Assessment of power and accuracy of methods for detection and frequency-estimation of null alleles Philippe Girard Æ Bernard Angers Received: 27 April 2007 / Accepted: 1 November 2007 / Published online: 1 December 2007 Ó Springer Science+Business Media B.V. 2007 Abstract Null alleles represent a common artefact of microsatellite-based analyses. Rapid methods for their detection and frequency estimation have been proposed to replace the existing time-consuming laboratory methods. The objective of this paper is to assess the power and accuracy of these statistical tools using both simulated and real datasets. Our results revealed that none of the tests developed to detect null alleles are perfect. However, combining tests allows the detection of null alleles with high confidence. Comparison of the estimators of null allele frequency indicated that those that account for unamplified individuals, such as the Brookfield2 estimator, are more accurate than those that do not. Altogether, the use of statistical tools appeared more appropriate than testing with alternative primers as null alleles often remain undetected following this laborious work. Based on these results, we propose recommendations to detect and correct datasets with null alleles. Keywords Detection tests  Estimators  Heterozygosity  Null alleles  Power  Sample size Abbreviations CI Confidence interval F NULL Null allele frequency (parameter of the frequency distribution) ^ F NULL Null allele frequency (estimation from a sample) H E-TOT Heterozygosity calculated with both null and visible alleles (parameter) H ˆ E-TOT Heterozygosity calculated with both null and visible alleles (estimation) H E-VIS Heterozygosity calculated with visible alleles only (parameter) H ˆ E-VIS Heterozygosity calculated with visible alleles only (estimation) H O Frequency of individuals having two visible alleles (parameter) H ˆ O Frequency of individuals having two visible alleles (estimation) HWE Hardy–Weinberg equilibrium k Total number of alleles MCT Micro-checker test N VIS Number of individuals having at least one visible allele (parameter) ^ N VIS Number of individuals having at least one visible allele (estimation) PCR polymerase chain reaction r CHAK Null allele frequency estimation according to the Chakraborty estimator r BROOK1 Null allele frequency estimation according to the Brookfield1 estimator r BROOK2 Null allele frequency estimation according to the Brookfield2 estimator TBR2 Brookfield2 test UT U-test Introduction Microsatellite markers are short-sequence tandem repeats of 1–6 nucleotides (Wyman and White 1980). Abundant in the P. Girard (&)  B. Angers GRIL, De ´partement des Sciences Biologiques, Universite ´ de Montre ´al, Succ. Centre-Ville, C.P. 6128, Montreal, QC, Canada H3C 3J7 e-mail: philippe.girard@umontreal.ca 123 Genetica (2008) 134:187–197 DOI 10.1007/s10709-007-9224-8