Genes of an unknown ancestor found in modern humans

Homo sapiens are likely to have bred with other ancient tribes much earlier than previously thought, according to new research. 

While it is known that DNA of the ancient tribes Neanderthals and Denisovans remains in the modern human genome, this was thought to have happened 50,000 years ago, when humans migrated from Africa to Eurasia, thereby interacting with these other tribes. It now seems likely that this interbreeding took place 200,000-300,000 years ago.

Professor Adam Siepel, one of the paper's authors, said: 'What I think is exciting about this work is that it demonstrates what you can learn about deep human history by jointly reconstructing the full evolutionary history of a collection of sequences from both modern humans and archaic hominins.' 

The researchers at Cold Spring Harbor Laboratory and Cornell University, both in New York, used DNA from the genomes of two Neanderthals, a Denisovan, and two modern-day African humans to obtain their findings. They found evidence of ancient humans in three percent of the Neanderthal genome. One percent of the Denisovan genome was inherited from the unknown ancestral species, and 15 percent of these sequences are still found in modern humans. 

To produce the findings published in PLOS Genetics, the team used a newly developed algorithm, ARGweaver-D. It uses Bayesian techniques to analyse ancestral recombination graphs and identifies regions where interbreeding is most likely to have taken place. It works well even on small sample numbers.

'This new algorithm... ARGweaver-D, is able to reach back further in time than any other computational method I've seen,' said Professor Siepel. 

The team also found that the modern human has traces of an unidentified tribe in its genome, suggested to be Homo erectus, although no certain conclusions can be made without DNA for this species.