In a remarkable double publication today in both Science and Nature, researchers report on recent collaborative successes with developing the beginnings of a catalog of the nuclear DNA for Neanderthals. Svante Pããbo of the Max Planck Institute for Evolutionary Anthropology, and Edward Rubin of the US Department of Energy Joint Genome Institute and Lawrence Berkeley National Laboratory, have been working on the same Neanderthal sample, using different technological strategies, in their attempts to define the genome. The test sample, found after an exhaustive search of 70 sets of archived materials for suitably preserved samples, is from a Neanderthal man who died some 38,000 years ago and whose bones were recovered from Vindija Cave in Croatia. Out of a likely 3.2 billion base pairs thought to make up the Neanderthal DNA chain, Pããbo's team has described 1 million base pairs; while Rubin's team, working at a slower pace and producing an online catalog for the results, has identified 60,000.
Neanderthals and DNA Sequencing
Neanderthals are our closest non-human ancestor, and they were residents of the earth both before and for about 100,000 years alongside of modern Homo sapiens (and at least 300,000 more alongside our other ancestors). Neanderthals disappeared from the planet about 30,000 years ago. While mitochondrial DNA (mtDNA) studies of Neanderthals have been sequenced for a number of years, these are the first such studies completed on nuclear DNA, a task once thought impossible given the scale of the project. mtDNA is found within the mitochondria of human cells, it doesn't change when inherited from your mother, and it is made up of about 16,000 base pairs. Nuclear DNA is stored in the nucleus of cells, is created in each individual by combining DNA from both parents and it is made up of over 3 billion base pairs. The Human Genome Project finished describing the 3 billion base pair sequence of modern human DNA in 2003 after thirteen years of investigations. In contrast, Pããbo and Rubin fully expect to have the sequencing of the Neanderthal genome completed by 2008, after only four years of study. They attribute this to newer and faster technologies, both developed for this project and in progress as this news is breaking.
Vindija Cave
The sequencing is being completed on a single fragment (2-4 grams) of leg bone recovered from Level G3 in Vindija Cave. Vindija Cave is a stratified cave in Croatia, with 14 levels dated between 25,000 and 45,000 years ago; four or five of those levels had hominin remains in them (both Neanderthals and Anatomically Modern Humans) when the cave was excavated in the 1970s. Level G3, from which the bone was taken, is thought to be dated between 38,000 and 45,000 years ago; the identifiable bone recovered from the level represent Neanderthals, and the artifacts have been classified as Mousterian. Based on all this, Level G3 is considered a Neanderthal-only level in Vindija cave. The bone used in this study is a fragment of a leg bone, itself AMS dated to 38,310 ± 2,130 BP years ago.Problems with the Attribution of Neanderthal?
Paleontologist Fred H. Smith (Loyola University), who participated in the morphological analysis of the materials from Vindija Cave in the 1980s and 90s, believes that this bone is likely Neanderthal, although the morphological characteristics were not necessarily clear-cut, and given the error margin in the dates, it could represent Anatomically Modern Human remains. When asked for a comment about this question, Dr. Pããbo spoke of his confidence that the bone is Neanderthal or at most mixed modern human and Neanderthal. "As Fred says, the morphology of the bone itself does not identify this as a Neandertal. But as Fred also says, the G3 layer in Vindija is commonly accepted to be Neandertal and 38,000 is old to be modern human in the Balkans. Also, the mtDNA sequences we find in the bone are typical Neandertal. So at the most, it could be a mixture, it could not be purely modern human. As we go on with the project, we will find out if there is evidence for interbreeding with modern humans in this individual."Addressing Ancient DNA
The difficulties in addressing ancient DNA (aDNA) are quite complex. The elegant double helix DNA chain breaks apart within a few months of an organism's death, and damage to DNA over time is not unexpected. Dr. Pããbo, speaking in a teleconference to reporters on November 13, described the search process. "We looked through around 70 different specimens of Neanderthals from around Europe and western Asia. Because these specimens are so valuable, we removed very tiny samples of just around 10 mg of bone and look for amino acid composition. ... [I]f that looks well preserved, if it looks like there's collagen in there and that the amino acids are not too much damaged, then we go on and remove a bigger sample of about 100 mg of bone and extract DNA from that."Then we do the crucial test of looking for how much Neandertal DNA is in there relative to contaminating modern human DNA. And for that we use our knowledge about the mitochondrial genome where we can tell the difference between Neandertal and modern human. We have found that in most of these bones we have a large proportion of contamination.
"But in this one bone from Vindija, we were very lucky to find that about 1-2 percent of the human DNA comes from contaminating modern DNA, and around 98% or 99% of the human DNA is of Neanderthal origin."
A Tool for the Future
The focus of this project has been on the sequencing--that is to say, on describing the patterns of the way the DNA fits together and (in Dr. Rubin's case) in cataloging and placing the data on the Internet for use by other scholars. Not much research on the DNA has been completed, although initial findings suggest that modern humans and Neanderthals last had much 'social interaction'--at least what would generate gene flow--about 400,000 years ago or some 300,000 years before the appearance of AMH. More recent mixing--that between AMH and Neanderthals--has not been ruled out, although no evidence has been found to date.The researchers believe the real worth of the project will begin when the genome is completed, and then can be compared to chimpanzee and modern human genome sequences. Then, Pããbo and Rubin believe, researchers will have the ability to find out what traits we have that Neanderthals didn't, that enabled our success on this planet.
Said Dr. Smith, "This is simply incredible work. Who would have thought 15 years ago we'd be sitting and discussing extracting nuclear DNA from an earlier form of life?"
For More Information
- Sequencing of Neanderthal DNA Begun, including the sources of this information
- Nature Focus: Neanderthal DNA
- Science: Neanderthal DNA Comes to Life
Comments