Recovering signatures of archaic hominin introgression using ancestral recombination graphs.

Authors

Yulin Zhang, Arjun Biddanda, Sarah A Johnson, Colm O'Dushlaine, Priya Moorjani

Published in

Science (New York, N.Y.). Pages eaef8874. Jul 30, 2026. Epub Jul 30, 2026.

Abstract

Admixture between modern humans and extinct hominins has shaped the genomes of present-day individuals, but reconstructing this history has been constrained by the scarcity of archaic samples and unadmixed outgroup populations. We introduce TRACE, a reference- and outgroup-free approach that uses features of ancestral recombination graphs to identify archaic ancestry. Simulations show TRACE has high precision and low false discovery rates. Applied to 1000 Genomes, TRACE recovers known Neanderthal and Denisovan introgression and uncovers ghost admixture from uncharacterized hominins in both Africans and non-Africans. Ghost ancestry persists in Neanderthal and Denisovan ancestry deserts, challenging their interpretation as Homo sapiens-specific regions. In Oceanians, TRACE finds deep lineages are enriched in Denisovan compared to Neanderthal regions, supporting super-archaic introgression. TRACE enables mapping archaic introgression without archaic genomes.

PMID:
42531349
Bibliographic data and abstract were imported from PubMed on 31 Jul 2026.

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