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Effects of microsatellite null alleles on assignment testing.

Jens Carlsson1

  • 1Duke University Marine Laboratory, Nicholas School of the Environment and Earth Sciences, 135 Duke Marine Laboratory Road, Beaufort, NC 28516-9721, USA. jens.carlsson@duke.edu

The Journal of Heredity
|June 7, 2008
PubMed
Summary

Microsatellite null alleles slightly reduce assignment test accuracy but may not alter overall outcomes. Use caution with these loci, preferring those less prone to null alleles for reliable genetic studies.

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Area of Science:

  • Population Genetics
  • Molecular Ecology
  • Bioinformatics

Background:

  • Microsatellite null alleles are prevalent across taxa and can distort genetic analyses.
  • Null alleles can inflate genetic differentiation (FST) and create false homozygotes.
  • Their impact on assignment testing, crucial for population structure inference, is less understood.

Purpose of the Study:

  • To investigate the effect of microsatellite null alleles on model-based clustering and Bayesian assignment tests.
  • To quantify the bias introduced by null alleles in assignment accuracy and FST estimation.

Main Methods:

  • Simulations were used to model the presence of null alleles at varying frequencies (0.000 to 0.913).
  • Assignment success rates were evaluated using STRUCTURE and GENECLASS software.
  • FST values were calculated to assess the impact on genetic differentiation estimates.

Main Results:

  • Null alleles significantly, though slightly, reduced the percentage of correctly assigned individuals in assignment tests.
  • Assignment power decreased by 0.2-1.0% for STRUCTURE and 2.4% for GENECLASS.
  • A small but significant overestimation of FST was observed in the presence of null alleles.

Conclusions:

  • Microsatellite null alleles have a minor impact on the overall outcome of assignment testing.
  • Loci with null alleles should be used cautiously as they reduce assignment power and FST accuracy.
  • Prioritizing loci less prone to null alleles is recommended for robust genetic studies.