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

DAIseg, a new reference-free HMM-based method, outperforms existing tools by jointly detecting Neanderthal and Denisovan introgressed segments in modern human genomes, revealing two Denisovan events in Papuans.

• Why it matters: Understanding archaic admixture is crucial for unraveling human evolutionary history, but current methods are limited to single ancestry detection and rely on reference genomes, hindering comprehensive analysis.
• What they did: The authors developed DAIseg, which uses only modern human genomes to simultaneously distinguish multiple waves of archaic introgression, validated through simulations and applied to Papuan populations.
• The result: DAIseg identified more archaic segments than previous methods and uncovered evidence for two Denisovan introgression events, enabling more accurate insights into archaic contributions to human evolution.