A study published in the American Journal of Human Genetics provides strong evidence that the ancestors of modern sub-Saharan African populations interbred with an unknown, extinct line of archaic humans. A team led by Jeffrey Wall (University of California, San Francisco) analyzed the genomic data of 1,667 individuals from around the world from the GenomeAsia 100K project. Instead of a direct comparison with the genomes of Neanderthals or Denisovans, they used a method based on linkage disequilibrium (LD) analysis to detect long, highly differentiated haplotypes - potential traces of archaic introgression, dubbed "putative ghost haplotypes" (PGHs). The analyses identified 2,319 such haplotypes, with significantly more of them - an average of 5 to 15 times - found in sub-Saharan Africans than in non-Africans. Significantly, the number was higher than predicted by computer simulations. The highest number of PGHs was recorded in representatives of the Khoe-San population, indicating that introgression occurred first in their ancestors, and then the archaic component spread to other African groups (including Pygmies and West, East and North African populations). However, the authors point out that their method does not clearly separate the influence of ancient population structures from actual interbreeding with archaic humans - further analysis of genomes from Central and Southern Africa will be necessary. At the same time, the researchers did not confirm earlier reports of the presence of traces of archaic introgression in the inhabitants of the Andaman Islands or Flores Island (where Homo floresiensis lived), despite deep sampling of these populations. The PGHs were mostly found outside the coding regions and were most likely removed by negative selection - confirming earlier findings that archaic DNA (e.g., Neanderthal) can be harmful to modern humans and linked to many diseases.