An archaic reference-free method to jointly infer Neanderthal and Denisovan introgressed segments in modern human genomes.

DAIseg, a new HMM-based method, jointly detects Neanderthal and Denisovan introgressed segments in modern human genomes, outperforming existing approaches in simulations and real data.

• Why it matters: Understanding archaic admixture is crucial for studying human evolution, but current methods typically detect only a single archaic ancestry and rely on reference genomes, limiting insights into multiple admixture events.
• What they did: The authors developed DAIseg, which uses only modern human reference genomes to distinguish multiple waves of archaic and recent admixture, and applied it to Papuan populations to identify Denisovan and Neanderthal segments.
• The result: DAIseg identified more archaic segments than previous methods and provided evidence for two Denisovan introgression events in Papuans, enabling more detailed analysis of archaic influence on human evolution.