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Indel-based evolutionary distance and mouse-human divergence.

Aleksey Y Ogurtsov1, Shamil Sunyaev, Alexey S Kondrashov

  • 1National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20892, USA.

Genome Research
|August 4, 2004
PubMed
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We developed a new method to measure evolutionary distance using insertions and deletions (indels). This approach accurately estimates divergence between DNA sequences, even with frequent large indel events.

Area of Science:

  • Evolutionary biology
  • Molecular evolution
  • Genomics

Background:

  • Estimating evolutionary distance is crucial for understanding species divergence.
  • Insertions and deletions (indels) are key drivers of genetic variation.
  • Saturation from frequent indels can complicate distance estimation.

Purpose of the Study:

  • To propose a novel method for estimating evolutionary distance based on indel accumulation.
  • To derive a maximal likelihood estimate for indel-based evolutionary distance.
  • To assess the accuracy of the method using mammalian sequence data.

Main Methods:

  • Utilizing differences in lengths of orthologous introns or delimited sequence segments.
  • Applying a maximal likelihood estimation framework.

Related Experiment Videos

  • Analyzing sequence divergence in terms of per site indel accumulation.

    • Main Results:

    • The method accurately recovers known evolutionary distance between rat and mouse (0.014 indels/site).
    • Mouse-human divergence is estimated to be four times greater than rat-mouse divergence.
    • Mouse-human evolutionary distance is calculated as 0.056 indels/site and approximately 0.8 substitutions/site.

    Conclusions:

    • The proposed method provides a precise estimation of indel-based evolutionary distance.
    • Saturation is not a significant obstacle for this method due to substantial long indel frequencies.
    • Mammalian evolutionary distances can be reliably quantified using indel accumulation, offering insights into divergence rates.