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 F Ped 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 (F Ped = 0.013opropIBD = 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.

Inbreeding depression of sperm traits in the zebra finch Taeniopygia guttata

“…Based on molecular data, this baseline appears to lie somewhere between F  = 0.05 to F  = 0.1 for our domesticated population (Knief et al. 2015), and probably slightly lower for the recently wild‐derived population (Forstmeier et al. 2007).…”

“…2000; Leberg and Firmin 2008; Knief et al. 2015) and agricultural sciences (Sewalem et al. 1999; König et al.…”

Meiotic recombination shapes precision of pedigree- and marker-based estimates of inbreeding

“…This estimate is specific to our captive population of zebra finches and should be adopted with caution for other populations. The aim of our example is to show how the precision and bias in predicting GWIBD (or fitness) declines when using typical microsatellite markers instead of 'ideal markers' (as can be derived from SNP panels; Knief et al, 2015). Essentially, we estimated how often our microsatellite markers would be IBS by chance alone (because of a limited number of allelic states) in the absence of any inbreeding, which renders marker IBS a less reliable predictor of marker IBD.…”

“…Throughout this paper we will mostly focus on an idealized scenario, where all inbreeding is fully defined and captured by the pedigree information and we will only briefly highlight the effects of related or inbred pedigree founders on Pedigree F. A more in-depth treatment of this issue can be found elsewhere and is outside the scope of the current study (see, for example, Powell et al, 2010;Thompson, 2013;Knief et al, 2015;Speed and Balding, 2015).…”

“…We used empirical data from 11 microsatellites genotyped in the seventh generation of our pedigree to estimate the IBD-IBS discrepancy and introduced this noise component into our simulations (Marker IBS 7 ). This allows us to compare the precision of (1) F from pedigrees of varying lengths, (2) multilocus homozygosity of 'ideal markers' (Knief et al, 2015), for example, derived from SNP panels (Marker IBD 7 ) and (3) multilocus homozygosity of typical microsatellite markers (Marker IBS 7 ) in predicting GWIBD 7 .…”