Neanderthals

How did a Neanderthal Gene for Antibodies Become Predominant in Humans?

Present day humans whose ancestors migrated out of Africa contain haplotypes with close matches to Neanderthal or Denisovan haplotypes in 2-5 % of their genome.

Our white blood cells make molecules called antibodies that bind to other molecules called antigens made by bacteria and viruses. Antibody binding aids in destroying the antigen-producing cell, and affords protection against pathogens. An antibody is made up of four protein molecules — two identical molecules of the immunoglobulin heavy chain, and two of the light chain. The IGH gene on our chromosome number 14 codes for the heavy chain protein.

All humans share the same African ancestors. Nevertheless, the predominant IGH gene found in East Asia and Europe, but not elsewhere, originated in the Neanderthals and not in our African ancestors. Who were the Neanderthals? And how did their IGH gene become predominant in East Asians and Europeans?

Researchers from Fudan University and the Chinese Academy of Sciences, Shanghai, China, addressed this question in a paper published on July 17 in the journal Molecular Biology and Evolution. Strikingly, they found that East Asians and Europeans had independently acquired the Neanderthal gene.

Hominins: extant and extinct

Hominins are all the species that emerged in our evolutionary line since it diverged about seven million years ago from the line leading to our closest cousins, the chimpanzees and bonobos. We, Homo sapiens, are the only surviving hominin. Neanderthals and Denisovans also were hominins, but they went extinct about 30,000 years ago.

An early hominin, Homo heidelbergensis, emerged in Africa from the still earlier Homo erectus. About 800 thousand years ago (kya, using kilo for thousand) the H. heidelbergensis population split. One sub-population migrated to Eurasia, became cold-adapted, and evolved into the Neanderthals and Denisovans. The other sub-population stayed in Africa and by 200 kya evolved into modern humans. For at least 20,000 generations humans did not exchange genes with either the Neanderthals and Denisovans. Denisovans diverged from Neanderthals about 640 kya.

Between 120 and 80 kya, humans migrated out of Africa into Eurasia, and came into contact with their Neanderthal and Denisovan cousins. DNA from skeletal remains dating to after the contact revealed that humans interbred with Neanderthals and Denisovans.

For comparison, the Mesopotamian civilization (‘beginning of history’) is less than 6 kya.

Genes and genomes

A DNA molecule is like a ladder with side rails made of a long series of alternating units of phosphate and deoxyribose (a sugar). Each sugar unit is chemically linked to one of four chemical bases — adenine (A), cytosine (C), guanine (G), and thymidine (T). Hydrogen bonds between the As and Cs on one side rail with the Ts and Gs on the other make the rungs. The A-T and G-C base-pairs hold the two DNA strands together.

A gene is a stretch of a few thousand base-pairs (kb). The sequence of bases on one strand specifies the sequence of amino acids in the protein encoded by the gene. A mutation is a change in the DNA sequence.

Our genome contains 23 DNA molecules which together have 3.2 billion base-pairs, and encode 22,000 genes. Each DNA molecule is the backbone of one of our 23 chromosomes. Every individual has two sets of the genome (46 chromosomes), one set inherited from the father and the other from the mother.

Neanderthal and Denisovan signatures

Experts can distinguish skeletal remains of Neanderthals from those of modern humans. They differ in the shape of the skull, inner ear bones (ossicles), and pelvis width.

DNA from Neanderthal bones shared 99.7 % identity with our DNA. This meant there were about 9.6 million base-pair differences across the 23 DNA molecules. Each lineage had accumulated its own suite of mutations following the split. For comparison, humans and chimps share 98.8%, and any two humans share 99.9%.

In 2010, DNA was sequenced from a finger bone found in the Denisova cave in the Altai Mountains of Siberia. It revealed a genome that differed equally from Neanderthal and human, and identified a new hominin, the Denisovan. Subsequently, DNA from other remains recovered from Russia, China (Tibet), and Laos were found to be Denisovan.

Also read: It Is Not Just Size That Separates the Human Brain From Other Living Primates

For two genomes differing in 3/1000 base-pairs, the alternative base-pairs can be used to define characteristic ‘haplotypes’. The haplotype present in a sufficiently long sequence can tell us whether the sequence is from a human, Neanderthal, or Denisovan.

The IGH gene of East Asians and Europeans came from Neanderthals

Present day humans whose ancestors migrated out of Africa contain haplotypes with close matches to Neanderthal or Denisovan haplotypes in 2-5 % of their genome. These genome segments have persisted since the time the ancestors interbred with Neanderthals and Denisovans in Eurasia.

Hundreds of non-African genomes were searched to determine whether a Neanderthal- or Denisovan-derived genome segment had attained a high frequency in any present-day population. A Neanderthal-derived 200 kb chromosome 14 segment, that included IGH, was predominant in East Asian and Europeans, but not in others.

The Neanderthal-derived haplotype found in East Asians, however, was slightly different from that found in Europeans. This implied that the ancestors of East Asians and Europeans independently interbred with Neanderthal populations bearing different IGH-linked haplotypes.

The Neanderthal IGH genes might have conferred better resistance to a geographically-restricted pathogen, resulting in their high frequencies today in East Asian and Europeans. Recall that Neanderthals resided for 700 ky in these geographies before our forebears arrived, and hence likely evolved better pathogen resistance.

Why is so little left of the Neanderthal/Denisovan contribution?

Given this success story, why have non-Africans retained so little of the Neanderthal or Denisovan genome contributions?

Consider two genes a and b that interacted in Homo heidelbergensis, and following the split, mutated into variants aA and bA in Africans, and aE and bE in Eurasians. Selection before contact ensured function was retained in the aA / bA and aE / bE pairs but not in aA / bE (and aE / bA). Consequently, hybrid progeny are weaker than non-hybrids, resulting in a gradual purging of aE and bE types. IGHE was an exception.

The exceptional occurring twice illustrates the power of pathogens in shaping our genomes.

Durgadas P Kasbekar is a retired scientist.

Early Humans in Africa May Have Interbred With a Mysterious, Extinct Species

A new study suggests that early humans living inside Africa may have interbred with archaic hominims, extinct species that are related to Homo sapiens.

One of the more startling discoveries arising from genomic sequencing of ancient hominin DNA is the realisation that all humans outside Africa have traces of DNA in their genomes that do not belong to our own species.

The approximately six billion people on Earth whose recent ancestry is not from Africa will have inherited between 1% and 2% of their genome from our closest but now extinct relatives: the Neanderthals. East Asians and Oceanians have also inherited a small amount of ancestry from the Denisovans, another close relative of Homo Sapiens.

Now a new study, published in Science Advances, suggests that early humans living inside Africa may also have interbred with archaic hominims. These are extinct species that are related to Homo sapiens.

Also Read: Will the Second Iteration of the Human Genome Project Usher in Greater Innovation?

The interbreeding outside Africa happened after our Homo sapiens ancestors expanded out of Africa into new environments. It was there they had sex with Neaderthals and the related Denisovans.

This led to new discoveries. Early genetic studies of people from across the globe had previously suggested that our current distribution was the result of a single expansion out of Africa around 100,000 years ago. But the identification of Neanderthal and Denisovan ancestry in modern Eurasians complicated things.

Homo Sapiens versus Neanderthals. Photo: Wikipedia, CC BY-SA

We still think that most – anywhere between about 92% and 98.5% – of the ancestry in people not living in Africa today does indeed derive from the out-of-Africa expansion. But we now know the remainder came from archaic species whose ancestors left Africa hundreds of thousands of years before that.

What was happening inside Africa?

Insights into interbreeding have been driven by the much greater availability of modern and ancient genomes from outside of Africa. That’s because the cold and dry environments of Eurasia are much better at preserving DNA that the wet heat of tropical Africa.

But our understanding of the relationship between ancient human ancestors within Africa, and their connection with archaic humans, is beginning to deepen. A 2017 study of ancient DNA from southern Africa investigated 16 ancient genomes from people alive over the last 10,000 years. This showed that the history of African populations was complex. There wasn’t just a single group of humans around in Africa when they expanded out 100,000 years ago.

It’s a result that was supported earlier this year by a paper examining ancient DNA from four individuals from what is now Cameroon. Taken together, this research suggests there were geographically diverse groups in Africa well before the main expansion out of the continent. And many of these groups will have contributed to the ancestry of people alive in Africa today.

In addition, it now appears that there was potentially gene-flow into ancient African Homo sapiens populations from an archaic ancestor. One way in which this could happen is for people to expand out of Africa, have sex with Neanderthals, and then migrate back into Africa. Indeed, this has been demonstrated in one recent study.

The new paper provides evidence that there may also have been gene-flow into the ancestors of West Africans directly from a mysterious archaic hominin. The researchers compared Neanderthal and Densiovan DNA with that from four contemporary populations from West Africa. Using some elegant mathematics, they then built a statistical model to explain the relationships between the archaic hominins and modern Africans.

Also Read: ‘Ghost’ Ancestors: African DNA Study Detects Mysterious Human Species

Interestingly, they suggest that 6%-7% of the genomes of West Africans is archaic in origin. But this archaic ancestry wasn’t Neanderthal or Denisovan. Their model suggested the additional ancestry came from an archaic population for which we don’t currently have a genome.

This ghost population likely split from the ancestors of humans and Neanderthals between 360,000 and 1.02 million years ago. That was well before the gene-flow event that brought Neanderthal DNA back into West Africa around 43,000 years ago – although the value of this could be anywhere between 0 and 124,000 years ago.

These dates position this ghost species as something akin to a Neanderthal, but that presumably was present within Africa, during the last 100,000 years. An alternative explanation is that the archaic hominin was present outside of Africa and interbred with populations there before they migrated back in.

Despite a raft of analyses that show that this result is not an artefact of either their methodology or some other genetic process, the authors are cautious about this result. They call for further analysis of both contemporary and ancient DNA from diverse populations in Africa.

Nevertheless, this research contributes to the ever-growing cannon of research demonstrating the promiscuous, species-crossing and complicated behaviours of the ancestors of all of us.

George Busby, senior research fellow in translational genomics, University of Oxford

This article is republished from The Conversation under a Creative Commons license. Read the original article.

‘Ghost’ Ancestors: African DNA Study Detects Mysterious Human Species

The discovery provides the latest evidence of humankind’s complicated genetic ancestry.

Washington: Scientists examining the genomes of West Africans have detected signs that a mysterious extinct human species interbred with our own species tens of thousands of years ago in Africa, the latest evidence of humankind’s complicated genetic ancestry.

The study indicated that present-day West Africans trace a substantial proportion, some 2% to 19%, of their genetic ancestry to an extinct human species – what the researchers called a “ghost population.”

“We estimate interbreeding occurred approximately 43,000 years ago, with large intervals of uncertainty,” said University of California, Los Angeles (UCLA) human genetics and computer science professor Sriram Sankararaman, who led the study published this week in the journal Science Advances.

Homo sapiens first appeared a bit more than 300,000 years ago in Africa and later spread worldwide, encountering other human species in Eurasia that have since gone extinct including the Neanderthals and the lesser-known Denisovans.

Previous genetic research showed that our species interbred with both the Neanderthals and Denisovans, with modern human populations outside of Africa still carrying DNA from both. But while there is an ample fossil record of the Neanderthals and a few fossils of Denisovans, the newly identified “ghost population” is more enigmatic.

Asked what details are known about this population, Sankararaman said, “Not much at this stage. We don’t know where this population might have lived, whether it corresponds to known fossils, and what its ultimate fate was,” Sankararaman added.

Sankararaman said this extinct species seems to have diverged roughly 650,000 years ago from the evolutionary line that led to Homo sapiens, before the evolutionary split between the lineages that led to our species and to the Neanderthals.

The researchers examined genomic data from hundreds of West Africans including the Yoruba people of Nigeria and Benin and the Mende people of Sierra Leone, and then compared that with Neanderthal and Denisovan genomes. They found DNA segments in the West Africans that could best be explained by ancestral interbreeding with an unknown member of the human family tree that led to what is called genetic “introgression.”

It is unclear if West Africans derived any genetic benefits from this long-ago gene flow.

“We are beginning to learn more about the impact of DNA from archaic hominins on human biology,” Sankararaman said, using a term referring to extinct human species. “We now know that both Neanderthal and Denisovan DNA was deleterious in general but there were some genes where this DNA had an adaptive impact. For example, altitude adaptation in Tibetans was likely facilitated by a Denisovan introgressed gene.”

Ancient Teenager the First Known Person with Parents of Two Different Species

Ancient DNA in a 50,000+ year old bone tells us that two species of early humans did produce offspring together. But how did a Neanderthal woman meet a Denisovan man? How did their respective communities interact? These are questions that now must be asked and investigated.

A new ancient DNA study published in Nature today reports the first known person to have had parents of two different species. The studied remains belonged to a girl who had a Neanderthal mother and a Denisovan father.

Neanderthals (Homo neanderthalensis) lived throughout Europe and Western Asia until around 30,000 years ago. This species lived in several different ecological zones, survived three glacial periods, and were excellent hunters and tool-makers.

Denisovans (Homo sapiens denisova), on the other hand, we know very little about. Thus far they have only been found in Denisova Cave in Sibera as tiny bone fragments. We don’t yet know what they looked like – nor exactly what they were capable of.

Neanderthal, Denisovans, and modern humans all shared a common ancestor more than 400,000 years ago.

Is this what Denisova 11’s mother looked like? A museum model of a Neanderthal woman. Credit: Shutterstock

Found in Denisova Cave, this child – known as “Denisova 11” – was at least 13 years of age at the time of her death. Analysis of a piece of her bone found that the girl died more than 50,000 years ago.

This discovery occurred through ancient DNA analysis, whereby a small piece of the teenager’s bone was pulverised, the DNA extracted, and then sequenced. The sequence was then compared to previously analysed samples from Neanderthals, modern humans, and Denisovans. Her genetic traits could only be explained if her mother was a Neanderthal and her father was a Denisovan.

Denisova 11 was a first generation Neanderthal-Denisovan woman – perhaps we could call her a “Neandersovan”?

Over many thousands of years, Denisova Cave in Siberia was occupied by Denisovans, Neanderthals and modern humans. Credit: Google Earth

Neighbours of modern humans

Neanderthals and Denisovans inhabited Eurasia until about 40,000 years ago when they were replaced by modern humans (Homo sapiens).

But before this replacement occurred, there appears to have been a fair bit of mingling going on whenever the different groups met.

Indeed, the ancestors of modern-day Oceanians and Asians contain Denisovan DNA, while present-day non-Africans contain 2-4% Neanderthal DNA.

Where ancient people roamed: the valley above the Denisova Cave archaeological site, Russia. Credit: Bence Viola

More mobile than we thought

The DNA of this girl — Denisova 11 — also suggests that there was some quite significant movement of Neanderthal groups between Western Europe and the East. Analysis of her DNA found that rather than being more closely related to a Neanderthal who lived in her home cave sometime prior to her birth, she instead showed more connections to those recovered in Western Europe.

This finding is interesting because most archaeological evidence indicates that Neanderthals – unlike modern humans – were not interested in long-distance movement. They don’t seem to have moved much beyond relatively constrained territories which provided everything they needed for day-to-day life.

Denisova 11 suggests that at least some major movement of ancient humans occurred between west and east. But when? And why?

And how did a Neanderthal woman meet a Denisovan man? How did their respective communities interact? These are questions that now must be asked and investigated.

Mystery girl

While this young girl has told us so much about her ancestors, we know very little about her.

Because it was only a small piece of one of her long bones found, we don’t know how she died. We can’t know if she suffered any serious illness in her short life, nor if she ever broke a bone.

We only know that she lived.

Michelle Langley, ARC DECRA Research Fellow, Griffith University

This article was originally published on The Conversation. Read the original article.

Scientists Hunt Down Genes Behind Humankind’s Big Brain

These genes, found only in people, appeared between three and four million years ago, just prior to a period when the fossil record demonstrates a dramatic brain enlargement in ancestral species in the human lineage.

Washington: Scientists have pinpointed three genes that may have played a pivotal role in an important milestone in human evolution: the striking increase in brain size that facilitated cognitive advances that helped define what it means to be human.

The three nearly identical genes, as well as a fourth nonfunctional one, are called NOTCH2NL genes, arising from a gene family dating back hundreds of millions of years and heavily involved in embryonic development.

The NOTCH2NL genes are particularly active in the reservoir of neural stem cells of the cerebral cortex, the brain’s outer layer responsible for the highest mental functions such as cognition, language, memory, reasoning and consciousness. The genes were found to delay development of cortical stem cells into neurons in the embryo, leading to the production of a higher number of mature nerve cells in this brain region.

“The cerebral cortex defines to a large extent what we are as a species and who we are as individuals. Understanding how it emerged in evolution is a fascinating question, touching at the basic origins of mankind,” said developmental neurobiologist Pierre Vanderhaeghen of Université Libre de Bruxelles and VIB/KULeuven in Belgium.

“It is the ultimate evolutionary question and it is thrilling to work in this area of research,” added biomolecular engineer David Haussler, scientific director of the University of California, Santa Cruz Genomics Institute and a Howard Hughes Medical Institute investigator.

The species Australopithecus afarensis, which combined ape-like and human-like traits and included the well-known fossil dubbed ‘Lucy’, lived in Africa at roughly the time these genes are estimated to have appeared.

“It would be great if we could sequence Lucy’s genome,” said UC-Santa Cruz biomolecular engineering research scientist Sofie Salama, while noting the improbability of doing that.

The genes are absent in people’s closest genetic relatives. None were found in monkeys or orangutans. A nonfunctional cousin of these genes was detected in gorillas and chimpanzees. But the researchers found the genes in two extinct species in the human lineage, Neanderthals and Denisovans.

NOTCH2NL gene abnormalities were found to be linked to neurological conditions including autism, schizophrenia and both abnormally large and abnormally small head size.

The findings on the NOTCH2NL genes were detailed in two studies published in the journal Cell.

(Reuters)

Warning Signs: How Early Humans First Began to Paint Animals

Figurative art may derive from Neanderthal hand prints and the hunter’s keen eye for perceiving animals.

Visual culture – and the associated forms of symbolic communication, are regarded by palaeo-anthropologists as perhaps the defining characteristic of the behaviour of Homo sapiens. One of the great mysteries of archaeology is why figurative art, in the form of the stunningly naturalistic animal depictions, appeared relatively suddenly around 37,000 years ago in the form of small sculpted objects and drawings and engravings on cave and rock shelter walls.

Since the discovery and authentication of such Palaeolithic art more than a century ago, theories have abounded as to what this meant to its Ice Age hunter-gatherer creators. But theories often say more about modern preconceptions regarding the function of art – how can we tell if we’re on the right track to understanding the remote and alien societies that created the first images?

In a radical new approach to the issue, we applied recent findings from visual neuroscience, perceptual psychology and the archaeology of cave art, that begin to make sense of the intriguing representations and forward what we hope can be tested scientifically.

Hands down

The first clue to their provenance came from the ancient hand marks (positive prints and negative stencils), which predate the earliest animal depictions by a considerable period. Recent dating shows that they were created by Neanderthals more than 64,000 years ago. The second clue came from the widespread inclusion of natural cave features – such as ledges and cracks – as parts of animal depictions. The final clue relates to the environment in which Upper Palaeolithic hunter-gatherers, along with other predators, were stalking the large herbivores – such as bison, deer and horses – that formed their prey and which often lay hidden in camouflage in the tundra environment.

We argue that hand marks initially supplied the idea to archaic humans that a graphic mark could act as a representation, however basic it was. This was a beginning of sorts – but how could hand marks give rise to the more complex animal depictions? We needed to be able to explain how that gap was bridged.

Seeing the unseen

Fortunately, the way hunters relate to the environment has changed little since early times in that they remain acutely sensitive to particular animal contours. So much so, that in challenging lighting situations – and where prey might be well camouflaged – the hunter becomes hypersensitive to such features.

In such ambiguous circumstances, it’s better to “see” an animal when it’s not there – to mistake a rock for a bear – than not see it. Such better-safe-than-sorry hair-trigger cues are cognitive adaptations that promote survival. In dangerous conditions, the human visual system becomes increasingly aroused and is even more easily triggered into accepting the slightest cue as an animal.

In short, we are preconditioned to interpret ambiguous shapes as animals. Recent evidence from visual neuroscience shows that when individuals are conditioned to see particular objects – faces, say – they are more likely to see them in ambiguous patterns. Upper Palaeolithic hunters conditioned themselves due to the need to detect animals, but this effect was reinforced by the suggestive features of the caves.

Caves are full of suggestive cues. They are dangerous places, often inhabited by predators, thereby stimulating increased arousal levels. Hunters entering the caves with an overactive visual system will have regularly “mistaken” the natural cave features for animals. The cave walls also simulated the outdoor environment, where hunters regularly had to be able to spot their prey in camouflage.

All the hunter needed to do to “complete” a depiction was to add one or two graphic marks to the suggestive natural features based on the visual imagery in their “mind’s eye”. A typical example of this can be seen at Chauvet cave where two giant deer (Megaloceros) are depicted by complementing the natural wall fissures (highlighted in brown) with lines (highlighted in black) painted onto the cave wall to complete the animal outlines. This potentially explains how the very first representational depictions arose.

Corroborating evidence

We’ve tried to combine our respective expertise in visual psychology and Palaeolithic art and, unlike many other theories, our approach is open to refutation. For example, if someone finds depictions of animals or similar that predate the first hand marks, this would overturn our main proposition. Similarly, if earlier figurative depictions come to light that do not derive from natural features, this would also challenge our theory.

But as we were making the final touches to our academic paper, valuable corroborative evidence came to light supporting the theory. Namely, the dating of a negative hand stencil and a geometric mark from the Monte Castillo cave art complex in Spain dating to a minimum of 64,000 years ago and almost certainly made by Neanderthals.

When later humans entered the same caves and saw these, the Neanderthals may literally have “handed on” to our own species the notion that a graphic mark could act as a figurative representation. Thanks to the primed visual system of the later hunter-gatherers – and the suggestive environment of the caves – it was Homo sapiens who took the final step creating the first complex figurative representations, with all the ramifications that followed for art and culture.

Derek Hodgson, Research Associate, University of York and Paul Pettitt, Professor in the Department of Archaeology, Durham University

This article was originally published on The Conversation. Read the original article.

The Evolutionary Advantage of Having Eyebrows

The evolution of the eyebrows performed an important function in expressing friendliness which might have helped early humans to colonise new environments.

Eyebrows, we all have them, but what are they actually for? While eyebrows help to prevent debris, sweat, and water from falling into the eye socket, they serve another important function too – and it’s all to do with how they move and human connection.

We already know that our modern minds often reflect the ways our ancestors needed to work together to survive in the distant evolutionary past. But it seems our anatomy reflects the importance of getting on with other people as well. As our new research published in Nature Ecology and Evolution suggests, the ability to look either intimidating or friendly is reflected in our bones – at least where the shape of the skulls is concerned.

We all know that ancient species of humans, such as Neanderthals, looked a little bit different from us. But the most obvious difference is that archaic humans possessed a pronounced and very distinctive brow ridge which contrasts with our own flat and vertical foreheads. And for scientists, this difference between us and them has been the hardest to explain. It was even famously said that Neanderthals would go unnoticed on a New York subway if only they could wear something like a hat to cover this distinctive feature.

Fossil modern human (left) and fossil Neanderthal crania (right). Author provided

But our latest research may have found an answer to explain why archaic humans had such a pronounced wedge of bone over their eyes (and why modern humans don’t). And it seems to be down to the fact that our highly movable eyebrows can be used to express a wide range of subtle emotions – which could have played a crucial role in human survival.

A sign of dominance

Research has already shown that humans today unconsciously raise their eyebrows briefly when they see someone at a distance to show we are not a threat. And we also lift our eyebrows to show sympathy with others – a tendency noticed by Darwin in the 19th century.

So with my colleagues Ricardo Godinho and Paul O’Higgins we looked at the iconic brow ridge of a fossilised skull (known as Kabwe 1) to find out more about its purpose. Ricardo used 3D engineering software, to shave back Kabwe’s huge brow ridge. And in doing so, found that Kabwe 1’s heavy brow offered no spatial advantage.

Model of a modern human cranium (left) shown next to a model of an archaic human (Kabwe 1) (right) Author provided

The brow ridges in archaic humans also serve no obvious function in relation to chewing or other practical mechanics – a theory commonly put forward to explain protruding brow ridges. As when the ridge was taken away there was no effect on the rest of the face when biting. This means that brow ridges in archaic humans must have had a social function – most likely used to display social dominance as is seen in other primates.

For our species losing the brow ridge probably meant looking less intimidating, but by developing flatter and more vertical foreheads our species could do something very unusual – move our eyebrows in all kinds of subtle and important ways.

Although the loss of the brow ridge may have initially been driven by changes in our brain or facial reduction, it subsequently allowed our eyebrows to make many different subtle and friendly gestures to people around us.

Expressing emotions

Illustration of grief from The Expression of Emotions in Man in Animals, Charles Darwin (1872).
Beinecke Rare Book & Manuscript Library, Yale University

This was a time when modern human groups began to exchange gifts across large regions. Being able to create distant friendships probably helped early humans to colonise new environments – as they had friends they could rely on and retreat back to. Historically speaking, these marked changes in the face occurred at a time when the emergence of important social changes began to take place. Mainly the collaboration between distantly related groups of humans.

Modern humans also lived in larger and more diverse groups than previous species reducing interbreeding. So the impact of friendly and mutually supportive relationships with people outside one’s own group were far reaching. And the development of mobile eyebrows may have been a key part of all these changes.

But these changes weren’t just exclusive to humans – the developments seen when wolves became domesticated are in some ways similar. Dogs have more waggy tails and flatter faces than wolves. And dogs who are better able to look cuter by raising their brows are more likely to be selected from shelters.

It seems then that for humans (and dogs), being able to get along with others was key to survival. And for our ancestors, the evolution of the eyebrows performed an important function in expressing friendliness. All of which forms part of a process of “self-domestication” – where our human brains, bodies and even anatomy reflects a drive to get on better with those around us.

Penny Spikins is Senior Lecturer in the Archaeology of Human Origins, University of York

This article was originally published on The Conversation. Read the original article.

Early Humans Mated With the Neanderthals’ Enigmatic Cousins. Twice.

A new study has found that ancient human populations mated with the Denisovans in two waves, contributing up to 5% of the modern human genome.

Scientists have discovered that ancient human populations intermixed with our close cousins, the elusive Denisovans, not just once but at two different times. And that this has led to certain modern human populations carrying upto 5% Denisovan DNA.

The Denisovans are ancient hominids who existed as recently as 40,000 years ago. New evidence shows that not only did they exist at the same time as Neanderthals and ancient humans, they also interbred with them.

The first indication of their existence was a bone fragment of a little finger that researchers found during a routine excavation for Neanderthal bones in the Denisova cave in the Altai mountains of Siberia in 2008. But the DNA extracted from the bone fragment revealed that the bone came from a species of hominids distinct from the Neanderthals. Researchers named them the Denisovans, after the cave where the bones fragments were found.

Our current knowledge of these hominids is based on just four pieces of bone: a finger bone, two molars, all of which yielded DNA, and a toe bone. But researchers have managed to extract almost the entire Denisovan genome from these bone fragments. They when compared the data with Neanderthal and human DNA and found a lot about the evolution and early lives of modern humans.

For example, they discovered that early humans diverged from a common ancestor of the Neanderthals and the Denisovans 600,000 years ago. And that the Neanderthals and Denisovans diverged from each other around 400,000 years ago.

However, the most exciting finding from the Denisovan DNA was from its comparison with modern human DNA. Researchers discovered that the Denisovan legacy lives on in the genes of many Asian groups, such as the Han Chinese and the Papuans.

A recent study conducted by a team led by Sharon Browning, a professor of biostatistics at the University of Washington, Seattle, advanced our understanding of the relations between ancient humans and the Denisovans. The researchers looked at DNA extracted from the Denisovan remains, compared it with the DNA of over 5,600 people across Eurasia and Oceania and found that populations from Melanesia and East Asia shared ancestry with the Denisovans.

Looking more closely at DNA regions that seemed to be of Denisovan origin, Browning discovered that there were two distinct signals of Denisovan DNA in modern human genomes in different populations.

One of the Denisovan molars that were excavated. Credit: Thilo Parg/Wikimedia Commons CC BY-SA 3.0

Data from the paper published in Cell showed that certain DNA regions of Chinese and Japanese populations were very similar to the DNA of the Denisovan woman whose finger bone was found in the Altai mountains.

Additionally, in these populations, they found weak signals of a second set of regions that seemed to be Denisovan in origin, but not as similar to the DNA from the Altai mountains. The Papuan population, on the other hand, showed strong signals for the latter type – regions in the DNA that were clearly Denisovan in origin but not related to the Altai female.

These observations indicate that ancient humans and the Denisovans mated with each other in at least two waves. One mating wave – which refers to the admixture of populations, not individuals, of Denisovans and humans – contributed to the DNA regions that are seen in Papuans and the East Asians. A second, possibly later mating wave involving a different Denisovan population contributed the DNA regions that are observed in only the East Asians.

According to Browning, this suggests that as ancient humans migrated through south Asia, they encountered and mated with one population of Denisovans. Progenies of this group migrated as far as Melanesia. This explains why current Melanesian populations have upto 5% Denisovan DNA in them. Humans migrating through a more northerly route in Asia probably encountered a second group of Denisovans, possibly somewhere near the Altai mountains and proceeded to East Asia, explaining why DNA regions in modern day Chinese and Japanese populations is very similar to the DNA extracted from the pinky bone in the Altai mountains.

A schematic of admixture events between humans and Neanderthals and Denisovans and their contributions to modern human DNA. Credit: Sharon Browning et al, Cell, 2018

Neanderthals and DNA

Browning did not stop at that. Using the genomic data of 5600 individuals from 23 populations and existing Neanderthal genome sequences, she tried to put together information regarding interbreeding between Neanderthals and ancient humans, quite like she did with the Denisovans. “Once I found two Denisovan waves, I thought we’d see something similar in the Neanderthals”, she told The Atlantic.

To her surprise, she found evidence for what seemed like only one wave of interbreeding between the Neanderthals and ancient humans. This was counter intuitive since scientists know that Neanderthals were distributed all across Europe and Asia. Thus, humans would have encountered multiple populations of Neanderthals as the spread through Europe and Asia.

Browning surmised that this might be because the genetic diversity within Neanderthals was very low compared to that of the Denisovans. For example, DNA extracted from Neanderthal bones as far apart as Croatia and Siberia were seen to be more similar to each other than the two Denisovan DNA regions that Browning found in her study, The Atlantic reported.

“Maybe the Neanderthals were more nomadic and their populations were mixing a lot, while the Denisovans stayed in particular places and didn’t mix”, Browning concluded.

Selective advantage

One of the more intriguing insights from the discovery of Denisovan DNA is related to a certain mutation that is frequent among the people of the Tibetan plateau.

In 2010, a team led by Rasmus Nielsen at University of California, Berkeley, found that a unique mutation in the EPAS1 gene allowed Tibetans to survive and thrive in high altitudes with only 60% of the oxygen found at sea level. While this mutation is found in 87% of all Tibetans, only 9% of the closely related Han Chinese exhibit it. The team called it the “strongest instance of natural selection documented in a human population”.

In a normal human being, the body steps up red blood cell (RBC) production when the environmental oxygen levels are low. If we were to continuously stay in a place with low oxygen levels such as the Tibetan plateau, it could lead to an overproduction of RBCs which could lead to viscous blood and hence stroke and high blood pressure. The mutation in the EPAS1 gene in Tibetans allows them to cope with low oxygen levels without suffering from stroke and high blood pressure by preventing their bodies from overproducing RBCs.

When Nielsen, who studies the molecular basis of evolution, attempted to find the origin of this mutation, he observed that the Denisovan version of the EPAS1 gene was almost an exact match for the Tibetan version. Moreover, the Tibetan version was very different from the Han Chinese version, despite the two populations having diverged as recently as 3000 years ago.

Thus, a Denisovan contribution allowed Tibetans to colonise a harsh environment – but the Denisovans themselves did not live in high altitudes. Nielsen postulated that the same gene may have helped them survive cold climates and coincidentally allowed the Tibetans to colonise the plateau – an example of the same gene performing multiple functions.

Neanderthals, Not Modern Humans, Were Europe’s First Painters

New analysis from Spain provides the strongest evidence yet that Neanderthals had the cognitive capacity to understand symbolic representation, a central pillar of human culture.

A colour-enhanced hand stencil from the Maltravieso Cave, made by a Neanderthal is seen in Pasiega, Spain in this photo obtained February 21, 2018. Credit: Univeristy of Southampton/Handout via Reuters

London: The world’s oldest known cave paintings were made by Neanderthals, not modern humans, suggesting our extinct cousins were far from being uncultured brutes.

A high-tech analysis of cave art at three Spanish sites, published on Thursday, dates the paintings to at least 64,800 years ago, or 20,000 years before modern humans arrived in Europe from Africa.

That makes the cave art much older than previously thought and provides the strongest evidence yet that Neanderthals had the cognitive capacity to understand symbolic representation, a central pillar of human culture.

A cave painting is seen inside a cave in Pasiega, Spain in this photo obtained February 21, 2018. Credit: Univeristy of Southampton/Handout via Reuters

“What we’ve got here is a smoking gun that really overturns the notion that Neanderthals were knuckle-dragging cavemen,” said Alistair Pike, professor of archaeological sciences at the University of Southampton, who co-led the study.

“Painting is something that has always been seen as a very human activity, so if Neanderthals are doing it they are being just like us,” he told Reuters.

While some archaeologists already viewed Neanderthals as more sophisticated than their commonplace caricature, the evidence until now has been inconclusive. With the data from the three Spanish cave sites described in the journal Science, Pike and colleagues believe they finally have rock-solid proof.

The early cave art at La Pasiega, Maltravieso and Ardales includes lines, dots, discs and hand stencils – and creating them would have involved specific skills, such as mixing pigments and selecting appropriate display locations.

The Neanderthals living in the same land that would one day give birth to Diego Velazquez and Pablo Picasso also needed the intellectual ability to think symbolically, like modern humans.

Scientists used a precise dating system based on the radioactive decay of uranium isotopes into thorium to assess the age of the paintings. This involved scraping a few milligrams of calcium carbonate deposit from the paintings for analysis.

Scientists sample cave painting material in a cave in Pasiega, Spain in this photo obtained February 21, 2018. Credit: Univeristy of Southampton/Handout via Reuters

A second related study published in Science Advances found that dyed and decorated marine shells from a different Spanish cave also dated back to pre-human times.

Taken together, the researchers said their work suggested that Neanderthals were “cognitively indistinguishable” from early modern humans.

Joao Zilhao of the University of Barcelona said the new findings meant the search for the origins of human cognition needed to go back to the common ancestor of both Neanderthals and modern humans more than 500,000 years ago.

Neanderthals died out about 40,000 years ago, soon after direct ancestors arrived in Europe. It is unclear what killed them off, although theories include an inability to adapt to climate change and increased competition from modern humans.

If they were still alive today, Pike believes they could well have gone on develop complex art and technology.

“If they had been given the time, the resources and the population, then they might have ended up in some version of the world we live in today.”

Fossil Jawbone Found in Israel Is the Oldest Modern Human Found Outside Africa

New discoveries are changing archaeologists’ ideas about the origins of our own species and our migration out of Africa. This fossil pushes Homo sapiens’ African exodus date back by 50,000 years.

A close-up view of the teeth accompanying the left maxilla of human remains from Misliya Cave in Israel, the oldest remains of our species Homo sapiens found outside Africa, is provided in this photo released on January 25, 2018. Credit: Handout via Reuters/ Israel Hershkovitz/Tel Aviv University

New fossil finds over the past few years have been forcing anthropologists to reexamine our evolutionary path to becoming human. Now the earliest modern human fossil ever found outside the continent of Africa is pushing back the date for when our ancestors left Africa.

The fossil, an upper left jawbone with most of the teeth attached, comes from Misliya Cave in Israel and dates to 177,000-194,000 years ago. This is considerably older than any other remains from our own species, Homo sapiens, ever discovered outside of Africa and it coincides with several other recent studies that are changing the view on our evolutionary origins and migration throughout the Old World.

African origins, then spreading from there

The earliest humans, referred to as hominins by anthropologists, lived around 6-7 million years ago in Africa. These early evolutionary ancestors are recognised as belonging to the human family mainly because their bones reveal clear signs of bipedalism: They walked on two feet. It was not until around 2 million years ago that human ancestors first migrated out of Africa and spread throughout the Old World.

Up until recently, anthropologists generally held that Homo sapiens first appeared around 200,000 years ago, in Africa. This was based on findings from genetic studies as well as fossil discoveries. Two sites in Ethiopia, Herto and Omo Kibish, have yielded early Homo sapiens fossils dated to between 160,000-195,000 years ago.

But in June of 2017, researchers dated fossils from the site of Jebel Irhoud in Morocco to around 315,000 years ago and attributed them to an early phase of Homo sapiens evolution. This unexpectedly early date pushed back the origin of our species by over 100,000 years.

Until recently, the earliest human fossils from our own species discovered outside of Africa dated to around 90,000-120,000 years ago. Two cave sites in Israel – Qafzeh and Skhul – have yielded numerous skeletons of early modern humans. The age of these sites would suggest that our species was restricted to Africa for as long as 200,000 years before migrating out of the continent. Other sites with Homo sapiens fossils from Asia and Europe are generally younger than the finds from the Middle East.

Now an international research team, of which I was a member, has reported finding an early modern human fossil at Misliya Cave in Israel dating as far back as 177,000-194,000 years ago. This date pushes back our species’ exodus from Africa by over 50,000 years.

High-tech analysis of ancient remains

The Misliya fossil is just part of one individual’s jawbone. To understand the significance of the find, we needed to be sure about when this individual lived and also what species they belonged to.

To start with, the stone tools associated with the fossil, of a type known as the Early Middle Paleolithic, indicated a considerable antiquity for the specimen. Similar tool kits from other sites in the Middle East generally date to older than 160,000 years ago. To establish the jawbone’s age more precisely, several independent dating techniques were applied to the fossil itself as well as the stone tools and sediments at the site. The results came back with ages that ranged between 177,000-194,000 years ago.

To diagnose which species the Misliya fossil might represent, we studied the original fossil using both traditional anthropological approaches as well as the latest technological advances. We micro-CT scanned and made 3-D virtual models of the specimen to visualize the internal structures of the teeth and quantify their shapes more precisely. The results of these analyses demonstrated very clearly that the Misliya fossil is a member of our own species.

All of the anatomical features in the Misliya fossil are consistent with it being a modern human, just like us. There is nothing in the fossil that would rule it out as a Homo sapiens. And some features in the Misliya fossil’s anterior teeth seem only to occur in Homo sapiens.

Our study found that these teeth lack several features that are found in earlier human species, including the Neanderthals. One of these characteristics is a thickening of the tooth crown along the edges on the inside surface of the incisor and canine. Anthropologists call this trait shoveling. We see shoveling on the teeth of previous species of hominins from before modern humans evolved. But we didn’t see it in the teeth from Misliya, supporting the idea that this jaw is from a Homo sapiens individual. Today some modern human populations actually do have shoveling on their teeth, while others do not; but in the fossil record, the only species that does not show shoveling is Homo sapiens.

Another trait we looked for is a small cusp at the base of the tooth crown on the inside surface of the incisor and canine. This feature is commonly seen in Neanderthals, but is absent in the Misliya fossil.

It’s the absence of these two dental features in the Misliya fossil, together with information from the other teeth and the jawbone itself, that tells us it came from a Homo sapiens.

Fitting more pieces into the puzzle

The findings at Misliya coincide with a recent genetic study that offered tantalizing evidence for the influx of genetic material into the Neanderthal gene pool from Africa. The researchers relied on ancient mitochondrial DNA extracted from a Neanderthal femur (leg bone) discovered in Germany. The African species involved was not clear, but the older dates for the earliest Homo sapiens fossils at Jebel Irhoud in Morocco make it clear that modern humans were already present in Africa at this time. These genetic results suggest the possibility of an earlier modern human migration out of Africa – at least as far back as 220,000 years ago and probably earlier.

While the Misliya fossil is younger than this, it provides the first fossil evidence confirming that modern humans left Africa considerably earlier than previously believed. This series of recent studies and discoveries from disparate sources are providing new insights into our own origins and dispersal around the globe.

Rolf Quam is associate professor of anthropology at Binghamton University, State University of New York.

This article was originally published on The Conversation. Read the original article.