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

By L. Waits, Gordon Luikart, P. Taberlet. Molecular Ecology, 2001

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Citations in the corpus

The role of genotypic diversity in determining grassland community structure under constant environmental conditions (2007, neutral): “(modified after Waits et al . 2001; L. P. Waits, pers.”
Estimating Population Size of Elusive Animals with DNA from Hunter‐Collected Feces: Four Methods for Brown Bears (2005, methodology): “We also computed the PI between siblings (PIsibs; Waits et al. 2001).”
Wildlife DNA forensics—bridging the gap between conservation genetics and law enforcement (2009, background): “However, important differences exist between human and non-human systems, particularly relating to levels of inbreeding (Ayres & Overall 1999, Waits et al. 2001) which require explicit consideration.”
Ecological investigations of grizzly bears in Canada using DNA from hair, 1995–2005: a review of methods and progress (2010, methodology): “Waits et al. (2001) developed a similar method to deal with this problem by considering the theoretical probability of a sibling genetic match based on population-level allele frequencies.”
Colonization History and Noninvasive Monitoring of a Reestablished Wolverine Population (2004, background): “Based on the obtained allele frequencies in the southern Norwegian wolverine population, the probability of identity across these nine loci was estimated to be as low as 1.29 × 10−5 for unrelated individuals and 7.8 × 10−3 for siblings (Waits et al. 2001).”
Abundance of humpback whales in Oceania using photo-identification and microsatellite genotyping (2012, background): “Given the large number of loci and the potential for false exclusion because of allelic dropout and other genotype error (Waits & Leberg 2000, Waits et al. 2001), the initial comparisons allowed for mismatches at up to 3 loci.”
The reintroduction of the Eurasian otter (Lutra lutra) into the Netherlands: hidden life revealed by noninvasive genetic monitoring (2010, background): “The probability of identity, P(ID), is the probability that two individuals drawn at random from a population have the same genotype at multiple loci (Creel et al. 2003; Taberlet and Luikart 1999; Waits et al. 2001 ).”
Demographic monitoring of an entire species (the northern hairy‐nosed wombat, Lasiorhinus krefftii) by genetic analysis of non‐invasively collected material (2003, background): “…only one offspring at a time and exhibit post-weaning dispersal (Johnson & Crossman, 1991), full siblings are likely to be sufficiently rare in the population that the actual PID may be closer to the estimate for unrelated individuals than in species with multiple litters (Waits et al., 2001).”
Remote collection of animal DNA and its applications in conservation management and understanding the population biology of rare and cryptic species (2003, methodology): “Studies to identify individuals by DNA fingerprinting can employ the statistic ‘probability of identity’ (PID), which enables the determination of the number of loci with given levels of heterozygosity required to distinguish confidently between a pair of individuals (Waits et al. 2001).”
Importance of a pilot study for non-invasive genetic sampling: genotyping errors and population size estimation in red deer (2006, background): “As advocated in Waits et al. (2001), the observed probability in the population ranged from unbiased PID to PID for siblings.”
Estimating population size by genotyping remotely plucked hair: the Eurasian badger (2004, methodology): “However, given the fact that PID-Sib is the upper limit of the possible ranges of PID in a population ( Waits, Luikart & Taberlet 2001 ) and that the two most informative loci were enough to distinguish the profiles of the animals captured in the core study area, we judged the seven loci to be suffi”
Snow leopard Panthera uncia predation on livestock and wild prey in a mountain valley in northern Nepal: implications for conservation management (2012, background): “Based on the observed allele frequencies of the applied loci, we estimated the probability of identity (PI) to be 4.8x10-6 for unrelated individuals and 0.03 for siblings, suggesting that different individuals could be distinguished reliably in the valley (cf. Waits et al. 2001).”
Current trends in microsatellite genotyping (2011, methodology): “HSNP Kruglyak (1997), Waits et al. (2001), Seddon et al. (2005) Parentage analysis 5 This estimate was obtained using SNPs with minor allele frequency >0.2.”
Catastrophic cat predation: A call for predator profiling in wildlife protection programs (2015, methodology): “GENECAP (Wilberg and Dreher, 2004) was used to detect genotyping errors in the capture-mark-recapture (CMR) data set and to calculate probability of identity P(ID) and probability of identity siblings P(ID)sib (Waits et al., 2001) for the 10 loci.”