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Related Experiment Videos

Constructing primate phylogenies from ancient retrovirus sequences.

W E Johnson1, J M Coffin

  • 1Department of Molecular Microbiology, Tufts University School of Medicine, Boston, MA 02111, USA.

Proceedings of the National Academy of Sciences of the United States of America
|September 1, 1999
PubMed
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Human endogenous retroviruses (HERVs) offer a powerful tool for tracing primate evolutionary history. Analyzing HERV sequences provides robust phylogenetic markers, revealing ancient viral infections and host relationships.

Area of Science:

  • Genomics
  • Evolutionary Biology
  • Virology

Background:

  • Modern human genomes contain thousands of endogenous retroviruses (HERVs), remnants of ancient primate viral infections.
  • Most HERVs are nonfunctional and selectively neutral, making them suitable for phylogenetic analysis.
  • Endogenous retroviruses (ERVs) offer phylogenetic insights through integration site polymorphism and nucleotide sequence comparison.

Purpose of the Study:

  • To utilize HERVs as phylogenetic markers for studying primate evolutionary history.
  • To explore the utility of noncoding long terminal repeats (LTRs) of ERVs in constructing phylogenetic trees.
  • To leverage the unique characteristics of HERVs for comparison with established primate phylogeny.

Main Methods:

  • Construction of phylogenetic trees using noncoding LTRs from multiple ERV loci.

Related Experiment Videos

  • Independent evolution of LTRs from a single ERV locus provides dual phylogenetic estimates.
  • Analysis of tree topology sensitivity to conversion events for recombination detection and correction.

    • Main Results:

    • Phylogenetic trees were constructed using ERV LTR sequences.
    • The independent evolution of LTRs allowed for multiple phylogenetic estimations from single loci.
    • Sensitivity to conversion events facilitated detection and correction for recombination.

    Conclusions:

    • HERVs serve as valuable and abundant phylogenetic markers for primate evolution.
    • ERV sequences, particularly LTRs, provide a robust method for reconstructing evolutionary history.
    • This approach offers a unique resource for understanding the co-evolution of Retroviridae and their hosts.