From The Telegraph, November 1, 2011:
The new study covers a larger part of the world than earlier research, and it is clear that it is not as simple as previously thought.
Professor Mattias Jakobsson, of Uppsala University in Sweden who conducted the study together with graduate student Pontus Skoglund, said hybridisation took place at several points in evolution and the genetic traces of this can be found in several places in the world.
He said: “We’ll probably be uncovering more events like these.
“Previous studies have found two separate hybridisation events between so-called archaic humans – different from modern humans in both genetics and morphology – and the ancestors of modern humans after their emergence from Africa.
“There was hybridisation between Neanderthals and the ancestors of modern humans outside of Africa and hybridisation between Denisovans and the ancestors of indigenous Oceanians.
“The genetic difference between Neanderthals and Denisovans is roughly as great as the maximal level of variation among us modern humans.”
The Uppsala scientists’ study demonstrates that hybridisation also occurred on the East Asian mainland.
The connection was discovered by using genotype data in order to obtain a larger data set.
Complete genomes of modern humans are only available from some dozen individuals today, whereas genotype data is available from thousands of individuals.
These genetic data can be compared with genome sequences from Neanderthals and a Denisovan which have been determined from archeological material.
Only a pinky finger and a tooth have been described from the latter.
Genotype data stems from genetic research where hundreds of thousands of genetic variants from test panels are gathered on a chip.
However, this process leads to unusual variants not being included, which can lead to biases if the material is treated as if it consisted of complete genomes.
Prof Jakobsson and Skoglund used advanced computer simulations to determine what this source of error means for comparisons with archaic genes and have thereby been able to use genetic data from more than 1,500 modern humans from all over the world.
Prof Jakobsson said: “We found that individuals from mainly Southeast Asia have a higher proportion of Denisova-related genetic variants than people from other parts of the world, such as Europe, America, West and Central Asia, and Africa.
“The findings show that gene flow from archaic human groups also occurred on the Asian mainland.”
Skoglund added: “While we can see that genetic material of archaic humans lives on to a greater extent than what was previously thought, we still know very little about the history of these groups and when their contacts with modern humans occurred.”
Because they find Denisova-related gene variants in south east Asia and Oceania, but not in Europe and America, the researchers suggest that hybridisation with Denisova man took place about 20 thousand years ago, but could also have occurred earlier.
This is long after the branch that became modern humans split off from the branch that led to Neanderthals and Denisovans some 300,000 to 500,000 years ago.
Prof Jakobsson said: “With more complete genomes from modern humans and more analyses of fossil material, it will be possible to describe our prehistory with considerably greater accuracy and richer detail.”
The findings were published in the online edition of the journal PNAS.