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Assessment of power and accuracy of methods for detection and frequency-estimation of null alleles

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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.

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Abbreviations

CI:

Confidence interval

F NULL :

Null allele frequency (parameter of the frequency distribution)

\(\hat{F}_{\text{NULL}} \) :

Null allele frequency (estimation from a sample)

H E-TOT :

Heterozygosity calculated with both null and visible alleles (parameter)

Ĥ E-TOT :

Heterozygosity calculated with both null and visible alleles (estimation)

H E-VIS :

Heterozygosity calculated with visible alleles only (parameter)

Ĥ E-VIS :

Heterozygosity calculated with visible alleles only (estimation)

H O :

Frequency of individuals having two visible alleles (parameter)

Ĥ 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)

\(\hat{N}_{\text{VIS}} \) :

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

rBROOK2 :

Null allele frequency estimation according to the Brookfield2 estimator

TBR2:

Brookfield2 test

UT:

U-test

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Acknowledgements

We thank Pascale Gibeau, Isabelle Bouthillier, Isabelle Gaudet, Geneviève Roy and Bénédicte Poncet for field and lab work. This work was supported by an NSERC research grant to BA. We are also grateful to Emilie Castonguay for very helpful comments. PG was financially supported by NATEQ, the Fond Étienne-Magnin, the Faculté des Études Supérieure of Université de Montréal and the Département des Sciences Biologiques.

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Correspondence to Philippe Girard.

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Girard, P., Angers, B. Assessment of power and accuracy of methods for detection and frequency-estimation of null alleles. Genetica 134, 187–197 (2008). https://doi.org/10.1007/s10709-007-9224-8

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  • DOI: https://doi.org/10.1007/s10709-007-9224-8

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