What a Small Brain Can Tell Us

New information about an early human skull sheds more light on the very first members of the human genus.  The skull, found in Dmanisi, Georgia in 2005, has now been freed from the stone casing that has preserved it for the past 1.8 million years. An international team led by David Lordkipanidze of the Georgian National Museum report its findings in the October 18 issue of the journal Science. 

Photo Caption: The Dmanisi D4500 early Homo cranium in situ. Photo courtesy of Georgian National Museum.

When the world first learned of early human remains in Georgia, the news came as a bit of a shock.  These early humans seemed quite similar to other remains found in Africa and dating to the same time.  That suggests they were able to travel and adapt to new settings. 

The latest analysis contains a new surprise.  The skull described in the new report has an unexpectedly small brain size, at or below the range usually seen as minimal for our genus.  At 546 cubic centimeters, its small brain widens our view of variability of humans at this time. 

Does this skull, identified as Skull 5 from Dmanisi, really measure up to being in the genus Homo at all? It is something else, like Australopithecus?  The researchers argue that it is clearly part of the genus Homo for the simple reason that Skull 5 is found with other, larger-brained skulls, all clearly part of the same community.  One Georgian brain was as large as 730 cc.  What this suggests is that Skull 5 is part of Homo but that our definition of Homo should be broadened. 

In fact, all this diversity at one site provides support for one side in an ongoing debate.  Are species defined broadly in terms of variability, or does small to moderate variation indicate separate species.  This finding supports the view that at least in terms of early humans, a species can be quite variable.      

Not too long ago, Lordkipanidze and his team took the opposite view.  They believed that these early humans from Georgia were a distinct species, what they called Homo georgicus.  The new paper retracts that claim, saying that the new evidence of variation in Georgia means that these fossils fit within the widened range variability of Homo erectus, a globally dispersed species.  More precisely, they see the Georgian samples as best classified as Homo erectus ergaster georgicus, part of the species Homo erectus but distinct because of modifications over time and because of location. 

Commenting on the variation in the skulls found almost literally on top of each other at Dmanisi, co-author Christoph Zollikofer notes that the skulls “look quite different from one another, so it's tempting to publish them as different species.  Yet we know that these individuals came from the same location and the same geological time, so they could, in principle, represent a single population of a single species,” Zollikofer said in a press release issued by the journal Science. 

The key claim advanced in the article, however, is that these samples from Georgia and Africa, together with other samples from Asia, are all part of one global species.  The report describes them as Homo erectus, seen as “a single but polymorphic lineage.” 

The diversity found in Georgia also suggests that the number of individuals in that region may have been larger than first thought, possibly numbering 10,000 or so.  And the small size of Skull 5’s brain suggests that they traveled all this way before brains began to expand.

The report, “A Complete Skull from Dmanisi, Georgia, and the Evolutionary Biology of Early Homo," is published in the 18 October 2013 issue of the journal Science, published by the American Association for the Advancement of Science.    

Denisovan DNA in Focus

Using new techniques to study ancient DNA, scientists have unraveled the genetic details of a young girl who lived in central Asia around 50,000 years ago. She is the only individual of her kind, a unique branch of the human family called the Denisovans, named for the cave where her remains were found in 2008.

What makes the research all the more startling is that only two teeth and one pea-size bone fragment has been found. But from those tiny fragments of humanity, the story of the Denisovans is being pieced together.

The new techniques were developed by Matthias Meyer, working at the Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology in Leipzig, a research program led by Svante Pääbo. DNA extracted from the bone fragment was separated into two strands that were amplified and analyzed separately, many times over, until a highly reliable sequence was determined.

Laboratory for the extraction of ancient DNA. [Image courtesy of Max Planck Institute for Evolutionary Anthropology].

Researchers claim that the result is as complete and accurate as the sequence of living human beings. Already, the new technique is being used to study other ancient remains, including samples of Neandertal DNA. Denisovans and Neandertals, distinct but closely related forms of humanity, overlapped with anatomically modern humans (AMH) and interbred with them.

New methods in genetics, including the technical breakthrough described in this paper, are opening new windows on the human family tree, which resembles an inter-grown vine more than a straight line of branches.

So accurate is the genetic analysis that researchers can reach some conclusions about other Denisovans, even though no samples exist for them. For one thing, despite their wide geographic spread, they apparently never reached high numbers. Their DNA lives on today in the faint echo of ancient interbreeding found in the uniquely-Denisovan sequences carried by those who live in the islands of southeast Asia.

No one knows what Denisovans looked like, but they probably resembled us in many ways. The Denisovan girl whose DNA was studied carried genes that are associated today with brown hair, brown eyes, and dark skin. Like us they had 23 pairs of chromosomes (compared to chimps with 24), making interbreeding more readily possible.

Denisova molar, distal. [Image courtesy of Max Planck Institute for Evolutionary Anthropology].

One of the more tantalizing aspects of the report is the light it sheds not on the Denisovans or the Neandertals but on us anatomically modern human beings who live today. Why did we survive and flourish culturally when they did not?

One explanation may lie in the genetic differences between us and them, which can be studied for the first time in detail. In this paper, researchers identify specific changes in genes that are associated with brain complexity, synaptic connections, and speech development. According to the paper, “it is thus tempting to speculate that crucial aspects of synaptic transmission may have changed in modern humans.” In other words, tiny differences in DNA led to still relatively small differences in brain function that led to huge differences in culture.

Future technical advances will continue to shed new light on the complex story of recent human ancestry. By gaining ever-higher clarity on the genetic differences between Neandertals, Denisovans, and modern humans, we will come to know the story of our humanity in greater detail.

The paper ends with this reflection: “This [work] should ultimately aid in determining how it was that modern humans came to expand dramatically in population size as well as culturally complexity which archaic humans eventually dwindled in numbers and became physically extinct.” The paper, “A High-Coverage Genome Sequence from an Archaic Denisovan Individual,” is published in the 30 August 2012 issue of Science, published by the American Association for the Advancement of Science.

How Old Is Art?

Confirmed dates for the world’s oldest art just got older, according to the report of an international research team published in the May 14 issue of the Proceedings of the National Academy of Sciences.

Dating back about 37,000 years, the art consists of engravings made in stone that has since fallen from the ceiling of a cave at Abri Castanet in southwestern France. While not as visually arresting as the more famous cave art found at Chauvet, the Castanet engravings are both older and represent what is very likely an earlier stage in the history of the Aurignacian culture, which spanned 40,000 to about 28,000 years ago. Some of the Chauvet paintings are now confirmed at between 30,000 and 32,000 years ago.

Credit: HTO. A replica of a painting, now in the public domain.

The Castanet engravings are both simpler artistically and were located in the general living area of the cave. The Aurignacian culture that created both the paintings and the engravings is known for is many forms of art. According to New York University anthropology professor Randall White, one of the study's co-authors, the Aurignacians "had relatively complex social identities communicated through personal ornamentation, and they practiced sculpture and graphic arts."

"But unlike the Chauvet paintings and engravings, which are deep underground and away from living areas, the engravings and paintings at Castanet are directly associated with everyday life, given their proximity to tools, fireplaces, bone and antler tool production, and ornament workshops," White said in press release issued by NYU.

With more refined archeological techniques, the story of the rise of human symbolic culture is likely to become more complex and more ancient. While there may well have been bursts of cultural creativity in which symbolic advance occurred rapidly, additional findings may also suggest a more steady rise in the story of human art. The study, entitled “Context and dating of Aurignacian vulvar representations from Abri Castanet, France,” appears in the May 14, 2012 edition of PNAS.

Spreading Farming, Spreading Genes

Agriculture probably originated in the Middle East about 11,000 years ago. Over the next six thousand years, it spread to other parts of the globe, including northern Europe, gradually replacing hunting and gathering as the primary means of human survival.

How did it spread? Were hunter-gatherers converted to the efficiencies of agriculture? Or did farmers from the south spread north, bringing their agriculture with them?

A new study suggests that farming spread because farmers moved. The movement was slow, taking five to six thousand years to reach Scandinavia. Early in the process, farmers of southern ancestry lived side by side with their more northerly human cousins, who still lived by hunting and gathering. Eventually, after a thousand years or so, farmers interbred with hunter-gatherers and farming became the dominant way of life.

The new study, which appears in the April 27 issue of Science, is based on an analysis of four skeletons, all found in Sweden and dating from about 5,000 years ago. Three were hunter-gatherers and one was a farmer. All of them lived their entire lives close to where they were buried, the hunter-gatherers in a flat grave and the farmer a stone megalith like the one pictured below.

Caption: Several hundred megalith tombs are known from the Falbygden area, including Gökhem and Valle parishes in Östergötland,Sweden.Credit: Göran Burenhult

"We know that the hunter-gatherer remains were buried in flat-bed grave sites, in stark contrast to the megalithic sites that the farmers built," said Mattias Jakobsson, a senior author from Uppsala University. "The farmer we analyzed was buried under such a megalith, and that's just one difference that helps distinguish the two cultures," Jakobsson said in a press release issued by the journal.

What is most significant in this study comes from an analysis of the human DNA extracted from the four skeletons. By studying their DNA, researchers found that the farmer belonged to a community with ancestral roots in the eastern Mediterranean, most closely resembling today's Greeks and Cypriots. The hunter-gatherers, on the other hand, were more like today’s northern Europeans, most closely resembling today's Finns. "What is interesting and surprising is that Stone Age farmers and hunter-gatherers from the same time had entirely different genetic backgrounds and lived side by side for more than a thousand years, to finally interbreed," Jakobsson said.

Caption: The skeleton belongs to a young female in her 20s, and can be dated to around 4,700 years ago. Credit: Göran Burenhult

"The results suggest that agriculture spread across Europe in concert with a migration of people," added Pontus Skoglund, also of Uppsala University. "If farming had spread solely as a cultural process, we would not expect to see a farmer in the north with such genetic affinity to southern populations."

The article, entitled "Origins and Genetic Legacy of Neolithic Farmers and Hunter-Gatherers in Europe," appears in the April 27 issue of Science, published by the American Association for the Advancement of Science.

A Million Years of Fire

One of our newest technologies has just shed new light on one of our oldest.

When did our human ancestors learn to control and use fire? Armed with the latest high tech tools, an international team of researchers has pushed the date back to 1 million years. That’s 300,000 years earlier than previous unambiguous dates.

The massive Wonderwerk Cave is in northern South Africa on the edge of the Kalahari. Previous excavations have shown extensive human occupation. Using the new techniques of micromorphological analysis and Fourier transform infrared microspectroscopy (mFTIR), researchers analyzed cave sediments at a far more detailed level than possible before.

Caption: This is a panoramic view of the entrance to Wonderwerk Cave, South Africa. Credit: H. Ruther. Usage Restrictions: None

In the cave sediments researchers found bits of ash from plants along with fragments of burned bone. Did the wind blow burning debris into the cave? The evidence—collected about 100 feet from the current opening of the cave—supports the conclusion that the fire burned in the cave. Also part of the proof: the surrounding surfaces are discolored.

”The analysis pushes the timing for the human use of fire back by 300,000 years, suggesting that human ancestors as early as Homo erectus may have begun using fire as part of their way of life," anthropologist Michael Chazan said in a press release from the University of Toronto.

According to the paper, "Through the application of micromorphological analysis and Fourier transform infrared microspectroscopy (mFTIR) of intact sediments and examination of associated archaeological finds— fauna, lithics, and macrobotanical remains—we provide unambiguous evidence in the form of burned bone and ashed plant remains that burning events took place in Wonderwerk Cave during the early Acheulean occupation, approximately 1.0 Ma. To date, to the best of our knowledge, this is the earliest secure evidence for burning in an archaeological context."

Caption: Interior of Wonderwerk Cave. Images courtesy of M. Chazan.

"The control of fire would have been a major turning point in human evolution," says Chazan. "The impact of cooking food is well documented, but the impact of control over fire would have touched all elements of human society. Socializing around a camp fire might actually be an essential aspect of what makes us human."

How important are fire and cooking for human evolution. A recent book, Catching Fire: How Cooking Made Us Human by Richard Wrangham, argues that cooking is essential to our humanity. Now in the paper published on April 2, the team concludes that its study “is the most compelling evidence to date offering some support for the cooking hypothesis of Wrangham.”

Their work is published as “Microstratigraphic evidence of in situ fire in the Acheulean strata of Wonderwerk Cave, Northern Cape Province, South Africa,” in the April 2, 2012 issue of the Proceedings of the National Academy of Sciences.

Genes, Hybrids, and Giant Tortoises

Charles Darwin visited the Galápagos Islands in 1835. As he moved from island to island, he saw the subtle differences between finches, tortoises, and other animals. These observations led to the discovery of the theory of evolution as an expanding “tree of life,” first sketched by Darwin in his notebook entry dated just two years later in 1837.

The great tortoises of the Galápagos could not fail to impress. The greatest of all, the tortoise Chelonoidis elephantopus, can live to be a hundred years old and grow to six feet and almost 900 pounds.

Until now, it was believed that whalers hunted the great C. elephantopus to extinction shortly after Darwin’s visit. Now, however, new research suggests that a few of the great tortoises may still be alive.

Caption: G. Becky tortoises are native to Isabela Island in the Galapagos chain and have more domed shape shell. Credit: Courtesy Yale University.

Researchers have found what they believe are direct offspring of purebred C. elephantopus tortoises. By testing the genes of living tortoises, researchers concluded that they were studying hybrids. One parent was from a related species, C. becki. But the other parent was clearly C. elephantopus. And since the living tortoises were still quite young, researchers were drawn to the obvious conclusion that the C. elephantopus parent lived until a few decades ago and may still be roaming the slopes of Isabela Island.

So now it’s a race against time to find surviving purebred C. elephantopus tortoises in hopes that enough of them still exist so the species—truly one of the great animal species—can be brought back from what seemed like extinction. According to the report, “purebred tortoises of the recently ‘extinct’ C. elephantopus from Floreana Island are very likely still alive today.”

Caption: This tortoise is a hybrid of G. Becky and C. elephantopus, a species native to Floreana Island some 200 miles away and thought to be extinct. Genetic analysis of tortoise population on Isabela Island suggests purebred individuals of C. elephantopus must still be alive on Isabela. Credit: Courtesy of Yale University

One interesting parallel. Using a similar approach, researchers have recently concluded that human beings are also hybrids. For example, many of us contain genes from our Neandertal ancestors. The big difference, of course, is that our interbreeding occurred tens of thousands of years ago. In either case, hybridization or interbreeding occurs when the twigs at the end of Darwin's tree of life come together. As evolutionary biologists are discovering, speciation (or branching) is critical to evolution, but so is interbreeding or hybridization.

According to the report, “To our knowledge, this is the first rediscovery of a species by way of tracking the genetic footprints left in the genomes of its hybrid offspring.” The report, "Genetic rediscovery of an ‘extinct’ Galápagos giant tortoise species," appears in the January 9, 2012 issue of Current Biology.

Evolutionary Fast-Track for Human Brains

More than 35 years ago, Allan Wilson and Mary-Claire King made an astonishing proposal. Maybe what separates humans and chimps is not just our genes. Maybe it’s also how our genes are expressed or regulated.

Research published in today’s issue of PLoS Biology builds on decades of intervening advances in evolution and genetics and take the question much further. The difference between humans and nonhuman primates in cognitive ability is explained in large part by differences in gene expression, especially during the critical periods when young brains are being formed.

Humans share many of their genes with other species, especially chimps. In fact, we share so many genes that it is hard to explain how we can be so different in terms of cognitive ability. If genes make all the difference, how can they explain the differences between chimp and human brains? And how can a mere six million years of human-chimp divergence give us enough time to accumulate enough genetic change?

The answer seems to lie in the relatively rapid evolution of differences in gene expression. In other words, while the genes themselves evolved slowly, the regulation of their expression evolved more rapidly. It’s not just the genes but their expression that’s important. It’s not just the evolution of genes but the evolution of gene expression that drives the rapid divergence between human and chimp brains.

This is especially true in the genes that control the development of the prefrontal cortex of the brain. In other words, there has been relatively rapid evolution in the genetic mechanisms that regulate genes directly responsible for the early-childhood neural development of the critically-important prefrontal cortex, which is involved in abstract thinking, planning, social intelligence, and working memory.

According to the article, “humans display a 3-5 times faster evolutionary rate in divergence in developmental patterns, compared to chimpanzees.” Most important, however, is the way this research identifies specific regulators that have evolved rapidly since human-chimp divergence. These regulators are “micro-RNAs,” some of which are specifically identified in the article, with the claim that “changes in the expression of a few key regulators may have been a major driving force behind rapid evolution of the human brain.”

According to the study’s senior author, Philipp Khaitovich, this finding suggests that "identifying the exact genetic changes that made us think and act like humans might be easier than we previously imagined." Kkaitovich was quoted in a press release issued by the journal, PLoS Biology.

The article is entitled "Micro-RNA-Driven Developmental Remodeling in the Brain Distinguishes Humans from Other Primates" and appears in the December 6 issue of PLoS Biology, where it is freely available to the public.