
Summary
This summary is machine-generated.

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We reconstructed the human phylome, detailing evolutionary relationships of human proteins and homologs across 39 eukaryotes. This analysis reveals gene duplication events and aids in understanding evolutionary transitions.

Area of Science:

  • Evolutionary biology
  • Genomics
  • Bioinformatics

Background:

  • Phylogenomics is crucial for understanding evolutionary relationships.
  • A complete phylome (all gene phylogenies in a genome) is valuable but challenging for large genomes.
  • Interpreting phylomes requires new methodologies.

Purpose of the Study:

  • To reconstruct the human phylome, encompassing all human proteins and their homologs.
  • To analyze evolutionary relationships among 39 eukaryotic genomes.
  • To develop and apply novel methods for orthology and paralogy determination.

Main Methods:

  • Utilized advanced phylogenetic techniques: alignment trimming, branch length optimization, evolutionary model testing, maximum likelihood, and Bayesian methods.
  • Applied a novel algorithm for deriving orthology and paralogy relationships independent of species phylogeny.

Related Experiment Videos

  • Assessed gene duplication events and their functional roles.

    • Main Results:

    • Reconstructed the human phylome, showing evolutionary links among 39 eukaryotes.
    • Supported key evolutionary hypotheses (Coelomata, Unikont) and primate-laurasatherian grouping.
    • Identified evidence for at least one to two whole genome duplication events before vertebrate radiation.
    • Derived orthology and paralogy relationships for human proteins.

    Conclusions:

    • Gene-sampling effects can influence phylogenomic analyses due to topological variations.
    • Duplicated gene families correlate with major evolutionary transitions.
    • The implemented pipeline is adaptable for other organisms.