Quantifying realized inbreeding in wild and captive animal populations

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KNIEF, Ulrich, Georg HEMMRICH-STANISAK, Michael WITTIG, Andre FRANKE, Simon C. GRIFFITH, Bart KEMPENAERS, W FORSTMEIER, 2015. Quantifying realized inbreeding in wild and captive animal populations. In: Heredity. 114(4), pp. 397-403. ISSN 0018-067X. eISSN 1365-2540. Available under: doi: 10.1038/hdy.2014.116

@article{Knief2015Quant-31076, title={Quantifying realized inbreeding in wild and captive animal populations}, year={2015}, doi={10.1038/hdy.2014.116}, number={4}, volume={114}, issn={0018-067X}, journal={Heredity}, pages={397--403}, author={Knief, Ulrich and Hemmrich-Stanisak, Georg and Wittig, Michael and Franke, Andre and Griffith, Simon C. and Kempenaers, Bart and Forstmeier, W} }

Knief, Ulrich Knief, Ulrich 2015 Kempenaers, Bart eng Forstmeier, W 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. Wittig, Michael 2015-06-01T13:18:43Z Franke, Andre Kempenaers, Bart Quantifying realized inbreeding in wild and captive animal populations Hemmrich-Stanisak, Georg Griffith, Simon C. Griffith, Simon C. Forstmeier, W 2015-06-01T13:18:43Z Franke, Andre Wittig, Michael Hemmrich-Stanisak, Georg

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