The earliest known homo sapiens had sex with Neanderthals and another close relative, the recently discovered Denisovans, according to genetic research at the Stanford University School of Medicine.
Although modern humans, Neanderthals and Denisovans share a common ancestor in Africa, the groups split into separate, distinct populations approximately 400,000 years ago. The Neanderthal lineage migrated northwestward into West Asia and Europe, and the Denisovan lineage moved northeastward into East Asia. The ancestors of modern man stayed in Africa until 65,000 years or so ago, when they expanded into Eurasia and then encountered the other human-like groups. In some cases, the rendezvous were amorous in nature.
A partial genome sequence of Neanderthals, who died out approximately 30,000 years ago, revealed that these trysts left as much as 4 percent Neanderthal DNA in the genetic blueprint of some present-day humans.The genome of another human cousin, the extinct Denisovans, made clear that up to 6 percent of some people's genomes are Denisovan in origin.
Researchers have found that these matings had a positive effect on modern human fitness. The cross breeding wasn't just a random event that happened, it gave something useful to the gene pool of the modern human - the introduction of new variants of immune system genes called the HLA class I genes which are critical for our body's ability to recognize and destroy pathogens. HLA genes are some of the most variable and adaptable genes in our genome, in part because the rapid evolution of viruses demands flexibility on the part of our immune system.
The HLA gene system, with its diversity of variants, provides a lot more detail about the history of populations than typical gene families.
Prior to the sequencing of the Neanderthal and Denisovan genomes, the researchers suspected that at least one HLA variant came from archaic humans. They determined that the variant known as HLA-B*73 is rare in present-day African populations but occurs with significant frequency in West Asian populations. The ethnic distribution of HLA-B*73 and its similarity across populations suggested that it came from a relatively recent co-mingling of modern human and archaic human DNA, which most likely would have happened outside of Africa.
But which archaic humans were the source of the HLA-B*73 gene type? The answer came in the genome sequence of the newly discovered human relative, the Denisovans, whose existence came to light in 2008 with the discovery of an unfamiliar finger bone and tooth in a cave in Siberia.
By comparing the HLA genes of the archaic humans with modern humans, researchers revealed that the HLA-B*73 allele likely came from cross breeding with Denisovans. Little is known about what the Denisovans looked like (a finger bone and a tooth are the only known fossils), but the genome sequence extracted from the finger bone gives insight into where they overlapped with modern humans. Gene flow from Denisovans into modern humans has its highest frequency of HLA-B*73 allele in West Asia, making that region the most likely site for the fortuitous mating.
Even in West Asian populations, the HLA-B*73 variant never represents more than 5 percent of all known variants of that gene. However, other human HLA types that arose from ancient matings are found in much greater frequencies, and certain traits coming from these archaic humans have become the dominant form.
A similar scenario is seen in some HLA gene types found in the Neanderthal genome, which was also sequenced from DNA extracted from ancient bones. These gene variants are common in European and Asian populations but rare in African populations. Within one class of HLA gene, researchers estimate that Europeans owe half of their variants to interbreeding with Neanderthals and Denisovans, Asians owe up to 80 percent and Papua New Guineans, up to 95 percent.