Over the past decade, there has been no shortage of studies focused on the relationship between Neanderthals and our own species, Homo sapiens. Researchers have dug deep into the fossil record and our genomes to uncover how closely related we are to the Neanderthals, whether we interacted with them, and even whether our two species shared offspring.

But what about the Neanderthals themselves? We know that beginning around 400,000 years ago, they occupied over 3 million square miles of Europe and Western Asia, from Spain to Iraq.  We know that they developed a unique tool technology and that they buried their dead.  But what we really don’t know is how they compared to each other:  were there in fact distinct Neanderthal sub-groups, shaped by the vastly different environments in which they lived?  Or can they all be considered a single, genetically similar population? These questions are addressed in the most recent issue of PLoS One by anthropologists from the Université de la Méditerranée in France, using a method that is both unique and comprehensive.

This study is of interest not only because it attempts to understand Neanderthal diversity, but also because it utilized data from a various sources.  First, the researchers collected data from the mitochondrial DNA sequences of 12 separate Neanderthal skeletons. These skeletons ranged in age from 29,000 to 100,000 years and were uncovered in various parts of the Neanderthal homeland, from Siberia to Spain.  The researchers then took physical measurements of the skeletons themselves. Finally, they developed and ran complex computer simulations based on the genetic and skeletal data, in an attempt to discover the most likely scenario for how Neanderthals evolved and spread across much of Eurasia.

The authors concluded that the most likely scenario for how the Neanderthals populated Europe and Western Asia involves three Neanderthal sub-groups: one centered in Western Europe, another in Southern Europe, and the final group in the Levant/Western Asia.  They propose that the Neanderthals within each of these sub-groups were more genetically — and perhaps physically — similar to each other than they were to members of another sub-group.  This is contrary to the idea that the Neanderthals were a single, uniform population.

This result begs the question of cultural distinctions between the sub-groups.  After all, if they were genetically and physically different from one another, it is entirely plausible that cultural differences, such as tool technologies, between the sub-groups also existed.  The authors hope to understand cultural differences between Neanderthal sub-groups in the same way as they’ve understood genetic and physical differences.  And, as more fossils are found and more DNA extracted, we will hopefully develop — with even more confidence — a clear picture on the origins and movements of Neanderthals.

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First came the Human Genome Project when, in the year 2000, an international team of scientists began mapping all 23 pairs of our chromosomes.  Then in 2005, the Chimpanzee Genome Project took off, attempting to do the same for the 24 chromosomes of our species’ closest living relative.  With intimate knowledge of the genetic make-up of both species, scientists could decipher the evolutionary changes that took place in the 7 million years since the time of our last shared ancestor.

Now, a joint research team led by Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology has gone one step further by mapping the complete genome of our nearest extinct relative. Pääbo and his colleagues announced the completion of a draft Neanderthal genome sequence today in Chicago at the annual meeting of the American Association for the Advancement of Science.

Neanderthals – our short, stocky, evolutionary cousins – lived in Europe during the harshest conditions of the Ice Age.  They survived in regions where few other animals could.  Neanderthals first came on the scene over 350,000 years ago, but seemed to dwindle in numbers with the arrival of humans about 40,000 years ago.  By 25,000 years ago they had disappeared completely.

But there are still many questions surrounding the fate of the Neanderthals.  While most scientists argue that Neanderthals were simply out-competed by the arriving humans, some believe that Neanderthals and early humans may have interbred, and that many modern Europeans have Neanderthal DNA interspersed throughout their genome.  Others believe that Neanderthals and early humans were in fact members of the same species, and should therefore have very similar DNA.

Solving the mystery has been no easy task. Because the archaeological samples available to Pääbo and his colleagues — three bone fragments from a cave in Croatia — are 30,000 years old, what little DNA they contain has been broken down into short fragments of just a few hundred base pairs each — a fraction of the billions that make up a complete genome.

Initially, the researchers focused on the mitochondrial DNA, because it is so prevalent in each cell.  When comparing the mitochondrial DNA of Neanderthals to that of modern humans, they found substantial differences between the two – indicating that humans and Neanderthals could not have been members of the same species.

However, the mitochondrial DNA represents only a fraction of the entire Neanderthal genome.  If we want to know the real genetic differences between humans and Neanderthals, then we’ll have to examine not just a small fraction, but the whole genome — all 46 chromosomes of it.

Working with 454 Life Sciences Corp of Branford, Conn., Pääbo and his team have devised a way to extract large amounts of nuclear DNA – DNA from the 23 pairs of chromosomes inside each cell – from prehistoric mammals, including Neanderthals.  All told, the two research teams have so far sequenced over 3 billion bases of Neanderthal nuclear DNA, constructing a ‘rough draft’ of the entire Neanderthal genome.

The sheer difficulty in completing such a task cannot be underestimated.  As soon as these Neanderthals died, tens of thousands of years ago, the DNA inside each cell began breaking down.  Up until recently, extracting the few remaining bits of DNA from fossils like these was virtually impossible.  Now, as Pääbo and others comb through the Neanderthal genome, we can embark on new chapter in the continuing saga surrounding the relationship between humans and Neanderthals.

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Neanderthal and Homo sapiens skeletons side by side. The thicker femurs, different eye sockets and barrel-shaped chest of our distant relatives are prominent in this comparison.

Mining the past: The Neanderthal Genome Project
The first invited speaker at the SMBE 2008 conference was Svante Pääbo of the Max Planck Institute for Anthropology in Germany. Pääbo and colleagues continue their incredible project to sequence the Neanderthal genome. Neanderthals are especially interesting in understanding our own history; they were another animal that walked upright, hunted with weapons, used clothes, and had culture, traits we consider very “human.” Pääbo presented some new findings that may change the way we think about our own history and that of our distant cousins, who went extinct around 25,000 years ago.

So far, the project has sequenced more than 3 billion Neanderthal DNA base pairs. The figure sounds impressive, and it is. However, sequencing ancient DNA is subject to contamination and in fact more than 99% of the DNA Paabo’s group extracts from Neanderthal bones is from bacteria, fungi or other organisms – including modern humans.

Scientists have debated for decades whether Neanderthals and humans interbred. So far, the Neanderthal genome does not show any evidence of having human ancestry. But the recent split between humans and Neanderthals has resulted in some sharing of genetic material between the species. That is, some people may share versions of SNPs with Neanderthals, but this sharing traces to a common ancestor who lived before the two species split about 800,000 years ago.

One especially interesting finding by Paabo’s group was in the so-called “language gene,” FOXP2. Humans have a very different version of FOXP2 than most other mammals, birds, and reptiles. Rare deletions in the gene cause people to have trouble with speaking and comprehension, providing support that the gene is important for language. Interestingly, other verbal mammals also have changes in FOXP2.
Scientists had thought the “human” version of FOXP2 arose within the last 200,000 years, since the origin of Homo sapiens and long after the human lineage split from Neanderthals. However, it turns out Neanderthals share the human version of FOXP2. These results indicate that something else happened in human history to make FOXP2 appear younger than it really is; and that this may not be related to the unique version of the gene shared by humans and Neanderthals.
So, is FOXP2 the gene that makes us unique from other animals? No. But could it still have played an important part in our own history? Probably. Just one of the many mysteries that evolutionary geneticists hope to answer.

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