Since short IBD segments are thought to be ancient, we wondered whether some IBD segments match bases of primate genomes, such as, chimpanzee and orang utan, or archaic genomes, such as, Neandertal and Denisova. Ancient short IBD segments may reveal gene flow between archaic genomes and ancestors of modern humans and, thereby, shed light on different out-of-Africa hypotheses (25). Bases of the ancestral chimpanzee and orang utan genomes were given as additional information in the 1000 Genomes Project data. 31X coverage sequencing data for the Denisova genome were provided by the Max Planck Institute for Evolutionary Anthropology (26). Again we restricted our analysis to chromosome 1 in order to comply with the Ft. Lauderdale agreement for use of unpublished data for method development. Denisova bases were called by the software package SAMtools (27). Considering only the SNVs of the 1000 Genomes Project, 0.3% of the Denisova bases were not determined, 89.7% matched bases of the human reference, and 10% matched either the human minor allele or were different from human alleles. The Neandertal genome (28) sequencing files were obtained from the European Bioinformatics Institute. Neandertal bases were again called by SAMtools but based on data with 1X coverage, resulting in lower quality than for the Denisova genome. At SNV loci of the 1000 Genomes Project, 33% of the Neandertal bases were not determined, 61% matched the human reference, and 6% matched the human minor allele or were different from human alleles.