Neanderthal Genes Influence Contemporary Humans’ Skull Shape, Brain Size


Individuals carrying these ancient ancestors’ DNA are more likely to have slightly elongated, rather than rounded, brains

The researchers are quick to point out that their findings don’t suggest a link between brain size or shape and behavior, but instead offer an exploration of the genetic evolution of modern brains (Philipp Gunz)

By Meilan Solly

smithsonian.com
December 14, 2018

Neanderthals may have gone extinct some 40,000 years ago, but thanks to long-ago species interbreeding, their genes live on in modern humans.

The implications of this genetic inheritance remain largely unclear, although previous studies have proposed links with disease immunity, hair color and even sleeping patterns. Now, Carl Zimmer reports for The New York Times, a study recently published in Current Biology offers yet another example of Neanderthals’ influence on Homo sapiens: Compared to individuals lacking Neanderthal DNA, carriers are more likely to have slightly elongated, rather than rounded, brains.

This tendency makes sense given Neanderthals’ distinctive elongated skull shape, which Science magazine’s Ann Gibbons likens to a football, as opposed to modern humans’ more basketball-shaped skulls. It would be logical to assume this stretched out shape reflects similarly protracted brains, but as lead author Philipp Gunz of Germany’s Max Planck Institute for Evolutionary Anthropology tells Live Science’s Charles Q. Choi, brain tissue doesn’t fossilize, making it difficult to pinpoint the “underlying biology” of Neanderthal skulls.

To overcome this obstacle, Gunz and his colleagues used computed tomography (CT) scanning to generate imprints of seven Neanderthal and 19 modern human skulls’ interior braincases. Based on this data, the team established a “globularity index” capable of measuring how globular (rounded) or elongated the brain is. Next, Dyani Lewis writes for Cosmos, the researchers applied this measure to magnetic resonance imaging (MRI) scans of around 4,500 contemporary humans of European ancestry, and then compared these figures to genomic data cataloguing participants’ share of Neanderthal DNA fragments.

Two specific genes emerged in correlation with slightly less globular heads, according to The New York Times’ Zimmer: UBR4, which is linked to the generation of neurons, and PHLPP1, which controls the production of a neuron-insulating sleeve called myelin. Both UBR4 and PHLPP1 affect significant regions of the brain, including the part of the forebrain called the putamen, which forms part of the basal ganglia, and the cerebellum. As Sarah Sloat explains for Inverse, the basal ganglia influences cognitive functions such as skill learning, fine motor control and planning, while the cerebellum assists in language processing, motor movement and working memory.

In modern human brains, PHLPP1 likely produces extra myelin in the cerebellum; UBR4 may make neurons grow faster in the putamen. Comparatively, Science’s Gibbons notes, Neanderthal variants may lower UBR4 expression in the basal ganglia and reduce the myelination of axions in the cerebellum—phenomena that could contribute to small differences in neural connectivity and the cerebellum’s regulation of motor skills and speech, the study’s lead author Simon Fisher of the Netherlands’ Max Planck Institute for Psycholinguistics tells Gibbons .

Still, the effects of such gene variations are probably negligible in living humans, merely adding a slight, barely discernible elongation to the skull.

“Brain shape differences are one of the key distinctions between ourselves and Neanderthals,” Darren Curnoe, a paleoanthropologist from Australia’s University of New South Wales who was not involved in the study, tells Cosmos, “and very likely underpins some of the major behavioural differences between our species.”

In an interview with The New York Times, Fisher adds that the evolution of UBR4 and PHLPP1 genes could reflect modern humans’ development of sophisticated language, tool-making and similarly advanced behaviors.

But, Gunz is quick to point out, the researchers are not issuing a decisive statement on the genes controlling brain shape, nor the effects of such genes on modern humans carrying fragments of Neanderthal DNA: “I don’t want to sound like I’m promoting some new kind of phrenology,” he tells Cosmos. “We’re not trying to argue that brain shape is under any direct selection, and brain shape is directly related to behaviour at all.”

Viewpoint: Human evolution, from tree to braid


If one human evolution paper published in 2013 sticks in my mind above all others, it has to be the wonderful report in the 18 October issue of the journal Science.

The article in question described the beautiful fifth skull from Dmanisi in Georgia. Most commentators and colleagues were full of praise, but controversy soon reared its ugly head.

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What was, in my view, a logical conclusion reached by the authors was too much for some researchers to take.

The conclusion of the Dmanisi study was that the variation in skull shape and morphology observed in this small sample, derived from a single population of Homo erectus, matched the entire variation observed among African fossils ascribed to three species – H. erectus, H. habilis and H. rudolfensis.

The five highly variable Dmanisi fossils belonged to a single population of H. erectus, so how could we argue any longer that similar variation among spatially and temporally widely distributed fossils in Africa reflected differences between species? They all had to be the same species.

I have been advocating that the morphological differences observed within fossils typically ascribed to Homo sapiens (the so-called modern humans) and the Neanderthals fall within the variation observable in a single species.

It was not surprising to find that Neanderthals and modern humans interbred, a clear expectation of the biological species concept.

But most people were surprised with that particular discovery, as indeed they were with the fifth skull and many other recent discoveries, for example the “Hobbit” from the Indonesian island of Flores.

It seems that almost every other discovery in palaeoanthropology is reported as a surprise. I wonder when the penny will drop: when we have five pieces of a 5,000-piece jigsaw puzzle, every new bit that we add is likely to change the picture.

Did we really think that having just a minuscule residue of our long and diverse past was enough for us to tell humanity’s story?

If the fossils of 1.8 or so million years ago and those of the more recent Neanderthal-modern human era were all part of a single, morphologically diverse, species with a wide geographical range, what is there to suggest that it would have been any different in the intervening periods?

Probably not so different if we take the latest finds from the Altai Mountains in Siberia into account. Denisova Cave has produced yet another surprise, revealing that, not only was there gene flow between Neanderthals, Denisovans and modern humans, but that a fourth player was also involved in the gene-exchange game.

The identity of the fourth player remains unknown but it was an ancient lineage that had been separate for probably over a million years. H. erectus seems a likely candidate. Whatever the name we choose to give this mystery lineage, what these results show is that gene flow was possible not just among contemporaries but also between ancient and more modern lineages.

Pit of Bones
A femur recovered from the famed “Pit of Bones” site in Spain yielded 400,000-year-old DNA

Just to show how little we really know of the human story, another genetic surprise has confounded palaeoanthropologists. Scientists succeeded in extracting the most ancient mitochondrial DNA so far, from the Sima de los Huesos site in Atapuerca, Spain.

The morphology of these well-known Middle Pleistocene (approximately 400,000 years old) fossils have long been thought to represent a lineage leading to the Neanderthals.

When the results came in they were actually closer to the 40,000 year-old Denisovans from Siberia. We can speculate on the result but others have offered enough alternatives for me to not to have to add to them.

The conclusion that I derive takes me back to Dmanisi: We have built a picture of our evolution based on the morphology of fossils and it was wrong.

We just cannot place so much taxonomic weight on a handful of skulls when we know how plastic – or easily changeable – skull shape is in humans. And our paradigms must also change.

The Panel of Hands at El Castillo Cave, Spain
Old assumptions are being challenged as new thinking emerges

Some time ago we replaced a linear view of our evolution by one represented by a branching tree. It is now time to replace it with that of an interwoven plexus of genetic lineages that branch out and fuse once again with the passage of time.

This means, of course, that we must abandon, once and for all, views of modern human superiority over archaic (ancient) humans. The terms “archaic” and “modern” lose all meaning as do concepts of modern human replacement of all other lineages.

It also releases us from the deep-rooted shackles that have sought to link human evolution with stone tool-making technological stages – the Stone Ages – even when we have known that these have overlapped with each other for half-a-million years in some instances.

The world of our biological and cultural evolution was far too fluid for us to constrain it into a few stages linked by transitions.

The challenge must now be to try and learn as much as we can of the detail. We have to flesh out the genetic information and this is where archaeology comes into the picture. We may never know how the Denisovans earned a living, after all we have mere fragments of their anatomy at our disposal, let alone other populations that we may not even be aware of.

What we can do is try to understand the spectrum of potential responses of human populations to different environmental conditions and how culture has intervened in these relationships. The Neanderthals will be central to our understanding of the possibilities because they have been so well studied.

A recent paper, for example, supports the view that Neanderthals at La Chapelle-aux-Saints in France intentionally buried their dead which contrasts with reports of cannibalistic behaviour not far away at El Sidron in northern Spain.

Here we have two very different behavioural patterns within Neanderthals. Similarly, modern humans in south-western Europe painted in cave walls for a limited period but many contemporaries did not. Some Neanderthals did it in a completely different way it seems, by selecting raptor feathers of particular colours. Rather than focus on differences between modern humans and Neanderthals, what the examples show is the range of possibilities open to humans (Neanderthals included) in different circumstances.

The future of human origins research will need to focus along three axes:

  • further genetic research to clarify the relationship of lineages and the history of humans;
  • research using new technology on old archaeological sites, as at La Chapelle; and
  • research at sites that currently retain huge potential for new discoveries.

Sites in the latter category are few and far between. In Europe at least, many were excavated during the last century but there are some outstanding examples remaining. Gorham’s and Vanguard Caves in Gibraltar, where I work, are among those because they span over 100,000 years of occupation and are veritable repositories of data.

There is another dimension to this story. It seems that the global community is coming round to recognising the value of key sites that document human evolution.

In 2012, the caves on Mount Carmel were inscribed on the Unesco World Heritage List and the UK Government will be putting Gorham’s and associated caves on the Rock of Gibraltar forward for similar status in January 2015. It is recognition of the value of these caves as archives of the way of life and the environments of people long gone but who are very much a part of our story.

Prof Clive Finlayson is director of the Gibraltar Museum and author of the book The Improbable Primate.

Gorham's Cave The UK government is to seek World Heritage status for Gorham’s and associated caves on the Rock

Neanderthals Passed Along Diabetes Risk Gene.


Kermanshah Pal Museum-Neanderthal

Scientists have determined that a variation of a gene that increases the risk of a person developing type 2 diabetes by 25 percent was likely introduced into human populations by Neanderthals more than 60,000 years ago. Half of people with a recent Native American lineage, including Latin Americans, have the gene, SLC16A11, as do 20 percent of East Asians. The newly seqeuenced, high quality Neanderthal genome, taken from a female toe found in Siberia‘s Denisova Cave, also included the variant, and researchers say that analysis suggests that Neanderthals introduced it into the human genome when they intermixed with modern humans, after the latter left Africa 60,000 to 70,000 years ago. According to the findings from the completed Neanderthal genome, roughly two percent of the genomes of today’s non-African humans are comprised of Neanderthal DNA.

Oldest human DNA found in Spain


 
A drawing shows what the species of Homo heidelbergensis might have looked like 400,000 years ago.
 
A drawing shows what the species of Homo heidelbergensis might have looked like 400,000 years ago.

STORY HIGHLIGHTS
 

There were no genetic tests 400,000 years ago, so our ancient relatives didn’t know as much about themselves as we know about them now.

Scientists have reconstructed a nearly complete mitochondrial genome of an ancient human relative, whose remains were found in Sima de los Huesos (“pit of bones”) in northern Spain. It is the oldest DNA to be recovered from an early humanlike species, authors of a study wrote in the journal Nature.

The ancient species that has revealed some of its genetic secrets, via bone fragments from a femur, is probably not directly linked to your family tree though.

“It’s quite clear that this is not a direct ancestor of people today,” said Svante Paabo, a biologist at the Max Planck Institute for Evolutionary Anthropology and senior author of the study.

Instead, he said, this representative of an early humanlike species, called Homo heidelbergensis, could be an ancestor of both Neanderthals and another group called the De nisovans.

The genetic relationship to Denisovans, discovered through this DNA research, is surprising because the Homo heidelbergensis remains found in the cave have many Neanderthal-like features. The only remnants of Denisovans come from Siberia — a long way from Spain.

“It’s sort of an open question really what this means, and I think further research into the nuclear genome of these hominins will address that,” Paabo said.

How they did it

Paabo and colleagues used a new method for sequencing ancient, degraded genetic material to put together the 400,000-year-old specimen’s mitochondrial genome. It is the oldest DNA ever found outside permafrost conditions — in other words, it was not permanently frozen.

“The retrieval of such ancient human DNA is a major technical achievement, and promises further recovery of such material from other fossils in this time range, both in the Sima and elsewhere, where we would not previously have expected it, or looked for it,” said Chris Stringer, researcher at the Natural History Museum in London, who was not involved in the study.

 

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Mitochondria are structures in cells that convert food energy into usable forms. DNA stored in the mitochondria is passed to children through the maternal line only (i.e., only moms can pass it on), so it’s only a small snapshot of inherited genes.

Genetic material in the cell’s nucleus comes from both parents and gives a fuller picture of genetic heritage.

To study genetics of our ancient predecessors, researchers have an easier time studying mitochondrial DNA because there are hundreds of times more copies of it in each cell.

“It’s a much bigger chance to find some fragments of this preserved,” Paabo said.

A skeleton of a Homo heidelbergensis representative from a cave site in Spain.
A skeleton of a Homo heidelbergensis representative from a cave site in Spain.

The method that researchers used involves separating the two strands of the DNA double helix. They then make a “library” from each of the two strands. If part of one strand is damaged, its analogue on the other strand — which is made of complementary genetic partners — may be intact.

“That is sort of the big trick involved,” Paabo said.

After sequencing the mitochondrial DNA, researchers then compared the result with genetic information about Neanderthals and Denisovans.

Since nuclear DNA encompasses more information about a person’s inheritance, a nuclear genome sequence from Homo heidelbergensis may reveal even more clearly how it is connected to other ancient humanlike species, he said.

But retrieving the nuclear DNA sequence will be challenging, study authors wrote. Just to get the mitochondrial DNA sequence, it took about two grams of bone — less than 0.1 ounce — even though hundreds of copies of this DNA are in every cell.

Still, Paabo said, the sequencing technique his group used “opens a possibility to now do this at many other sites, and really begin to understand earlier human evolution.”

Relationship to other species

Researchers thought initially the mitochondrial DNA of the Homo heidelbergensis specimen would share a common ancestor with Neanderthals. Neanderthals lived in Europe beginning as much as 300,000 years ago, Paabo said. (Homo sapiens, our species, first appeared in Africa between 100,000 and 200,000 years ago.)

Instead, researchers discovered through the DNA that this specimen is closer to the Denisovans, a group related to the Neanderthals.

A likely explanation is that in Eastern Eurasia this species gave rise to Denisovans, and in Western Eurasia they were the ancestors of Neanderthals, Paabo said. But more research needs to be done to verify that theory.

Humans, Neanderthals related to yet another group

Little is known about the Denisovans. Although some of their remains were found in southern Siberia, their genetic signature is only found today on islands in the Pacific.

Paabo was also the senior author on a 2012 study in the journal Science analyzing the Denisovan genome. That research suggested that human ancestors and the Denisovans’ ancestors must have branched off from one another as much as 700,000 years ago — although that number is vague. Still, it seems that the Denisovans must have mated with indigenous people in Papua New Guinea and Australia, Paabo said.

About 3% to 5% of the DNA of people from Melanesia (islands in the southwest Pacific Ocean), Australia and New Guinea as well as aboriginal people from the Philippines comes from the Denisovans.

On the other hand, everyone who lives outside Africa today probably has some Neanderthal DNA in them, Paabo said in 2012.

The bottom line, Paabo said, is that the relationships between these early human relatives — Homo heidelbergensis, Neanderthals and Denisovans — are not clear-cut.

“It’s going to be a more complex history that one will eventually clarify with the help of DNA,” he said.

New study explains why men’s noses are bigger than women’s.


Human noses come in all shapes and sizes. But one feature seems to hold true: Men’s noses are bigger than women’s. A new study from the University of Iowa concludes that men’s noses are about 10 percent larger than female noses, on average, in populations of European descent. The difference, the researchers believe, comes from the sexes’ different builds and energy demands: Males in general have more lean , which requires more oxygen for muscle tissue growth and maintenance. Larger noses mean more oxygen can be breathed in and transported in the blood to supply the muscle.

The researchers also note that males and females begin to show differences in nose size at around age 11, generally, when puberty starts. Physiologically speaking, males begin to grow more lean muscle mass from that time, while females grow more fat mass. Prior research has shown that, during puberty, approximately 95 percent of body weight gain in males comes from fat-free mass, compared to 85 percent in females.

“This relationship has been discussed in the literature, but this is the first study to examine how the size of the nose relates to body size in males and females in a longitudinal study,” says Nathan Holton, assistant professor in the UI College of Dentistry and lead author of the paper, published in the American Journal of Physical Anthropology. “We have shown that as body size increases in males and females during growth, males exhibit a disproportionate increase in nasal size. This follows the same pattern as energetic variables such as oxygenate consumption, basal metabolic rate and daily energy requirements during growth.”

It also explains why our noses are smaller than those of our ancestors, such as the Neanderthals. The reason, the researchers believe, is because our distant lineages had more muscle mass, and so needed larger noses to maintain that muscle. Modern humans have less lean muscle mass, meaning we can get away with smaller noses.

“So, in humans, the nose can become small, because our bodies have smaller oxygen requirements than we see in archaic humans,” Holton says, noting also that the rib cages and lungs are smaller in modern humans, reinforcing the idea that we don’t need as much oxygen to feed our frames as our ancestors. “This all tells us physiologically how have changed from their ancestors.”

Holton and his team tracked nose size and growth of 38 individuals of European descent enrolled in the Iowa Facial Growth Study from three years of age until the mid-twenties, taking external and internal measurements at regular intervals for each individual. The researchers found that boys and girls have the same nose size, generally speaking, from birth until puberty percolated, around age 11. From that point onward, the size difference grew more pronounced, the measurements showed.

“Even if the is the same,” Holton says, “males have larger noses, because more of the body is made up of that expensive tissue. And, it’s at puberty that these differences really take off.”

https://i1.wp.com/cdn.physorg.com/newman/gfx/news/2013/thebigmaleno.jpg

Holton says the findings should hold true for other populations, as differences in male and female physiology cut across cultures and races, although further studies would need to confirm that.

Prior research appears to support Holton’s findings. In a 1999 study published in the European Journal of Nutrition, researchers documented that males’ energy needs doubles that of females post-, “indicating a disproportional increase in energy expenditure in during this developmental period,” Holton and his colleagues write.

Another interesting aspect of the research is what it all means for how we think of the nose. It’s not just a centrally located adornment on our face; it’s more a valuable extension of our lungs.

“So, in that sense, we can think of it as being independent of the skull, and more closely tied with non-cranial aspects of anatomy,” Holton says.

What Neandertal DNA can teach about race, autism, and more?


london-bicycle-elevated-highway-screenshotPaleoanthropologists used to pray that they would unearth big troves of intact Neandertal skeletons and well-preserved artifacts that they could comb for clues to the origins of the human race. But these days, they can often get as much or more information straight from the DNA in bone fragments.

Case in point: the newly published genome study in Science from Matthias Meyer and Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology and their international team of colleagues. Using a novel DNA sequencing technique that works particularly well with degraded specimens, they examined the genome of a seven-year-old girl who died more than 74,000 years ago, using a surviving sliver from one of her finger bones. That girl’s bone fragment was one of the few pieces of evidence that in 2010 revealed the existence of the ancient Denisovan people — contemporaries of the Neandertals who overlapped with them in eastern Asia.

 

Matthias Meyer at work in the laboratory. (Credit: Max Planck Inst. for Evol. Anthro.)

Yet from that extraordinarily humble source, the Max Planck scientists have drawn a wealth of insights. They learned, for instance, that the Denisovans were probably dark-skinned, unlike the pale Neandertals. Because the girl had two X chromosomes, one from each parent, the scientists were able to infer that the Denisovan population had relatively little genetic diversity. Living natives of Papua New Guinea, Australia, and some southeast Asian islands derived about 6 percent of their genes from the Denisovans, yet the Denisovans seem to have contributed nothing of lasting value to the DNA of people in other parts of the world. Comparison with the Denisovan DNA also allowed the researchers to recognize that Europeans carry somewhat fewer genes from Neandertals than do East Asians and Native Americans.

Such discoveries are endlessly fascinating to some of us. But I can also understand that many people might reasonably question why any of these details matter. After all, Neandertals and our other ancient ancestors have been extinct for 30,000 years or longer. Why should we care so much about their DNA? Is there any practical value to be had from these studies?

I’ll argue that there is, and that it might be especially useful in helping us to develop more enlightened attitudes about racial differences and autism. To explain why, it may be useful to start by reviewing some of the major current ideas about how humans evolved in the first place.

Overview of our origins

Fifteen or 20 years ago, it might have been easier to find a rough consensus among paleoanthropologists about this topic than it is today precisely because of the recent bounty of fossil and DNA discoveries. All that information has answered some important questions and filled in a level of detail that might once have seemed inconceivable, but curiously enough, some of the broad strokes in the big picture have become less clear.

Roughly speaking, in Africa 1.7-2 million years ago, the earliest primitive members of the genus Homo appeared. They were small, hairy people who might look a bit apelike by our standards of beauty, but they had bigger brains and more tools than the upright Australopithecus species before them. The Homo erectus people were successful enough to spread out of Africa and migrate across Asia, and are responsible for some of the ancient fossils given names such as “Peking man.” Nevertheless, they were probably something of a false start for the spread of humanity as we now it.

 

The more relevant development came between 400,000 and 800,000 years ago, with a new wave of African emigration into the Middle East and Asia by a group of people with even bigger brains and better tools. They gave rise to the brawny, brow-ridged Neandertal people, Europe’s first inhabitants. Yet they also spawned at least one other Asian group, the Denisovans. (It wouldn’t be too surprising anymore if still more sibling groups contemporary to the Neandertals and Denisovans turned up elsewhere in Asia.) Meanwhile, humans also continued to prosper and evolve in Africa, and by 80,000 years ago, ones with a fully modern appearance had appeared and started their own exodus into the rest of the Old World.

What happened next is the stuff of archaeologists’ heated arguments. The oldest theory is the multiregional hypothesis strongly advocated by Milford Wolpoff of the University of Michigan in Ann Arbor. It claims that as different in appearance as moderns, Neandertals, Denisovans, and even the early Homo erectus might seem, they were all still members of the same human species. Over time, the modern traits predominated but some of the traits in local populations that had adaptive value (such as shorter, thicker bodies in cold climates) were retained and might bear some connection to physical differences seen in populations around the world today.

In the 1980s, however, a starkly opposing theory emerged largely, though not exclusively, from studies of mitochondrial DNA in living populations. (Mitochondria, the organelles in animal cells that create chemical energy, carry their own unique sets of genes, completely separate from the DNA in the nucleus for the rest of the cell’s genes.) Those analyses suggested that the maternal bloodlines of everyone alive today converged back on Africa less than 100,000 years ago, with no trace of a genetic contribution from local groups elsewhere. That conclusion spawned the “out of Africa” model, according to which scientists such as Chris Stringer of the Natural History Museum in London argued that when the anatomically modern humans colonized Asia and Europe, they displaced the Neandertals and other ancient residents without breeding with them. Whether the moderns had directly exterminated the ancients or simply outcompeted them for resources was anybody’s guess, but interbreeding was effectively nonexistent.

The out-of-Africa model and its mitochondrial DNA evidence proved highly persuasive to many anthropologists. Disagreements remained fierce, but during the 1990s it was often presented as the default explanation for human origins, even though almost everyone acknowledged how counterintuitive it seemed that modern humans would so completely refrain from mixing with creatures that looked so much like them. Mostly, scientists chalked it up to some obscure biological or behavioral speciation barrier.

DNA twists the plot

Ironically, one type of DNA evidence helped put the out-of-Africa model on top but later DNA evidence helped knock it back down. If brief, when Svante Pääbo and other researchers began the painstaking work of recovering nuclear DNA from Neandertal bones and sequencing it, they discovered that on average about 4 percent of living people’s genes are derived from Neandertals. (The telling exception was in people of modern African descent, whose genes were generally less than 1 percent Neandertal, which is what one might expect if the mixing would have occurred primarily outside Africa.)

Four percent might not sound like much, but it is substantially more than an out-of-Africa scenario with strict replacement rather than interbreeding would seem to allow. It’s remotely possible that this mixture is an artifact of old, unequal mixing of what became Neandertal genes within the ancestral African population (although anthropologist John Hawks has explained on his blog why that situation seems unlikely). The more likely explanation, though, is that some level of interbreeding did occur. For that reason, Stringer and other defenders of the concept now refer to a modified “mostly out of Africa” model that acknowledges some interbreeding but considers it largely trivial in extent and consequences.

That same evidence has, of course, only reinvigorated the multiregional hypothesis (though one might wonder why the percentage of ancient humans’ genes in us isn’t then higher). It has also nourished a popular new “assimilationist” school of thought that pragmatically splits the difference between multiregionalism and out-of-Africanism. The assimilationist model says that when the anatomically modern humans left Africa 80,000 years ago, they retained their own identity but also mixed to a degree with the older human populations they encountered. Both the modern and ancient groups became locally varying patchworks of physical traits and technologies. In the end, the ancients’ societies were too disrupted to survive but some of their genes persist in us.

The question of when and how humans emerged over the past few hundred thousand years is therefore considerably more complicated and less settled than it might have seemed a couple of decades ago. The same can be said for the closely related question about whether Neandertals, for example, represent their own species (Homo neanderthalensis) or just a subspecies (Homo sapiens neanderthalensis) alongside our own (Homo sapiens sapiens) – or whether, as Wolpoff would have it, virtually all of Homo has been one big species that has varied overtime.

Why we should care

Even if the science of human origins is still a work in progress, the accumulating information about how we got here and indeed what constitutes a member of the human race offers some useful perspectives on matters of scientific and ethical importance.

Perspective on the age of humanity. One small point that studies of the DNA of Neandertals and other ancient people illuminate is just how old or young we humans are as a species. The paleontological record indicates that the mean survival time for a mammalian species is about a million years, though some have lasted ten times that long. If we emerged only within the past 100,000 years or less, then Homo sapiens is indeed an amazingly young and precocious lot. And a loose, handwaving argument might therefore be made that we also probably have a commensurately long future ahead of us.

On the other hand, if Wolpoff is right and we are part of a species that has been around for two million years, then we are much more senior. It might make us look at the extinction rates with a little more sense of urgency.

Perspective on our nonprogressive evolution. The molecular study of our evolution also helps to drive home how unexceptional our biological history has been. Many icons of human evolution unintentionally reinforce a misleading sense of progress — witness the classic March of Progress illustration by Rudolph Zallinger that shows a modern human leading a Neanderthal and other “less evolved” ancestors.

But that sense really changes if we and Neandertals are seen as sibling groups, diverging but also sometimes re-merging throughout history. Our evolutionary history looks much less progressive and more like that of other species.

Perspective on race. For centuries (at least), arguments over race have invoked inappropriate biological concepts to make or defend distinctions among peoples — and distinctions in how they should be treated. They have likened races to subspecies to justify their inherent biological reality, along with some allegedly biological superiority, inferiority, or “otherness.”

A simple refutation of that idea has been the proof that the diversity of genetic characteristics within racial groups is greater than the diversity separating them: human races are not well enough defined and different enough to be meaningful biological groups. For that reason, many scientists now argue that race is not a biological concept but rather a social concept that sometimes carries biomedical consequences.

(Here’s what that means, if it isn’t immediately clear: In a society that mistreats the dark-skinned in general, for instance, black people may be at higher risk for diseases of poverty without having an intrinsic susceptibility to them. But an example that is perhaps less obvious is that of sickle-cell anemia, which is more common in those of black African descent than in those of white European descent. That’s because many people whose ancestors lived in regions where malaria was prevalent carry mutations for sickle-cell anemia that offer some protection from the parasite. But not all of those people are racially black and not all blacks carry the mutation. Sickle-cell information campaigns target predominantly black populations because society doesn’t accurately group people in terms of “ones whose ancestors had a lot of malaria.” In this case, race is a flawed but useful proxy for that nonexistent classification — but not because of the biological characteristics of the race as such.)

The foregoing is all true only in terms of race as we understand the concept today, however. If the multiregionalists and the assimilationists are right, then the Neandertals, Denisovans, and other ancient people we displaced may not have been separate species of person at all. They may instead have been races so different from modern humanity that they really were akin to other subspecies. Differences in their anatomical, genetic, behavioral, and intellectual traits would surely dwarf any seen in the world today among Homo sapiens. Color me naïve, but I would like to think that these insights might help to strengthen the spirit of color-blind brotherhood we ought to feel for one another.

(And in anticipation of a query I can feel coming: no, hypothetically, I would not be in favor of summarily treating Neandertals as second-class citizens if ever we could use technology to clone one. Neandertals were people and therefore, in my opinion, would deserve to be fully enfranchised. However, the question shows how ethically fraught such high-tech resurrections could be.)

Perspective on neurodiversity. In the course of their recent analysis of the Denisovan DNA, Meyer and Pääbo identified 23 highly conserved areas of the human genome that seem to be unique to our kind. Eight of those contain genes that previous studies have tied to nerve growth and other aspects of brain function. And three of the conserved genes — ADSL, CBTNAP2, and CNTNAP2 — have been implicated in some forms of autism.

Those correlations are not entirely surprising. Looking at the artwork and artifacts left by Neandertals, some archaeologists have argued that they seemed to lack a capacity for symbolic thought. Others such as John J. Shea disagree and suggest that the differences between modern and ancient thinking may have been exaggerated. Nevertheless, whatever evolutionary changes marked the emergence of modern humans, it’s likely they involved at least some important changes to our cognitive, linguistic, and social abilities. One might expect to find genes for those traits to be altered or absent in older types of humans.

I want to be perfectly clear on this point: this discovery absolutely does not mean that the Denisovans, Neandertals, and other ancients were autistic. Nor does it mean that autistic people exhibit prehistoric thinking. Rather, what it underscores is that normal modes of human thought occupy a broad continuum.

The “neurotypical” way in which most people see the world today is only one way of doing it. As enlightened studies of autism repeatedly drive home, we need to appreciate those variations as part of our human spectrum rather than just labeling them defective or abnormal.

With or without all our cognitive abilities, the Neandertals and Denisovans survived under amazingly hostile conditions for hundreds of thousands of years. Their different ways of thinking may have been dominant throughout long stretches of the past, and might even have had advantages over our own under their circumstances. The lesson that these ancients offer is that we should broaden our minds about how broad minds can be.

Source: Smart Planet

 

Genome Brings Ancient Girl to Life


In a stunning technical feat, an international team of scientists has sequenced the genome of an archaic Siberian girl 31 times over, using a new method that amplifies single strands of DNA. The sequencing is so complete that researchers have as sharp a picture of this ancient genome as they would of a living person’s, revealing, for example that the girl had brown eyes, hair, and skin. “No one thought we would have an archaic human genome of such quality,” says Matthias Meyer, a postdoc at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. “Everyone was shocked by the counts. That includes me.”

That precision allows the team to compare the nuclear genome of this girl, who lived in Siberia’s Denisova Cave more than 50,000 years ago, directly to the genomes of living people, producing a “near-complete” catalog of the small number of genetic changes that make us different from the Denisovans, who were close relatives of Neandertals. “This is the genetic recipe for being a modern human,” says team leader Svante Pääbo, a paleogeneticist at the institute.

Ironically, this high-resolution genome means that the Denisovans, who are represented in the fossil record by only one tiny finger bone and two teeth, are much better known genetically than any other ancient human—including Neandertals, of which there are hundreds of specimens. The team confirms that the Denisovans interbred with the ancestors of some living humans and found that Denisovans had little genetic diversity, suggesting that their small population waned further as populations of modern humans expanded. “Meyer and the consortium have set up the field of ancient DNA to be revolutionized—again,” says Beth Shapiro, an evolutionary biologist at the University of California, Santa Cruz, who was not part of the team. Evolutionary geneticist Sarah Tishkoff of the University of Pennsylvania agrees: “It’s really going to move the field forward.”

Pääbo’s group first gave the field a jolt in May 2010 by reporting a low-coverage sequence (1.3 copies on average) of the composite nuclear genome from three Neandertals. They found that 1% to 4% of the DNA of Europeans and Asians, but not of Africans, was shared with Neandertals and concluded that modern humans interbred with Neandertals at low levels.

Just 7 months later, the same group published 1.9 copies on average of a nuclear genome from a girl’s pinky finger bone from Denisova Cave. They found she was neither a Neandertal nor a modern human—although bones of both species had been found in the cave—but a new lineage that they called Denisovan. The team found “Denisovan DNA” in some island Southeast Asians and concluded that their ancestors also interbred with the ancestors of Denisovans, probably in Asia.

But these genomes were too low quality to produce a reliable catalog of differences. Part of the problem was that ancient DNA is fragmentary, and most of it breaks down into single strands after it is extracted from bone.

Meyer’s breakthrough came in developing a method to start the sequencing process with single strands of DNA instead of double strands, as is usually done. By binding special molecules to the ends of a single strand, the ancient DNA was held in place while enzymes copied its sequence. The result was a sixfold to 22-fold increase in the amount of Denisovan DNA sequenced from a meager 10-milligram sample from the girl’s finger. The team was able to cover 99.9% of the mappable nucleotide positions in the genome at least once, and more than 92% of the sites at least 20 times, which is considered a benchmark for identifying sites reliably. About half of the 31 copies came from the girl’s mother and half from her father, producing a genome “of equivalent quality to a recent human genome,” says paleoanthropologist John Hawks of the University of Wisconsin, Madison, who was not part of the team.

Now, the view of the ancient genome is so clear that Meyer and his colleagues were able to detect for the first time that Denisovans, like modern humans, had 23 pairs of chromosomes, rather than 24 pairs, as in chimpanzees. By aligning the Denisovan genome with that of the reference human genome and counting mutations, the team calculated that the Denisovan and modern human populations finally split between 170,000 and 700,000 years ago.

The researchers also estimated ancient Denisovan population sizes by using methods to estimate the age of various gene lineages and the amount of difference between the chromosomes the girl inherited from her mother and father. They found that Denisovan genetic diversity, already low, shrank even more 400,000 years ago, reflecting small populations at that time. By contrast, our ancestors’ population apparently doubled before their exodus from Africa.

The team also counted the differences between Denisovans and chimps, and found that they have fewer differences than do modern people and chimps. The girl’s lineage had less time to accumulate mutations, and the “missing evolution” suggests she died about 80,000 years ago, although the date is tentative, says co-author David Reich, a population geneticist at Harvard University. If this date—the first proof that a fossil can be directly dated from its genome—holds up, it is considerably older than the very rough dates of 30,000 to more than 50,000 years for the layer of sediment where the fossils of Denisovans, Neandertals, and modern humans all were found.

The team says the new genome confirms their previous findings, showing that about 3% of the genomes of living people in Papua New Guinea come from Denisovans, while the Han and Dai on mainland China have only a trace of Denisovan DNA. Furthermore, the team determined that Papuans have more Denisovan DNA on their autosomes, inherited equally often from both parents, than on their X chromosomes, inherited twice as often from the mother. This curious pattern suggests several possible scenarios, including that male Denisovans interbred with female modern humans, or that these unions were genetically incompatible, with natural selection weeding out some of the X chromosomes, Reich says.

The new genome also suggests one odd result. By using the detailed Denisovan genome to sharpen the view of their close cousins the Neandertals, the team concludes that living East Asians have more Neandertal DNA than Europeans have. But most Neandertal fossils are from Europe; paleoanthropologist Richard Klein of Stanford University in Palo Alto, California, calls the result “peculiar.”

Most exciting to Pääbo is the “nearly complete catalog” of differences in genes between the groups. This includes 111,812 single nucleotides that changed in modern humans in the past 100,000 years or so. Of those, eight were in genes associated with the wiring of the nervous system, including those involved in the growth of axons and dendrites and a gene implicated in autism. Pääbo is intrigued in particular by a change in a gene that is regulated by the so-called FOXP2 gene, implicated in speech disorders. It is “tempting to speculate that crucial aspects of synaptic transmission may have changed in modern humans,” the team wrote. Thirty-four genes are associated with disease in humans. The list suggests some obvious candidates for gene-expression studies. “The cool thing is that it isn’t an astronomically large list,” Pääbo says. “Our group and others will probably be able to analyze most of them in the next decade or two.”

Back in Leipzig, the mood is upbeat, as researchers pull fossil samples off the shelf to test anew with “Matthias’s method.” First on Pääbo’s list: Neandertal bone samples, to try to produce a Neandertal genome to rival that of the little Denisovan girl.

Source: Scientific American.