(1) Parentage analyses
Parentage was assigned using Cervus 3.0 (Kalinowski, Taper, & Marshall,
2007) based on autosomal loci. Cervus compares likelihood ratios of two
most likely candidate parents and assigns parentage based on statistical
thresholds generated during the simulation analysis. For Cervus
analysis, we used a simulation of 100,000 offspring, an error rate of
0.01, 90% relaxed and 95% strict confidence level, and accounted for
relatedness of candidate mothers and fathers. Relatedness was calculated
with the R package related 1.0 (Pew, Muir, Wang, & Frasier, 2015) using
Wang’s estimator r (Wang, 2002). This estimator was chosen
because it performed best in simulations, showing the highest
correlation between observed and expected values for our set of loci.
Additionally, we used Colony 2.0.6.5 (Jones & Wang, 2010) to verify
parentage assignments from Cervus. Unlike Cervus, Colony reconstructs a
full pedigree, inferring sibship and parentage among individuals by
comparing the likelihood of different clusters of individuals and
maximizing group rather than pairwise likelihoods. For this analysis, we
used an error rate of 0.01, male and female polygyny, and a sibship size
prior of 1.6, calculated as the average number of young per family group
in our study population. For both Cervus and Colony analyses, the set of
candidate fathers included all sampled adult males plus the oldest
subadult male from Group 6 that had dispersed from his natal group in
the beginning of the study and could have sired offspring by the end of
the sampling period. The set of candidate mothers included all adult
females that shared their mtDNA haplotype with candidate offspring. For
seven offspring (Supplementary Table 1), the mothers were known because
they were seen nursing them. To test the reliability of our parentage
estimates, we ran the analyses twice, with and without the respective
set of known mother-offspring pairs. Combined non-exclusion probability
for the set of 16 autosomal loci (with chr01b excluded) was
9.9x10-5 for the first parent,
3.4x10-7 for the second parent, and
9.0x10-12 for the parent pair, calculated using
Cervus.
Additionally, we used the data for the X-linked locus chrXa to check for
allelic mismatches between candidate parents and offspring. This locus
was treated separately because neither Cervus nor Colony can handle a
mixture of autosomal and sex-linked loci.