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Journal of Heredity Advance Access originally published online on June 4, 2008
Journal of Heredity 2008 99(6):616-623; doi:10.1093/jhered/esn048
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© The American Genetic Association. 2008. All rights reserved. For permissions, please email: journals.permissions@oxfordjournals.org.

Effects of Microsatellite Null Alleles on Assignment Testing

Jens Carlsson

From the Duke University Marine Laboratory, Nicholas School of the Environment and Earth Sciences, 135 Duke Marine Laboratory Road, Beaufort, NC 28516-9721

Address correspondence to J. Carlsson at the address above, or e-mail: jens.carlsson{at}duke.edu.

Microsatellite null alleles are found to a varying degree across all taxa. They are problematic as they may inflate measures of genetic differentiation and create false homozygotes. Although there are several methods for correcting allele frequencies for null alleles and enable estimations of FST, much less is known about how null alleles affect assignment testing. Data presented here, based on simulations, show that the percentage of correctly assigned individuals in model-based clustering and Bayesian assignment methods were slightly, though significantly, reduced in the presence of null alleles (frequency range from 0.000 to 0.913). The bias in assignment tests caused by null alleles lead to a slight reduction in the power to correctly assigned individuals (0.2 and 1.0 percent units for STRUCTURE- and 2.4 percent units for GENECLASS-based assignment tests). Further, the presence of null alleles caused a small, however, significant overestimation of FST. Consequently, microsatellite loci affected by null alleles would probably not alter the overall outcome of assignment testing and could therefore be included in these types of studies. Nevertheless, loci prone to null alleles should be used with caution as they lower the power of assignment tests and alter the accuracy of FST, and loci less prone to null alleles should always be preferred.

Corresponding Editor: Jose V. Lopez

Received March 12, 2008
Accepted May 5, 2008


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