Author Topic: Neanderthals in the News  (Read 4695 times)

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Neanderthals in the News
« on: November 10, 2015, 04:47:35 PM »
If the old thread with the same name ever re-surfaces, I'll merge it with this one. Meanwhile, two new papers from different teams have (possibly, since these results are provisional at the moment) very similar things to tell us about how modern non-African humans came to have the particular level of contribution from the Neanderthal genome that we see.

"How Admixture with Neanderthals May Have Affected Human Populations" | Social Evolution Forum/The Evolution Institute


Modern Homo sapiens skull faces Homo neanderthalensis skull

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One of the most fascinating aspects of the human genome is what it reveals about our enigmatic extinct siblings, the Neanderthals. Two bioRxiv preprints (Harris and Nielsen, and Juric et al.) out just this week have given us new insights into the effects of Neanderthal admixture on ancient Homo sapiens populations, with implications for the phylogenetic relationships between the two hominins. Even though these are still provisional findings, I think they’re significant enough to warrant discussion in an evolution forum, and I’m delighted to write my first post here about them.

In case you’re not up to date on the latest Neanderthal research, a bit of background is in order. The latest estimates indicate that Neanderthals and humans likely shared a last common ancestor sometime between 550-765 kya. From the sequencing of Neanderthal mitochondrial and nuclear genomes, we’ve learned that as modern humans spread out of Africa there was subsequent hybridization between human and Neanderthal groups in Europe and Asia resulting in varying degrees (~2-4%) of Neanderthal ancestry among contemporary non-African populations. We have also learned that Neanderthal populations were quite small, maintaining an effective population size of just ~1,000 for about 400,000 years (see reference list at the end of this post for citations and further reading).

How did admixture with Neanderthals affect human populations? Some of the alleles from Neanderthal populations appear to provide an adaptive advantage to non-Africans, particularly those for hair and skin color. However, these are only a tiny fraction of Neanderthal-derived alleles. There are large, conserved swathes of the human genome where Neanderthal ancestry appears to be depleted, implying that there is selection against the majority of Neanderthal-derived functional alleles. But what does this selection mean for our evolutionary history? Was it due to hybrid incompatibility between the Neanderthals and humans? Or were those alleles also deleterious in Neanderthals?

[Continues . . .]
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Re: Neanderthals in the News
« Reply #1 on: November 10, 2015, 09:17:04 PM »
A lot of prior knowledge is needed to completely understand this, and there was one word, introgression, the meaning of which I could only vaguely infer from the context. However, it has become clearer on second reading, and it is fascinating that two approaches have reached similar conclusions. I watch this space in anticipation of further research.
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Re: Neanderthals in the News
« Reply #2 on: January 07, 2016, 11:50:18 PM »
Some good and some not so good from our beetle-browed relatives.

"Neanderthal genes gave modern humans an immunity boost, allergies" | Science Daily

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When modern humans met Neanderthals in Europe and the two species began interbreeding many thousands of years ago, the exchange left humans with gene variations that have increased the ability of those who carry them to ward off infection. This inheritance from Neanderthals may have also left some people more prone to allergies.

The discoveries reported in two independent studies in the American Journal of Human Genetics on January 7 add to evidence for an important role for interspecies relations in human evolution and specifically in the evolution of the innate immune system, which serves as the body's first line of defense against infection.

[Continues . . .]
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Re: Neanderthals in the News
« Reply #3 on: January 08, 2016, 06:12:08 AM »
What a really interesting read!  Thank you so much for sharing it with us.
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Re: Neanderthals in the News
« Reply #4 on: February 17, 2016, 09:19:25 PM »
What a really interesting read!  Thank you so much for sharing it with us.

You're welcome, Bluenose:)

* * *

More about the good and bad that come from Neanderthal genetic contributions: "Our hidden Neandertal DNA may increase risk of allergies, depression" | Science

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Depressed? Your inner Neandertal may be to blame. Modern humans met and mated with these archaic people in Europe or Asia about 50,000 years ago, and researchers have long suspected that genes picked up in these trysts might be shaping health and well-being today. Now, a study in the current issue of Science details their impact. It uses a powerful new method for scanning the electronic health records of 28,000 Americans to show that some Neandertal gene variants today can raise the risk of depression, skin lesions, blood clots, and other disorders.

Neandertal genes aren’t all bad. “These variants sometimes protect against a disease, sometimes make people more susceptible to disease,” says paleogeneticist Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. Two other new studies identified three archaic genes that boost immune response. And most archaic genes that persist in humans were likely beneficial in prehistoric times. But some now cause disease because modern lifestyles and environments are so different.

[Continues . . .]
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Re: Neanderthals in the News
« Reply #5 on: February 18, 2016, 11:18:02 AM »
The mixing of early anatomically modern humans (AMH) with Neanderthals means that the genetic contributions went both ways. A paper published online yesterday presents evidence of AMH contribution to a Neanderthal genome. This interbreeding occurred much earlier than any previously discovered.

"Early gene flow from modern humans into Neanderthals" | EurekAlert

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Scenario of interbreeding between modern humans and Neanderthals: Neanderthal DNA in present-day humans outside Africa originates from interbreeding that occurred 47,000 - 65,000 years ago (green arrow). Modern human DNA in Neanderthals is likely a consequence of earlier contact between the two groups roughly 100,000 years ago (red arrow). Image Credit: Ilan Gronau

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Using several different methods of DNA analysis, an international research team has identified an interbreeding event between Neanderthals and modern humans that occurred an estimated 100,000 years ago, which is tens of thousands of years earlier than other such events previously documented. They suggest that some modern humans left Africa early and mixed with Neanderthals. These modern humans later became extinct and are therefore not among the ancestors of present-day people outside Africa who left Africa about 65,000 years ago.

"We knew from Neanderthal DNA found in the genomes of humans outside Africa that Neanderthals and humans have interbred. This interbreeding is estimated to have happened less than 65,000 years ago, around the time that modern human populations spread across Eurasia from Africa. We now find evidence for a modern human contribution to the Neanderthal genome. This is likely the result of much earlier interbreeding", says Sergi Castellano from the Max Planck Institute for Evolutionary Anthropology, who co-led the study.

[Continues . . .]

The full paper is available for free from Nature: "Ancient gene flow from early modern humans into Eastern Neanderthals" | Nature

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Re: Neanderthals in the News
« Reply #6 on: March 16, 2016, 10:49:36 PM »
Another intriguing discovery about Neanderthal genetics comes from the ancient bones found in the Sima de los Huesos ("pit of bones") in Spain, which was mentioned in the previous thread on this topic because of the possible evidence of prehistoric murder found there.

The abstract of the paper in Nature:

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A unique assemblage of 28 hominin individuals, found in Sima de los Huesos in the Sierra de Atapuerca in Spain, has recently been dated to approximately 430,000 years ago. An interesting question is how these Middle Pleistocene hominins were related to those who lived in the Late Pleistocene epoch, in particular to Neanderthals in western Eurasia and to Denisovans, a sister group of Neanderthals so far known only from southern Siberia. While the Sima de los Huesos hominins share some derived morphological features with Neanderthals, the mitochondrial genome retrieved from one individual from Sima de los Huesos is more closely related to the mitochondrial DNA of Denisovans than to that of Neanderthals. However, since the mitochondrial DNA does not reveal the full picture of relationships among populations, we have investigated DNA preservation in several individuals found at Sima de los Huesos. Here we recover nuclear DNA sequences from two specimens, which show that the Sima de los Huesos hominins were related to Neanderthals rather than to Denisovans, indicating that the population divergence between Neanderthals and Denisovans predates 430,000 years ago. A mitochondrial DNA recovered from one of the specimens shares the previously described relationship to Denisovan mitochondrial DNAs, suggesting, among other possibilities, that the mitochondrial DNA gene pool of Neanderthals turned over later in their history.

Press release: "Analysis of nuclear DNA from Sima de los Huesos hominins provides evidence of their relationship to Neanderthals" | ScienceDaily

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Previous analyses of the hominins from Sima de los Huesos in 2013 showed that their maternally inherited mitochondrial DNA was distantly related to Denisovans, extinct relatives of Neanderthals in Asia. This was unexpected since their skeletal remains carry Neanderthal-derived features. Researchers of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, have since worked on sequencing nuclear DNA from fossils from the cave, a challenging task as the extremely old DNA is degraded to very short fragments. The results now show that the Sima de los Huesos hominins were indeed early Neanderthals. Neanderthals may have acquired different mitochondrial genomes later, perhaps as the result of gene flow from Africa.

Until now it has been unclear how the 28 400,000-year-old individuals found at the Sima de los Huesos ("pit of bones") site in Northern Spain were related to Neanderthals and Denisovans who lived until about 40,000 years ago. A previous report based on analyses of mitochondrial DNA from one of the specimens suggested a distant relationship to Denisovans, which is in contrast to other archaeological evidence, including morphological features that the Sima de los Huesos hominins shared with Neanderthals.

[Continues . . .]

. . . And an article about this find: "Oldest ever human genome sequence may rewrite human history" | New Scientist

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The oldest ever human nuclear DNA to be reconstructed and sequenced reveals Neanderthals in the making – and the need for a possible rewrite of our own origins.

The 430,000-year-old DNA comes from mysterious early human fossils found in Spain’s Sima de los Huesos, or “pit of bones”.

[. . .]

The results suggest they are more closely related to ancestors of Neanderthals than those of Denisovans – meaning the two groups must have diverged by 430,000 years ago. This is much earlier than the geneticists had expected.

It also alters our own timeline. We know that Denisovans and Neanderthals shared a common ancestor that had split from our modern human lineage. In light of the new nuclear DNA evidence, Meyer’s team suggests this split might have happened as early as 765,000 years ago.

[Continues . . .]
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Re: Neanderthals in the News
« Reply #7 on: April 10, 2016, 07:08:10 PM »
A new study shows that the Y chromosome of Neanderthal appears to have left no trace in anatomically modern humans (AMH). There are a few hypotheses that have been advanced to explain this, including the possibility that there were some genes in their Y chromosome that were incompatible with AMH.

"Missing Y chromosome kept us apart from Neanderthals" | New Scientist

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Modern humans diverged from Neanderthals some 600,000 years ago – and a new study shows the Y chromosome might be what kept the two species separate.

It seems we were genetically incompatible with our ancient relatives – and male fetuses conceived through sex with Neanderthal males would have miscarried. We knew that some cross-breeding between us and Neanderthals happened more recently – around 100,000 to 60,000 years ago.

Neanderthal genes have been found in our genomes, on X chromosomes, and have been linked to traits such as skin colour, fertility and even depression and addiction. Now, an analysis of a Y chromosome from a 49,000-year-old male Neanderthal found in El Sidrón, Spain, suggests the chromosome has gone extinct seemingly without leaving any trace in modern humans.

This could simply be because it drifted out of the human gene pool or, as the new study suggests, it could be because genetic differences meant that hybrid offspring who had this chromosome were infertile – a genetic dead end.

[Continues . . .]

The abstract of the paper, which is available for free at the link:

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Sequencing the genomes of extinct hominids has reshaped our understanding of modern human origins. Here, we analyze ∼120 kb of exome-captured Y-chromosome DNA from a Neandertal individual from El Sidrón, Spain. We investigate its divergence from orthologous chimpanzee and modern human sequences and find strong support for a model that places the Neandertal lineage as an outgroup to modern human Y chromosomes—including A00, the highly divergent basal haplogroup. We estimate that the time to the most recent common ancestor (TMRCA) of Neandertal and modern human Y chromosomes is ∼588 thousand years ago (kya) (95% confidence interval [CI]: 447–806 kya). This is ∼2.1 (95% CI: 1.7–2.9) times longer than the TMRCA of A00 and other extant modern human Y-chromosome lineages. This estimate suggests that the Y-chromosome divergence mirrors the population divergence of Neandertals and modern human ancestors, and it refutes alternative scenarios of a relatively recent or super-archaic origin of Neandertal Y chromosomes. The fact that the Neandertal Y we describe has never been observed in modern humans suggests that the lineage is most likely extinct. We identify protein-coding differences between Neandertal and modern human Y chromosomes, including potentially damaging changes to PCDH11Y, TMSB4Y, USP9Y, and KDM5D. Three of these changes are missense mutations in genes that produce male-specific minor histocompatibility (H-Y) antigens. Antigens derived from KDM5D, for example, are thought to elicit a maternal immune response during gestation. It is possible that incompatibilities at one or more of these genes played a role in the reproductive isolation of the two groups.
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Re: Neanderthals in the News
« Reply #8 on: April 20, 2016, 12:06:47 AM »
A new paper describes one of the ways that anatomically modern humans may have been involved in the extinction of Neanderthals: by giving them nasty new bugs.

"Neanderthals may have been infected by diseases carried out of Africa by humans" | Phys.org

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A new study suggests that Neanderthals across Europe may well have been infected with diseases carried out of Africa by waves of anatomically modern humans, or Homo sapiens. As both were species of hominin, it would have been easier for pathogens to jump populations, say researchers. This might have contributed to the demise of Neanderthals.

Researchers from the universities of Cambridge and Oxford Brookes have reviewed the latest evidence gleaned from pathogen genomes and DNA from ancient bones, and concluded that some infectious diseases are likely to be many thousands of years older than previously believed.


[Continues . . .]

A pre-print version of the full paper is available for free: "Neanderthal Genomics Suggests a Pleistocene TimeFrame for the First Epidemiologic Transition" | American Journal of Physical Anthropology (PDF)
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Re: Neanderthals in the News
« Reply #9 on: April 20, 2016, 01:56:41 AM »
That's how we got rid of Native Americans - with smallpox and other bugs. Effective strategy.

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Re: Neanderthals in the News
« Reply #10 on: May 26, 2016, 06:30:23 AM »
Our robust cousins of old built circles of broken off stalagmites deep inside a cave.


Image Credit: Ettienne Fabre - SSAC

"Neanderthals built cave structures — and no one knows why" | Nature

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Neanderthals built one of the world’s oldest constructions — 176,000-year-old semicircular walls of stalagmites in the bowels of a cave in southwest France. The walls are currently the best evidence that Neanderthals built substantial structures and ventured deep into caves, but researchers are wary of concluding much more.

“The big question is why they made it,” says Jean-Jacques Hublin, a palaeoanthropologist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany who was not involved in the study, which is published online in Nature on 25 May 1. “Some people will come up with interpretations of ritual or religion or symbolism. Why not? But how to prove it?”

Speleologists first discovered the structures in Bruniquel Cave in the early 1990s. They are located about a third of a kilometre from the cave entrance, through a narrow passage that at one point requires crawling on all fours. Archaeologists later found a burnt bone from an herbivore or cave bear nearby and could detect no radioactive carbon left in it — a sign that the bone was older than 50,000 years, the limit of carbon dating. But when the archaeologist leading the excavation died in 1999, work stopped.

[Continues . . .]
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Re: Neanderthals in the News
« Reply #11 on: July 09, 2016, 05:47:08 PM »
A new paper presents some fairly strong evidence from a cave in Belgium of cannibalism by Neanderthals.

There is a press release that can be found at ScienceDaily: ("Cannibalism among late Neanderthals in northern Europe"). That brief article doesn't answer the question that came to my mind--how do we know that it was Neanderthals butchering Neanderthals, and not early anatomically modern humans butchering Neanderthals? The full paper is available for free, however: "Neandertal cannibalism and Neandertal bones used as tools in Northern Europe" | Scientific Reports. The authors of the paper say that there is no evidence of anatomically modern humans being in the area of the cave at the time.

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Re: Neanderthals in the News
« Reply #12 on: August 09, 2016, 05:37:52 AM »
A couple of recent stories, neither one of which is particularly solid, but I guess most of you know by now that I have an interest in anything to do with this branch of the family tree:

"Neanderthal skulls and brains may have developed just like ours" | New Scientist

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Evidence from Neanderthals’ skulls suggests that their large brains grew in the same way as ours do. That in turn suggests that Neanderthals were perhaps not so cognitively different from us – although not everyone agrees with this interpretation.

We know that Neanderthal brains were roughly the same size as ours, making them the largest among all known extinct human species. To get a sense for how they grew over an individual’s life, Christoph Zollikofer at the University of Zurich, Switzerland, and his colleagues looked at 15 Neanderthal skulls. Six belonged to adults and nine to children; the youngest was an individual who died just weeks after birth, the oldest a child who died aged roughly 12.

Using software, they generated 3D casts of the brain case – effectively allowing them to study changes in the rough shape of the Neanderthal brain through childhood. They then compared the findings with patterns of brain development in modern children.

The team found evidence that at birth, Neanderthal brains were subtly but significantly longer, wider and flatter than modern human brains. Subsequently, though, the Neanderthal brain developed rather like ours: certain regions, including the cerebellum, expanded quickly during childhood and then became some of the slowest-growing areas in early adulthood.

[Continues . . .]

Later in the story, we learn that a different study using some of the same specimens produced different results, and so putting too much weight on this later study may not be justified.

* * *

For those interested in the development of clothing:

"Ice age fashion showdown: Neanderthal capes versus human hoodies" | New Scientist

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An analysis of animal remains at prehistoric hominin sites across Europe suggests modern humans clad themselves in snug, fur-trimmed clothing, while Neanderthals probably opted for simple capes.

Even so, the finding suggests our extinct cousin was far more sophisticated than once thought.

[Continues . . .]

"Religion is fundamentally opposed to everything I hold in veneration — courage, clear thinking, honesty, fairness, and above all, love of the truth."
— H. L. Mencken


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Re: Neanderthals in the News
« Reply #13 on: August 23, 2016, 04:05:19 AM »
There seems to be evidence that schizophrenia appeared in anatomically modern humans after we diverged from the Neandertals.

"Schizophrenia emerged after humans diverged from Neanderthals" | ScienceDaily

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Schizophrenia poses an evolutionary enigma. The disorder has existed throughout recorded human history and persists despite its severe effects on thought and behavior, and its reduced rates of producing offspring. A new study in Biological Psychiatry may help explain why-comparing genetic information of Neanderthals to modern humans, the researchers found evidence for an association between genetic risk for schizophrenia and markers of human evolution.

"This study suggests that schizophrenia is a modern development, one that emerged after humans diverged from Neanderthals," said John Krystal, Editor of Biological Psychiatry. "It suggests that early hominids did not have this disorder."

The cause of schizophrenia remains unknown, but researchers know that genetics play a significant role in the development. According to senior author Ole Andreassen from the University of Oslo in Norway and University of California, San Diego, some think that schizophrenia could be a "side effect" of advantageous gene variants related to the acquisition of human traits, like language and complex cognitive skills, that might have increased our propensity to developing psychoses.

[Continues . . .]
"Religion is fundamentally opposed to everything I hold in veneration — courage, clear thinking, honesty, fairness, and above all, love of the truth."
— H. L. Mencken


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Re: Neanderthals in the News
« Reply #14 on: August 23, 2016, 11:54:30 AM »
^ Very interesting. :smilenod:
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