Data from: Quantifying realized inbreeding in wild and captive animal populations

Most molecular measures of inbreeding do not measure inbreeding at the
scale that is most relevant for understanding inbreeding depression—namely
the proportion of the genome that is identical-by-descent (IBD). The
inbreeding coefficient FPed obtained from pedigrees is a valuable
estimator of IBD, but pedigrees are not always available, and cannot
capture inbreeding loops that reach back in time further than the
pedigree. We here propose a molecular approach to quantify the realized
proportion of the genome that is IBD (propIBD), and we apply this method
to a wild and a captive population of zebra finches (Taeniopygia guttata).
In each of 948 wild and 1057 captive individuals we analyzed available
single-nucleotide polymorphism (SNP) data (260 SNPs) spread over four
different genomic regions in each population. This allowed us to determine
whether any of these four regions was completely homozygous within an
individual, which indicates IBD with high confidence. In the highly
nomadic wild population, we did not find a single case of IBD, implying
that inbreeding must be extremely rare (propIBD=0–0.00094, 95% CI). In the
captive population, a five-generation pedigree strongly underestimated the
average amount of realized inbreeding (FPed=0.013