Fourth strand in European gene mix (Nature.com)

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Fourth strand in European gene mix (Nature.com)

Postby Marshall on November 16th, 2015, 2:49 pm 

http://www.nature.com/ncomms/2015/15111 ... troduction

Recent find based on DNA from old bones. Article is currently open-access (not behind pay wall).

This was covered in several popular online media today, giving simplified summaries. But I either don't understand or don't trust the summaries.
http://www.bbc.com/news/science-environment-34832781
The BBC summary is not bad but at one point they say 3000 BP when they meant 3000 BC (i.e. 5000 years before present---western migration of Yamnaya herders)

The Nature article seems to be talking about a four-way mix of groups identified by their DNA as distinct populations. They use abbreviations:
ANE ancient north eurasians
WHG western hunter-gatherers
EF early farmers (came in from Levant around 7000 BP)
CHG caucasus hunter-gatherers (genes brought in by herding population wave around 3000 BC = 5000 BP)

It's the CHG that these authors want to add to the picture. They go so far as to suggest that the Indo-Aryan language group may have come in with westward migration of CHG-descended herders. Also plague.

==quote==

We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic–Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers ~45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers ~25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe ~3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.

==endquote==
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Re: Fourth strand in European gene mix (Nature.com)

Postby Marshall on November 16th, 2015, 3:56 pm 

==quote==

Ancient genomes from Eurasia have revealed three ancestral populations that contributed to contemporary Europeans in varying degrees1. Mesolithic individuals, sampled from Spain all the way to Hungary1, 2, 3, belong to a relatively homogenous group, termed western hunter-gatherers (WHG). The expansion of early farmers (EF) out of the Levant during the Neolithic transition led to major changes in the European gene pool, with almost complete replacement in the south and increased mixing with local WHG further north1, 2, 3, 4, 5. Finally, a later wave originating with the Early Bronze Age Yamnaya from the Pontic steppe, carrying partial ancestry from ancient North Eurasians (ANE) and ancestry from a second, undetermined source, arrived from the east, profoundly changing populations and leaving a cline of admixture in Eastern and Central Europe1, 3, 6. This view, which was initially based on a handful of genomes, was recently confirmed by extensive surveys of Eurasian samples from the Holocene5, 7.

Here, we extend our view of the genetic makeup of early Europeans by both looking further back in time and sampling from the crossroads between the European and Asian continents. We sequenced a Late Upper Palaeolithic (‘Satsurblia’ from Satsurblia cave, 1.4-fold coverage) and a Mesolithic genome (‘Kotias’ from Kotias Klde cave, 15.4-fold) from Western Georgia, at the very eastern boundary of Europe. We term these two individuals Caucasus hunter-gatherers (CHG). To extend our overview of WHG to a time depth similar to the one available for our samples from the Caucasus, we also sequenced a western European Late Upper Palaeolithic genome, ‘Bichon’ (9.5-fold) from Grotte du Bichon, Switzerland. These new genomes, together with already published data, provide us with a much-improved geographic and temporal coverage of genetic diversity across Europe after the Last Glacial Maximum (LGM)8. We show that CHG belong to a new, distinct ancient clade that split from WHG ~45 kya and from Neolithic farmer ancestors ~25 kya. This clade represents the previously undetermined source of ancestry to the Yamnaya, and contributed directly to modern populations from the Caucasus all the way to Central Asia.

==endquote==
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Re: Fourth strand in European gene mix (Nature.com)

Postby wolfhnd on November 16th, 2015, 5:27 pm 

Very interesting articles but I'm curious about your personal reflections on the relevancy of ancestry?
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Re: Fourth strand in European gene mix (Nature.com)

Postby Marshall on November 16th, 2015, 8:01 pm 

Relevancy to what? Relevance has to be defined in relation to something. This is archeology, reconstructing the past by studying old stones and old bones. To some people it's intrinsically interesting and to others it is not.

To me it's interesting that until 7000 BP there was a fairly uniform population from Spain to Hungary, the WHG.
Over the years I've heard a lot about these people. Found in caves in Spain recently. They even got over into British Isles.

"Mesolithic individuals, sampled from Spain all the way to Hungary1, 2, 3, belong to a relatively homogenous group, termed western hunter-gatherers (WHG)."

They were already established 45,000 BP, presumably, because it says the newly identified group split off from them around 45,000 BP. But then around 7000 BP a lot of Farmers flooded in and actually REPLACED much of the WHG in parts of Europe, esp in south, and MIXED with them in other parts:

"The expansion of early farmers (EF) out of the Levant during the Neolithic transition led to major changes in the European gene pool, with almost complete replacement in the south and increased mixing with local WHG further north1, 2, 3, 4, 5."

We still have no indication when and whence the group of European-and-related languages came in---Greek, Latin, Celtic, Norse, Russian, Persian, Sanskrit, Spanish, French etc etc.

What they are telling us in this paper and what is apparently now expert consensus is that that language group came in with the YAMNAYA herders, who were horse-riders, with bronze age tech, lactose tolerant, and came off the Pontic steppes (grasslands around the Black Sea and Caspian Sea I guess)

I just came across this popular article in phys org it might interest you because talks about recognizable traits:
http://phys.org/news/2015-06-ancient-dn ... -skin.html
It is about the Yamnaya influx. about 5000 BP. Have to go, back later.
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Re: Fourth strand in European gene mix (Nature.com)

Postby Marshall on November 16th, 2015, 11:03 pm 

WH, the topic is archaeology here. Your post is off-topic here and belongs in medicine forum. I will help you start a thread there by moving the post and giving it a title like
"Catalog of human genetic variation could improve diagnosis"

The topic here is not "ancestry" in the usual sense of knowing who someone's forebears were, it is reconstructing the past migrations mixing of ancient groups, reconstructing HISTORY.

BTW genetic analysis seems to indicate that the earliest European H Sapiens (the WHG) were dark skinned and blue eyed.

Light skin genes (from CHG) came in with the Herders (who tended to be brown-eyed) and the Farmers.
". Like EF, but in contrast to WHG, CHG carry a variant of the SLC24A5 gene17 associated with light skin colour (rs1426654, see Supplementary Note 6). This trait, which is believed to have risen to high frequency during the Neolithic expansion18, may thus have a relatively long history in Eurasia, with its origin probably predating the LGM."

I don't know how seriously to take that. It's what they say in the article.

Seems like a drastic reconstruction.
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Re: Fourth strand in European gene mix (Nature.com)

Postby wolfhnd on November 16th, 2015, 11:32 pm 

Ok I get your point and appreciate your comments but I'm still interested in why you find this topic "intrinsically interesting"? I think we can dispense with some of the formalities or professionalism for a moment without degrading the quality of the forums? If you don't want to answer that's fine as I assume you posted it to get expert input on the reliability of the articles which I would also be interested in but which is something I can add nothing to.
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Re: Fourth strand in European gene mix (Nature.com)

Postby Marshall on November 17th, 2015, 12:09 am 

From the BBC news item, based on this paper in Nature:
"The Yamnaya transformed the gene pools of northern and central Europe, such that some populations, like Norwegians, owe around 50% of their ancestry to these Steppe pastoralists."

For convenience I'll bring forward the links and abbreviations:
http://www.nature.com/ncomms/2015/15111 ... troduction

Recent find based on DNA from old bones. Article is currently open-access (not behind pay wall).

This was covered in several popular online media today, giving simplified summaries. But I either don't understand or don't trust the summaries.
http://www.bbc.com/news/science-environment-34832781
The BBC summary is not bad but at one point they say 3000 BP when they meant 3000 BC (i.e. 5000 years before present---western migration of Yamnaya herders)

The Nature article seems to be talking about a four-way mix of groups identified by their DNA as distinct populations. They use abbreviations:

WHG western hunter-gatherers (ancient inhabitants of Europe)
EF early farmers (came in from Levant around 7000 BP)
CHG caucasus hunter-gatherers (genes brought in by herding population wave around 3000 BC = 5000 BP)
ANE ancient north eurasians, the other component of the Yamnaya herders of around 5000 BP

It's the CHG that these authors want to add to the picture. They go so far as to suggest that the Indo-Aryan language group may have come in with westward migration of CHG-descended herders. Also plague.
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Re: Fourth strand in European gene mix (Nature.com)

Postby vivian maxine on November 17th, 2015, 9:08 am 

Thank you, Marshall for the review. The story of Europe's development is the story of our development. The Yamnaya - I don't remember that name but do remember about the people on the Steppes. Somewhere I have a story of their horsemanship. They were not "johnny-come-latlies" to the scene. They were developing quite a civilization long before they came down to join the other Europeans. I remember once reading that the Basque language may have originated there but the idea seems to have died a-borning as I've heard no more about it.

A good story for a rainy day.
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Re: Fourth strand in European gene mix (Nature.com)

Postby vivian maxine on November 17th, 2015, 10:27 am 

Marshall, I just saw this in today's Science Daily. It is likely a different publisher's repeat of your story. I only add it in case there is anything new in it. If not, and you want to remove it, feel free to do so.

http://www.sciencedaily.com/releases/20 ... ce+News%29

The Caucasus hunter-gatherer genome showed a continual mixture with the ancestors of early farmers in the Levant area ..... This ends, however, around 25,000 years ago, just before the time of the last peak Ice Age. ..... There followed a long Caucasus hunter-gatherer isolation period.
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Re: Fourth strand in European gene mix (Nature.com)

Postby Marshall on November 17th, 2015, 12:44 pm 

vivian maxine » Tue Nov 17, 2015 7:27 am wrote:Marshall, I just saw this in today's Science Daily. It is likely a different publisher's repeat of your story. I only add it in case there is anything new in it. If not, and you want to remove it, feel free to do so.

http://www.sciencedaily.com/releases/20 ... ce+News%29

The Caucasus hunter-gatherer genome showed a continual mixture with the ancestors of early farmers in the Levant area ..... This ends, however, around 25,000 years ago, just before the time of the last peak Ice Age. ..... There followed a long Caucasus hunter-gatherer isolation period.


So the CHG population was "ICE-o-lated"! : ^)
It's isolated populations (Darwin discovered in the Galapagos islands?) that are able to diverge and develop distinctive characteristics.

Thanks Vivian, that Science Daily piece is definitely talking about the same research.

I'm far from expert in these matters but I can tell it's interesting and the Science Daily perspective fits right in with the BBC commentary and the scholarly article in Nature.com.
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Re: Fourth strand in European gene mix (Nature.com)

Postby vivian maxine on November 17th, 2015, 12:55 pm 

I'm glad it fit. I understand Science Daily better than Nature. All those abbreviations and equations are over my head, especially the equations. I hope Science Daily is reliable reporting.
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Re: Fourth strand in European gene mix (Nature.com)

Postby Marshall on November 17th, 2015, 2:32 pm 

Indeed the Science Daily piece you found http://www.sciencedaily.com/releases/20 ... ce+News%29
struck me (FWIW) as entirely consistent with the Nature.com article and better written for our purposes. Much easier to understand. I hadn't seen it before.
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Re: Fourth strand in European gene mix (Nature.com)

Postby vivian maxine on November 17th, 2015, 2:45 pm 

Good. Now we see how all these people got along - or didn't.
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