Archaeology Magazine - Neanderthal Genome Decoded

Paleogenetics shows our ancient cousins aren't so extinct

[image]

Researchers Johannes Krause and Anne Butthof of the Max Planck Institute in Leipzig, Germany, insert a plate containing a DNA solution into a gene sequencer. (Courtesy Max Planck Institute for Evolutionary Anthropology/Frank Vinken)

For anyone who has ever looked at the hair on their knuckles and wondered if there might be a smidgen of Neanderthal in their genes, the recent publication of the Neanderthal genome provides some important answers. After four years of work, an international research team led by Svante Pääbo of the Max Planck Institute of Evolutionary Anthropology in Leipzig, Germany, has sequenced about 60 percent of the DNA that formed the building blocks of the Neanderthal lineage. The genome will allow scientists to better understand the biology of our closest extinct relatives, and provide a new point of reference for learning how our species, Homo sapiens, evolved. The study shows that Neanderthals are not as extinct as everyone thought. Somewhere between one and four percent of the DNA in people who are ethnically non-African comes from Neanderthals. In other words, they live on in some of us.

The DNA comes from three bones found in Croatia's Vindija Cave in the 1970s; all were non-identifiable fragments of limb bones. Two of them were radiocarbon dated—one to between 34,000 and 42,000 years ago and the other to between 43,000 and 45,000 years ago. The DNA studies revealed that each bone belonged to a different individual, all of them were probably women, and that two of them likely shared a relative on their mothers' side. The research team identified several areas of modern human genomes that seem to have conferred some kind of adaptive advantage and were passed on throughout the population of Homo sapiens around the time they were coming into contact with Neanderthals. Some of those regions include genes that affect cognitive functions and the ability to metabolize food into energy. One important difference between the Neanderthal and modern genomes was in a gene labelled RUNX2. That gene plays a role in the shape of the skull, rib-cage, and shoulder joint—parts of the anatomy where Neanderthals differ from modern humans. Mutations to RUNX2 may have given Homo sapiens the anatomy that makes us unique among hominids.

[image]

A sample was taken from a Neanderthal bone for DNA analysis. The bone powder was mixed with chemical solution to remove the DNA. (Courtesy Max Planck Institute for Evolutionary Anthropology/Frank Vinken)

The study compared the Neanderthal DNA to the genomes of five modern humans from around the globe (three non-Africans: French, Han Chinese, and Polynesian, and two Africans: Yoruba and San). The results showed that all non-Africans share a similar amount of Neanderthal DNA, indicating that this contribution to the gene pool took place before Homo sapiens migrated across the world. The most likely scenario, according to the research group, is that a small number of Homo sapiens left Africa between 100,000 and 80,000 years ago and encountered Neanderthals in the Middle East, where the two populations interbred before Homo sapiens moved into the rest of Eurasia. The lack of Neanderthal DNA in the two African genomes probably means that the population was dense enough that either people did not move back into Africa once they left, or the DNA of those who did come back was diluted in the continent's large human gene pool.

The research team cautions against drawing any racist conclusions based on their results. "It's not as if there are places in the genome where all non-Africans have Neanderthal ancestry and all Africans do not have Neanderthal ancestry," says geneticist David Reich of Harvard University. "In fact, each non-African today seems to have their Neanderthal ancestry in a different place in the genome." He also points out that there is no single Neanderthal gene that all non-Africans share.

Now that Pääbo's team has established protocols for preventing contamination of DNA samples and methods for assembling ancient gene sequences, future work should proceed much more quickly. They plan to re-sequence the Neanderthal genome several more times to eliminate any errors. The team also plans to do experiments that will tell them how the differences in the genome would have affected the physical attributes of Neanderthals. As the technology for gene sequencing becomes cheaper and faster, the techniques Pääbo's group has developed will allow archaeologists to routinely take DNA samples from the bones they uncover, creating more points of comparison between modern humans and our ancestors. Having more genomes to work with will make it easier to track down when particular mutations took place, as well as help us understand what drove those changes.

[image]

Geneticist Svante Pääbo confers with archaeologist Marco de la Rasilla at El Sidrón Cave in Spain, one of the sites that has yielded Neanderthal DNA. (© El Sidron Research Team)

Another way that paleogenetic research is changing the way scientists learn about human evolution is by allowing geneticists to identify new human lineages from unidentifiable pieces of bone, as Pääbo and Johannes Krause, also from the Max Planck Institute, did in March when they announced they had retrieved DNA from a 30,000-year-old finger bone from Denisova Cave in Siberia. So far, they have only sequenced the mitochondrial DNA (the DNA from the organelles that convert food to energy inside the body's cells) from the Denisova individual, but it appears to be from a 1 million-year-old strain of mitochondria that does not appear in any known Neanderthal or Homo sapiens individual. The discovery was surprising because it may indicate that a type of hominid unknown in the fossil record left Africa sometime around a million years ago and migrated to Asia, where it lived side by side with Neanderthals and Homo sapiens. "Maybe it is an oversimplification to talk about particular migrations out of Africa," says Pääbo. "There might have been more or less continuous gene flow or migration." Taken together, the Neanderthal genome and the Denisova DNA seem to be moving ideas about human evolution in a different direction. "What unfolds is that the human family tree we thought was so clear-cut will morph to become more like a bush," says Stephan Schuster, a geneticist at Penn State University who is not affiliated with the research team. "There will be many different versions of human."

Deciding whether the Denisova hominid is different enough from Neanderthals and modern humans to be called a separate species based on its genes alone is going to be tricky. "There is no metric where you say �this percentage of divergence is a new species,'" says Pääbo. "I think it will always be a bit murky." Defining the term "species" is fraught with all kinds of problems especially when referring to people who lived thousands of years ago. Paleoanthropologists rely mainly on measurements of bone shape and size to make assumptions about what makes one hominid different enough from another to call them separate species. "It seems pretty obvious that if a paleontologist can find a tooth and name a new species, then finding the genome provides millions of times more information, so you ought to be able to define a species," says John Hawks, a geneticist at the University of Wisconsin who is not part of the research team. Another possibility advocated by Hawks is that the Denisova individual is simply a Neanderthal with an old form of mitochondria. Soon, Krause and Pääbo will know if that is the case. They are already at work recovering the complete Denisova genome, and they hope to have a draft sequence in a few months.

Zach Zorich is a senior editor at ARCHAEOLOGY.