Conservation Genetics

, Volume 5, Issue 4, pp 539–543 | Cite as

Counting Alleles with Rarefaction: Private Alleles and Hierarchical Sampling Designs

  • Steven T. Kalinowski


The number of alleles (allelic richness) in a population is a fundamental measure of genetic variation, and a useful statistic for identifying populations for conservation. Estimating allelic richness is complicated by the effects of sample size: large samples are expected to have more alleles. Rarefaction solves this problem. This communication extends the rarefaction procedure to count private alleles and to accommodate hierarchical sampling designs.

allelic richness estimation genetic diversity rarefaction sample size species diversity species richness 


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  1. Castric V, Bernatchez L (2003) The rise and fall of isolation by distance in the anadromous brook charr (Salvelinus fontinalis Mitchill). Genetics, 163,983–996.PubMedGoogle Scholar
  2. Comps B, Gömöry D, Letouzey J, Thiébaut B, Petit RJ (2001) Diverging trends between heterozygosity and allelic richness during postglacial colonization in the European beech. Genetics, 157,389–397.PubMedGoogle Scholar
  3. Cornuet JM, Luikart G (1996) Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics, 144,2001–2014.PubMedGoogle Scholar
  4. El Mousadik A, Petit RJ (1996) High level of genetic differen-tiation for allelic richness among populations of the argan tree [Argania spinosa (L.)Skeels ]endemic to Morocco. Theor. Appl.Genet., 92,832–839.Google Scholar
  5. Gotelli NJ, Colwell RK (2001) Quantifying biodiversity: pro-cedures and pitfalls in the measurement and comparison of species richness. Ecol.Lett., 4,379–391.Google Scholar
  6. Heck KL, Van Belle G, Simberloff D (1975) Explicit calculation of the rarefaction diversity measurement and the determi-nation of the suffcient sample size. Ecology, 56, 1459–1461.Google Scholar
  7. Hurlbert SH (1971) The nonconcept of species diversity:a critique and alternative parameters. Ecology, 52, 577–586.Google Scholar
  8. Jin L, Baskett ML, Cavalli-Sforza LL, Zhivotovsky LA, Feld-man MW, Rosenberg NA (2000) Microsatellite evolu-tion in modern humans: a comparison of two data sets from the same populations. Ann.Hum.Genet., 64, 117–134.PubMedGoogle Scholar
  9. King TL, Kalinowski ST, Schill WB, Spidle AP, Lubinski BA (2001) Population structure of Atlantic salmon (Salmo salar L.):a rangewide perspective from microsatellites. Mol. Ecol., 10, 807–821.Google Scholar
  10. Leberg PL (2002) Estimating allelic richness: effects of sample size and bottlenecks. Mol. Ecol., 11,2445–2449.PubMedGoogle Scholar
  11. Petit R, El Mousadik A, Pons O (1998) Identifying populations for conservation on the basis of genetic markers. Conserv. Biol., 12, 844–855.Google Scholar
  12. Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW (2002) Genetic structure of human populations. Science, 298, 2381–2385.PubMedGoogle Scholar
  13. Smith W, Grassle JF (1977) Sampling properties of a family of diversity measures. Biometrics, 33, 283–292.Google Scholar
  14. Simberloff D (1979) Rarefaction as a distribution-free method of expressing and estimating diversity. In: Ecological Diver-sity in Theory and Practice. (eds. Grassle JF, Patil GP, Smith W, Taillie C), International Co-operative Publishing House, Fairland, Maryland.Google Scholar
  15. Tipper JC (1979) Rarefaction and rare ction –the use and abuse of a method in paleoecology. Paleobiology, 5, 423–434.Google Scholar

Copyright information

© Kluwer Academic Publishers 2004

Authors and Affiliations

  • Steven T. Kalinowski
    • 1
  1. 1.Department of EcologyMontana State UniversityBozemanUSA

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