Our results show that the information provided by dense SNP maps is generally higher and more uniformly distributed than with standard microsatellite panels composed of about 400 markers. This increased information comes at a cost of increased computational complexity. At least 100 times as many iterations are required and each iteration took 10–20 times longer for the SNP maps as for the microsatellite. For example, 100,000 iterations took 3.4 hours for the microsatellites, 30 hours for the Illumina SNPs, and 68 hours for the Affymetrix SNPs. While the increased time for each iteration is likely due to the increased number of markers, the increase in required iterations may be due to the reduced information of the SNP markers. This could be tested by comparing convergence with a dense microsatellite map.
