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

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DNA from Neandertal relative may shake up human family tree


By Ann Gibbons 11 September 2015 10:15 am 19 Comments
LONDON—In a remarkable technical feat, researchers have sequenced DNA from fossils in Spain that are about 300,000 to 400,000 years old and have found an ancestor—or close relative—of Neandertals. The nuclear DNA, which is the oldest ever sequenced from a member of the human family, may push back the date for the origins of the distinct ancestors of Neandertals and modern humans, according to a presentation here yesterday at the fifth annual meeting of the European Society for the study of human evolution.

Ever since researchers first discovered thousands of bones and teeth from 28 individuals in the mid-1990s from Sima de los Huesos (“pit of bones”), a cave in the Atapuerca Mountains of Spain, they had noted that the fossils looked a lot like primitive Neandertals. The Sima people, who lived before Neandertals, were thought to have emerged in Europe. Yet their teeth, jaws, and large nasal cavities were among the traits that closely resembled those of Neandertals, according to a team led by paleontologist Juan-Luis Arsuaga of the Complutense University of Madrid. As a result, his team classified the fossils as members of Homo heidelbergensis, a species that lived about 600,000 to 250,000 years ago in Europe, Africa, and Asia. Many researchers have thought H. heidelbergensis gave rise to Neandertals and perhaps also to our species, H. sapiens, in the past 400,000 years or so.

But in 2013, the Sima fossils’ identity suddenly became complicated when a study of the maternally inherited mitochondrial DNA (mtDNA) from one of the bones revealed that it did not resemble that of a Neandertal. Instead, it more closely matched the mtDNA of a Denisovan, an elusive type of extinct human discovered when its DNA was sequenced from a finger bone from Denisova Cave in Siberia. That finding was puzzling, prompting researchers to speculate that perhaps the Sima fossils had interbred with very early Denisovans or that the “Denisovan” mtDNA was the signature of an even more ancient hominin lineage, such as H. erectus. At the time, researchers at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, who had obtained the mtDNA announced that they would try to sequence the nuclear DNA of the fossils to solve the mystery.

After 2 years of intense effort, paleogeneticist Matthias Meyer of the Max Planck Institute for Evolutionary Anthropology has finally sequenced enough nuclear DNA from fossils of a tooth and a leg bone from the pit to solve the mystery. The task was especially challenging because the ancient DNA was degraded to short fragments, made up of as few as 25 to 40 single nucleotides. (Nucleotides—also known as base pairs—are the building blocks of DNA.) Although he and his colleagues did not sequence the entire genomes of the fossils, Meyer reported at the meeting that they did get 1 million to 2 million base pairs of ancient nuclear DNA.

They scanned this DNA for unique markers found only in Neandertals or Denisovans or modern humans, and found that the two Sima fossils shared far more alleles—different nucleotides at the same address in the genome—with Neandertals than Denisovans or modern humans. “Indeed, the Sima de los Huesos specimens are early Neandertals or related to early Neandertals,” suggesting that the split of Denisovans and Neandertals should be moved back in time, Meyer reported at the meeting.

Researchers at the meeting were impressed by this new breakthrough in ancient DNA research. “This has been the next frontier with ancient DNA,” says evolutionary biologist Greger Larson of the University of Oxford in the United Kingdom.

The close affinity with Neandertals, but not with Denisovans or modern humans, suggests that the lineage leading to Neandertals was separate from other archaic humans earlier than most researchers have thought. That means that the ancestors of modern humans also had to split earlier than expected from the population that gave rise to Neandertals and Denisovans, who were more closely related to each other than they were to modern humans. (Although all three groups interbred at low levels after their evolutionary paths diverged—and such interbreeding may have been the source of the Denisovan mtDNA in the first Sima fossil whose DNA was sequenced.) Indeed, Meyer suggested in his talk that the ancestors of H. sapiens may have diverged from the branch leading to Neandertals and Denisovans as early as 550,000 to 765,000 years ago, although those results depend on different mutation rates in humans and are still unpublished.

That would mean that the ancestors of humans were already wandering down a solitary path apart from the other kinds of archaic humans on the planet 100,000 to 400,000 years earlier than expected. “It resolves one controversy—that they’re in the Neandertal clade,” says paleoanthropologist Chris Stringer of the Natural History Museum in London. “But it’s not all good news: From my point of view, it pushes back the origin of H. sapiens from the Neandertals and Denisovans.” The possibility that humans were a distinct group so early shakes up the human family tree, promising to lead to new debate about when and where the branches belong.

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Fossil teeth place humans in Asia '20,000 years early'
By Paul Rincon
Science editor, BBC News website
14 October 2015

The 47 human teeth were found sealed in a cave, beneath 80,000-year-old stalagmites
Fossil finds from China have shaken up the traditional narrative of humankind's dispersal from Africa.
Scientists working in Daoxian, south China, have discovered teeth belonging to modern humans that date to at least 80,000 years ago.
This is 20,000 years earlier than the widely accepted "Out of Africa" migration that led to the successful peopling of the globe by our species.
Details of the work are outlined in the journal Nature.
We need to re-think our models. Maybe there was more than one Out of Africa migration
Dr María Martinón-Torres, UCL
Several lines of evidence - including genetics and archaeology - support a dispersal of our species from Africa 60,000 years ago.
Early modern humans living in the horn of Africa are thought to have crossed the Red Sea via the Bab el Mandeb straits, taking advantage of low water levels.
All non-African people alive today are thought to derive from this diaspora.
Now, excavations at Fuyan Cave in Daoxian have unearthed a trove of 47 human teeth.
Ancient diaspora
"It was very clear to us that these teeth belonged to modern humans [from their morphology]. What was a surprise was the date," Dr María Martinón-Torres, from University College London (UCL), told BBC News.
"All the fossils have been sealed in a calcitic floor, which is like a gravestone, sealing them off. So the teeth have to be older than that layer. Above that are stalagmites that have been dated using uranium series to 80,000 years.
This means that everything below those stalagmites must be older than 80,000 years old; the human teeth could be as old as 125,000 years, according to the researchers.
Skhul skullImage copyrightScience Photo Library
Image caption
Modern humans reached the Levant 125,000 years ago, but this migration has been regarded as a failed foray outside Africa
In addition, the animal fossils found with the human teeth are typical of the Late Pleistocene - the same period indicated by the radioactive dating evidence.
Some fossils of modern humans that predate the Out of Africa migration are already known, from the Skhul and Qafzeh caves in Israel. But these have been regarded as part of a failed early dispersal of modern humans who probably went extinct.
However, the discovery of unequivocally modern fossils in China clouds the picture.
"Some researchers have proposed earlier dispersals in the past," said Dr Martinón-Torres.
"We really have to understand the fate of this migration. We need to find out whether it failed and they went extinct or they really did contribute to later people.
"Maybe we really are descendents of the dispersal 60,000 years ago - but we need to re-think our models. Maybe there was more than one Out of Africa migration."
'Game-changer'
Prof Chris Stringer, from London's Natural History Museum said the new study was "a game-changer" in the debate about the spread of modern humans.
"Many workers (often including me) have argued that the early dispersal of modern humans from Africa into the Levant recorded by the fossils from Skhul and Qafzeh at about 120,000 years ago was essentially a failed dispersal which went little or no further than Israel."
"However, the large sample of teeth from Daoxian seem unquestionably modern in their size and morphology, and they look to be well-dated by uranium-thorium methods to at least 80,000 years. At first sight this seems to be consistent with an early dispersal across southern Asia by a population resembling those known from Skhul and Qafzeh.
"But the Daoxian fossils resemble recent human teeth much more than they look like those from Skhul and Qafzeh, which retain more primitive traits. So either there must have been rapid evolution of the dentitions of a Skhul-Qafzeh type population in Asia by about 80,000 years, or the Daoxian teeth represent a hitherto-unsuspected early and separate dispersal of more modern-looking humans."
Dr Pontus Skoglund, from the department of genetics at Harvard Medical School, told BBC News: "The genetic evidence we have puts strong constraints on some aspects of human history, but less so on the timing of the out of Africa event. Most genetic reconstructions based on modern data relies on assumptions on the mutation rate, for which there are still some real uncertainties.
"In terms of direct genetic evidence, we already have a 45,000 year-old genome from Siberia (Ust Ishim) and a ~40,000 year old individual from Europe (Oase) that are consistent with being from now-mostly-extinct lineages. "
"The conclusion is perhaps that the genetics does allow an 80,000 year old East Asian population to contribute some ancestry to present-day people, but I think not very much. It is a very interesting discovery that is hard to fit in our current thinking, but not impossible. We are just starting to cope with this data point."
Dr Martinón-Torres said the study could also shed light on why it took Homo sapiens another 40,000 years to settle Europe.
Perhaps the presence of the Neanderthals kept our species out of westernmost Eurasia until our evolutionary cousins started to dwindle in number. However, it's also possible that modern humans - who started out as a tropical species - were not as well-conditioned as the Neanderthals for the icy climate in Europe.
She noted that while modern humans occupied the warmer south of China 80,000 years ago, the colder regions of central and northern China appear to be settled by more primitive human groups who may have been Asian relatives of the Neanderthals.

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‘Virtual fossil’ reveals last common ancestor of humans and Neanderthals
Date:
December 18, 2015
Source:
University of Cambridge
Summary:
New digital techniques have allowed researchers to predict structural evolution of the skull in the lineage of Homo sapiens and Neanderthals, in an effort to fill in blanks in the fossil record, and provide the first 3D rendering of their last common ancestor. The study suggests populations that led to the lineage split were older than previously thought.

The 'virtual fossil' of last common ancestor of humans and Neanderthals.
Credit: Aurélien Mounier
New digital techniques have allowed researchers to predict structural evolution of the skull in the lineage of Homo sapiens and Neanderthals, in an effort to fill in blanks in the fossil record, and provide the first 3D rendering of their last common ancestor. The study suggests populations that led to the lineage split were older than previously thought.

We know we share a common ancestor with Neanderthals, the extinct species that were our closest prehistoric relatives. But what this ancient ancestral population looked like remains a mystery, as fossils from the Middle Pleistocene period, during which the lineage split, are extremely scarce and fragmentary.

Now, researchers have applied digital "morphometrics" and statistical algorithms to cranial fossils from across the evolutionary story of both species, and recreated in 3D the skull of the last common ancestor of Homo sapiens and Neanderthals for the first time.

The "virtual fossil" has been simulated by plotting a total of 797 "landmarks" on the cranium of fossilised skulls stretching over almost two million years of Homo history -- including a 1.6 million-year-old Homo erectus fossil, Neanderthal crania found in Europe and even 19th century skulls from the Duckworth collection in Cambridge.

The landmarks on these samples provided an evolutionary framework from which researchers could predict a timeline for the skull structure, or 'morphology', of our ancient ancestors. They then fed a digitally-scanned modern skull into the timeline, warping the skull to fit the landmarks as they shifted through history.

This allowed researchers to work out how the morphology of both species may have converged in the last common ancestor's skull during the Middle Pleistocene -- an era dating from approximately 800,000 to 100,000 years ago.

The team generated three possible ancestral skull shapes that corresponded to three different predicted split times between the two lineages. They digitally rendered complete skulls and then compared them to the few original fossils and bone fragments of the Pleistocene age.

This enabled the researchers to narrow down which virtual skull was the best fit for the ancestor we share with Neanderthals, and which timeframe was most likely for that last common ancestor to have existed.

Previous estimates based on ancient DNA have predicted the last common ancestor lived around 400,000 years ago. However, results from the 'virtual fossil' show the ancestral skull morphology closest to fossil fragments from the Middle Pleistocene suggests a lineage split of around 700,000 years ago, and that -- while this ancestral population was also present across Eurasia -- the last common ancestor most likely originated in Africa.

The results of the study are published in the Journal of Human Evolution.

"We know we share a common ancestor with Neanderthals, but what did it look like? And how do we know the rare fragments of fossil we find are truly from this past ancestral population? Many controversies in human evolution arise from these uncertainties," said the study's lead author Dr Aurélien Mounier, a researcher at Cambridge University's Leverhulme Centre for Human Evolutionary Studies (LCHES).

"We wanted to try an innovative solution to deal with the imperfections of the fossil record: a combination of 3D digital methods and statistical estimation techniques. This allowed us to predict mathematically and then recreate virtually skull fossils of the last common ancestor of modern humans and Neanderthals, using a simple and consensual 'tree of life' for the genus Homo," he said.

The virtual 3D ancestral skull bears early hallmarks of both species. For example, it shows the initial budding of what in Neanderthals would become the 'occipital bun': the prominent bulge at the back of the skull that contributed to elongated shape of a Neanderthal head.

However, the face of the virtual ancestor shows hints of the strong indention that modern humans have under the cheekbones, contributing to our more delicate facial features. In Neanderthals, this area -- the maxillia -- is 'pneumatized', meaning it was thicker bone due to more air pockets, so that the face of a Neanderthal would have protruded.

Research from New York University published last week showed that bone deposits continued to build on the faces of Neanderthal children during the first years of their life.

The heavy, thickset brow of the virtual ancestor is characteristic of the hominin lineage, very similar to early Homo as well as Neanderthal, but lost in modern humans. Mounier says the virtual fossil is more reminiscent of Neanderthals overall, but that this is unsurprising as taking the timeline as a whole it is Homo sapiens who deviate from the ancestral trajectory in terms of skull structure.

"The possibility of a higher rate of morphological change in the modern human lineage suggested by our results would be consistent with periods of major demographic change and genetic drift, which is part of the history of a species that went from being a small population in Africa to more than seven billion people today," said co-author Dr Marta Mirazón Lahr, also from Cambridge's LCHES.

The population of last common ancestors was probably part of the species Homo heidelbergensis in its broadest sense, says Mounier. This was a species of Homo that lived in Africa, Europe and western Asia between 700,000 and 300,000 years ago.

For their next project, Mounier and colleagues have started working on a model of the last common ancestor of Homo and chimpanzees. "Our models are not the exact truth, but in the absence of fossils these new methods can be used to test hypotheses for any palaeontological question, whether it is horses or dinosaurs," he said.

Story Source:

The above post is reprinted from materials provided by University of Cambridge. The original story is licensed under a Creative Commons Licence. Note: Materials may be edited for content and length.

Mysterious Species May Have Interbred With Humans
By Nathaniel Scharping | December 18, 2015 3:16 pm

An artist’s depiction of what a member of the Red Deer Cave people may have looked like. (Credit: Peter Schouten)
The history of human evolution keeps getting more complicated.

Researchers this week announced the discovery of a thigh bone that could serve as evidence of a new branch in the our family tree. The femur was dated to around 14,000 years ago, challenging the notion that other species of ancient humans died out after modern humans appeared. Instead, this find suggests that our distant cousins may have co-existed with several other species of hominins for quite some time.

Area Known For Archaeological Finds

The femur was unearthed in Red Deer Cave, which is located near the southwest Chinese city of Maludong. The cave is named after the extinct species of deer the ancient cave’s inhabitants may have once hunted. In 2012, researchers discovered well-preserved skulls with a curious mix of ancient and modern features in the cave. The area around the cave has also produced revolutionary finds, such as the discovery of another possible species earlier this year in the nearby Longlin cave.

Here’s what we know about the cave’s ancient inhabitants: The Red Deer Cave people had prominent brow ridges, no chins and thick skulls, much like Neanderthals, but also possessed frontal lobes reminiscent of modern humans. The odd combination of features suggested to researchers that they had found a completely new species.

“In short, they’re anatomically unique among all members of the human evolutionary tree,” said Darren Curnoe, an evolutionary biologist and a co-author of the study, in an interview with National Geographic.

The discovery of the femur strengthens researchers’ theory that the remains discovered at Red Deer Cave belong to a completely new species. The bone is dated to around the same time period as previous finds in the area, yet looks very similar to bones from Homo habilis, a species that died out 1.5 million years ago.

Debate Still Ongoing

The apparent contradiction has caused controversy among scientists, some of whom argue that the Red Deer Cave people do not, in fact, represent a new species. Instead, they believe that they are simply another variation of modern humans, who have been shown to possess a wide range of features. Difficulties in extracting DNA from the Red Deer Cave bones has made the dispute hard to resolve.

Another theory holds that the Red Deer Cave people are a hybrid of modern humans and a more ancient species, indicating that our ancestors interbred with other species.

Yunnan province, the region of China where the remains were discovered, is also home to other unique species due to its geographic isolation and the presence of natural boundaries such as mountains, valleys and rivers. The Red Deer Cave people could have migrated out of Africa with other hominins two million years ago and remained tucked away in their remote homeland away from other species, allowing them to survive for much longer as a distinct species.

The controversy over the Maludong discovery mirrors the dispute over another human ancestor that likely existed in the same time period, Homo floresienses. Found in 2003 in Indonesia, H. floresienses stood between three and four feet tall and possessed many characteristics that differentiated them from modern humans, such as their lack of a defined chin. At the time of their discovery, there was an intense debate centered on whether they were distinct enough to merit their own species. Today, it is largely accepted that the specimens do make up an entirely new species.

It seems that modern humans had a few contemporaries. Why our species ended up on top is still a measure of some debate, but it is a question worth pondering. If things had gone differently, we all may have ended up looking like this.

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Human-Neanderthal relationships may be at root of modern allergies
Three genes inherited from our Neanderthal cousins may cause modern carriers to have an overly-sensitive immune system susceptible to allergies

The genes are thought to have spread through modern humans when small groups of pioneers who left Africa met and had sex with Neanderthals already long at home in Eurasia.
The genes are thought to have spread through modern humans when small groups of pioneers who left Africa met and had sex with Neanderthals already long at home in Eurasia. Photograph: AFP/Getty Images
Ian Sample Science editor

Passionate encounters between ancient humans and their burly cousins, the Neanderthals, may have left modern people more prone to sneezes, itches and other allergies, researchers say.

The curious legacy comes from three genes that crossed into modern humans after their distant ancestors had sex with Neanderthals, or their close relatives the Denisovans, more than 40,000 years ago.

The prehistoric couplings left all non-Africans today carrying 1-6% of Neanderthal DNA. People whose ancestors never left the continent would not have crossed paths with Neanderthals or the Denisovans, a mysterious group of humans who lived in and around Siberia at the same time.

The three genes are among the most common strands of Neanderthal and Denisovan-like DNA found in modern humans, suggesting they conferred an evolutionary advantage. They probably boosted the immune system, since the genes are involved in the body’s first line of defence against pathogens such as bacteria and fungi.

But people who carry the three genes seem to pay a price in the form of an overly-sensitive immune system. One study by the US genetics company 23andme found that carriers of the genes were more likely to have asthma, hay fever and other allergies.

The genes are thought to have spread through modern humans when small groups of pioneers who left Africa met and had sex with Neanderthals already long at home in Eurasia. Unlike the new arrivals, the Neanderthals had spent 200,000 years adapting to life in the region, and their immune systems had become tuned to the new infections they faced.

“A small group of modern humans leaving Africa would not carry much genetic variation,” said Janet Kelso, who led the research at the Max Planck Institute for evolutionary Anthropology in Leipzig. “You can adapt through mutations, but if you interbreed with the local population who are already there, you can get some of these adaptations for free.”

Kelso’s team scanned the genomes of modern day humans for evidence of Neanderthal or Denisovan genes and then looked at how common they were in people from around the world. Among the three immune system genes that stood out, two closely matched Neanderthal DNA. The most common was found in all non-Africans, the other only in Asians. The third gene was more similar to Denisovan DNA and much rarer, found in only a handful of people from Asia who took part in the study.


Discovery of oldest human DNA in Spanish cave sheds light on evolution
Read more
The findings suggest that modern humans inherited Neanderthal and Denisovan genes in three waves depending on where and when the groups met. The genes proved so beneficial that they remain in our genomes to this day. The study is reported in the American Journal of Human Genetics.

The work is backed up by separate research published in the same journal by scientists at the Pasteur Institute in Paris. Geneticist Lluis Quintana-Murci analysed DNA from participants in the 1000 Genomes Project and compared their DNA with ancient human genomes. He focused specifically on 1500 immune genes and found that most adaptations occurred in the past 6,000 to 13,000 years, when humans shifted from a hunter-gatherer lifestyle to farming.

But Quintana-Murci said the most striking discovery was of the same three genes that Kelso found. In his study, the trio of genes were among the most common Neanderthal or Denisovan DNA found in modern people.

“Interbreeding with archaic humans does indeed have functional implications for modern humans,” Kelso said. “The most obvious consequences have been in shaping our adaptation to our environment - improving how we resist pathogens and metabolise novel foods.”

For all the benefits they bring, the downsides of Neanderthal genes might not be so bad. “They might have increased our susceptibility,” said Kelso. “But I wouldn’t go so far as to say Neanderthals gave us allergies.”

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How Culture Wars May Have Killed Off the Neanderthals

What happened to the Neanderthals? They left their African homes and migrated into Europe 350,000 to 600,000 years ago, well ahead of modern humans, who showed up only about 45,000 years ago. But within about 5,000 years of our arrival, the indigenous Neanderthals had disappeared.

Anthropologists have proposed that they may have been done in by terrible epidemics or an inability to adapt to climate changes of the era, but a new study, published in the Proceedings of the National Academy of Sciences, now suggest culture wars of a sort might have spelled the end.

The researchers came to their conclusion after creating mathematical models that demonstrated that it wasn’t necessary for the humans to outnumber the locals in order to prevail. A smaller band of humans with a more highly developed level of culture could eventually push out the Neanderthals, the models showed.

The edge wasn’t just raw intelligence. Archeological findings have shown that brain size was essentially the same for humans and Neanderthals, and recent paleo-anthropological studies suggest that Neanderthals were capable of a range of advanced intellectual behaviors typically associated with early modern humans.

But a more fully developed culture among humans could have led to being able to gather territory or hunt over a larger area, or a higher level of tool-making. And better tools probably meant better weapons.

“Presumably there was a lot of violence going on at that time,” says Marcus Feldman, professor of in the School of Humanities and Sciences at Stanford University. “I assume it wasn’t only constructive things done with tools. A hand axe can be used for constructive purposes and destructive purposes.”

Looking at the results of the modeling, the researchers concluded that a small population of humans with a high level of sophistication could have overwhelmed a larger, established population of Neanderthals that had been getting by with a lower level of cultural sophistication.

And the rich probably got richer in some sense, because a growing population of humans could support a higher level of cultural sophistication. The modeling also suggests then that it was not necessarily a genetic mutation that changed the human brain and provided a leg up for humans over Neanderthals, as has been suggested, Feldman says.

“They are presumably the last close relatives to us, before humans dominated the world.”

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Your Neanderthal inheritance could affect your mood, your skin and your smoking habits
Neanderthal legacy
A new study finds Neanderthal DNA influences many physical traits in people of Eurasian heritage. (Michael Smeltzer / Vanderbilt University)
Deborah Netburn
It's been 40,000 years since the Neanderthals disappeared, but their lingering genetic legacy may be influencing your health.

If you are of Asian or European descent, about 2% of your genome came from your Neanderthal ancestors, scientists say. Now, new evidence suggests this inheritance affects a broad range of health disorders including skin disease, your ability to fight infection and even your risk of addiction and depression.

"Some of the associations we found made a lot of sense when we saw them, but the ones that affected neurological and psychiatric traits -- those were surprising," said Tony Capra, a computational geneticist at Vanderbilt University in Nashville who oversaw the research.

About 50,000 years ago, the anatomically modern humans who left Africa encountered Neanderthal settlements somewhere in the Middle East, scientists believe. The question of whether the two groups interbred was debated in scientific circles for decades, until 2010 when researchers found clear evidence of Neanderthal DNA sequences in people alive today.

Since then, genetic archaeologists have been trying to determine what instructions these Neanderthal genes contain code for and why they have been preserved over so many millenniums.

The new study, published Thursday in the journal Science, is based on data collected by the eMerge network, which includes the medical records and matching DNA sequences of 28,000 people in the U.S. The researchers also worked with a previously published map of all the places where genetic variants derived from Neanderthals had been found in the human genome.

Armed with these two data sets, the team analyzed each of the 28,000 individuals in the consortium and determined whether they had the signatures of Neanderthal DNA in any of the known spots on the genome. Then, they looked for patterns that would indicate whether having these Neanderthal variants meant a person was more or less likely to have been diagnosed with a specific disease.

It stands to reason that the Neanderthal versions of genes would function differently from their modern human counterparts. After all, Neanderthals had been living in northern latitudes for thousands of years before anatomically modern humans arrived, giving the Neanderthals plenty of time to adapt to the unique environment and its pathogens.

Most geneticists believe that at least some of the Neanderthal DNA variants that remain in the human genome were able to spread because they provided some advantage to our ancestors after they left Africa.

"We know when you move a population into a new environment, the bodily systems that are involved directly with that environment are most likely to change quickly," Capra said.

Indeed, the strongest signal the researchers found involved a Neanderthal variant that improves the blood's ability to clot, or coagulate. Today, too much clotting is considered a disorder because it increases risk of stroke, pulmonary embolisms and pregnancy complications, but tens of thousands of years ago, this hypercoagulation might have served our ancestors well.

"Coagulation is one of the first immune responses the body has to a wound," Capra said. A clot not only stops bleeding, it also sends messages to the immune system "to join the fight against pathogens."

He added that the ability to form a scab quickly would have been useful for keeping unfamiliar germs out of the body.

The researchers also discovered an association between Neanderthal versions of genes and keratosis, which are skin lesions that can form after too much exposure to the sun. Keratosis is caused by a dysfunction in a type of cell called a keratinocyte that protects the skin from UV radiation. However, in the low-light conditions of the north, this mistake might have allowed more light to reach the skin, enhancing the production of vitamin D, Capra said.

Some of the findings were more difficult to explain. For example, the study authors wrote that Neanderthal variants were associated with an increased risk of mood disorders, tobacco addiction and a relatively strong effect on depression.

If you are picturing hopeless Neanderthals wandering around in a cloud of cigarette smoke, don't.

"It's very hard to project backwards," said Joshua Akey, a professor of genome sciences at the University of Washington in Seattle and a co-author on the study. "It's hard to know what the consequences of having that variation 40,000 years ago might have been."

Still, the idea that neurological and psychiatric traits are influenced by Neanderthal DNA is one of the most intriguing conclusions of the study, said Rasmus Nielsen, who studies evolutionary theory and genetics at UC Berkeley.

"That is interesting because it suggests that there were more differences in those traits between humans and Neanderthals than in other traits, suggesting perhaps that we are somewhat cognitively differentiated from Neanderthals," Nielsen said in a statement.

The researchers also found that Neanderthal DNA variants had a subtle but real association with disorders including obesity, respiratory infections, and the hardening of the arteries known as coronary atherosclerosis. However, in these cases the Neanderthal variants account for less than 1% of the overall risk.

That may not sound like a lot, but it's significant, said Dr. Gail Jarvik, head of the Division of Medical Genetics at the University of Washington and an author on the paper.

"We now know that Neanderthal variants tweak your risk of certain disorders," she said.

At the same time, she noted that it's possible we acquired some good traits from our Neanderthal relatives.

"We looked at associations with diseases, not associations with getting along with people or other traits," she said.

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Mysterious Cave Rings Show Neanderthals Liked To Build

May 26, 20165:00 AM ET

CHRISTOPHER JOYCE

Researchers found numerous ring-like structures inside France's Bruniquel Cave. They believe they were built by Neanderthals some 176,000 years ago.
Etienne FABRE - SSAC
Here's a mystery found in a French cave. It appears that a group of Neanderthals walked into that cave about 176,000 years ago and started building something. Neanderthals were our closest living relatives but they weren't known as builders or cave explorers.

Scientists identify the forms as "constructions," but they can't figure out what they were for.

It was in 1990 when a French archaeologist first ventured deep into Bruniquel Cave in southwestern France. Spelunkers had just broken through the entrance, which apparently had been obstructed for millennia. The archaeologist traveled deep into the cave, over 1,000 feet. There he discovered something strange — someone had broken stalagmites from the floor and arranged them in two large ovals. But he died before he could fully explore the site.

Twenty-three years later, in 2013, a crew of scientists managed to get back to the site. Geologist Dominique Genty with France's National Center for Scientific Research (CNRS) was there.

"It was very strange," he says, "it was kind of obvious that it was not natural."

The team found the circles of stone spikes, almost like 2-foot-high fences. But they found more than the original discoverer. There were more stone fragments lying in piles nearby. It was like a huge Lego set, a Neanderthal Lego set, because all of this calcite stone dated back 176,000 years — long before modern humans arrived in Europe.

Writing in the journal Nature, the team says it's the most complex Neanderthal structure ever found. "We know now," says Genty, "that they were able to make a sort of elaborate construction," more elaborate than anything Neanderthals had been known to make.

A 3D reconstruction shows the structures built inside the cave.

Xavier Muth/Pascal Mora
Why did they build it?

There are only clues. For example, the stalagmite pieces all showed signs of being burned. Was it a ritual? Or perhaps it was a sort of fireplace, to warm them or maybe to repel cave bears. Genty says no one knows.

Then there's the location, more than 1,000 feet from the cave entrance. Archaeologist Marie Soressi with Leiden University in the Netherlands is a Neanderthal expert and says that's astonishing.

"What is most surprising for me is that this discovery is showing that Neanderthals ventured underground and far away from any source of natural light," says Soressi. While Neanderthals no doubt took shelter in caves, they were never to known to go that deep, so far from light.

The scientists found pieces of burned animal bone at the site, which they think could have been used as torches because the fatty interior of bone burns.

Soressi points out that recent discoveries keep stoking the argument that Neanderthals were in fact not dumb throwbacks compared to modern humans. "I think ... we have by now many different lines of evidence to show that Neanderthals, and even Neanderthals 200,000 years ago, had cognitive abilities not so different from our direct ancestors."

[NeonLX]

"What is most surprising for me is that this discovery is showing that Neanderthals ventured underground and far away from any source of natural light," says Soressi. While Neanderthals no doubt took shelter in caves, they were never to known to go that deep, so far from light.

The scientist says from his comprehensive observations via a WABAC machine set to the Neanderthal era.

[Pele'sDaughter]

My bet is on an event such as this:

https://en.wikipedia.org/wiki/Near-Earth_supernova

[Iamwhomiam]

Ooo... Galactic Warming!

[seemslikeadream]

Inbred Neanderthals left humans a genetic burden
Non-African human populations today have marginally lower fitness thanks to Neanderthal inheritance
Date:
June 6, 2016
Source:
Genetics Society of America
Summary:
The Neanderthal genome included harmful mutations that made the hominids around 40 percent less reproductively fit than modern humans, according to new estimates. Non-African humans inherited some of this genetic burden when they interbred with Neanderthals, though much of it has been lost over time. The results suggest that these harmful gene variants continue to reduce the fitness of some populations today. The study also has implications for management of endangered species.

The Neanderthal genome included harmful mutations that made the hominids around 40% less reproductively fit than modern humans, according to estimates published in the latest issue of the journal Genetics. Non-African humans inherited some of this genetic burden when they interbred with Neanderthals, though much of it has been lost over time. The results suggest that these harmful gene variants continue to reduce the fitness of some populations today. The study also has implications for management of endangered species.

"Neanderthals are fascinating to geneticists because they provide an opportunity to study what happens when two groups of humans evolve independently for a long time--and then come back together," says study leader Kelley Harris, of Stanford University. "Our results suggest that inheriting Neanderthal DNA came at a cost."

Previous studies of DNA extracted from Neanderthal remains revealed that these Eurasian hominids were much more inbred and less genetically diverse than modern humans. For thousands of years, the Neanderthal population size remained small, and mating among close relatives seems to have been common.

Then, 50,000-100,000 years ago, groups of anatomically modern humans left Africa and moved to the homelands of their distant Neanderthal cousins. The two groups interbred, mingling their previously distinct genomes. But though a small fraction of the genome of non-African populations today is Neanderthal, their genetic contribution is uneven. Neanderthal sequences are concentrated in certain parts of the human genome, but missing from other regions.

"Whenever geneticists find a non-random arrangement like that, we look for the evolutionary forces that caused it," says Harris.

Harris and her colleague Rasmus Nielsen (University of California, Berkeley / University of Copenhagen) hypothesized that the force in question was natural selection. In small populations, like the Neanderthals', natural selection is less effective and chance has an outsized influence. This allows weakly harmful mutations to persist, rather than being weeded out over the generations. But once such mutations are introduced back into a larger population, such as modern humans, they would be exposed to the surveillance of natural selection and eventually lost.

To quantify this effect, Harris and Nielsen used computer programs to simulate mutation accumulation during Neanderthal evolution and to estimate how humans were affected by the influx of neanderthal genetic variants. The simulations incorporated data on the mutation rates, genome properties, and population dynamics of hominids.

The results suggest that Neanderthals carried many mutations with mild, but harmful effects. The combined effect of these weak mutations would have made Neanderthals at least 40% less fit than humans in evolutionary terms--that is, they were 40% less likely to reproduce and pass on their genes to the next generation.

Related conclusions were reached in an independent study that used very different methods, led by Ivan Juric at the University of California, Davis. This work is currently being peer reviewed and is available at the pre-publication preprint server bioRxiv.

Harris and Nielsen's simulations also suggest that humans and Neanderthals mixed much more freely than originally thought. Today, Neanderthal sequences make up approximately 2% of the genome in people from non-African populations. But Harris and Nielsen estimate that at the time of interbreeding, closer to 10% of the human migrants' genome would have been Neanderthal. Because there were around ten times more humans than Neanderthals, this number is consistent with the two groups acting as as single population that interbred at random. Recent DNA evidence has confirmed that the Neanderthal contribution to Eurasian genomes was higher in the past.

Although most of the harmful mutations bequeathed by our Neanderthal ancestors would have been lost within a few generations, a small fraction likely persists in people today. Harris and Nielsen estimate that non-Africans may have historically had approximately 1% lower reproductive fitness due to their Neanderthal heritage. This is in spite of the small number of Neanderthal gene variants thought to be beneficial today, including genes related to immunity and skin color.

The results also have implications for conserving endangered species. Many vulnerable populations in fragmented habitats face similar genetic problems to the Neanderthals: inbreeding, low genetic diversity, and accumulation of harmful mutations. One management strategy for overcoming these problems is genetic rescue--improving the health of an inbred population by outcrossing it with other populations.

"Genetic rescue is designed to move gene variants from an outbred population to an inbred population," says Harris. "Our results suggest managers must ensure that this movement only goes one way; otherwise harmful mutations from the inbred population may lower the fitness of the outbred group."

[NeonLX]

^^^^Maybe that's why I have such shitty teeth.

[seemslikeadream]

The Neanderthal in the Mirror
Our evolutionary cousin is no longer a blundering caveman. Recent research has painted a picture of a human ancestor with culture, art, and advanced cognitive skills.

By Lydia Pyne | August 1, 2016

On August 3, 1908, the first near-complete Neanderthal skeleton was discovered in a cave near the village of La Chapelle-aux-Saints in south central France, during a survey of the region’s Paleolithic archaeological sites.

For decades prior, prehistorians had collected bits and pieces of curious but not-quite-human fossils from museums and excavations alike—the odd skull here, a scrap of tooth there. In 1863, the mélange of bones was finally given its own species designation, Homo neanderthalensis. Forty-five years later, the La Chapelle discovery was the first Neanderthal specimen found in an original archaeological context and the first to be expertly excavated and carefully studied. Because the body was arranged in a flexed, fetal position and carefully placed in the floor of the cave, excavators argued that fossil—nicknamed the Old Man—had been purposefully buried by his Neanderthal contemporaries.

More than any other single individual, the Old Man of La Chapelle has shaped the way that science and popular culture have thought about Neanderthals. But why? What is it about this Neanderthal’s story that is so special? In short, the Old Man was the right fossil found at the right time. He was—and still is—offered as a key bit of evidence in debates about evolution and human origins. He quickly became a scientific touchstone, an archetype for how science and popular culture create celebrity fossils. I explore the stories of similarly spectacular paleoanthropological finds in my new book Seven Skeletons: The Evolution of the World’s Most Famous Human Fossils.

Once they had excavated the fossil, the discoverers sent the Old Man remains to Marcellin Boule, an eminent expert in human evolution at the Muséum National d’Histoire Naturelle in Paris, for careful study. Boule spent two years examining the fossil, and his initial analysis of the La Chapelle Neanderthal would shape the perception of our evolutionary cousins for a hundred years—preconceptions that contemporary archaeologists and paleoanthropologists are doing their utmost to counter.

Boule concluded that Neanderthals were sad specimens of nature. He argued that the species was stooped in its posture and stunted in its culture. Boule’s conclusions quickly turned into the pop-culture caricature that we tend to associated with the Neanderthal species. The image of a hunched, cave-dwelling lout barely capable of brandishing a club quickly caught the public’s imagination in the early 20th century thanks, in no small part, to the portrayal of Neanderthals in museums and in the press. (How could a creature so primitive as a Neanderthal, the logic went, have something as complex as a culture that involved burying the dead?) It was no wonder, Boule’s work implied, that the species went extinct, especially compared with the superior Homo sapiens.

The conclusions Boule drew from his analysis of the La Chapelle skeleton couldn’t have been more wrong.

Today, we’re rather used to the idea that Neanderthals had a vibrant culture, but science and society’s acceptance of each new piece of the Neanderthal story is an uphill battle, thanks to the Old Man’s early days in the public’s eye. We now have archaeological evidence that Neanderthals built structures; that they had sophisticated hunting strategies, fire-starting technologies, and art; and, of course, that they buried their dead. Analyses of Neanderthal DNA show us more and more similarities between ourselves and Neanderthals, with every indication that modern humans and Neanderthals interbred in their evolutionary history. Every “human” behavior we can claim to separate ourselves from our Pleistocene relatives, we eventually find in Neanderthals, blurring the line between human and not.

Decades of researchers have studied the Old Man since Boule’s original analysis. Every new iteration of the Neanderthal’s story humanizes him, turning the fossil from a dim troglodyte into a dignified paleo patriarch. The more we study the Old Man, the more the differences between our species melt away.

Tolerance of smoke may have given us an edge over Neanderthals
People around a campfire
Not healthy in a cave, especially not for Neanderthals

By Colin Barras

Where there’s fire there’s often smoke – which might have been bad news for Neanderthals and other ancient hominins. Modern humans carry a genetic mutation that reduces our sensitivity to cancer-causing chemicals found in wood smoke. But Neanderthals and Denisovans apparently lacked the mutation.

Harnessing fire was one of the key events in hominin prehistory. Fire offered light, warmth, better protection from predators and the possibility of easier-to-digest cooked food. But smoke is something to be wary of. “Even today, smoke inhalation increases susceptibility to lung infections,” says Gary Perdew at Pennsylvania State University.

It might have been a significant problem during the Stone Age, given that hominins often lighted fires in caves or other enclosed areas. “If you were in a cave trying to cook, the amount of smoke you’d breathe in would be ridiculous,” says Perdew.

Our species, Homo sapiens, might have been particularly well suited to those conditions, though. Perdew and his colleagues looked at the genomes of three Neanderthals and a Denisovan, and compared them with genomes from living people and one member of our species who lived 45,000 years ago.

The researchers found that this ancient member of our species already carried a mutation not seen in either Neanderthals or Denisovans. It occurs in the AHR gene, which produces a receptor that helps regulate our response to carcinogenic polycyclic aromatic hydrocarbons often found in wood smoke.

Toxic effect
The team inserted human and Neanderthal versions of the AHR gene into animal cells in the lab and examined how the cells responded when exposed to these carcinogens. The Neanderthal version proved to be far more likely to cause the production of enzymes that induce a toxic effect.

“We were surprised that the differences between the two were so large,” says Perdew. For some compounds there was a 1000-fold difference in the toxic response.

That raises the intriguing idea that, at some point in the past, our species picked up the AHR mutation and so became far better than other hominins at coping with the toxic effects of wood smoke. But Perdew stresses this is only a possibility.

“There’s no evidence I can point to that says if hominins didn’t have this mutation, they would have died of respiratory infection,” he says. “There are no Neanderthals around to explore the idea.”

Perdew and his colleagues are now engineering mice to carry the human form of AHR. “In the long run it would be nice to have a mouse with the Neanderthal version too. Then we could run some smoke-inhalation studies,” he says.

Last year, Karen Hardy at the Autonomous University of Barcelona in Spain and her colleagues found flecks of charcoal in deposits scraped from ancient hominin teeth at Qesem Cave in Israel. Their presence is consistent with the idea that the hominins there inhaled smoke from their fires.

“Qesem Cave was a place where natural features of the cave likely helped to limit the effects of smoke,” Hardy says – fires were set beneath a natural “chimney” that would draw most smoke away. But even so, the hominins clearly were exposed to smoke pollution. “The detrimental effects of smoke inhalation known about today could have been disastrous for them in terms of survival and reproduction,” says Hardy.

[NeonLX]

Dang. I was thinking it would be a blast to do a few bowls with one of my Neanderthal cousins. Maybe brownies would be a better choice.

[Nordic]

Interesting. Maybe I've got more Neanderthal and Desovian DNA in me because I have an extremely low tolerance to smoke.