Assessing Parent Numbers from Offspring Genotypes: The Importance of Marker Polymorphism

Department of Zoology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria.
The Journal of heredity (Impact Factor: 2.09). 04/2009; 100(2):197-205. DOI: 10.1093/jhered/esn095
Source: PubMed


Methods to infer parent numbers from offspring genotypes either determine the minimum number of parents required to explain
alleles and multilocus genotypes detected in the offspring or use models to incorporate information on population allele frequencies
and allele segregation. Disparate results by different approaches suggest that one or perhaps all methods are subject to bias.
Here, we investigate the performance of minimum parent number estimates, maximum likelihood, and Bayesian analyses (programs
COLONY and PARENTAGE) with respect to marker information content in simulated data sets without knowledge of parental genotypes.
Offspring families of different sizes were assumed to share one parent and to be sired by 1 or 5 additional parents. All methods
committed large errors in terms of underestimation (minimum value) and overestimation (COLONY), or both (PARENTAGE) of parent
numbers, unless the data were highly informative, and their relative performances depended on full-sib group sizes and sire
numbers. Increasing the number of markers with low gene diversity (He ≤ 0.68) yielded only slow improvement of the results, but all 3 methods performed well with 5–7 markers of He = 0.84. We emphasize the importance of high marker polymorphism for inferring parent numbers and individual parent contributions,
as well as for the detection of monogamous reproduction.

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    • "respectively , while COLONY (both PLS and FPLS) inferred S of 0–0.07 through overestimation of the minimum number of sires required to explain a progeny array. This sort of bias had already been documented for the latter approach earlier (Sefc & Koblmuller, 2009; Whitehead et al., 2015). The obtained results show that even for markers with high levels of polymorphism (sufficient for the identification of genotypes), a high proportion of genetically identical individuals in a population suffering from a strong genetic bottleneck may bring uncertainty to the estimation of mating system parameters based on genetic data. "
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