Relatedness and inbreeding
The inbreeding coefficient (Fis ) was calculated
with GENETIX v4.05.2 (Belkhir et al., 2004) on all genotyped females and
one offspring per nest (n=665). Pairwise relatedness coefficients
(r ) were calculated with the R package related v1.0. (Pew
et al., 2015) for all parent pairs found using COLONY, using sample
allele frequency. Simulations were performed based on the observed
allele frequency to determine which of the four relatedness estimators
implemented in the package performs best on our data (i.e. is the
closest to expected relatedness values). A hundred simulated genotypes
for each of the four relationships were generated and their rcoefficient was calculated (parent-offspring, expected r = 0.5;
full-sibling, expected r = 0.5, half-sibling, expected r =
0.25, unrelated, expected r = 0). The Wang estimator, which
yielded the best fit to expected relatedness values, was then used for
relatedness calculation of reconstructed parent pairs (Supplementary
Data 3). Relatedness of reconstructed vs potential parent pairs was
calculated, and a two-tailed Student’s t-test on the mean was performed
to test for significant differences between the two relatedness
distributions. To explore the effect of relatedness on fitness, clutch
size, total number of hatchlings, and number of dead embryos were
plotted against the relatedness of parent pairs. Additionally, the
relatedness of pairs involving i) a male that mated with multiple
partners (within a season or across seasons), ii) a female that mated
with multiple partners (within a season or across seasons), iii) the
female and dominant male from clutches with multipaternity, and iv) a
female that that nested over several years, were compared with the
relatedness of all the reconstructed parent pairs to determine whether
any of these behaviours led to a deviation of the observed relatedness,
and significant differences on the mean relatedness were tested with a
two-tailed Student’s t-test.
Results