Recent genetic analysis suggests that humans mated with the mysterious Denisovans not once, but twice:
Asian genomes carry introgressed DNA from Denisovans and Neanderthals
East Asians show evidence of introgression from two distinct Denisovan populations
South Asians and Oceanians carry introgression from one Denisovan population
I can’t read the whole paper, because it’s paywalled, but if correct, this is quite the change. Previously, only small amounts of Denisovan were detected in East Asians, while large amounts (2-6%) were detected in Oceanians (ie, Melanesians, Papuans, and Australian Aborigines.)
Statistical analysis of genomic DNA sequences from different Asian populations indicates that at least two distinct populations of Denisovans existed, and that a second introgression event from Denisovans into humans occurred. A study of Han Chinese, Japanese and Dai genomes revealed that modern East Asian populations include two Denisovan DNA components: one similar to the Denisovan DNA found in Papuan genomes, and a second that is closer to the Denisovan genome from the Altai cave. These components were interpreted as representing separate introgression events involving two divergent Denisovan populations. South Asians were found to have levels of Denisovan admixture similar to that seen in East Asians, but this DNA only came from the same single Denisovan introgression seen in Papuans. …
The Denisovans, in case you’re new here, are a human species similar to the Neanderthals who lived… well, we’re not sure exactly where they lived, other than the Altai Cave, Siberia. We also don’t know what they looked like, because we have only found a few of their bones–a finger bone and some teeth–but they might have looked a bit like the Red Deer Cave People. Remarkably, though, these were in good enough condition (Siberia preserves things very well,) to allow scientists to extract sufficient DNA to determine that they are indeed a human species, but one that split from the ancestors of Homo sapiens about 600,000-750,000 years ago, and from the Neanderthals about 200,000 years later.
Just as Homo sapiens mated with Neanderthals, so Denisovans mated with Neanderthals and Homo sapiens–the human family tree is growing increasingly complex.
We don’t know exactly where these interbreeding events happened, since we know so little about the Denisovans (at least one of the Neanderthal interbreeding events probably happened in the Middle East, given that all non-Africans [and some Africans] have Neanderthal DNA,) but a clue lies in the DNA of the Negrito peoples.
The Negritoes are a variety of peoples who live in south east Asia and, like the Pygmies of Africa, are rather short. Some of them, like the Aeta of the Philippines, have almost Papuan levels of Denisovan admixture, while others, like the Onge of India, have almost none. Assuming the Negritos are related to each other and not just isolated examples of island dwarfism, this suggests that the interbreeding event really did take places somewhere east of the major Indonesian islands of Sumatra and Borneo (which probably weren’t islands at the time, but connected to the mainland). The Denisovans may have been clever enough to build boats and cross the Wallace Line, surviving in the more isolated islands of Indonesia and the Philippines.
On a related note, the article I just linked to from John Hawks, “This is where Scientists Might Find the Next Hobbits,” is truly excellent:
In May, an international team of scientists led by Thomas Ingicco revealed new archaeological findings from Kalinga, in the northernmost part of Luzon, Philippines. Until now, scientists have mostly assumed that the Philippines were first inhabited by modern humans, only after 100,000 years ago. But the artifacts unearthed by Ingicco and coworkers were much older, more than 700,000 years old. …
Luzon was never connected to the Asian mainland, even when sea level was at its lowest during the Ice Ages. To get there, ancient hominins had to float. Who were they, and how did they get there?
I recommend you read the whole thing.
What’s all of this Denisovan DNA good for, anyway? Quoting Wikipedia again:
The immune system’s HLA alleles have drawn particular attention in the attempt to identify genes that may derive from archaic human populations. Although not present in the sequenced Denisova genome, the distribution pattern and divergence of HLA-B*73 from other HLA alleles has led to the suggestion that it introgressed from Denisovans into humans in west Asia. As of 2011, half of the HLA alleles of modern Eurasians represent archaic HLA haplotypes, and have been inferred to be of Denisovan or Neanderthal origin. The apparent over-representation of these alleles suggests a positive selective pressure for their retention in the human population. A higher-quality Denisovan genome published in 2012 reveals variants of genes in humans that are associated with dark skin, brown hair, and brown eyes – consistent with features found with Melanesians today. A study involving 40 Han Chinese and 40 people of ethnic Tibetan background identified a region of DNA around the EPAS1 gene that assists with adaptation to low oxygen levels at high altitude found in Tibetans is also found in the Denisovan genome. In Papuans, introgressed Neanderthal alleles have highest frequency in genes expressed in the brain, whereas Denisovan alleles have highest frequency in genes expressed in bones and other tissues.
It is a great era in genetics.