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Reliability assessment of null allele detection: inconsistencies between and within different methods
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
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2014 (English)In: Molecular Ecology Resources, ISSN 1755-098X, Vol. 14, no 2, 361-373 p.Article in journal (Refereed) Published
Abstract [en]

Microsatellite loci are widely used in population genetic studies, but the presence of null alleles may lead to biased results. Here, we assessed five methods that indirectly detect null alleles and found large inconsistencies among them. Our analysis was based on 20 microsatellite loci genotyped in a natural population of Microtus oeconomus sampled during 8years, together with 1200 simulated populations without null alleles, but experiencing bottlenecks of varying duration and intensity, and 120 simulated populations with known null alleles. In the natural population, 29% of positive results were consistent between the methods in pairwise comparisons, and in the simulated data set, this proportion was 14%. The positive results were also inconsistent between different years in the natural population. In the null-allele-free simulated data set, the number of false positives increased with increased bottleneck intensity and duration. We also found a low concordance in null allele detection between the original simulated populations and their 20% random subsets. In the populations simulated to include null alleles, between 22% and 42% of true null alleles remained undetected, which highlighted that detection errors are not restricted to false positives. None of the evaluated methods clearly outperformed the others when both false-positive and false-negative rates were considered. Accepting only the positive results consistent between at least two methods should considerably reduce the false-positive rate, but this approach may increase the false-negative rate. Our study demonstrates the need for novel null allele detection methods that could be reliably applied to natural populations.

Place, publisher, year, edition, pages
2014. Vol. 14, no 2, 361-373 p.
Keyword [en]
heterozygosity, bottleneck, microsatellite loci, genotyping errors, null alleles, Microtus oeconomus
National Category
Natural Sciences
URN: urn:nbn:se:uu:diva-220981DOI: 10.1111/1755-0998.12177ISI: 000331469500013OAI: oai:DiVA.org:uu-220981DiVA: diva2:707735
Available from: 2014-03-25 Created: 2014-03-24 Last updated: 2014-03-25Bibliographically approved

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Dabrowski, MichalUmer, Husen Muhammad
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Computational and Systems BiologyDepartment of Cell and Molecular Biology
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