Introgression of archaic haplotypes into human populations is an already known phenomenon, with some haplotypes even providing a selective advantage such as adaptation to living in high altitudes or haplotypes carrying alleles of genes involved in the immune-system.
Most published methods for identification of archaic haplotypes rely on ancient DNA samples from the archaic population, to compare the modern samples with. Here we present a method for identifying regions of modern whole genome sequences that have been introgressed into a subset of modern humans from an ancestor with a long history of separation from the modern human lineage, and apply it to Oceanian genomes. The method takes advantage of the fact that introgressed regions show different patterns of LD and a high density of SNPs private to the population that received the introgression. For the Oceanian samples, we look for regions that have a clear excess of variants not seen in any 1000 Genomes Project sample, in order to identify regions introgressed from archaic populations other than Neanderthals, after the separation of Oceanians from other modern Asian ancestral populations.
We identify tens of Mb of potentially private introgressed sequence for each of the individuals in the study. The regions will be compared to regions found by other methods traditionally used for identifying introgressed regions, to known archaic sequences from ancient DNA, to each other to understand their diversity, and to other modern human sequences to estimate their original separation time.