The Real Question: Who Didn't Have Sex with Neanderthals?

[seemslikeadream]

Scientists to grow 'mini-brains' using Neanderthal DNA

Geneticists hope comparing prehistoric and modern biology will help them understand what makes humans unique

Hannah DevlinLast modified on Fri 11 May 2018 17.12 EDT

Kennis models of Homo sapiens (left) and a Neanderthal man. Photograph: Kevin Webb/NHM Image Resources/The Natural History Museum, London
Scientists are preparing to create “miniature brains” that have been genetically engineered to contain Neanderthal DNA, in an unprecedented attempt to understand how humans differ from our closest relatives.

In the next few months the small blobs of tissue, known as brain organoids, will be grown from human stem cells that have been edited to contain “Neanderthalised” versions of several genes.

The lentil-sized organoids, which are incapable of thoughts or feelings, replicate some of the basic structures of an adult brain. They could demonstrate for the first time if there were meaningful differences between human and Neanderthal brain biology.

“Neanderthals are the closest relatives to everyday humans, so if we should define ourselves as a group or a species it is really them that we should compare ourselves to,” said Prof Svante Pääbo, director of the genetics department at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, where the experiments are being performed.

Pääbo previously led the successful international effort to crack the Neanderthal genome, and his lab is now focused on bringing Neanderthal traits back to life in the laboratory through sophisticated gene-editing techniques.

The lab has already inserted Neanderthal genes for craniofacial development into mice (heavy-browed rodents are not anticipated), and Neanderthal pain perception genes into frogs’ eggs, which could hint at whether they had a different pain threshold to humans. Now the lab is turning its attention to the brain.

“We’re seeing if we can find basic differences in how nerve cells function that may be a basis for why humans seem to be cognitively so special,” said Pääbo.

The research comes as the longstanding stereotype of Neanderthals as gormless and thuggish is being rewritten by emerging evidence that they buried their dead, produced cave art and had brains that were larger than our own.

Svante Pääbo
Prof Svante Pääbo, director of evolutionary genetics at the Max Planck Institute for Evolutionary Anthropology. Photograph: Christian Jungeblodt
In the basement beneath Pääbo’s office, scientists are working to extract DNA – the code of life – from ancient human and animal fossils excavated at sites across the world. The team’s success relies on taking obsessive precautions against contamination: a speck of dust floating in through a window can contain more DNA than the few milligrams of powdered ancient bone under analysis. Researchers shower and don spacesuit-style uniforms before entering rooms kept sterile by UV lights and a sophisticated air filtration system.

It was under these stringent working conditions in 2010 that his team reassembled the code of the Neanderthal genome from heavily degraded samples taken from four females who lived in Europe tens of thousands of years ago.

The genome revealed Neanderthals interbred with our ancestors – and successfully enough that all non-Africans today carry 1-4% of Neanderthal DNA. And since people acquired slightly different genes, collectively about a third of the Neanderthal genome is still floating around in modern populations.

However, there are also genetic dead zones: large stretches of the Neanderthal genome that nobody inherited, possibly because they conferred disadvantages to health, fertility, cognition or physical appearance.

Quick guide
Evolutionary timeline

“We want to know whether among those things, is there something hiding there that really sets us apart?” Pääbo said. “Is there a biological basis for why modern humans went on to become millions and eventually billions of people, spread across the world and have culture?”

It is not certain that the contrasting fates of the two species are linked to differences in cognition, but Pääbo said: “It’s tempting to think that, yes.”

The latest work focuses on differences in three genes known to be crucial for brain development. Using the editing technique Crispr, changes have been introduced into human stem cells to make them closer to Neanderthal versions.

The stem cells are coaxed using chemical triggers to become neurons, which spontaneously clump together and self-organise into miniature brain-like structures that grow to a few millimetres in diameter. The lack of any sensory input means the internal wiring is haphazard and varies from one blob to the next.

“You start the organoid growing and leave it for nine months and see what happens,” said Gray Camp, a group leader at the institute who is overseeing the organoid experiments. “You don’t get a well-formed human brain at all, but you see multiple regions have kind of formed; you can study the synapses and electrical activity and early developmental differences.”

The scientists will compare the Neanderthalised organoids and the fully human ones to assess the speed at which the stem cells divide, develop and organise into three-dimensional brain structures and whether the brain cells wire up differently.

“A dream result would be that the [genetic] changes make for longer or more branched neuronal outgrowth,” said Pääbo. “One would say it would be a biological basis for why our brain would function differently.”

The work won’t reveal which species is “smarter”, but could hint at differences in the ability to plan, socialise and use language.

The lab is also looking at how Neanderthal genes that are commonly found in the DNA of people with European and Asian ancestry influence brain development. By growing organoids from cells taken from living people and looking at how the Neanderthal genes switch on and off, the team can see whether a person’s brain development is subtly influenced by their ancient Neanderthal ancestry.

“We can regrow your Neanderthal brain,” said Camp. “We can monitor that and resurrect the functionality of those neanderthal genes.”

Guardian graphic
The team are not the first to contemplate resurrecting Neanderthal biology. The Harvard professor George Church previously suggested that a cloned Neanderthal baby could be created if an “adventurous female human” were prepared to act as a surrogate. Such a scenario, Pääbo counters, is not only ethically unpalatable but unachievable with today’s technology, which allows for only a handful of genetic edits at a time rather than the 30,000 required for fully Neanderthal tissue.

Pääbo said he finds comments like Church’s frustrating because “then other people like me have to look like the boring, non-visionary guy, saying it’s not possible and think about the ethics.”

Do blobs of brain come with their own ethical considerations? “Yes, at some point one can of course ask, when does a developing brain become an individual? But that is far into the future.”

Modern humans and Neanderthals split into separate lineages around 400,000 years ago, with our ancestors remaining in Africa and the Neanderthals moving north into Europe. About 60,000 years ago, the archaeological record reveals, there was a mass migration of modern humans out of Africa that brought the two species face-to-face once more. The revelation that Neanderthals interbred with humans and were far more sophisticated than previously thought has led some to suggest the two lineages should be merged into a single species, but Pääbo and others disagree.

“Yes, there’s growing evidence that Neanderthals, particularly towards the end of their history, did some form of art,” he said. “But if I’m a little mean, I would say they did some art but it was very modern art because I can’t see what it depicts.”

And there is no evidence of Neanderthals having set out to explore the world’s oceans, as humans did at least 100,000 years ago, a feat that perhaps has as much to do with mindset as with being inventive enough to build a boat.

“It is very risky to set out into the Pacific and look for something when you don’t know there’s something out there,” Pääbo said. “Neanderthals were reasonable, like other mammals. They didn’t go out into the ocean without seeing anything on the other side. To me, the biggest question in human history is, why did we become this crazy?”

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https://www.independent.co.uk/news/scie ... 1534957611

A bone belonging to a very unusual teenage girl has once again shaken up our understanding of human history.

Around 50,000 years ago, Eurasia was home to two very distinct groups of humans, separated by thousands of years of evolution – the Neanderthals and the Denisovans.

Now analysis of a bone fragment from a Siberian cave has revealed the girl it came from had a Neanderthal mother and a Denisovan father.

Scientists have been gradually unpicking the complicated relationships of our distant ancestors, using ancient DNA.

Increasingly, these efforts have suggested few displayed any form of prejudice when selecting partners.

"But I never thought we would be so lucky as to find an actual offspring of the two groups,” says Dr Viviane Slon, one of the researchers behind the discovery at the Max Planck Institute for Evolutionary Anthropology.

Denisova Cave, which is so far the only place physical evidence of the mysterious Denisovans been unearthed, has proved to be a treasure trove of human history.

The bone fragment, “Denisova 11”, that the new study was based on was discovered there by Russian archaeologists in 2012 before being taken to Germany for genetic analysis.

The key message from the new discovery, outlined in the journal Nature, is that not only was interbreeding happening, it was happening a lot.

“To find an actual hybrid of such a mating in a still sparse fossil record must surely indicate that these matings could not have been rare events, at least when the populations met each other, under whatever circumstances,” said Professor Chris Stringer, an expert in human origins based at the Natural History Museum, who was not involved in the research.

Analysis of the genome also revealed that the Denisovan father of the girl, who was 13 at the time of death, had at least one Neandertal ancestor further back in his family tree, meaning there were multiple instances of interbreeding within this one family.

"Neanderthals and Denisovans may not have had many opportunities to meet,” said Professor Svante Paabo, a pioneer in the exploration of ancient human DNA who also worked on the new study.

“But when they did, they must have mated frequently – much more so than we previously thought."

Professor Mark Thomas, an evolutionary geneticist at University College London who was not involved in the research, said the evidence for interbreeding between ancient human lineages can be seen to this day in the DNA of modern people.

Around 5 per cent of DNA in some people today, particularly those from Papua New Guinea, is thought to be Denisovan in origin.

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Neanderthals and Humans Were Hooking Up Way More Than Anyone Thought


NO REUSE - Neanderthal family
Way more sex happened between Neanderthals and the ancestors of modern humans across Europe and Asia than scientists originally thought, a new study finds.

Scientists initially thought that interbreeding among the two groups was more isolated to a particular place and time — specifically, when they encountered each other in western Eurasia shortly after modern humans left Africa. This idea stemmed from the fact that the genomes of modern humans from outside Africa are only about 2 percent Neanderthal, on average.

Subsequent research, however, has found that Neanderthal ancestry is 12 to 20 percent higher in modern East Asians compared to modern Europeans. [In Images: The First Bone from a Neanderthal-Denisovan Hybrid]

"There's been a lot of debate as to why East Asians seem to have a bit more Neanderthal ancestry than Europeans," said senior study author Joshua Schraiber, a population geneticist at Temple University in Philadelphia. "There've been two competing ideas. One is that East Asians happen to interbreed more with Neanderthals. The other is that, of the multiple ancestral populations of Europeans, one had very little Neanderthal ancestry, diluting the [overall] Neanderthal contribution."

To shed light on this question of interbreeding, scientists developed computer simulations that modeled how DNA would get shared during a range of numbers of encounters between modern humans and Neanderthals. Then, they looked into which models best fit modern human genetic databases.

The researchers suggested the patterns of Neanderthal DNA inheritance seen in modern humans are best explained by not one, but multiple, independent episodes of interbreeding between Neanderthal and modern humans, first and foremost in the Middle East, but also later in both Europe and East Asia. The dilutive effect likely also played some role in why there is less Neanderthal ancestry in modern Europeans than in modern East Asians, Schraiber told Live Science. In other words, both multiple interbreeding episodes and dilutive effects might have occurred, contrary to what was previously thought.

This scenario of multiple episodes of interbreeding between modern humans and Neanderthals fits in with the emerging view that various human lineages had complex and frequent interactions. For example, recent work found the mysterious human lineage known as the Denisovans apparently contributed to the modern human gene pool at least twice, leaving behind two distinct genetic component — one mostly in Papuan and Australian aboriginal populations, the other primarily in East Asian populations.

More research is needed to explain why some Neanderthal DNA was kept in the human genome and some was purged, the scientists noted. For instance, previous work suggested that evolution weeded out a great deal of Neanderthal DNA from modern human genomes. One theory for this is that Neanderthal DNA was of less benefit to modern humans as their environments changed over time. Another theory posits that harmful mutations were more common in Neanderthals due to inbreeding, Schraiber said.

The scientists detailed their findings online Nov. 26 in the journal Nature Ecology & Evolution.

In Photos: Neanderthal Burials Uncovered
Denisovan Gallery: Tracing the Genetics of Human Ancestors
Image Gallery: Our Closest Human Ancestor
Original article on Live Science.
https://www.yahoo.com/news/neanderthals ... 00886.html

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Neanderthals Should Join Homo Sapiens on the Family Tree

New findings from fossils and DNA should expand our thinking about our species.

Faye FlamJuly 30, 2019, 7:00 PM CDT


Life before selfies.
Photographer: Sebastian Willnow/AFP, via Getty Images


Faye Flam is a Bloomberg Opinion columnist. She has written for the Economist, the New York Times, the Washington Post, Psychology Today, Science and other publications. She has a degree in geophysics from the California Institute of Technology.
Read more opinion Follow @fayeflam on Twitter

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The term “Homo sapiens” is no longer working so well. Neither is the closely related term, “modern humans,” used to describe us and fossils of long-dead people who looked something like us. It’s not just that “sapiens” means wise, and there’s no evidence that our species is any wiser than any of the other kinds of humans that walked the planet. The problem is bigger than that. It’s hard to be objective about ourselves, even for scientists.

I started considering the trouble after seeing a Twitter discussion among paleontologists who appeared to be upset by the way journalists had used “modern humans” about a new claim that fossils found in Greece date back 210,000 years.

What should journalists have called them? There’s no great answer from human history. The story has just become too messy.

Just a few years ago we had a nice neat understanding: Some 200,000 years ago, Homo sapiens arose amid a wealth of other kinds of humans – most notably Neanderthals in Europe and a group called Denisovans who lived in parts of Asia. But our kind, allegedly through our wisdom or some other attribute, won out, and, some 60,000 years ago, started to spread through the world, replacing Neanderthals and various other “also ran” humans.

Or so we thought.

Then scientists learned to read bits of DNA scraped from fossils and found, oops, what we thought of as our species was mating with Neanderthals, Denisovans and any other human species we came in contact with. This complicates everything, including the question of who gets to be included in our species category.

To further confuse us, some people who look distinctly like us – modern humans – got up and left for Europe before 210,000 years ago, back when it was thought only Neanderthals and other non-sapiens lived up there. The finding, announced in the journal Nature this month, follows another fragmentary find that would put modern humans in the region well before 100,000 years ago.

And therein lies the terminology problem. “Modern humans” has long implied a group of people that look like us, with our distinct rounded skulls, small jaws and chins. And also implies our single, direct ancestral lineage.

And now the DNA evidence and fossils together show a patchwork of different human species or sub-species, interbreeding and contributing to our ancestry, as well as people who look a lot like us branching off early in Europe, perhaps not contributing to our ancestry at all.

It’s not universally agreed upon that those early people in Greece were all that much like us. The fossil in question – a part of a skull – was found in the 1970s and showed the rounded shape more like people today than like Neanderthals or Denisovans. New technology allowed researchers to finally get their surprisingly early date.

There are plenty of skeptics who want more evidence than a single skull to show that such a migration happened more than 210,000 years ago, as the authors of the paper suggested. Others find it plausible. University of Wisconsin paleoanthropologist John Hawks said it fits with genetic evidence showing that Neanderthals had genes from so-called modern humans.

There’s that term again. “It makes them seem more like people,” Hawks said of Neanderthals. Should we just call them all “people” till we get that figured out?

Our genus-species name, Homo sapiens, is just as bad, said Hawks, as it’s sometimes synonymous with modern humans, and sometimes it’s broader. Some scientists want to include Denisovans and Neanderthals as kinds of Homo sapiens rather than as separate species. And if the DNA evidence is right, many prehistoric people considered them part of the family.

One thing the fossil record is telling us is that mixing across species is not weird. It happens, after all, between different species of cats, of elephants, and between dogs and wolves. Which makes it hard to neatly categorize things into species – especially ourselves.

The new narrative of our origins contains a mystery at the center, because genetic evidence shows we are not a diverse species. Despite our mixed-up origins, all 7 billion of us are closely related. How did diverse populations – perhaps even multiple species – end up such a homogeneous lot?

Perhaps when they sort out the mystery, scientists can rethink all our terms and give us more precise ones. They would earn that title of “sapiens.”

This column does not necessarily reflect the opinion of the editorial board or Bloomberg LP and its owners.
https://www.bloomberg.com/opinion/artic ... amily-tree

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'All bets now off' on which ape was humanity's ancestor
By Pallab Ghosh Science correspondent, BBC News

Composite of Australopithecus anamensis skull and faceCMNH/MattCrow
The discovered skull (R) with an artist's rendering (L) of what Anamensis might have looked like
Researchers have discovered a nearly complete 3.8-million-year-old skull of an early ape-like human ancestor in Ethiopia.

An analysis of the new specimen challenges ideas about how the first humans evolved from ape-like ancestors.

The current view that an ape named Lucy was among a species that gave rise to the first early humans may have to be reconsidered.

The discovery is reported in the journal Nature.

The skull was found by Prof Yohannes Haile-Selassie at a place called Miro Dora, which is in the Mille District of Ethiopia's Afar Regional State.

The scientist, who's affiliated to the Cleveland Museum of Natural History in Ohio, US, said he immediately recognised the significance of the fossil.

"I thought to myself, 'oh my goodness - am I seeing what I think I am seeing?'. And all of a sudden I was jumping up and down and that was when I realised that this was what I had dreamt," he told BBC News.

Prof Haile-Selassie says the specimen is the best example yet of the ape-like human ancestor called Australopithecus anamensis - the oldest known australopithecine whose kind may have existed as far back as 4.2 million years ago.

It had been thought that A. anamensis was the direct ancestor of a later, more advanced species called Australopithecus afarensis, which in turn has been considered a direct ancestor of the first early humans in the grouping, or genus, known as Homo, and which includes all humans alive today.

Four views on the nearly complete skullCleveland Museum of Natural History
Different aspects of the new specimen's face and view (bottom-left) looking at its upper-jaw from below. The creature had protruding jaws and small earholes
The discovery of the first afarensis skeleton in 1974 caused a sensation. She was nicknamed Lucy by researchers after the Beatles song, Lucy in the Sky With Diamonds, which was playing at the excavation site.

Hailed as "the first ape to have walked", Lucy captured the public's attention. But writing a commentary in Nature, Prof Fred Spoor, of London's Natural History Museum, said that anamensis "looks set to become another celebrated icon of human evolution".

The reason for this likely elevated status is because we can now say that anamensis and afarensis actually overlapped in time. The former did not evolve directly into the latter in a neat linear manner, as previously supposed.

The realisation comes about through the reinterpretation that the new fossil brings to bear on a previously discovered 3.9-million-year-old skull fragment. That fragment had been assigned to anamensis. Scientists can now see it is actually the remains of an afarensis, pushing this species' origin deeper into the past.

It's apparent now the two species must have co-existed for at least 100,000 years.

Prof Yohannes Haile-Selassie holding the skull he found
Cleveland Museum of Natural History
I thought to myself 'Oh my goodness, am I seeing what I think I'm seeing?'

What most likely happened was that a small group of anamensis isolated itself from the main population and over time evolved into afarensis because of adaptations to local conditions. The two types rubbed along for a while before the remnant anamensis died out.

The finding is important because it suggests that additional overlaps with other advanced ape-like species may also have occurred, increasing the number of potential evolutionary routes to the first humans.

In short, although this latest discovery does not disprove that Lucy's kind gave rise to the Homo group, it does bring other recently named species into contention. Prof Haile-Selassie agreed that "all bets are now off" as to which species is humanity's direct ancestor.

He explained: "For a long time, afarensis was considered the best candidate as an ancestor to our kind, but we are not in that position any more. Now we can look back at all the species that might have existed at the time and examine which one may have been most like the first human."

LucyP.PLAILLY/E.DAYNES/SPL
The remains of an ape named Lucy thought to be the ancestor of the first humans
Presentational white space
The term "missing link" drives anthropologists crazy when they hear anyone, especially journalists, use it to describe a fossil that is part-ape and part-human.

Indeed Dr Henry Gee, a senior editor at Nature, once threatened to "rip my liver out and eat it with onions, borlotti beans and a glass of claret" if I did so when reporting a previous discovery.

There are many reasons for Henry's irritation, but chief among them is the recognition that there are many links in the chain of human evolution and most if not nearly all of them are still missing.

Anamensis is the latest in a string of recent discoveries that shows that there was no smooth line of ascent to modern humans.

The truth is far more complex and far more interesting. It tells a story of evolution "trying out" different "prototype" human ancestors in different places until some of them were resilient and clever enough to withstand the pressures wrought by changes in climate, habitat and food scarcity - and evolve into us.

Prof Haile-Selassie is one of the few African scientists working in human evolution. He is now a recognised name but he says it's hard for well qualified African researchers to get the necessary financial backing from Western-based research funding organisations.

"Most of the fossil evidence related to our origin comes from Africa and I think Africans should be able to use the resources available in their own continent and advance their career in palaeoanthropology. Their limitations getting to this field of study is usually funding," he told me.

https://www.bbc.com/news/science-environment-49486980

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How differences in the genetic 'instruction booklet' between humans and Neanderthals influenced traits
by Spencer Turney, Vanderbilt University


Neanderthal
Reconstruction of Neanderthal man. Credit: public domain
When it comes to our differences from Neanderthals, most of what we know comes from comparing fossils. But fossils can only tell us about bones and not whole living organisms.

That's changing thanks to a new paper from a team of genomics researchers at Vanderbilt, who have developed a first-of-its-kind computational method. Their approach uses Neanderthal DNA that remains in those bones to find differences in how genes are controlled between modern humans and Neanderthals. This newfound ability to study changes in the on/off "instructions" for genes, also known as gene regulation, helps identify differences that fossils alone cannot tell us.

The research appears today in the journal Nature Ecology & Evolution.

Developed by Tony Capra, associate professor of Biological Sciences, and his team at Vanderbilt, the computational technique compares thousands of human genomes and the few Neanderthal genomes available. This allows for deeper understanding of how genomes differ in function and how certain traits changed between humans and our close relatives.

"Up until now, it has been challenging to interpret how individual genetic differences between humans and our close relatives relate to differences in our traits," noted Capra. "Our new technique integrates the effects of many genetic variants together to give a more holistic look at what differences in our DNA mean about differences in our biology. This is helping us understand how our species changed across the last few hundred thousand years."

Using their new computational technique, the team uncovered a diverse array of differences between human and Neanderthal immune, skeletal, cardiovascular and reproductive systems. Lending support to the approach, some of the findings are consistent with known differences from fossils, such as the shorter stature of Neanderthals. The team found that how and when genes are active changed much more than the genes themselves, and in some cases these changes were likely the result of different environmental pressures.

The research builds on previous work from Capra's team, who in 2016 found that DNA inherited from Neanderthals influences disease risk in modern humans—also proving the ability to use electronic health record data in evolutionary studies.

The next step for the new research, according to Capra, is to apply the method across the wide range of ancient human DNA available today—not just Neanderthals.

"Increasing our understanding of what makes our ancestors both different and similar to us will give us an increasingly relevant and timely view on what happened to make us human," added Capra. "The ability to read this 'instruction booklet' for how genes were induced or repressed will set the stage for future research and could even one day lead to significant therapeutic implications."
https://phys.org/news/2019-10-differenc ... thals.html

Long stretches of Neanderthal and Denisovan DNA helped Homo sapiens adapt
Denisovans and Neanderthals passed extra copies of some DNA to modern humans.

Kiona N. Smith - 10/21/2019, 9:45 AM

Global map of Denisovan gene frequency in modern human genomes
Image courtesy of Jacobsson and Skoglund/Proceedings of the National Academy of Sciences
University of Washington geneticist PingHsun Hsieh and his colleagues found Neanderthal and Denisovan versions of some genes in the genomes of people from Melanesia. These versions have several thousand base pairs of DNA that have been duplicated or deleted in the normal human versions. Most of this altered DNA is in or near genes related to metabolism, development, the life cycle of cells, communication among cells, or the immune system.

Those gene variants are surprisingly common among Melanesian peoples, and that could mean that their effects were useful enough that natural selection favored passing them along.

DNA from the Denisovans

As Homo sapiens first ventured beyond Africa, they encountered other hominins already living in Europe and Asia, and those encounters left their mark on our modern genomes. Most people from outside Africa carry a little Neanderthal DNA (it makes up about one to four percent of the average non-African genome), and some people from East Asian, Melanesian, and indigenous Australian populations also have a bit of DNA inherited from Denisovans (about one to five percent of the average genome; it’s highest in Melanesian and indigenous and Australian people). Some of that DNA probably stuck with us for tens of thousands of years because it somehow helped our species adapt to new environments and challenges.

How does this DNA differ from the version found in modern humans? Thanks to the Neanderthal and Denisovan genomes recovered from ancient bones and teeth, scientists can recognize certain alleles that belong to our extinct cousins. Usually, when scientists talk about Neanderthal or Denisovan genes, they’re talking about alleles with small differences from the Homo sapiens version—sometimes just a single nucleotide (one “letter” in the genetic code).

Sometimes those small changes don’t make a difference, but other times they’re enough to code for a different protein or cause a gene to be active under different conditions.

Hsieh and his colleagues looked for larger differences, in which tens of thousands of base pairs had either disappeared from the chromosome or had been repeated more times than usual. Geneticists call such changes copy-number variations, and they can be bad news; too many or too few copies of most genes can cause health problems or increase the risk of cancer. But some of the copy-number variations that Melanesian peoples inherited from Neanderthals and Denisovans actually seem to have been helpful.

DNA: The gift that keeps on giving

Hsieh and his colleagues studied genomes from modern people, looking for copy-number variants that showed up in the genomes of Neanderthals or Denisovans. They focused on those that appeared in modern people from outside Africa but not in modern people from Africa, whose ancestors wouldn’t have run into Neanderthals or Denisovans. They found a total of 51 such chunks of genetic code.

Hsieh and his colleagues were especially curious about Melanesia because the average Melanesian person has a higher percentage of Denisovan DNA in their genome (between three and five percent) than the average member of any other group of people. In a sample of Melanesian people’s genomes from research databases, they found 37 copy-number variations that showed up in a larger portion of the population than you’d expect just by random genetic chance.

In other words, it looked like natural selection had acted in favor of those 37 pieces of DNA, making them more common because they somehow helped people live and reproduce more successfully.

Of those 37 apparently helpful sets of duplicated DNA, 19 appeared to have originally come from the Neanderthal or Denisovan genomes. “It is tempting to hypothesize that [DNA] introgression from other hominins may have played a key role in helping humans [who were] migrating out of Africa adapt to new environments by serving as a reservoir of beneficial alleles,” wrote Hsieh and his colleagues.

But there’s still a large gap between seeing that a genetic variant is likely to have been helpful enough for natural selection to kick in and being able to say exactly what that variant does. It is, however, possible to make some general predictions based on which genes are nearby. Based on that, it looks like most of the copy-number variants affect genes—associated with things like metabolism, the immune system, and embryonic development. So far, however, Hsieh and his colleagues can’t be sure of the details.

The complex history of chromosome 16

One of the largest and most complex sequences in the study appears to be somehow associated with iron regulation during the development of an embryo. The 383-base-pair sequence (which contains two copied sections of DNA) happens to be located near a spot on chromosome 16 that’s already prone to rearrangements. Those rearrangements are associated with the second most common genetic cause of autism that we know of, which affects about one percent of diagnosed people.

Based on what we know about how quickly DNA changes over time, Hsieh and his colleagues say that between 500,000 and 2.5 million years ago, a complex series of changes happened on chromosome 16 in the Denisovans. Some genes got copied, others got deleted, and still others just got rearranged. Eventually, about 60,000 to 170,000 years ago, the resulting alleles got passed to Homo sapiens, likely somewhere between southeast Asia and Melanesia. Today, the Denisovan variant shows up in about 80 percent of people in the lowlands of New Guinea.

That section of chromosome 16 already had its own copy-number variant in humans, which originated around 280,000 years ago. As a result of the extra DNA, that area of the genome was already vulnerable to having its code rearranged. Hsieh and his colleagues suggest that the altered DNA could influence how often the genetic code gets rearranged. But that benefit could also impact the frequency of autism among Melanesians, although it’s much, much too early to draw firm conclusions.

What is increasingly clear, however, is that many modern people still carry aspects of our extinct hominin relatives with us. The next step is to unravel exactly how those surviving bits of ancient DNA may still influence the lives and health of modern populations.
https://phys.org/news/2019-10-differenc ... thals.html

[seemslikeadream]

Neanderthal glue was a bigger deal than we thought
Technology seems to have been a routine part of Neanderthal life.

Kiona N. Smith - 10/22/2019, 11:50 AM
Color photo of a roll of birch bark, a puddle of tar, and a spear with birch tar securing the point.
This replica shows how Neanderthals might have used birch tar to haft a projectile point.
Paul R. B. Kozowyk
Fifty-thousand years ago, a Neanderthal living in Northwestern Europe put sticky birch tar on the back side of a sharp flint flake to make the tool easier to grip. Eventually, that tool washed down the Rhine or Meuse Rivers and out into the North Sea. In the 21st century, dredging ships scooped it up along with tons of sand, other stone tools, and fossilized bones, then dumped the whole pile on Zandmotor Beach in the Netherlands.

Despite all of that, the birch tar still clung to the flake, and it provides evidence that Neanderthals used a complex set of technology to make elaborate tools.

Living on the edge

Making birch tar at all is a fairly complex process. It takes multiple steps, lots of planning, and detailed knowledge of the materials and the process. So the fact that archaeologists have found a handful of tools hafted using birch tar tells us that Neanderthals were (pardon the pun) pretty sharp.

But the Zandmotor Beach flake tells us more than that. Making birch tar adhesive for tools was so routine that Neanderthals would do it even for a simple domestic tool like a small flake—even in the extreme environment of Ice Age Northwestern Europe, in the shadow of glaciers at the very northern edge of where Neanderthals could survive. And all the while, they were using fairly advanced methods for more efficient production.

“Despite [the] mounting evidence, the degree of Neanderthal technological expression is still under debate,” notes the new paper by archaeologist Marcel Niekus and his colleagues (Niekus is at the Netherlands-based Foundation for Stone Age Research). “The Neanderthal tar finds provide evidence of a complex technology so ingrained in their behavior that it was maintained at the limits of their ecological tolerance: glacial northwestern Europe.”

There’s not much room left to debate Neanderthals’ intelligence in the face of evidence that they used fire and created art. But a technology like producing tar adhesive—only one component of a complex, multi-piece tool—requires more than brains. Anthropologists usually assume that such technologies require a larger, relatively sedentary population; hunter-gatherers could still pull it off, but they’d need to live in larger groups, and move around less, than the archaeological record suggests for Neanderthals.

As far as we know, Neanderthals lived in relatively small groups, with a sparse population scattered across the Eurasian landscape. Based on the shape of their femurs, they walked much more than modern hunter-gatherers. Most anthropologists wouldn’t expect them to be able to develop, much less routinely practice, a technology that’s every bit as complicated as pottery or metallurgy. But it now appears that they did.

High-tech and efficient

When Niekus and his colleagues examined the thick black tar with a micro-CT scan, they noticed fine grains of charcoal, sand, and iron oxide mixed in with the tar. Those contaminants were mixed in very evenly, as if they’d been worked into the tar while it was molten and flowing. To manage that kind of thorough mixing, birch tar would have to reach temperatures of 350ºC or more. The amounts of chemical compounds like botulin and lupeol in the tar also suggest a temperature in that range. To get the tar that hot, Neanderthals must have produced it in a relatively high-tech way.

As a study earlier this year pointed out, it’s really not very hard to make birch bark tar; burning a roll of birch bark next to a flat rock will do the trick. But that’s also a super inefficient way of making tar; Niekus and his colleagues—who tried their hands at tar production for the sake of science—estimate that it would have taken ten hours to make enough tar just to haft a single flake. If Neanderthals were going to the trouble of putting tar on a small, everyday domestic tool like a flake (whether to attach it to a haft or just to make a simple grip), then producing tar in usable amounts must have been routine. And that means they probably found a more efficient way to go about it.

The most efficient way to get tar from birch bark is to heat the roll of bark in a clay vessel buried inside an earthen mound. It’s a more complicated process, which requires more steps, more planning, and more detailed technical knowledge, but it also makes more tar more quickly, and with about 40 times less bark required for the same amount of tar. It’s also the only method that produced temperatures hot enough to explain the fine grains of sand and charcoal mixed with the tar (360ºC inside the vessel and 310ºC inside the bark roll).

The mother of invention

So the Zandmotor Beach flake suggests that Neanderthals were using Stone Age high-tech to make adhesives for their multi-part tools (which were pretty high-tech in their own right). It involved a complex process of gathering birch bark and heating it to extract the tar, then using the tar to haft a tool or shape a grip. That would have taken a lot of time and energy, yet “the technological investment must be worth the trouble,” wrote Niekus and his colleagues.

That’s especially true in an extreme environment like glacial Northwestern Europe 50,000 years ago, where resources where scarce and uncertain, and just surviving at a basic level must have been a challenge. But Niekus and his colleagues suggest that the cold, inhospitable environment may actually have pushed the Neanderthals to develop more complex tools, and more efficient ways of producing them, in order to make a living.
https://arstechnica.com/science/2019/10 ... e-thought/

Long stretches of Neanderthal and Denisovan DNA helped Homo sapiens adapt
Denisovans and Neanderthals passed extra copies of some DNA to modern humans.

Kiona N. Smith - 10/21/2019, 9:45 AM

Global map of Denisovan gene frequency in modern human genomes
Image courtesy of Jacobsson and Skoglund/Proceedings of the National Academy of Sciences
University of Washington geneticist PingHsun Hsieh and his colleagues found Neanderthal and Denisovan versions of some genes in the genomes of people from Melanesia. These versions have several thousand base pairs of DNA that have been duplicated or deleted in the normal human versions. Most of this altered DNA is in or near genes related to metabolism, development, the life cycle of cells, communication among cells, or the immune system.

Those gene variants are surprisingly common among Melanesian peoples, and that could mean that their effects were useful enough that natural selection favored passing them along.

DNA from the Denisovans

As Homo sapiens first ventured beyond Africa, they encountered other hominins already living in Europe and Asia, and those encounters left their mark on our modern genomes. Most people from outside Africa carry a little Neanderthal DNA (it makes up about one to four percent of the average non-African genome), and some people from East Asian, Melanesian, and indigenous Australian populations also have a bit of DNA inherited from Denisovans (about one to five percent of the average genome; it’s highest in Melanesian and indigenous and Australian people). Some of that DNA probably stuck with us for tens of thousands of years because it somehow helped our species adapt to new environments and challenges.

How does this DNA differ from the version found in modern humans? Thanks to the Neanderthal and Denisovan genomes recovered from ancient bones and teeth, scientists can recognize certain alleles that belong to our extinct cousins. Usually, when scientists talk about Neanderthal or Denisovan genes, they’re talking about alleles with small differences from the Homo sapiens version—sometimes just a single nucleotide (one “letter” in the genetic code).

Sometimes those small changes don’t make a difference, but other times they’re enough to code for a different protein or cause a gene to be active under different conditions.

Hsieh and his colleagues looked for larger differences, in which tens of thousands of base pairs had either disappeared from the chromosome or had been repeated more times than usual. Geneticists call such changes copy-number variations, and they can be bad news; too many or too few copies of most genes can cause health problems or increase the risk of cancer. But some of the copy-number variations that Melanesian peoples inherited from Neanderthals and Denisovans actually seem to have been helpful.

DNA: The gift that keeps on giving

Hsieh and his colleagues studied genomes from modern people, looking for copy-number variants that showed up in the genomes of Neanderthals or Denisovans. They focused on those that appeared in modern people from outside Africa but not in modern people from Africa, whose ancestors wouldn’t have run into Neanderthals or Denisovans. They found a total of 51 such chunks of genetic code.

Hsieh and his colleagues were especially curious about Melanesia because the average Melanesian person has a higher percentage of Denisovan DNA in their genome (between three and five percent) than the average member of any other group of people. In a sample of Melanesian people’s genomes from research databases, they found 37 copy-number variations that showed up in a larger portion of the population than you’d expect just by random genetic chance.

In other words, it looked like natural selection had acted in favor of those 37 pieces of DNA, making them more common because they somehow helped people live and reproduce more successfully.

Of those 37 apparently helpful sets of duplicated DNA, 19 appeared to have originally come from the Neanderthal or Denisovan genomes. “It is tempting to hypothesize that [DNA] introgression from other hominins may have played a key role in helping humans [who were] migrating out of Africa adapt to new environments by serving as a reservoir of beneficial alleles,” wrote Hsieh and his colleagues.

But there’s still a large gap between seeing that a genetic variant is likely to have been helpful enough for natural selection to kick in and being able to say exactly what that variant does. It is, however, possible to make some general predictions based on which genes are nearby. Based on that, it looks like most of the copy-number variants affect genes—associated with things like metabolism, the immune system, and embryonic development. So far, however, Hsieh and his colleagues can’t be sure of the details.

The complex history of chromosome 16

One of the largest and most complex sequences in the study appears to be somehow associated with iron regulation during the development of an embryo. The 383-base-pair sequence (which contains two copied sections of DNA) happens to be located near a spot on chromosome 16 that’s already prone to rearrangements. Those rearrangements are associated with the second most common genetic cause of autism that we know of, which affects about one percent of diagnosed people.

Based on what we know about how quickly DNA changes over time, Hsieh and his colleagues say that between 500,000 and 2.5 million years ago, a complex series of changes happened on chromosome 16 in the Denisovans. Some genes got copied, others got deleted, and still others just got rearranged. Eventually, about 60,000 to 170,000 years ago, the resulting alleles got passed to Homo sapiens, likely somewhere between southeast Asia and Melanesia. Today, the Denisovan variant shows up in about 80 percent of people in the lowlands of New Guinea.

That section of chromosome 16 already had its own copy-number variant in humans, which originated around 280,000 years ago. As a result of the extra DNA, that area of the genome was already vulnerable to having its code rearranged. Hsieh and his colleagues suggest that the altered DNA could influence how often the genetic code gets rearranged. But that benefit could also impact the frequency of autism among Melanesians, although it’s much, much too early to draw firm conclusions.

What is increasingly clear, however, is that many modern people still carry aspects of our extinct hominin relatives with us. The next step is to unravel exactly how those surviving bits of ancient DNA may still influence the lives and health of modern populations.
https://arstechnica.com/science/2019/10 ... ens-adapt/

[seemslikeadream]

Neanderthals were master fire-starters, cave chemistry suggests
BY TOM METCALFE31 OCTOBER 2019

Neanderthals were masters at making and controlling fires, suggests new research that found distinctive hydrocarbons from ancient hearths in a cave inhabited up to 60,000 years ago. The study gives weight to the theory that Neanderthals and other early humans were skilled at making fires, rather than just exploiting natural wildfires.

Although it’s sometimes argued that only Homo sapiens could control fires for warmth, light, cooking and tool-making – a skill known as pyrotechnology – the study indicates otherwise. ‘Our research has strengthened the idea that Neanderthals were able to control fire,’ says lead author Alex Brittingham from the University of Connecticut, US.

It also casts doubt on the idea that an inability to make fires contributed to Neanderthals dying out about 40,000 years ago. ‘At least some Neanderthals had the ability to control fire in the same way that modern humans did,’ Brittingham says. ‘If this behaviour was similar between the two species, there is no reason to believe it led to the extinction of the Neanderthals.’

The researchers studied polycyclic aromatic hydrocarbons (PAHs) in floor sediments at Lusakert-1, a cave in Armenia where Neanderthals lived between 40,000 and 60,000 years ago. Light PAHs, with three or four aromatic rings, disperse in the air and are caused by wildfires, explains geochemist Michael Hren from the University of Connecticut, a co-author of the study.

But heavy PAHs, with five or more aromatic rings, take more energy to create and disperse only a few metres. They are usually caused by burning wood on hot hearth fires – and the researchers found that heavy PAHs occurred independently of light PAHs in the cave. ‘We have people living in this cave, burning fires for food, for warmth … if they were relying on frequent lightning strikes to get fire, then we would have seen a more abundant background fire signal,’ Hren said. ‘We did not see that.’

Instead, they found that heavy PAHs occurred alongside concentrations of Neanderthal artifacts, including charcoal and bone fragments. ‘It really tells us that they were having fires locally.’

Archaeologist Andrew Sorensen from the University of Leiden, the Netherlands, who was not involved in the research, says the technique of studying PAH levels in sediments has great potential for studying other Neanderthal sites, ‘to really get a better idea of what is going on with Palaeolithic fire-use’. But because natural wildfires could be rekindled in hearth fires almost endlessly, this research alone is not final proof that Neanderthals had complete control of fire, he adds.

The mastery of fire by early humans is a hot topic. A 2016 study suggested Neanderthals used powdered magnesium dioxide as a fire lighter, and a 2018 study led by Sorensen proposed that distinctive marks on Neanderthal tools from around 50,000 years ago were evidence of fire-making.

The new technique could also help determine if the use of fire arose more than once. ‘Throughout the archaeological record we see the independent development of different behaviours,’ – including animal domestication, Brittingham says. ‘Pyrotechnology could have undergone a similar process, and may have developed independently in different Palaeolithic populations.’
https://www.chemistryworld.com/news/nea ... 95.article

Yet More Evidence That Neanderthal Bling Included Eagle Talons
Artist’s depiction of a Neanderthal female and male wearing jewelry made from eagle talons.

Illustration: Lou-Octavia Mørch
New fossil evidence suggests the Neanderthal practice of collecting eagle talons, which were likely worn as jewelry or used to create powerful symbols, was more extensive than previously thought. Remarkably, the dating of these artifacts suggests modern humans might have copied this practice.

New evidence presented on Friday in Science Advances bolsters a theory that suggests Neanderthals used eagle talons as symbolic decorations, which they may have worn as necklaces, earrings, or other forms of personal adornment. Evidence of this cultural practice among the Neanderthals has been found elsewhere, but the new find—a lone eagle toe bone pulled from Foradada Cave in Spain—is the first to be found in the Iberian Peninsula. What’s more, at 39,000 years old, it’s possibly the most “modern” known example of talon use among the Neanderthals, appearing at the very end of their long reign.

That said, an anthropologist Gizmodo spoke to said it’s not clear if these particular Neanderthals used eagle talons for symbolic or decorative reasons, saying more supporting evidence is needed.

That Neanderthals made their own jewelry is hardly a surprise. Other archaeological evidence suggests they made cave paintings and decorated themselves with feathers. What’s more, modern humans arriving in Europe might have even acquired some of their technological know-how from Neanderthals, including the lissoir—a specialized bone for working tough animal hides. Fascinatingly, and as the new paper proposes, modern humans may have also adopted the Neanderthal practice of using eagle talons as jewelry.

The lone eagle toe bone with cut marks.

Image: Antonio Rodríguez-Hidalgo
Evidence of eagle talon use among the Neanderthals has been found before. That includes at sites in France and Croatia, both of which date back to well over 100,000 years ago. The could say oldest ancestors of Neanderthals in Eurasia date back to 400,000 years ago.

“This paper builds on earlier work, including mine, that shows that Neandertals exploited raptor talons presumably for symbolic reasons,” said Eugene Morin, an anthropologist at Trent University in Canada who wasn’t involved with the new study, in an email to Gizmodo. “What’s new here is that for the first time this behavior is documented in Iberia. The paper also shows that it existed among Châtelperronian Neandertals, likely the very last Neandertals in the region. In other words, the paper extends the geographical and temporal range for this behavior.”

Indeed, the new study co-authored by Antonio Rodríguez-Hidalgo from the Institute of Evolution in Africa (IDEA) expands the timeframe within which Neanderthals collected eagle talons, a period that stretches from 130,000 to 39,00 years ago. The Neanderthals went extinct shortly thereafter.

“The evidence of symbolic behavior—in burials, art, or for personal adornment—among archaic human species is scarce,” explained Rodríguez-Hidalgo in an email to Gizmodo. “Each new find is a new piece of the great puzzle. The findings of Foradada cave, in Spain, represent the most recent case of use of eagle talons as ornaments by the Neanderthals.”

It’s important to point out that Rodríguez-Hidalgo and his colleagues did not actually uncover eagle talons in Foradada Cave. Rather, they found indirect evidence in the form of a single eagle phalanx, or toe bone, to which a talon was once attached. The scientists documented specific cut marks made onto this bone as evidence that the Neanderthals manually extracted the talon, in this case from the left leg of a Spanish Imperial Eagle.

Multiple views of the toe bone and associated cut marks.
Image: A. Rodríguez-Hidalgo et al., 2019/Science Advances
It’s possible that Neanderthals made these marks while butchering an eagle for food, but the authors ruled this out due to the “complete lack of nutritional value of a bird’s lower extremities,” according to the new paper. It’s also possible that the talons were used as tools, such as for piercing or needling, but the authors thought this unlikely. Neanderthals “used very few tools made with bone, at least as far as we know now,” Rodríguez-Hidalgo told Gizmodo, adding that the “Neanderthals chose the eagle talons, because it was a deliberate decision, because it was important to choose eagles by their significance.”

John Stewart, an associate professor of paleoecology and environmental change at Bournemouth University who wasn’t involved with the research, said an important aspect of the study is that, as far as he knows, it’s the first time cut marks on bird bones have been analyzed with a scanning technology developed by biologist Silvia Bellow from the Natural History Museum in the UK.

“This makes it a lot more convincing than previous suggested claims,” Stewart told Gizmodo.

The authors don’t know if these talons were used to create necklaces or if they were worn as earrings or bracelets, but these ornaments “transmitted a message that the members of the group could understand and that other Neanderthals, at least from southern Europe, could understand,” Rodríguez-Hidalgo said. “Unfortunately, we do not have a Rosetta Stone to decode this message.”

David Frayer, an anthropologist at the University of Kansas who wasn’t involved with the new research, said he was “happy” to read about this new evidence, but he had some concerns.

First off, some archaeologists aren’t convinced that the Châtelperronian layer in Foradada Cave can be linked to Neanderthals, “so this paper will not sway them,” Frayer wrote to Gizmodo.

Secondly, Frayer wasn’t thrilled that the authors were unable to find an actual eagle talon. Back in in 2015, Frayer and his colleagues did just that, publishing a study detailing the discovery of several eagle talons in Croatia’s Krapina Cave that were dated to 130,000 years old. Talons are “much more informative,” said Frayer, “but this was just a phalanx.” By itself, the cut marks on the toe bone “does not say much about symbolic intentions.”

Without other supporting evidence, Frayer is “not convinced these are anything but butchering marks, but I am not a specialist in cut marks as they relate to butchering,” he said. “I agree they were not eating eagles, but I would like to have seen more. It is too bad they have yet to find talons at Foradada Cave.”

Indeed, more evidence would certainly help the authors to bolster their case, but this is still an important piece that can be added to the puzzle. In total, archaeologists have now collected 24 pieces like this, revealing the Neanderthal fascination with these majestic birds.
https://gizmodo.com/yet-more-evidence-t ... 1839537075