Two groups of researchers have done what many thought impossible: They have sequenced more than 1 million bases of nuclear DNA from a Neandertal fossil. The data, reported this week in Science and Nature, support the view that Neandertals diverged from our own ancestors at least 450,000 years ago. One group has fresh evidence that Neandertals and modern humans may have interbred.
The breakthrough owes a large debt to a burgeoning field known as paleometagenomics, as well as to faster sequencing technology. Until now, researchers have gleaned genetic information from ancient fossils by painstakingly purifying DNA from samples before sequencing it. This ensures that DNA from microbes and other contaminants does not pop up in the final sequence. But with paleometagenomics, researchers can feed DNA information from an unpurified sample into a computer and have the computer filter out foreign DNA.
Two years ago, Edward Rubin, head of the Department of Energy Joint Genome Institute in Walnut Creek, California, approached Svante Pääbo, a paleogeneticist at the Max Planck Institute of Evolutionary Anthropology in Leipzig, Germany, about applying paleometagenomics to Neandertal DNA. Pääbo shared a sample from a 38,000-year-old Neandertal fossil with Rubin, and the two teams embarked on parallel but different analyses.
In Rubin's lab, postdoctoral fellow James Noonan first created a library of Neandertal DNA incorporated into live bacteria that reproduce the DNA, creating an endless supply. The team employed a new, massively parallel technique called pyrosequencing, which uses pulses of light to read the sequence of thousands of bases at once. Sophisticated computer programs then compared the sequence fragments to available DNA databases and identified potential Neandertal ones based on their similarity to modern human sequence.
Pääbo and his Leipzig colleague Ed Green also employed pyrosequencing and computers to pick out Neandertal DNA. But instead of using bacterial libraries, they coated tiny beads with Neandertal DNA fragments and amplified each fragment for sequencing.
As expected, the Neandertal and human genomes proved more than 99.5% identical. Rubin's team calculated that the most recent common ancestor of the two human species lived about 700,000 years ago, whereas Green's analysis of 1 million bases found a more recent divergence time, about 465,000 to 569,000 years ago. As to the question of interbreeding, Rubin's group found no sign of it, but Pääbo's group did. "Taken at face value, our data can be explained by gene flow from modern humans into Neandertals," most likely from modern humans fathering children with Neandertal females, says Pääbo.
For Neandertal genomics to come into its own, however, Pääbo, Rubin, and others must demonstrate that their sequences are real and not a mosaic of errors due to degradation that occurs as DNA ages, sequencing mistakes, or contamination from modern humans who have handled the fossils, says genomicist Stephan Schuster of Pennsylvania State University in State College. Nonetheless, "this is great stuff," says molecular evolutionist Alan Cooper of the University of Adelaide, Australia. "It opens the way for much more work on identifying uniquely human genetic changes."