Admixed Americans show archaic alleles proportional to European and Indigenous American ancestry. African ancestry tracts contain almost no archaic alleles. Denisovan alleles denser in Indigenous American than European segments. East Asians have most archaic sites, Europeans fewest. Peruvians carry highest archaic density due to 77% Indigenous ancestry. Neanderthal alleles equal in European and Indigenous segments. Five genomic regions with high archaic density shared across 20+ admixed individuals in Indigenous tracts. Archaic alleles in genes like CNTNAP2, LRRK2 targeted by selection in Americans. PBS identifies adaptive archaic introgression in immunity, brain, metabolism genes. PEL and MXL show higher archaic frequencies than East Asians in select loci. Heterosis unlikely explains high archaic frequencies in most regions. Neutral simulations confirm selection signals exceed drift. 79-81% of high-PBS archaic sites overlap confirmed introgression tracts. Indigenous Americans mirror East Asian archaic profiles including extra Denisovans. Archaic variation absent in African segments mirrors out-of-Africa bottlenecks. Admixed genomes mirror unadmixed archaic patterns by ancestry source.
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