SUPPLEMENTARY MATERIAL
Supplementary Methods
Tests for Adherence to Analytical Assumptions
Microsatellite data were initially tested for adherence to assumptions of downstream analyses
using a panel of 102 breeding adults sampled in 2007. We initially tested for departures from
Hardy-Weinberg equilibrium (HWE) using ARLEQUIN version 3.11 (Excoffier et al. 2005)
and linkage equilibrium using GENEPOP version 4.0 (Rousset 2008). P values from multiple
comparisons were Bonferroni corrected. Two loci (Pru03 and Pru21) had heterozygote
deficits and significant departures from HWE, as well as consistent mismatches across
families in the reconstructed pedigrees, suggesting the presence of null alleles. These loci
were removed from further relatedness analyses. Tests for linkage disequilibrium indicated
that three pairs of loci were linked (Table S1) and a GenBank BLASTn (Altschul et al. 1997)
search of the zebra finch genome indicated that each linked pair shared a chromosome.
KININFOR v.1 (Wang 2006) estimates the power of an individual locus to discriminate
between two types of relationships. Based on the power of each of the linked loci to
distinguish full-siblings from unrelated dyads using relatedness estimates, we removed the
least informative loci from each of the three pairs of linked loci (Pru12, Pru15 and Pru24)
from further analyses (Table S1).
Table S1
Pairs of loci having significant results in linkage disequilibrium tests. Chromosome number
inferred from NCBI BLASTn search of zebra finch genome. Power of locus to distinguish
full-sibling from unrelated pairs.
Linked Loci
Chromosome
Power
Pru07
Pru24
1
1
0.38
0.33
Pru12
Pru25
3
3
0.36
0.46
Pru15
Pru34
1a
1a
0.35
0.38
Pedigree reconstruction
A total of 1197 individuals were genotyped at fourteen loci (Holleley et al. 2009) across all
sampling years (2005-08), with many of these individuals present in multiple years. The
locus Pru21 was excluded from parentage analyses because of a high frequency of null
alleles and allelic dropout. Parentage was initially assigned using CERVUS (Kalinowski et
al. 2007) to identify parents from the whole sample of adults (within each year) and then the
top three candidate male and female parents were examined manually and assigned
unequivocally on the basis of matching loci (and invariably matched with putative maternity
[through the presence of a brood patch] and social-group membership). Despite the number
of close relatives in many social groups, given the high number of loci used and their
variability (Table 1), all offspring for whom parents were assigned, could be readily assigned
to just a single female and male parent from the population, with even other close relatives
typically mismatching at multiple loci. We adopted the conservative approach of not
assigning maternity or paternity to any individuals where the best candidate mismatched at
more than one locus, and these individuals were not included in the pedigree. However, we
did include seven out of 284 offspring who mismatched with a candidate parent at a single
locus, on the basis of a low level of mutation and genotyping errors. For no offspring did we
ever find more than a single male or female that matched at all bar one locus, i.e. even though
there were many close relatives in family groups, the number of loci used and their variability
were informative enough to reliably distinguish between them. The pedigree that was
established across years by assigning direct relationships between parents and offspring was
used to calibrate relatedness measures and to validate disperser identification (see Results).
Supplementary Results
Table S2
Correlation coefficients for comparisons between values of relatedness from pedigrees (r)
and genetic estimates of relatedness (R). Methods include two likelihood approaches ("D",
Milligan 2003; "T", Wang 2007), and five moment estimators ("L", Li et al. 1993), ("LR",
Lynch & Ritland 1999), ("Q", Queller & Goodnight 1989), ("R", Ritland 1996), and ("W",
Wang 2002). All seven correlations were significant at the 0.01 level.
Method
Correlation Coefficient
T
D
L
LR
Q
R
W
0.776
0.785
0.780
0.732
0.798
0.513
0.793
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