Parentage analyses
COLONY was run with 23 loci in the same configuration as for marker set calibration, to assign candidate mother-offspring relationships and to infer the genotype of unknown parents. For genotyped mothers (n=107), an offspring assignment probability threshold of 0.9 was used based on the results of the above calibration. For genotypes that were reconstructed, COLONY only provides a probability per locus. A probability threshold of 0.9 is usually a good choice for conservative results, however, in our case, this threshold would discard 93% of the genotypes. Thus, probability thresholds from 0.4 to 0.9 were examined to determine the best trade-off between conservative and robust results (i.e. number of samples retained) (Supplementary Data 2). Finally, only reconstructed loci with a probability superior to 0.8 were retained for the analyses, while the others were considered as missing data. Like genotyped individuals, individuals with missing data at more than 3 loci were discarded.
Finally, the dataset was checked for inconsistencies (for example, when more than one mother was found for a single nest) and the least likely relationship (i.e. with the lowest probability) was removed. Ultimately, a parent-offspring relationship was only retained when both parents (assigned or reconstructed) passed the different thresholds: 0.9 for assigned mothers, 0.8 for reconstructed loci, and less than 3 missing loci for a given genotype.
From parentage assignments, OSR, female and male reproduction frequencies were determined. Additionally, within-season parameters such as multipaternity, female nesting interval, and the number of partners for males, were reported. The effect of multipaternity on fitness parameters (clutch size, number of hatchlings, number of dead embryos) was investigated by performing a two-tailed Student’s t-test on the average.