Science. 2026 Aug 27; 393(6814): eaef8874.

Roland Heynkes 29.8.2026, CC BY-SA-4.0 DE

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Gliederung

NR BADF

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

TI Recovering signatures of archaic hominin introgression using ancestral recombination graphs

QU Science. 2026 Aug 27; 393(6814): eaef8874. DOI: 10.1126/science.aef8874

AB 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.

SP englisch

VT

RESEARCH ARTICLE SUMMARY

Editor’s summary

Since the sequencing of Neanderthal and Denisovan genomes, extensive gene flow between archaic hominins and humans has become increasingly apparent. However, early episodes of gene flow can obfuscate later signals, and introgression is still difficult to detect without a reference genome. Zhang et al. developed TRACE, a method that uses ancestral recombination graphs to identify introgression in humans without archaic reference genomes. They found introgressed regions from a ghost lineage of hominins in all modern human populations that surprisingly overlapped regions previously identified as lacking Neanderthal and Denisovan introgression, called "deserts." This work also supported previous evidence of superarchaic ancestry within Denisovan introgressed regions. - Corinne Simonti

Structured Abstract

INTRODUCTION

The sequencing of Neanderthal and Denisovan genomes has revealed extensive interbreeding between modern humans and now-extinct archaic hominins, transforming our understanding of human evolutionary history. However, many archaic populations that contributed to modern human ancestry—particularly those lacking preserved fossils or DNA—remain uncharacterized. Existing computational methods cannot detect these contributions as they rely on either an archaic reference genome or an unadmixed outgroup. As a result, the full extent and complexity of archaic introgression remain unknown.

RATIONALE

Ancestral recombination graphs (ARGs) encode the full genealogical history of a set of samples across the genome, providing a record of the ancestral population relationships over time. Gene flow from a deeply divergent archaic source is expected to leave two distinctive signatures in the ARG: (i) unusually deep coalescent branches, reflecting the long evolutionary separation between the introgressing lineage and the recipient population, and (ii) long stretches of the genome over which introgressed lineages persist as contiguous haplotypes, reflecting the limited number of recombination events since the gene flow event. We developed TRACE (Tracking Archaic Contributions via ARG Estimation), a reference- and outgroup-free method that identifies introgressed archaic segments in contemporary genomes by scanning inferred ARGs for these signatures.

RESULTS

We validate TRACE by performing extensive simulations and show that it has high precision and low false discovery rate across a range of demographic scenarios and parameters. Applied to data from the 1000 Genomes Project, TRACE recovers the known signatures of Neanderthal introgression in all non-Africans and Denisovan introgression in Asians and Oceanians, with population-level patterns consistent with prior estimates.

Beyond these established signals, TRACE identifies extensive segments of ghost archaic ancestry—from a previously uncharacterized hominin lineage—in both African and non-African populations. We find ghost ancestry persists within Neanderthal and Denisovan ancestry deserts, genomic regions previously interpreted as depleted of archaic introgression and thought to be specific to Homo sapiens. This challenges the prevailing interpretation of these regions and suggests that selection acting against introgressed ancestry has not been uniform across all archaic sources. In Oceanian populations, TRACE detects a substantial enrichment of unusually deep coalescent lineages within Denisovan ancestry segments compared with Neanderthal segments, consistent with a model of super-archaic gene flow into modern humans through Denisovans. Together, these results point to multiple layers of introgression—both direct and mediated through other archaic groups—that have shaped modern human genomes.

CONCLUSION

TRACE is a genealogy-based method for mapping archaic ancestry without the need for archaic reference genomes, revealing hidden layers to our evolutionary past. Using ARGs inferred from modern genomes alone, the method recovers signatures of introgression from archaic hominins for whom no DNA is available, including ghost and super-archaic lineages. With continued progress in ARG reconstruction, TRACE will increasingly advance our understanding of the legacy of extinct populations to present-day human genetic diversity.

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