Altai Neanderthal genome shows gene flow from modern humans 1.0–7.1%. No modern human gene flow detected in Denisovan or European Neanderthals. Gene flow source split early from African ancestors like San and Yoruba. Young African haplotypes in Altai Neanderthal coalesce 100,000–230,000 years ago. Altai Neanderthal shares 5.4% more derived alleles with Africans than Denisovan. European Neanderthals share fewer derived alleles with Africans than Altai Neanderthal. Introgressed segments overlap FOXP2 gene linked to language. Longest introgressed segment includes NR5A2 transcription factor under selection in humans. Neanderthals and Denisovans underwent long-term population decline. Archaic populations had less efficient purifying selection than modern humans. Altai Neanderthal population isolated in Siberia. Interbreeding likely in Near East or Levant 120,000 years ago. Modern humans reached China 120,000 years ago enabling archaic admixture. Altai Neanderthal diverged from European Neanderthals 110,000 years ago post-introgression. Denisovan received gene flow from deeply divergent archaic hominin over 1 million years old.