We focused only on individuals and families from non-inbred populations, which means that inbreeding coefficients were assumed zero. The program genedrop in Morgan 2.8.2 [Thompson, 1995; Thompson, 2000b; Thompson, 2005] was used for generating marker genotypes for the simulated data sets. For each individual, we simulated 400 microsatellite markers based on Rutgers map positions and allele frequencies from the version 10 CEPH data at ftp://ftp.cephb.fr/ceph_genotype_db/. These markers were chosen randomly, subject to the condition that they were separated by an average of 10cM. Except where otherwise noted, we used all 400 markers for further analyses.
