Reconstructing the genetic history of late Neanderthals

Jovialis

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Abstract

Although it has previously been shown that Neanderthals contributed DNA to modern humans1,2, not much is known about the genetic diversity of Neanderthals or the relationship between late Neanderthal populations at the time at which their last interactions with early modern humans occurred and before they eventually disappeared. Our ability to retrieve DNA from a larger number of Neanderthal individuals has been limited by poor preservation of endogenous DNA3 and contamination of Neanderthal skeletal remains by large amounts of microbial and present-day human DNA3,4,5. Here we use hypochlorite treatment6 of as little as 9 mg of bone or tooth powder to generate between 1- and 2.7-fold genomic coverage of five Neanderthals who lived around 39,000 to 47,000 years ago (that is, late Neanderthals), thereby doubling the number of Neanderthals for which genome sequences are available. Genetic similarity among late Neanderthals is well predicted by their geographical location, and comparison to the genome of an older Neanderthal from the Caucasus2,7 indicates that a population turnover is likely to have occurred, either in the Caucasus or throughout Europe, towards the end of Neanderthal history. We find that the bulk of Neanderthal gene flow into early modern humans originated from one or more source populations that diverged from the Neanderthals that were studied here at least 70,000 years ago, but after they split from a previously sequenced Neanderthal from Siberia2 around 150,000 years ago. Although four of the Neanderthals studied here post-date the putative arrival of early modern humans into Europe, we do not detect any recent gene flow from early modern humans in their ancestry.

https://www.nature.com/articles/nature26151

It's behind a paywall, but here's an article on it:

Researchers at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, have sequenced the genomes of five Neandertals that lived between 39,000 and 47,000 years ago. These late Neandertals are all more closely related to the Neandertals that contributed DNA to modern human ancestors than an older Neandertal from the Altai Mountains that was previously sequenced. Their genomes also provide evidence for a turnover in the Neandertal population towards the end of Neandertal history.

Due to the limited number of specimens and difficulties in obtaining endogenous DNA from such old material, the number of Neandertals for which nuclear genomes have been sequenced is still limited. Since 2010 whole genome sequences have been generated for four Neandertals from Croatia, Siberia and the Russian Caucasus. This study adds five new genomes representing Neandertals from a wider geographic range and from a later time period than what was previously obtained.

New methods for the removal of contaminating DNA from microbes and present-day humans that were developed by the Leipzig group have now enabled the researchers to sequence the genomes of five Neandertals from Belgium, France, Croatia, and Russia that are between 39,000 and 47,000 years old. These therefore represent some the latest surviving Neandertals in Europe.

Having genomes from multiple Neandertals allows the researchers to begin to reconstruct Neandertal population history. "We see that the genetic similarity between these Neandertals is well-correlated with their geographical location. By comparing these genomes to the genome of an older Neandertal from the Caucasus we show that Neandertal populations seem to have moved and replaced each other towards the end of their history", says first author, Mateja Hajdinjak.

The team also compared these Neandertal genomes to the genomes of people living today, and showed that all of the late Neandertals were more similar to the Neandertals that contributed DNA to present-day people living outside Africa than an older Neandertal from Siberia. Intriguingly, even though four of the Neandertals lived at a time when modern humans had already arrived in Europe they do not carry detectable amounts of modern human DNA. "It may be that gene flow was mostly unidirectional, from Neandertals into modern humans", says Svante Pääbo, Director at the Max Planck Institute for Evolutionary Anthropology.

"Our work demonstrates that the generation of genome sequences from a large number of archaic human individuals is now technically feasible, and opens the possibility to study Neandertal populations across their temporal and geographical range", says Janet Kelso, the senior author of the new study.

Read more at: https://phys.org/news/2018-03-genomes-late-neandertals-insights-neandertal.html#jCp
 
I find the dating of the Spy Neanderthal quite young.
The Spy cave was excavated before carbon dating existed, and we have only stratigraphical chronology.
So, I suspect this Neanderthal was dated directly from the bones.
Between Neanderthal and Aurignacian at Spy there is an intermediate layer of a modern humans industry that appeared in other parts of Europe as well.
Aurignacians were in Southern Germany allready ca 43 ka.
Appearantly it took them a long time to get from there to Belgium.
And all this time, they didn't interbreed with the European Neanderthals.

My pics of the Spy cave :

spy 047.JPG spy 046.JPG
attachment.php

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the Spy cave and Goyet cave are along siderivers of the Meuse-Sambre valley with sometimes steep cliffs on both sides of that valley
I guess these siderivers were corridors for game to cross the Meuse-Sambre valley
 
Thanks for sharing the latest news but as we keep seeing change is the key word of what's happening. There appears to be supplementary material as part of Nature's Abstract. I've just downloaded it and if it seems current I'll post it. It's an exciting time.
 
[h=3][FONT=Open Sans, sans-serif]​Fantastic pictures in my hint I saw this abstract and thought it might have a link to your pictures. I'll keep looking and thanks formsharing. .[/FONT]
[FONT=Open Sans, sans-serif]Abstract[/FONT]
[/h][FONT=&quot]In Eurasia, the period between 40,000 and 30,000 BP saw the replacement of Neandertals by anatomically modern humans (AMH) during and after the Middle to Upper Paleolithic transition. The human fossil record for this period is very poorly defined with no overlap between Neandertals and AMH on the basis of direct dates. Four new 14C dates were obtained on the two adult Neandertals from Spy (Belgium). The results show that Neandertals survived to at least ≈36,000 BP in Belgium and that the Spy fossils may be associated to the Lincombian–Ranisian–Jerzmanowician, a transitional techno‐complex defined in northwest Europe and recognized in the Spy collections. The new data suggest that hypotheses other than Neandertal acculturation by AMH may be considered in this part of Europe. Am J Phys Anthropol, 2009. © 2008 Wiley‐Liss, Inc.
[/FONT]

Citing Literature
 
I have been saying for 10 years (since I started getting interested in population genetics) that Neanderthals probably had several subspecies, and that Homo sapiens are likely to have interbred with them times and again at various locations. Consequently, sequencing just one or a few Neanderthal genomes would not provide a clear picture of how much Neanderthal admixture is present in modern humans.

This study confirms that modern humans are closer to Late Neanderthals, and especially to two specimens (Spy in Belgium and Mezmaiskaya in the Pontic Steppe, close to the Yamna-Maykop boundary). Therefore it would appear, based on this still very partial data, that Homo sapiens got their Neanderthal admixture mostly in these two regions. Aurignacian Cro-Magnons (haplogroups CT, C1a, C1b, I) could have mixed with Neanderthals around Namur (Goyet and Spy) in Belgium. Another branch blended in the North Caucasus, whose population became the was overtaken later by R1a and R1b tribes (Mesolithic East Europeans), who then spread this 2nd set of Neanderthal genes across Europe, West Asia and South Asia during the Bronze Age.

I haven't had time to read the whole article in detail yet. Did anyone see if they recalculated the percentage of Neanderthal ancestry in modern Europeans and Asians based on these new samples?
 
I have been saying for 10 years (since I started getting interested in population genetics) that Neanderthals probably had several subspecies, and that Homo sapiens are likely to have interbred with them times and again at various locations. Consequently, sequencing just one or a few Neanderthal genomes would not provide a clear picture of how much Neanderthal admixture is present in modern humans.
This study confirms that modern humans are closer to Late Neanderthals, and especially to two specimens (Spy in Belgium and Mezmaiskaya in the Pontic Steppe, close to the Yamna-Maykop boundary). Therefore it would appear, based on this still very partial data, that Homo sapiens got their Neanderthal admixture mostly in these two regions. Aurignacian Cro-Magnons (haplogroups CT, C1a, C1b, I) could have mixed with Neanderthals around Namur (Goyet and Spy) in Belgium. Another branch blended in the North Caucasus, whose population became the was overtaken later by R1a and R1b tribes (Mesolithic East Europeans), who then spread this 2nd set of Neanderthal genes across Europe, West Asia and South Asia during the Bronze Age.
I haven't had time to read the whole article in detail yet. Did anyone see if they recalculated the percentage of Neanderthal ancestry in modern Europeans and Asians based on these new samples?
the results have to be taken with caution, as the authors state themselves
but there are new techniques now to study Neanderthal DNA in detail
I'm confident more will follow in the next months and years
 
The recent Supplementals have expanded on each of the primary source materials. It's interesting that expansion of one site after another has it's own history. the digs and the procedures continue to offer clues long after there first discovery. I hope to review each of the sites and try to identify the population pathways. Thank you for expanding the horizons of this information.
Spy (Belgium)
The cave of Spy is one of the richest prehistoric sites in Belgium and located only 20
kilometres from the Troisième caverne of Goyet in the Mosan Basin. The first human remains
were discovered in stratigraphic context and in association with lithic material in 188613.
Since then, numerous excavations have been carried out at the site14. Mousterian, LRJ and
Aurignacian industries have been identified at Spy8. The two incomplete adult Neandertal
skeletons, Spy I and Spy II, were found in the deepest level of the terrace of the Spy cave13.
Spy 94a was identified during the reassessment of the Spy collections in 200915. It is
an upper right molar (M3) with an associated alveolar bone that was directly radiocarbon
dated to 39,150-37,880 cal BP (one standard deviation error, GrA-32623) and attributed to the
Spy I Neandertal15. Recent re-dating of both Spy Neandertals makes them the youngest
Neandertals identified in Northwestern Europe and contemporaneous with the transitional
LRJ industry.H
 
Spy was the 2nd place in history where Neanderthals were found and identified as a species different from modern humans.
 
I have been saying for 10 years (since I started getting interested in population genetics) that Neanderthals probably had several subspecies, and that Homo sapiens are likely to have interbred with them times and again at various locations. Consequently, sequencing just one or a few Neanderthal genomes would not provide a clear picture of how much Neanderthal admixture is present in modern humans.

This study confirms that modern humans are closer to Late Neanderthals, and especially to two specimens (Spy in Belgium and Mezmaiskaya in the Pontic Steppe, close to the Yamna-Maykop boundary). Therefore it would appear, based on this still very partial data, that Homo sapiens got their Neanderthal admixture mostly in these two regions. Aurignacian Cro-Magnons (haplogroups CT, C1a, C1b, I) could have mixed with Neanderthals around Namur (Goyet and Spy) in Belgium. Another branch blended in the North Caucasus, whose population became the was overtaken later by R1a and R1b tribes (Mesolithic East Europeans), who then spread this 2nd set of Neanderthal genes across Europe, West Asia and South Asia during the Bronze Age.

I haven't had time to read the whole article in detail yet. Did anyone see if they recalculated the percentage of Neanderthal ancestry in modern Europeans and Asians based on these new samples?

You might be right, but I am not sure if this paper supports your view. They say Neanderthals moved a lot by the end, and since they last known refuges were in Western Europe, that means they moved west-wards. Admixture was calculated to have happened around 50-60 kya, so it seems to me this article points to admixture events to the east of these areas.

I also don't understand why you think that similarity between these Neanderthals and the ones that interbred with homo sapiens might change Neanderthal DNA percentage results. Could you elaborate?
 
You might be right, but I am not sure if this paper supports your view. They say Neanderthals moved a lot by the end, and since they last known refuges were in Western Europe, that means they moved west-wards. Admixture was calculated to have happened around 50-60 kya, so it seems to me this article points to admixture events to the east of these areas.

I am not sure what you mean. Yes, Neanderthals moved a lot (as did Sapiens, who colonised Earth from Africa during the Late Paleolithic). But these genomes are of Late Neanderthals, around the time Sapiens reached Europe. So they would be the ones who would have interbred with Sapiens, not older subspecies that got replaced.

I also don't understand why you think that similarity between these Neanderthals and the ones that interbred with homo sapiens might change Neanderthal DNA percentage results. Could you elaborate?

Because the Neanderthal genomes that were tested before were considerably older and did not belong to Neanderthal subspecies that actually met groups of Sapiens. If modern Europeans have 3-4% of DNA from those older Neanderthals, who were so closely related to the later Neanderthals who came from the East, then it is only logical to assume that modern Europeans are more similar to the Neanderthals they actually encountered. That might raise the percentage of Neanderthal DNA in modern Eurasians by a few percents.
 
I am not sure what you mean. Yes, Neanderthals moved a lot (as did Sapiens, who colonised Earth from Africa during the Late Paleolithic). But these genomes are of Late Neanderthals, around the time Sapiens reached Europe. So they would be the ones who would have interbred with Sapiens, not older subspecies that got replaced.

What I meant is that the paper that first established that non-Africans have Neanderthal ancestry calculated that admixture happened around 50-60kya. This date, combined with a more or less consistent admixture percentage across non-Africans, is why they hypothesized admixture had happened before the non-African split into different populations. You are suggesting they were wrong. You said admixture happened in differentiated populations, and in Europe.

However it seems they do not reject the earlier model. These new genomes are from 39-47kya. Assuming dates are correct, these Neanderthals lived after the admixture event(s), but they are more similar to the admixture Neanderthals. However, the authors said European Neanderthal populations were replaced, and since these new genomes were the latest there, it means arrived from somewhere else, most likely east. This places them closer to the SW Asia region where admixture was hypothesized to have happened. So that explains the additional similarity without necessarily meaning admixture took place in Europe, or with European populations. That's why I said I don't think this paper provides evidence your point.
 

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