Extended Data Figure 1. Three features used in the Conditional Random Field for predicting Neandertal ancestry.

Feature 1: Patterns of variation at a single SNP. Sites where a panel of sub-Saharan Africans carries the ancestral allele and where the sequenced Neandertal and the test haplotype carry the derived allele are likely to be derived from Neandertal gene flow. Feature 2: Haplotype divergence patterns. Genomic segments where the divergence of the test haplotype to the sequenced Neandertal is low while the divergence to a panel of sub-Saharan Africans is high are likely to be introgressed. Feature 3: we search for segments that have a length consistent with what is expected from the Neandertal-into-modern human gene flow 2,000 generations ago, corresponding to a size of about 0.05cM = (100cM/Morgan)/(2000 generations).