DOI: 10.5061/dryad.2ht96
title: Data from: Relative accuracy of three common methods of parentage analysis in natural populations

description: Parentage studies and family reconstructions have become increasingly
 popular for investigating a range of evolutionary, ecological and
 behavioral processes in natural populations. However, a number of
 different assignment methods have emerged in common use, and the accuracy
 of each may differ in relation to the number of loci examined, allelic
 diversity, incomplete sampling of all candidate parents, and the presence
 of genotyping errors. Here we examine how these factors affect the
 accuracy of three popular parentage inference methods (COLONY, FaMoz and
 an exclusion-Bayes’ theorem approach by Christie et al. (2010a)) to
 resolve true parent-offspring pairs using simulated data. Our findings
 demonstrate that accuracy increases with the number and diversity of loci.
 These were clearly the most important factors in obtaining accurate
 assignments explaining 75-90% of variance in overall accuracy across 60
 simulated scenarios. Furthermore, the proportion of candidate parents
 sampled had a small but significant impact on the susceptibility of each
 method to either false positive or false negative assignments. Within the
 range of values simulated, COLONY outperformed FaMoz, which outperformed
 the exclusion-Bayes’ theorem method. However, with 20 or more highly
 polymorphic loci, all methods could be applied with confidence. Our
 results show that for parentage inference in natural populations, careful
 consideration of the number and quality of markers will increase the
 accuracy of assignments and mitigate the effects of incomplete sampling of
 parental populations.
description: N500_adults_20percentSimulated data - N500 low diversity population with 20% of adults sampled and 20 microsatellite loci. The first 10 and 15 loci were subset for analyses with 10 and 15 loci.N500_adults_40percentSimulated data - N500 low diversity population with 40% of adults sampled and 20 microsatellite loci. The first 10 and 15 loci were subset for analyses with 10 and 15 loci.N500_adults_60percentSimulated data - N500 low diversity population with 60% of adults sampled and 20 microsatellite loci. The first 10 and 15 loci were subset for analyses with 10 and 15 loci.N500_adults_80percentN500_adults_100percentSimulated data - N500 low diversity population with 100% of adults sampled and 20 microsatellite loci. The first 10 and 15 loci were subset for analyses with 10 and 15 loci.N1000_adults_20percentSimulated data - N1000 high diversity population with 20% of adults sampled and 20 microsatellite loci. The first 10 and 15 loci were subset for analyses with 10 and 15 loci.N1000_adults_40percentSimulated data - N1000 high diversity population with 40% of adults sampled and 20 microsatellite loci. The first 10 and 15 loci were subset for analyses with 10 and 15 loci.N1000_adults_60percentSimulated data - N1000 high diversity population with 60% of adults sampled and 20 microsatellite loci. The first 10 and 15 loci were subset for analyses with 10 and 15 loci.N1000_adults_80percentSimulated data - N1000 high diversity population with 80% of adults sampled and 20 microsatellite loci. The first 10 and 15 loci were subset for analyses with 10 and 15 loci.N1000_adults_100percentSimulated data - N1000 high diversity population with 20% of adults sampled and 20 microsatellite loci. The first 10 and 15 loci were subset for analyses with 10 and 15 loci.N500_juveniles_0.1percenterrorSimulated data - N500 low diversity offspring with 0.1% genotyping error rates. The first 10 and 15 loci were subset for analyses with 10 and 15 loci.N500_juveniles_1.0percenterrorSimulated data - N500 low diversity offspring with 1.0% genotyping error rates. The first 10 and 15 loci were subset for analyses with 10 and 15 loci.N1000_juveniles_0.1percenterrorSimulated data - N1000 high diversity offspring with 0.1% genotyping error rates. The first 10 and 15 loci were subset for analyses with 10 and 15 loci.N1000_juveniles_1.0percenterrorSimulated data - N1000 high diversity offspring with 1.0% genotyping error rates. The first 10 and 15 loci were subset for analyses with 10 and 15 loci.Methods resultsResults of parentage analyses using simulated data - Results from COLONY, FaMoz and an exclusion-Bayes' theorem approach by Christie et al. (Mol. Ecol. Res. 2010, 10, 115-128) to resolve true parent-offspring pairs under 60 simulated scenarios that incrementally simulate the number of loci, allelic diversity , adult sample size and genotyping error.Supp.Mat. R-ScriptsSupplementary R-script for processing software outputs of COLONY, FaMoz and an exclusion-Bayes theorem approach by Christie et al. (Mol. Ecol. Res. 2010, 10, 115-128). Script also includes details of the Generalized Linear Model to assess the relative variance attributed to different factor affecting the accuracy of assignments.