Data from: Meiotic recombination shapes precision of pedigree- and marker-based estimates of inbreeding
Knief, Ulrich; Kempenaers, Bart; Forstmeier, Wolfgang (2016), Data from: Meiotic recombination shapes precision of pedigree- and marker-based estimates of inbreeding, Dryad, Dataset, https://doi.org/10.5061/dryad.67f9c
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 Pedigree and Marker F. In zebra finches, where the genome contains large blocks which are rarely broken up by recombination, the Mendelian noise was large (nearly twofold larger standard deviations compared to humans) and Pedigree F thus less precise than in humans, where cross-overs are distributed more uniformly along chromosomes. Effects of meiotic recombination on Marker F were reversed, such that the same number of molecular markers yielded more precise estimates of GWIBD in zebra finches than in humans. As a consequence, in species inheriting large blocks that rarely recombine, even small numbers of microsatellite markers will often be more informative about inbreeding and fitness than large pedigrees.