Calibration of the set of loci
To test the accuracy of the motherhood assignment provided by the
software COLONY v.2.0.6.6 (Jones and Wang, 2010), we calibrated the
assignment probability based on known mother-offspring relationships.
The probability of assignment of a mother was plotted against its true
motherhood, based on the known mother-offspring relationships from the
field, which involved 58 mothers and 275 hatchlings from 105 nests.
COLONY uses a full likelihood model to assign sibship and parentage
relationships using multilocus genotype data. Its algorithm allows for
missing data and genotyping errors. Three long runs were performed with
high likelihood precision, allowing polygamy for both sexes under an
inbreeding model, and assuming an error rate of 0.01 for both allelic
dropout and genotyping error. It is assumed that hatchlings sampled in
2010/11 did not reach sexual maturity by 2020/21 based on the mean age
at maturity of 25 years (Chaloupka et al., 2004), therefore, we did not
consider the occurrence of overlapping generations. All the hatchlings
were considered as potential offspring and all the females were
candidate mothers.
To determine the effect of genotyping errors on the accuracy of
motherhood assignment, the above calibration was run with three
different subsets of markers to determine which one would best perform
in assigning true mother-offspring relationships: subset 1 comprised all
23 loci described in Dolfo et al. (2023); in subset 2 the loci which
were deviant from Hardy-Weinberg equilibrium, as emphasized by the
authors, were removed, leaving 14 loci (list in Supplementary Data 1);
in subset 3 the loci which were given the highest error rate by COLONY
were removed (CMY19, CMY22, and CMY35), leaving 20 loci. Based on this
calibration (Supplementary Data 1) all 23 loci were retained for the
analyses.