Take a look at the second installment of 23andMe’s Human Prehistory 101 series.  23andMe’s creative team (led by chief illustrator Ariana Killoran) recently released “Out of (Eastern) Africa.”  With this new installment, we pick up where the previous video left off, when humans were starting to take their first tentative steps beyond the shores of Africa and into the unknown.

We begin this second episode around 60,000 years ago, when early human groups were exploring Africa for food and other resources. Just a few thousand years later, a few people journeyed even farther, heading east into the Arabian Peninsula, Asia, Europe and beyond. The common theme here? Things were changing for our human ancestors, who had previously stayed relatively confined to their homeland but now they were on the move. Around the time they first set foot in Asia, humans in Africa began creating sophisticated stone tools and art the likes of which had never been seen before.

As humans ventured into uncharted territory, they may have encountered other species who bore some resemblance to themselves.  In Asia, they may have run into Homo erectus, a distant relative that had journeyed into Asia from Africa almost 2 million years earlier.  In Europe humans likely came across the Neanderthals, another related species that had been braving the cold northern latitudes of Europe and western Asia for hundreds of thousands of years.

Our story continues as we see where various human populations settled over the next several thousand years, and gives us a peek at the difficulties that awaited them as the harsh Ice Age approached. Subsequent episodes will document how our human ancestors survived the harsh Ice Age conditions and how the innovation of agriculture and development of language laid the groundwork for the genetic diversity we see today.  Enjoy this latest installment and stay tuned for future episodes of Human Prehistory 101!

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The Neanderthals have always held a special place in the field of anthropology.  The skeletal remains of our short, stocky evolutionary relatives have been found everywhere from Spain to Iraq.

Their physical likeness to our own species, and the possibility that humans and Neanderthals may have interacted, has long fascinated experts and enthusiastic novices alike.  But simply studying their skeletal remains and artifacts seemed to leave more questions than answers.

More than 10 years ago an international team of scientists became the first to extract and analyze ancient DNA (aDNA) from a Neanderthal skeleton. By examining the mitochondrial DNA (mtDNA) — which is more abundant in our cells than our nuclear DNA and therefore more likely to preserve — they found that there were enough genetic differences between this Neanderthal and modern humans to classify the two as separate species.

Since this initial foray into Neanderthal genetics there have been attempts to improve aDNA analysis, with the goal of filling in the gaps that traditional anthropological techniques had been unable to.  Earlier this year, scientists at the Max Planck Institute for Evolutionary Anthropology became the first to sequence the entire Neanderthal mitochondrial genome – no easy feat. Now scientists have taken aDNA analysis to the next level by developing a novel technique to extract it more easily, yielding the most comprehensive and accurate results to date.  Along the way, they have uncovered some intriguing clues to the possible fate of the Neanderthals. Their results are reported in the July 17 issue of Science.

This new study, also led by Max Planck Institute scientists, centers around a novel method for finding and extracting that elusive aDNA from Neanderthal remains. The study took advantage of a new kind of aDNA extraction process, called Primer Extension Capture (PEC). This technique has many advantages over the others, primarily because it allows the aDNA to be completely isolated from all the other molecular junk  that can accumulate over time. This yields highly accurate results with much less effort. So instead of simply using this technique on one Neanderthal individual, they analyzed five.

The remains they chose had been excavated from a variety of locations, from Croatia to Germany to Spain and Russia.  Most of the remains were between 35,000 and 40,000 years old, which is very close to when Neanderthals were believed to have disappeared from most of their range.  They also examined Neanderthal remains from Russia that dated to between 60,000 and 70,000 years old.

After successfully extracting and analyzing the DNA of these remains, the researchers came to a few startling conclusions.  First, the level of genetic diversity among the samples was exceedingly low.  In fact, the amount of genetic diversity of the Neanderthal samples was less than one-third the diversity we see in modern humans today. For example, two of the samples — one from Croatia and the other from Germany — had identical mtDNA genomes. For two individuals living nearly 1,000 miles apart, this is quite unusual; unless there wasn’t much variation in mtDNA in the first place.

The authors of this report think this genetic homogeneity means that there were far fewer Neanderthals living in Europe and western Asia than they’d previously thought. Based on their analysis of the five individuals, the they estimated that the total population size of Neanderthals in Europe 35,000 years ago may have had as few as 3,500 females (because mtDNA is passed down maternally, it cannot be used to estimate male population size).

The authors believe there are two possible explanations for this small population size.  The first is that, over the 400,000 year history of Neanderthals, their population may have always been small.  After all, for much of their existence they survived harsh ice age conditions, so low population size may have been necessary for survival.

But the authors offer an alternate explanation as well. They think this small population size is the result of long-term population decline, perhaps beginning about 40,000 years ago and continuing until Neanderthals were wiped out. To test their hypothesis, the researchers re-analyzed the Neanderthal mtDNA genomes and found that their protein-encoding genes had evolved much more quickly than those of humans or chimpanzees since the three species split, millions of years ago.

This high rate of evolution, the authors argue, was not present in the older Russian Neanderthal sample.  This fact implies a pattern of decline in population size, not a population that had been small from the start. These results support their idea that the Neanderthal numbers were on the decline.  Without direct evidence, they can only speculate as to the cause of of their decline, but the scientists believe it may be tied to the arrival of humans in Europe and western Asia about 40,000 years ago.

Today most experts believe the Neanderthals were being out-competed by the incoming humans, who had superior technology and language skills.  Over time, the Neanderthals were forced to move to more isolated regions in the mountains of France and Spain.  By 30,000 years ago, only a few traces remained.  Soon after, they were gone.  This study reveals some compelling evidence that humans were in fact responsible – whether directly or indirectly – for the demise of the Neanderthals.

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It is estimated that there are up to 8,000 distinct languages spoken around the world today.  At birth, the human mind is capable of learning and understanding any of these languages; an impressive feat given how uniquely complex they are.  The fact that humans are able to understand and communicate with one another in such a way that even our closest primate relatives cannot has long been supposed to be the result of some sort of genetic distinction separating us from the rest of the animal kingdom. 

In 2002, scientists believed they had found this genetic distinction in the form of a gene called FOXP2.  Their early studies suggested that FOXP2 was linked to the development of language in humans, and in humans’ ability to manipulate the brain, lungs, and vocal chords to make the complicated suite of sounds and movements resulting in speech.

However, the expression of FOXP2 in humans – and its presence in other species – is anything but simple.  Research has revealed that FOXP2 isn’t expressed just in the brain, but in a host of other tissues and organs throughout the body.  Moreover, FOXP2 isn’t unique to humans, but is found in many species, from chimpanzees to field mice.  It’s the version of FOXP2 we humans carry that is distinct from those of other species.  So it is the differences in FOXP2 across species that has been at the heart of scientific research into the origins of complex language.

A few years after the FOXP2 gene’s possible role in promoting complex language skills was announced in 2002, scientists analyzing ancient DNA extracted from Neanderthals, our closest fossil ancestors, found that they had the same version of FOXP2 as humans.  This discovery was revolutionary, as it meant that humans may not have been the first species capable of complex speech and language. It also pushed back the appearance of this version of FOXP2 to at least 350,000 years ago.

Recently, the focus of genetic research into FOXP2 has focused on the specific role FOXP2 plays in our language ability.  Was it involved in enhancing our cognitive abilities?  Our motor skills? Our breathing patterns?  The results of scientists’ most recent effort to uncover the answers to these questions are in the May 29th issue of Cell, in a paper published by researchers from the Max-Planck Institute of Evolutionary Anthropology.

In order to advance our understanding of FOXP2, the scientists chose to examine its expression in mice, a surprisingly strong model for many human biological systems.  The chief difference in FOXP2 between humans and many other species such as mice boils down to two changes in the gene.  At some point in human prehistory, these changes arose and quickly became universal in the FOXP2 of humans.

To see what effect those changes might have had, the Max Planck scientists altered the copies of FOXP2 in mice to be identical to the copies of FOXP2 in humans.  They then examined any changes that took place surrounding the cognition and vocal skills of the genetically altered mice, to see how they might be affected by the supposedly advanced copy of FOXP2.  And, while the linguistic skills of the mice failed to rival our own, the scientists did see some surprising changes.  First, they found that the altered mice showed changes in their brain circuitry that bore some similarity to that of humans.  And perhaps most intriguing, the altered mice had distinct ultrasonic vocalizations that differed from their unmodified brethren.  Ultrasonic vocalizations, sometimes referred to as chirps or squeaks, are used by mice to communicate to each other, such as to warn of a predator.  When the young altered mice were separated from their mothers, something that usually elicits many such squeaks, they emitted ultrasonic vocalizations that were distinctly different in intensity and frequency than their counterparts.  The authors argue that the altered FOXP2 in the mice was influencing the type of squeaks that they were making when separated from their mothers.  And the scientists therefore believe there is some kind of connection to language development.

But what does all this mean to humans?  The past several years of research into FOXP2 has revealed that human patients who carry at least one non-functional version of the gene (i.e., the version of the gene found in species other than humans) have problems producing the facial movements necessary to form words.  It had been thought that part of the function of FOXP2 in humans was to develop motor control needed to articulate our mouths, vocal chords, and esophagus to produce complex language.  Many experts have also proposed that FOXP2 in humans plays a role in the development of both the lungs and the esophagus – both of which are vital to speech.  This most recent study shows that by simply tweaking FOXP2 in mice, we see a noticeable change in how they communicate.

Clearly, there is much more work to be done and many more questions to be answered.  In the future, these researchers envision going even further to understand exactly how FOXP2 influences our ability to communicate with each other.  Their next goal?  To understand the exact mechanics behind the version of FOXP2 found in humans, so that they can finally piece together its importance in giving us the power of speech.

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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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The Spittoon has pointed out several times in the last few months (here, here and here) that when researchers look for evidence of interbreeding between early humans and Neanderthals, they often fail to find any.

But there are still a number of geneticists who would like us to pay heed to the words of former defense secretary Donald Rumsfeld, who once pointed out that “the absence of evidence is not evidence of absence.”

During a briefing for science writers this morning at Stanford University, geneticist Bruce Lahn argued that interbreeding with Neanderthals may have introduced into the human gene pool a mutation that appears to confer an evolutionary advantage with regard to brain development.

“We argue that in modern humans there may actually be some Neanderthal genes,” Lahn said at the Council for the Advancement of Science Writing’s New Horizons in Science briefings.

Lahn based his argument on a gene known as microcephalin. Because certain mutations in the gene can cause underdevelopment of the brain, microcephalin is assumed to be involved in that organ’s development.

Lahn described research that he and several colleagues first described two years ago in the Proceedings of the National Academy of Sciences. The researchers sequenced microcephalin in 89 people from populations around the world. They found that the sequences fell into two very different groups — so different, in fact, that they apparently traced back to a common ancestor older than the human species itself.

Moreover, each of the two groups appeared to have a very distinct history of its own. One appeared to have arisen about a million years ago, and diversified at a steady pace since then. The other group, however, appeared to have arisen just 37,000 years ago and spread rapidly throughout 70% of the human population. That kind of pattern suggests what evolutionary biologists call a “selective sweep,” the introduction of an advantageous genetic variant that quickly wipes out older versions of the gene.

Usually when geneticists see a selective sweep in action, the new variant appears to arise out of the pre-existing one. But in this case, Lahn argues, the new genetic variation traces back to a common ancestor that precedes both populations. He believes Neanderthals could have been that population, and that they could have transferred the “new” variation to the into the human gene pool through interbreeding about 40,000 years ago.

It’s just a hypothesis at this point — and one that many geneticists consider difficult to confirm. But if ongoing efforts to sequence the Neanderthal genome find a version of the microcephalin gene identical to the one that is currently sweeping through the human population, Lahn will have strong evidence for his claim.

Photo: K. Mowbray

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Despite mounting genetic evidence that modern humans are not descended from Neanderthals, there are still some who argue that our two species interbred when both roamed Europe about 35,000 years ago.

A report appearing tomorrow in the journal Cell puts another nail in that theory’s coffin. Svante Paabo’s group at the Max Planck Institute for Anthropology in Germany has produced the first-ever complete sequence of a Neanderthal’s mitochondrial genome. Their analysis shows that the last common ancestor of humans and Neanderthals walked the Earth on the order of 660,000 years ago – hundreds of millennia earlier than the most recent common ancestor of all humans living today.

Mitochondrial DNA is passed down intact from mother to child. All people living today can use mitochondrial DNA to trace their maternal line back to the Mother of all Mothers (MoM), who probably lived about 175,000 years ago in eastern Africa.

When working with ancient DNA, researchers have to contend with several technical problems. Contamination by DNA from laboratory workers must be carefully avoided. And even if contamination is controlled, the inevitable chemical breakdown of DNA that has been buried for thousands of years can skew results. Lead author Richard Green and his colleagues avoided both of these pitfalls by sequencing the mitochondrial DNA nearly 35 times over.

“For the first time, we’ve built a sequence from ancient DNA that is essentially without error,” Green said in a statement.

The authors say that their success at sequencing the mitochondrial genome of a Neanderthal will help in their ultimate goal of sequencing the species’ much larger and more complicated nuclear genome, which could then be compared with a modern human genome to identify genes that were important in the emergence of Homo sapiens.

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The place of Neanderthals in the story of human evolution has been hotly debated for decades.  A distant cousin to our species, Neanderthals had already been in Europe over 250,000 years when Homo sapiens first arrived there 35,000 years ago.

Often called Cro-Magnoids, these first Europeans are believed by many scientists to have out-competed the Neanderthals, gradually driving them to extinction. The alternative theory, that Neanderthals and early humans are more closely related and may have even interbred upon meeting, is less popular, though it hasn’t yet been ruled out.  In order to resolve this debate, scientists have turned to genetics and methods of ancient DNA analysis to help them answer the questions surrounding the relationships between Neanderthals and Cro-Magnoids.

However, the practice of extracting and analyzing ancient DNA remains tricky and fraught with skepticism.  One of the main problems is contamination – anyone who touches fossilized remains runs the risk of contaminating it with his or her own DNA.  So how can we tell if scientists are analyzing the right DNA? A new study in this week’s PLOS One attempts to rectify the contamination problem in a novel way by analyzing the DNA of everyone who touched a fossil for comparison in order to rule out contamination. It will also help us better understand the genetic connection between Cro-Magnoids and Neanderthals.

The Italian team, led by David Caramelli, analyzed DNA from a 28,000-year-old Homo sapiens Cro-Magnoid individual found in Piglacci Cave in Italy.  They also analyzed the DNA of everyone who had touched the remains since its 2003 discovery.  What they found was that the Cro-Magnoid individual was genetically similar to most modern Europeans.  The Cro-Magnoid DNA was also distinct from the researchers’ DNA sequences, showing that none of them had contaminated the sample. When the DNA of the Piglacci Cro-Magnoid individual was compared to previous analyses of Neanderthal DNA, the researchers found that the Cro-Magnoid individual has much more in common genetically with modern European humans than with Neanderthals. These results are important for several reasons.

• First, this is one of the first studies to have obtained a reliable and contaminant-free sample of DNA from a 28,000-year-old Cro-Magnoid.  It will hopefully satisfy the skeptics who had claimed contamination will always be a possibility.
• Second, the genetic similarity of the Cro-Magnoid to modern Europeans, combined with its lack of similarity to Neanderthals, helps solidify the theory that the two ancient groups were not closely related.  Previous studies comparing Neanderthal DNA to modern human DNA have also turned up no genetic similarity.
• Third, the body of evidence now shows that Neanderthals didn’t contribute any DNA to the Cro-Magnoid OR modern human gene pool. Indeed, Caramelli and his colleagues point out that “the burden of proof is now on those who maintain that Neanderthals might have contributed to the modern gene pool.”

Together, the current scientific evidence suggests that instead of merging with Cro-Magnoids Neanderthals must have simply died out, unable to compete with the Cro-Magnoids’ superior technology and greater population size.  The archaeological record shows Neanderthals becoming less and less prevalent around 35,000 years ago, and by 30,000 years ago, they disappear completely.

After their rivals’ disappearance, Cro-Magnoid humans would have to cope with hardships of their own, as the Last Ice Age was approaching its peak.  They would be relegated to the southern fringes of Europe for 5,000 years, awaiting the warming temperatures that would allow them to repopulate the continent.

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