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