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

The proportion of an individual’s genome that is identical-by-descent (GWIBD) can be estimated from pedigrees (inbreeding coefficient “Pedigree F”) or molecular markers (“Marker F”), but both estimators come with error. Assuming unrelated pedigree founders, Pedigree F is the expected proportion of GWIBD given a specific inbreeding constellation. Meiotic recombination introduces variation around that expectation (Mendelian noise) and related pedigree founders systematically bias Pedigree F downwards. Marker F is an estimate of the actual proportion of GWIBD but it suffers from the sampling error of markers plus the error that occurs when a marker is homozygous without reflecting common ancestry (identical-by-state). We here show via simulation of a zebra finch and a human linkage map that three aspects of meiotic recombination (independent assortment of chromosomes, number of cross-overs and their distribution along chromosomes) contribute to variation in GWIBD and thus the precision of ...