api‐calc 1.0: a computer program for calculating the average probability of identity allowing for substructure, inbreeding and the presence of close relatives

Abstract

Individual identification via DNA profiling is important in molecular ecology, particularly in the case of noninvasive sampling. A key quantity in determining the number of loci required is the probability of identity (PIave), the probability of observing two copies of any profile in the population. Previously this has been calculated assuming no inbreeding or population structure. Here we introduce formulae that account for these factors, whilst also accounting for relatedness structure in the population. These formulae are implemented in api‐calc 1.0, which calculates PIave for either a specified value, or a range of values, for FIS and FST.

Bridging the gaps between non-invasive genetic sampling and population parameter estimation

“…Fortunately, underestimation of abundance caused by the shadow effect can be identified using population level statistics such as probability of identity (PI) and probability of identity of siblings (PI SIB ), and eliminated by increasing the number of variable molecular markers used to produce a molecular tag (Mills et al 2000). One problem with using the probability of identity statistics is that they are population level statistics which assume no inbreeding, or population structure, and most populations have some undetected level of subdivision or structured composition, whether created by landscapes, social behaviour or territorial dynamics (Ayres and Overall 2004). Ayres and Overall (2004) developed a new and more robust probability of identity test (PI AVE ) which take into account these factors, as well as the relatedness structure of the population.…”

“…One problem with using the probability of identity statistics is that they are population level statistics which assume no inbreeding, or population structure, and most populations have some undetected level of subdivision or structured composition, whether created by landscapes, social behaviour or territorial dynamics (Ayres and Overall 2004). Ayres and Overall (2004) developed a new and more robust probability of identity test (PI AVE ) which take into account these factors, as well as the relatedness structure of the population. However, these statistics are seldom used in the literature and have not been thoroughly evaluated in natural populations.…”

Concordance study between the ParaDNA ® Intelligence Test, a Rapid DNA profiling assay, and a conventional STR typing kit (AmpFlSTR ® SGM Plus ® )

“…The multi-locus probability of identity (system PI), calculated by multiplying the individual PI values of each locus, is often used as a measure of the discriminatory ability of a profiling system [18]. The PI for the ParaDNA Intelligence Test system was calculated at 3.71 x10 -7 suggesting the average probability of observing a random matching profile (PM) from this population was about 1 in 2.7 million.…”

“…Polymorphism Information Content (PIC) was calculated in Excel following [17]. Probability of Identity (PI) was calculated using ApiCalc [18]. Power of Discrimination (PD) and Power of Exclusion (PE) were calculated following [19].…”

Studies on Genetic Diversity and Phylogenetic Relationships of Korean Native Chicken using the Microsatellite Marker

“…API-CALC ver 1.0 (Ayres and Overall, 2004) 프로그램을 사용하여 동일개체 출현빈도를 계산하였으며, DISPAN (Ota, 1993, Nei, 1983 프 로그램을 통해 각 집단에 대하여 유전적 거리는 NeighborJoining 방법 (Saitou and Nei, 1987 …”