Abstract
Nuclear SSRs are notorious for having relatively high frequencies of null alleles, i.e. alleles that fail to amplify and are thus recessive and undetected in heterozygotes. In this paper, we compare two kinds of approaches for estimating null allele frequencies at seven nuclear microsatellite markers in three French Fagus sylvatica populations: (1) maximum likelihood methods that compare observed and expected homozygote frequencies in the population under the assumption of Hardy-Weinberg equilibrium and (2) direct null allele frequency estimates from progeny where parent genotypes are known. We show that null allele frequencies are high in F. sylvatica (7.0% on average with the population method, 5.1% with the progeny method), and that estimates are consistent between the two approaches, especially when the number of sampled maternal half-sib progeny arrays is large. With null allele frequencies ranging between 5% and 8% on average across loci, population genetic parameters such as genetic differentiation (F ST) may be mostly unbiased. However, using markers with such average prevalence of null alleles (up to 15% for some loci) can be seriously misleading in fine scale population studies and parentage analysis.
This is a preview of subscription content, log in via an institution to check access.
References
Asuka Y, Tani N, Tsumura Y, Tomaru N (2004) Development and characterization of microsatellite markers for Fagus crenata Blume. Mol Ecol Notes 4:101–103
Brookfield JFY (1996) A simple new method for estimating null allele frequency from heterozygote deficiency. Mol Ecol 5:453–455
Callen DF, Thompson AD, Shen Y, Phillips HA, Richards RI, Mulley JC, Sutherland GR (1993) Incidence and origin of null alleles in the (AC)n microsatellite markers. Am J Hum Genet 52:922–927
Chakraborty R, De Andrade M, Daiger SP, Budowle B (1992) Apparent heterozygote deficiencies observed in DNA typing data and their implications in forensic applications. Ann Hum Genet 56:45–57
Chapuis M-P, Estoup A (2007) Microsatellite null alleles and estimation of population differentiation. Mol Biol Evol 24:621–631
Dakin EE, Avise JC (2004) Microsatellite null alleles in parentage analysis. Heredity 93:504–509
Dempster AP, Laird NM, Rubin DB (1977) Maximum likelihood from incomplete data via the EM algorithm. J R Stat Soc 39:1–38
De Sousa SN, Finkeldey R, Gailing O (2005) Experimental verification of microsatellite null alleles in Norway spruce (Picea abies [L.] Karst.): Implications for population genetic studies. Plant Mol Biol Rep 23:113–119
Kalinowski ST, Taper ML (2006) Maximum likelihood estimation of the frequency of null alleles at microsatellite loci. Conserv Genet 7:991–995
Magri D, Vendramin GG et al (2006) A new scenario for the quaternary history of European beech populations: palaeobotanical evidence and genetic consequences. New Phytol 171:199–221
Marshall TC, Slate J, Kruuk LEB, Pemberton JM (1998) Statistical confidence for likelihood-based paternity inference in natural populations. Mol Ecol 7:639–655
Pastorelli R, Smulders MJM, Van’t Westende WPC, Vosman B, Giannini R, Vettori C, Vendramin GG (2003) Characterization of microsatellite markers in Fagus sylvatica L. and Fagus orientalis Lipsky. Mol Ecol Notes 3:76–78
Rousset F (2008) Genepop’007: a complete re-implementation of the genepop software for Windows and Linux. Mol Ecol Resour 8:103–106
Summers K, Amos W (1997) Behavioral, ecological, and molecular genetic analyses of reproductive strategies in the Amazonian dart-poison frog, Dendrobates ventrimaculatus. Behav Ecol 8:260–267
Tanaka K, Tsumura Y, Nakamura T (1999) Development and polymorphism of microsatellite markers for Fagus crenata and the closely related species, F. japonica. Theor Appl Genet 99:11–15
Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370
Wagner AP, Creel S, Kalinowski ST (2006) Estimating relatedness and relationships using microsatellite loci with null alleles. Heredity 97:336–345
Acknowledgements
Data used for this paper were generated in the course of the European project DYNABEECH (Contract QLRT-1999-01210) and of a national project supported by the French Bureau des Ressources Génétiques (project BRG No. 88-2003-2004, AIP 223). A meeting for co-writing of this paper was supported by the European Commission through the Network of Excellence EVOLTREE (contract number: 016322) under the Sixth Framework Programme. We thank B. Jouaud, A. Roig (INRA, Avignon, France) and R. Pastorelli (CNR, Firenze, Italy) for laboratory work, as well as J. Glaubitz, and one anonymous reviewer for detailed comments on a previous version of the manuscript.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Oddou-Muratorio, S., Vendramin, G.G., Buiteveld, J. et al. Population estimators or progeny tests: what is the best method to assess null allele frequencies at SSR loci?. Conserv Genet 10, 1343–1347 (2009). https://doi.org/10.1007/s10592-008-9648-4
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10592-008-9648-4