Quantifying realized inbreeding in wild and captive animal populations

Abstract

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<propIBD=0.064), as expected given that pedigree founders were already related. We suggest that this SNP-based technique is generally useful for quantifying inbreeding at the individual or population level, and we show analytically that it can capture inbreeding loops that reach back up to a few hundred generations.

Figure 1

Each histogram shows the mean heterozygosity of every individual in a population for a particular gene region (four regions per population). The wild population (n=948 individuals, a–d) contains no individual that is fully homozygous in any of the four gene regions (identical-by-state, IBS=0). In contrast, between 2.8 and 11.0% of the 1057 individuals of the captive population (e–h) are fully homozygous in a given gene region indicating homozygosity by descent and hence inbreeding (dark bars). Gene regions are not the same between the two populations, but were matched for the number of SNPs genotyped per region. n=67 SNPs for (a) RALDH2 and (e) Tgu1, n=56 SNPs for (b) RALDH3 and (f) Tgu1A, n=75 SNPs for (c) TGFBR2 and (g) Tgu2, n=62 SNPs for (d) CTNNB1 and (h) Tgu4.