Recovering signatures of archaic hominin introgression using ancestral recombination graphs

• 成果类型: Article
• 署名作者: Zhang, Yulin; Biddanda, Arjun; Johnson, Sarah A.; O'Dushlaine, Colm; Moorjani, Priya
• 署名单位: University of California System; University of California Berkeley; Johns Hopkins University; University of California System; University of California Berkeley
• 刊物名称: SCIENCE
• ISSN/ISSBN: 0036-8075; 1095-9203
• DOI: 10.1126/science.aef8874
• 发表日期: 2026-08-27
• 页码: eaef8874
• 关键词: coverage neanderthal genome; evolutionary history; admixture; sequence; adaptation; reveals; models; NDUTU; dna

摘要

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 demonstrate that TRACE achieves 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 that deep lineages are enriched in Denisovan compared with Neanderthal regions, supporting super-archaic introgression. TRACE enables mapping of archaic introgression without archaic reference genomes.