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, b...

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Bibliographic Details
Published in:Heredity 2015-04, Vol.114 (4), p.397-403
Main Authors: Knief, U, Hemmrich-Stanisak, G, Wittig, M, Franke, A, Griffith, S C, Kempenaers, B, Forstmeier, W
Format: Article
Language:English
Subjects:
Animal populations
Animals
Birds
Female
Finches - genetics
Genetics, Population
Genomes
Genotype
Haplotypes
Inbreeding
Male
Models, Genetic
Molecular biology
Original
Pedigree
Polymorphism
Polymorphism, Single Nucleotide
Sequence Analysis, DNA
Taeniopygia guttata
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Summary: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
ISSN:0018-067X
1365-2540
DOI:10.1038/hdy.2014.116