Estimating the probability of identity among genotypes in natural populations: cautions and guidelines

• Published in: Molecular Ecology
• Main Authors: Waits, L. P., Luikart, G., Taberlet, P.
• Other Authors: Laboratoire d'Ecologie Alpine (LECA), Université Joseph Fourier - Grenoble 1 (UJF)-Université Savoie Mont Blanc (USMB Université de Savoie Université de Chambéry )-Centre National de la Recherche Scientifique (CNRS), Department of Fish and Wildlife Resources, University of Idaho Moscow, USA
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2001
• Subjects: DNA fingerprinting; match probability; microsatellites; noninvasive genetic sampling; population estimation; probability of identity; WOMBAT LASIORHINUS-KREFFTII; MICROSATELLITE ANALYSIS; GENETIC-VARIATION; BROWN BEARS; DNA; AFLP; HAIR; INDIVIDUALS; DIVERSITY; BLACK; [SDE.BE]Environmental Sciences/Biodiversity and Ecology; [SDV.BID]Life Sciences [q-bio]/Biodiversity; [SDV.EE]Life Sciences [q-bio]/Ecology; environment; Canis lupus; Ursus arctos
• Online Access: https://hal.science/halsde-00279799; https://doi.org/10.1046/j.1365-294X.2001.01185.x

Times Cited: 153 International audience 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).