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Introgressions from Neanderthals and Denisovans were detected in modernhumans. Introgressions from other archaic hominins were also implicated,however, identification of which poses a great technical challenge. Here, weintroduced an approach in identifying introgressions from all possible archaichominins in Eurasian genomes, without referring to archaic hominin sequences.We focused on mutations emerged in archaic hominins after their divergence frommodern humans (denoted as archaic-specific mutations), and identifiedintrogressive segments which showed significant enrichment of archaic-specificmutations over the rest of the genome. Furthermore, boundaries ofintrogressions were identified using a dynamic programming approach topartition whole genome into segments which contained different levels ofarchaic-specific mutations. We found that detected introgressions shared morearchaic-specific mutations with Altai Neanderthal than they shared withDenisovan, and 60.3% of archaic hominin introgressions were from Neanderthals.Furthermore, we detected more introgressions from two unknown archaic homininswhom diverged with modern humans approximately 859 and 3,464 thousand yearsago. The latter unknown archaic hominin contributed to the genomes of thecommon ancestors of modern humans and Neanderthals. In total, archaic homininintrogressions comprised 2.4% of Eurasian genomes. Above results suggested acomplex admixture history among hominins. The proposed approach could alsofacilitate admixture research across species.

Genome-wide Scan of Archaic Hominin Introgressions in Eurasians Reveals Complex Admixture History