Estimating the probability of identity among genotypes in natural populations: cautions and guidelines
Abstract
Individual identification using DNA fingerprinting methods is emerging as a critical tool in conservation genetics and molecular ecology. Statistical methods that estimate the probability of sampling identical genotypes using theoretical equations generally assume random associations between alleles within and among loci. These calculations are probably inaccurate for many animal and plant populations due to population substructure. We evaluated the accuracy of a probability of identity (P(ID)) estimation by comparing the observed and expected P(ID), using large nuclear DNA microsatellite data sets from three endangered species: the grey wolf (Canis lupus), the brown bear (Ursus arctos), and the Australian northern hairy‐nosed wombat (Lasiorinyus krefftii). The theoretical estimates of P(ID) were consistently lower than the observed P(ID), and can differ by as much as three orders of magnitude. To help researchers and managers avoid potential problems associated with this bias, we introduce an equation for P(ID) between sibs. This equation provides an estimator that can be used as a conservative upper bound for the probability of observing identical multilocus genotypes between two individuals sampled from a population. We suggest computing the actual observed P(ID) when possible and give general guidelines for the number of codominant and dominant marker loci required to achieve a reasonably low P(ID) (e.g. 0.01–0.0001).
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Probability of identity values were low for all sites, except Zanzibar where PI was 0.014, and were adequate for population studies.
“PIs were low for all sites (PI < 0.01, except in Zanzibar PI = 0.014) and therefore adequate for population studies (Waits et al. 2001).”
From Population genetics of the brooding coral Seriatopora hystrix reveals patterns of strong genetic differentiation in the Western Indian Ocean (2021) · cites this paper as Waits et al. 2001
Cites
AFLP: a new technique for DNA fingerprinting
Vos, P., Hogers, R. C. J., Bleeker, M., Reijans, M., van de Lee, T., Hornes, M., Frijters, A., Pot, J., Paleman, J., Kuiper, M. T. R., et al. (1995) · Nucleic Acids Research · doi:10.1093/nar/23.21.4407 · Cited by 12,433 · see citing works
ESTIMATION OF AVERAGE HETEROZYGOSITY AND GENETIC DISTANCE FROM A SMALL NUMBER OF INDIVIDUALS
Nei, M. (1978) · Genetics · doi:10.1093/genetics/89.3.583 · Cited by 11,499 · see citing works
Nowak, R. (2018) · doi:10.1353/book.59141 · Cited by 4,102 · see citing works
Reliable genotyping of samples with very low DNA quantities using PCR
Taberlet, P. (1996) · Nucleic Acids Research · doi:10.1093/nar/24.16.3189 · Cited by 1,491 · see citing works
Self-citationNoninvasive genetic sampling: look before you leap
Taberlet, P., Waits, L. P., & Luikart, G. (1999) · Trends in Ecology & Evolution · doi:10.1016/s0169-5347(99)01637-7 · Cited by 1,081 · see citing works
Self-citationAFLP genotyping and fingerprinting
Mueller, U. G., & Wolfenbarger, L. L. (1999) · Trends in Ecology & Evolution · doi:10.1016/s0169-5347(99)01659-6 · Cited by 967 · see citing works
Schönswetter, P., Popp, M., & Brochmann, C. (2006) · Journal of Biogeography · doi:10.1111/j.1365-2699.2006.01462.x · Cited by 694 · see citing works
Microsatellite analysis of genetic variation in black bear populations
Paetkau, D., & Strobeck, C. (1994) · Molecular Ecology · doi:10.1111/j.1365-294x.1994.tb00127.x · Cited by 658 · see citing works
Microsatellites and their application to population genetic studies
Bruford, M. W., & Wayne, R. K. (1993) · Current Opinion in Genetics & Development · doi:10.1016/0959-437x(93)90017-j · Cited by 607 · see citing works
Estimating population size by genotyping faeces
Kohn, M. H., York, E. C., Kamradt, D. A., Haught, G., Sauvajot, R. M., & Wayne, R. K. (1999) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.1999.0686 · Cited by 574 · see citing works
Genetic tagging of free-ranging black and brown bears
Woods, J. G., Paetkau, D., Lewis, D. L., McLellan, B. N., Proctor, M. F., & Strobeck, C. (1999) · Cited by 566 · see citing works
First Course in Population Genetics
Li, C. C. (1976) · Medical Entomology and Zoology · Cited by 535 · see citing works
Noninvasive genetic tracking of the endangered Pyrenean brown bear population
Taberlet, P., Camarra, J.-J., GRIFFIN, S., et al. (1997) · Molecular Ecology · doi:10.1111/j.1365-294x.1997.tb00141.x · Cited by 494 · see citing works
Self-citationESTIMATING ANIMAL ABUNDANCE USING NONINVASIVE DNA SAMPLING: PROMISE AND PITFALLS
Mills, L. S., Citta, J. J., Lair, K. P., Schwartz, M. K., & Tallmon, D. A. (2000) · Ecological Applications · doi:10.1890/1051-0761(2000)010[0283:eaaund]2.0.co;2 · Cited by 488 · see citing works
Gagneux, P., Boesch, C., & Woodruff, D. S. (1997) · Molecular Ecology · doi:10.1111/j.1365-294x.1997.tb00140.x · Cited by 386 · see citing works
Genetic tagging of humpback whales
Palsbøll, P. J., Allen, J. M., Bérubé, M., et al. (1997) · Nature · doi:10.1038/42005 · Cited by 380 · see citing works
Interpreting DNA evidence: statistical genetics for forensic scientists
(1999) · Choice Reviews Online · doi:10.5860/choice.36-6266 · Cited by 367 · see citing works
Taylor, A. C., Sherwin, W. B., & Wayne, R. K. (1994) · Molecular Ecology · doi:10.1111/j.1365-294x.1994.tb00068.x · Cited by 329 · see citing works
Population Genetics in Forensic DNA Typing
Lewontin, R. C., & Hartl, D. L. (1991) · Science · doi:10.1126/science.1845040 · Cited by 314 · see citing works
Lander, E. S. (1989) · Nature · doi:10.1038/339501a0 · Cited by 286 · see citing works
Reed, J. Z., Tollit, D., Thompson, P. M., et al. (1997) · Molecular Ecology · doi:10.1046/j.1365-294x.1997.00175.x · Cited by 275 · see citing works
Interpreting DNA Evidence: Statistical Genetics for Forensic Scientists
Nichols, R. A. (1999) · Heredity · doi:10.1038/sj.hdy.6885562 · Cited by 255 · see citing works
Variation in Genetic Diversity across the Range of North American Brown Bears
Paetkau, D., Waits, L. P., Clarkson, P. L., et al. (1998) · Conservation Biology · doi:10.1111/j.1523-1739.1998.96457.x · Cited by 254 · see citing works
Self-citationThe Utility of DNA Typing in Forensic Work
Chakraborty, R., & Kídd, K. K. (1991) · Science · doi:10.1126/science.1763323 · Cited by 243 · see citing works
Waits, L. P., Taberlet, P., Swenson, J. E., et al. (2000) · Molecular Ecology · doi:10.1046/j.1365-294x.2000.00892.x · Cited by 243 · see citing works
Self-citationPlucked hair samples as a source of DNA: reliability of dinucleotide microsatellite genotyping
Goossens, B., Waits, L. P., & Taberlet, P. (1998) · Molecular Ecology · doi:10.1046/j.1365-294x.1998.00407.x · Cited by 232 · see citing works
Self-citationBiases associated with population estimation using molecular tagging
Waits, J. L., & Leberg, P. L. (2000) · Animal Conservation · doi:10.1111/j.1469-1795.2000.tb00103.x · Cited by 227 · see citing works
Gerloff, U., Schlötterer, C., Rassmann, K., Rambold, I., Hohmann, G., Fruth, B., & Tautz, D. (1995) · Molecular Ecology · doi:10.1111/j.1365-294x.1995.tb00247.x · Cited by 223 · see citing works
Ernest, H. B., Penedo, M. C. T., May, B., Syvanen, M., & Boyce, W. M. (2000) · Molecular Ecology · doi:10.1046/j.1365-294x.2000.00890.x · Cited by 216 · see citing works
Jeffreys, A. J., Turner, M. R., & Debenham, P. G. (1991) · PubMed · Cited by 172 · see citing works
Review of DNA‐based census and effective population size estimators
Schwartz, M. K., Tallmon, D. A., & Luikart, G. (1998) · Animal Conservation · doi:10.1111/j.1469-1795.1998.tb00040.x · Cited by 166 · see citing works
Self-citationClonal diversity in a Rhododendron ferrugineum L. (Ericaceae) population inferred from AFLP markers
Escaravage, N., Questiau, S., Pornon, A., et al. (1998) · Molecular Ecology · doi:10.1046/j.1365-294x.1998.00415.x · Cited by 154 · see citing works
DNA Technology in Forensic Science
National Research Council (1992) · National Academies Press eBooks · doi:10.17226/1866 · Cited by 151 · see citing works
Foran, D. R., Minta, S. C., & Heinemeyer, K. S. (1997) · Medical Entomology and Zoology · Cited by 147 · see citing works
Microsatellite Analysis of Paternity and Reproduction in Arctic Grizzly Bears
Craighead, L., Paetkau, D., Reynolds, H. V., et al. (1995) · Journal of Heredity · doi:10.1093/oxfordjournals.jhered.a111578 · Cited by 144 · see citing works
Noninvasive genetic tracking of the endangered Pyrenean brown bear population
Taberlet, P., Camarra, J.-J., Griffin, S., et al. (1997) · Molecular Ecology · doi:10.1046/j.1365-294x.1997.00251.x · Cited by 136 · see citing works
Self-citationHeterozygote deficiency, population substructure and their implications in DNA fingerprinting
Chakraborty, R., & Li, J. (1992) · Human Genetics · doi:10.1007/bf00197257 · Cited by 134 · see citing works
Power of Sign Surveys to Monitor Population Trends
Kendall, K. C., Metzgar, L. H., Patterson, D. A., et al. (1992) · Ecological Applications · doi:10.2307/1941877 · Cited by 122 · see citing works
The genetics of transferrins in cattle
Jamieson, A. J. (1965) · Heredity · doi:10.1038/hdy.1965.54 · Cited by 119 · see citing works
On the Probability of Matching DNA Fingerprints
RISCH, N. J., & Devlin, B. (1992) · Science · doi:10.1126/science.1738844 · Cited by 116 · see citing works
Taylor, A. C., Horsup, A. B., Johnson, C. N., et al. (1997) · Molecular Ecology · doi:10.1046/j.1365-294x.1997.00146.x · Cited by 96 · see citing works
Genetic Structure and Migration in Native and Reintroduced Rocky Mountain Wolf Populations
Forbes, S. H., & Boyd, D. K. (1997) · Conservation Biology · doi:10.1046/j.1523-1739.1997.96296.x · Cited by 95 · see citing works
DNA Fingerprinting: A Review of the Controversy
Roeder, K. (1994) · Statistical Science · doi:10.1214/ss/1177010488 · Cited by 86 · see citing works
Effects of population structure on DNA fingerprint analysis in forensic science
Nichols, R. A., & Balding, D. J. (1991) · Heredity · doi:10.1038/hdy.1991.37 · Cited by 73 · see citing works
The Evaluation of Forensic DNA Evidence
National Research Council (1996) · National Academies Press eBooks · doi:10.17226/5141 · Cited by 46 · see citing works
Principles and Recent Advances in Human DNA Fingerprinting
Jeffreys, A. J., Royle, N. J., Patel, I., et al. (1991) · Proceedings of the Fourth International Symposium on Polarization Phenomena in Nuclear Reactions · doi:10.1007/978-3-0348-7312-3_1 · Cited by 44 · see citing works
Donnelly, P. (1995) · Heredity · doi:10.1038/hdy.1995.100 · Cited by 33 · see citing works
Self-organized criticality in ecology and evolution
Fukami, T., Zimmermann, C. R., Russell, G. J., et al. (1999) · Trends in Ecology & Evolution · doi:10.1016/s0169-5347(99)01672-9 · Cited by 12 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
SNPs in ecology, evolution and conservation
Morin, P. A., Luikart, G., Wayne, R. K., & the SNP workshop group (2004) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2004.01.009 · Cited by 1,080 · see citing works
Self-citationReliable microsatellite genotyping of the Eurasian badger (<i>Meles meles</i>) using faecal DNA
Frantz, A. C., Pope, L. C., Carpenter, P. J., Roper, T. J., Wilson, G. J., Delahay, R. J., & Burke, T. (2003) · Molecular Ecology · doi:10.1046/j.1365-294x.2003.01848.x · Cited by 266 · see citing works
Van OPPEN, M. J. H., BONGAERTS, P., UNDERWOOD, J. N., PEPLOW, L. M., & COOPER, T. F. (2011) · Molecular Ecology · doi:10.1111/j.1365-294x.2011.05050.x · Cited by 183 · see citing works
Lucchini, V., Galov, A., & Randi, E. (2004) · Molecular Ecology · doi:10.1046/j.1365-294x.2004.02077.x · Cited by 132 · see citing works
Berger, B., Berger, C., Hecht, W., Hellmann, A., Rohleder, U., Schleenbecker, U., & Parson, W. (2014) · Forensic Science International: Genetics · doi:10.1016/j.fsigen.2013.07.002 · Cited by 46 · see citing works
Ruiz-González, A., Madeira, M. J., Randi, E., Urra, F., & Gómez-Moliner, B. J. (2013) · European Journal of Wildlife Research · doi:10.1007/s10344-012-0683-6 · Cited by 37 · see citing works
van der Ven, R. M., Flot, J.-F., Buitrago-López, C., & Kochzius, M. (2021) · Heredity · doi:10.1038/s41437-020-00379-5 · Cited by 26 · see citing works
- Authors
- Waits, L. P., Luikart, G., & Taberlet, P.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Corresponding author
- Waits, Lisette P.
- Venue
- Molecular Ecology
- Publisher
- Wiley
- Published
- 2001-01
- Volume
- 10
- Issue
- 1
- Pages
- 249-256
- ISSN
- 0962-1083 (ISSN-L)
- 1365-294X
- OpenAlex
- W2046403313
- Cited by
- 1,437
- References
- 48
- Citations by year
- 2026: 51 · 2025: 57 · 2024: 72 · 2023: 50 · 2022: 86 · 2021: 89 · 2020: 70 · 2019: 72 · 2018: 73 · 2017: 61 · 2016: 67 · 2015: 70 · 2014: 88 · 2013: 60 · 2012: 86
- FWCI
- 10.58
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Molecular Ecology (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion)
- Funders
- National Science Foundation
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- probability of identity, DNA fingerprinting, microsatellite markers, population substructure, allele association, individual identification, threatened species, grey wolf, brown bear, conservation genetics
- MeSH terms
- Animals, Ursidae, Genetics, Population, Marsupialia, Probability, Models, Statistical, Bias, DNA Fingerprinting, Microsatellite Repeats, Wolves
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
