The worlds of ancient and modern DNA exploration have collided in spectacular fashion in the past few months. Last week saw the publication of a long-awaited draft genome of the Neanderthal, an archaic hominin from about 40,000 years ago1. Just three months earlier, researchers in Denmark reported the genome of a 4,000-year-old Saqqaq Palaeo-Eskimo2 that was plucked from the Greenland permafrost and sequenced in China using the latest technology.

Neanderthals once bred with Homo sapiens. Credit: PHOTOLIBRARY

As researchers compare these ancient genomes with the ever-expanding number from today's humans, they expect to gain insights into human evolution and migration — with more discoveries to come as they decipher DNA from other branches of the human evolutionary tree. "For the first time, ancient and modern genetic research is going hand in hand," says Eske Willerslev, whose team at the University of Copenhagen led the Palaeo-Eskimo sequencing project. "It is really a fantastic time."

Already, analysis of the Neanderthal genome has helped to resolve a debate about whether there was interbreeding between Neanderthals and Homo sapiens: genome comparisons suggest that the two groups mated an estimated 45,000–80,000 years ago in the eastern Mediterranean area. The sequencing study, from a consortium led by Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, found that the genomes of non- African H. sapiens today contain around 1–4% of sequence inherited from Neanderthals.

The breakthroughs have been driven by the plummeting cost of sequencing, together with new strategies for reducing or detecting contamination by near-identical modern human DNA. These days, labs such as Pääbo's and Willerslev's might piece together a complete genome from the degraded scraps of DNA present in ancient bone, hair or teeth in as little as a month. Researchers from geneticists to fossil specialists can't wait for more.

For the first time, ancient and modern genetic research is going hand in hand. ,

Some hope to use ancient–modern genome comparisons to chart splits in human populations and how they might have correlated with climatic changes. "I call this molecular stratigraphy," says Jeffrey Long, a genetic anthropologist at the University of New Mexico in Albuquerque. "I then want to use this relative chronology of genetic events to compare to the palaeoclimate of Earth's biomes."

For Willerslev, ancient genomes offer the opportunity to trace prehistoric migration routes. By comparing the ancient Saqqaq genome with those of modern human populations, Willerslev and his team linked it to the present-day Chukchi people of Siberia, revealing that ancestors of this group trekked from eastern Siberia to Greenland about 5,500 years ago. "The genomes will allow us to test theories about peoples and migrations debated for a century," says Willerslev. "In the next five years, we will see a whole spectrum of discoveries." For example, the work could reveal whether the first Native Americans included migrants from Europe who crossed the ice-age Atlantic Ocean.

Pääbo and his team had nearly completed the Neanderthal genome by early 2009, about four years after the sequencing effort began. But, to carry out their analysis, the researchers raced to sequence five genomes of people from diverse modern populations in Europe, Asia and Africa. By comparing these to the Neanderthal genome, they found 78 protein-altering sequence changes that seem to have arisen since the divergence from Neanderthals several hundred thousand years ago, plus a handful of other genomic regions that show signs of positive selection in modern humans. These are linked to sperm motility, wound healing, skin function, genetic transcription control and cognitive development. The team also found that only the modern African genomes lacked segments of Neanderthal ancestry, indicating that interbreeding between the two groups probably occurred after humans migrated out of Africa.

That revelation is likely to revive the debate about whether or not the two groups are separate species, says anthropologist Fred Smith of Illinois State University in Normal, who has studied Neanderthals in Europe. Smith thinks that they are a subspecies of H. sapiens. Now that the genomes can be compared, it will be possible to investigate the genetic roots of some shared features. For instance, he points to the development of the occipital bun, a bulge at the back of the skull that is found in Neanderthals and in some modern humans. "We need to look and clarify certain characteristics in Neanderthal morphology with genetics," he says.

Most researchers in the field anticipate that the next ancient human genome will be completed by Pääbo's group, from a tiny finger bone found in a cave in the Altai Mountains in southern Siberia. In March, the group reported the mitochondrial DNA sequence from this individual3, an unknown hominin that, so far, does not genetically match either Neanderthals or H. sapiens and may represent a new species. The team dated the bone to about 40,000 years ago, but others say that the sediments around the bone may be as old as 100,000 years. There is speculation that the bone could be the remains of an older species of Homo, perhaps even of a remnant population of Homo heidelbergensis, known in Europe from 300,000 to 500,000 years ago, or of Homo erectus, found as early as 1.8 million years ago from Africa to Indonesia. A full sequence may help to resolve this.

Obtaining the genome of a human ancestor this old was previously unimaginable. "I honestly believe this new era will change our view of human evolution," Willerslev says.

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