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Mean d(2) and divergence time: transformations and standardizations.

B D Neff1

  • 1Department of Biology, University of Western Ontario, London, Ontario N6A 5B7, Canada. bneff@uwo.ca

The Journal of Heredity
|April 10, 2004
PubMed
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Mean d(2), a measure of parental haplotype relatedness, effectively predicts divergence time over long evolutionary scales. While heterozygosity is better for short periods, mean d(2) excels at detecting longer-term genetic divergence.

Area of Science:

  • Population Genetics
  • Evolutionary Biology
  • Molecular Ecology

Background:

  • Inbreeding and outbreeding fitness consequences are key biological questions.
  • Mean d(2) is a novel relatedness measure suited for microsatellite markers.
  • Its utility for detecting inbreeding vs. outbreeding depression requires further investigation.

Purpose of the Study:

  • To identify optimal standardization and transformations for mean d(2).
  • To evaluate mean d(2) as a measure of parental lineage divergence time.
  • To compare mean d(2) with heterozygosity for detecting genetic divergence over various timescales.

Main Methods:

  • Simulations were used to test mean d(2) performance.
  • Appropriate standardization coefficients and transformations were identified.

Related Experiment Videos

  • Mean d(2) was evaluated as a predictor of divergence time up to 10,000 generations.

    • Main Results:

    • Mean d(2) linearly predicts divergence time.
    • Logarithm transformation is recommended for homoscedasticity.
    • Mean d(2) outperforms heterozygosity for divergence times over 1,000 generations.
    • Gene flow as low as 1% can impair divergence time estimation.

    Conclusions:

    • Mean d(2) is a valuable tool for estimating long-term divergence times.
    • Standardization and transformation enhance mean d(2) precision.
    • Careful consideration of gene flow is crucial when using genetic relatedness measures.