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Mars
30-09-14, 10:16
I'm wondering what contemporary population has the clearest connection to the farmers who came to Europe 8,000 years ago from the Fertile Crescent. Any ideas?

Angela
30-09-14, 15:11
Well, since the academics say over and over again that the ancient samples we have cluster with modern day Sardinians, I suppose they're the best candidate.

Here's the PCA from Lazaridis et al:
https://lh4.googleusercontent.com/-r4BFSXC2SnI/U52vsEP-ggI/AAAAAAAAAmM/jhLYu5dx88U/w350-h331-no/Ancient_human_genomes_suggest_three_ancestral_popu lations_Fig1b_small.png

It's too small an image, but if you enlarge it on your computer you can see what I mean.
Probably better to take a look at it in the paper.
http://www.nature.com/nature/journal/v513/n7518/full/nature13673.html

Or we can go with EEF levels:
6673

Ashkenazi 93%, Sicilians 90%, Sardinians 82%, Spanish 81%, Greeks 79% and down from there.

The Sicilians score higher because of additional "doses" they got later, probably mostly, although not only during the Metal Ages through mainland Greece and the Islands as vectors. (The Maltese would fit in here as well.)

The Ashkenazi are a special case. It's complicated. They may be preserving the genetic signal of the ancient Near East better than other populations.

John Doe
30-09-14, 15:18
Well, since the academics say over and over again that the ancient samples we have cluster with modern day Sardinians, I suppose they're a good candidate.

Or we can go with EEF levels:
6673

But don't forget that EEF is a hybrid of the Neolithic component and of the Mesolithic WHG component. Therefore it might not best represent the Basal Eurasian component, considering the fact that EEF is merely a hybrid.

Angela
30-09-14, 16:25
We don't have the genome of an early farmer in the Near East. The closest we have is Stuttgart. Plus, we don't know yet where the various elements came together to form EEF. For all we know, it could have all happened in the Near East.

One can only answer questions based on the currently available data.

John Doe
30-09-14, 16:33
We don't have the genome of an early farmer in the Near East. The closest we have is Stuttgart. Plus, we don't know yet where the various elements came together to form EEF. For all we know, it could have all happened in the Near East.

One can only answer questions based on the currently available data.

Alright, but from what I know one of the components that make up EEF is a Mesolithic component that is WHG like, please correct me if I'm wrong though.

Mars
30-09-14, 16:59
Thanks for your replies folks, but they lead me to one more question... What is basal eurasian? Pardon my ignorance...

Aberdeen
30-09-14, 17:13
Thanks for your replies folks, but they lead me to one more question... What is basal eurasian? Pardon my ignorance...

You can read the paper that discusses the concept at David Reich's Harvard genetics website. I'd give you the link, except that I'm having trouble with my new computer. But just search under David Reich.

sparkey
30-09-14, 17:25
Sardinians are a near-perfect (~99%) genetic snapshot of people in Southern Europe before the "ANE" migration into Europe ("Ancient North Eurasian"--sometimes associated with Y-DNA haplogroup R and/or Indo-European languages, although not always exclusively). Every other group, including Sicilians, Ashkenazi Jews, and Basques, have significantly more ANE. The only thing that keeps the Sardinians from having the most Neolithic farmer ancestry is that they also have significant European hunter-gatherer mixed in (~17%).

Angela
30-09-14, 17:37
Alright, but from what I know one of the components that make up EEF is a Mesolithic component that is WHG like, please correct me if I'm wrong though.

I don't see how any of that changes the answer to the question, but...

Lazaridis et al found that this model is the best fit for the evidence we have so far:
http://3.bp.blogspot.com/-YbYK8NzQNAY/UrihRsR5eSI/AAAAAAAAJbo/TYynaV4cO4Y/s1600/model.png

As you can see, EEF is estimated to possess 44% plus or minus 10% "Basal Eurasian". The rest is from the "West Eurasian" branch from which WHG also stemmed. So the additional lineage or lineages would be related to WHG.

Some admixture might and probably did take place in Europe, (10-20%?) but the farmers in the Near East would have already been an admixture of "Basal Eurasian" and some Unknown Hunter Gatherers from the same ancient branch of humanity as the WHGs of Europe. (Mind, the Basal Eurasians would also have been hunter gatherers. People seem to have trouble keeping in mind that everyone was once a hunter-gatherer. We don't know if the "Basal Eurasians" alone developed farming. I would doubt it; I think they are much too old for that. So, the inventors of farming and animal husbandry, upon which all of the remainder of our history is built, would have most likely been an admixture of "Basal Eurasian" HG and "West Eurasian" HG.)

This is all discussed in the supplement starting on page 59.
http://biorxiv.org/content/biorxiv/suppl/2013/12/23/001552.DC1/001552-3.pdf

.
As we get more ancient genomes, I'm sure that their models will change. That's one of the hallmarks of this group.

John Doe
30-09-14, 17:48
Ed. Could a moderator please remove this? It's a double post. Thanks.



I don't see how any of that changes the answer to the question, but...

Lazaridis et al found that this model is the best fit for the evidence we have so far:
http://3.bp.blogspot.com/-YbYK8NzQNAY/UrihRsR5eSI/AAAAAAAAJbo/TYynaV4cO4Y/s1600/model.png

As you can see, EEF is estimated to possess 44% plus or minus 10% "Basal Eurasian". The rest is from the "West Eurasian" branch from which WHG also stemmed. So the additional lineage or lineages would be related to WHG.

Some admixture might and probably did take place in Europe, (10-20%?) but the farmers in the Near East would have already been an admixture of "Basal Eurasian" and some Unknown Hunter Gatherers from the same ancient branch of humanity as the WHGs of Europe. (Mind, the Basal Eurasians would also have been hunter gatherers. People seem to have trouble keeping in mind that everyone was once a hunter-gatherer. We don't know if the "Basal Eurasians" alone developed farming. I would doubt it; I think they are much too old for that. So, the inventors of farming and animal husbandry, upon which all of the remainder of our history is built, would have most likely been an admixture of "Basal Eurasian" HG and "West Eurasian" HG.)

This is all discussed in the supplement starting on page 59.
http://biorxiv.org/content/biorxiv/suppl/2013/12/23/001552.DC1/001552-3.pdf

As we get more ancient genomes, I'm sure that their models will change. That's one of the hallmarks of this group.

Oh, I see... Thanks for the detailed information, from this map I can see that EEF component isn't exactly descended from WHG, but from a related HG which stems from the same common ancestor with WHG (west Eurasian), as well as from Basal Eurasian thanks. Yeah, we must remember that we still don't know everything, and that not all the cards are on the table yet.

P.S This means that most of the EEF component is descended from this unknown west Eurasian HG, and only 10% of it (plus minus 44%) comes from the Basal Eurasians?

Angela
30-09-14, 17:53
This is a link to the 2013 preprint which contains a link to the Supplement where the meat of the analysis can be found. The published 2014 version is behind a paywall.
http://biorxiv.org/content/early/2013/12/23/001552.figures-only

For discussions of Basal Eurasian, just use the search engine here.

Here is one thread where it was discussed...
http://www.eupedia.com/forum/threads/30466-Ancient-human-genomes-suggest-three-ancestral-populations-for-present-day-Europeans?highlight=Basal+Eurasians

If you read the supplement carefully, you'll see that Lazaridis tried to use far southern Bedouins as the reference population because they have so little ANE, but the problem is that they are recently SSA admixed, so it wasn't really satisfactory.

I think we're really just going to have to wait for some more ancient genomes. Problem is, the warmer the climate the less likely they survive.

John Doe
30-09-14, 17:56
This is a link to the 2013 preprint which contains a link to the Supplement where the meat of the analysis can be found. The published 2014 version is behind a paywall.
http://biorxiv.org/content/early/2013/12/23/001552.figures-only

For discussions of Basal Eurasian, just use the search engine here.

Here is one thread where it was extensively discussed...
http://www.eupedia.com/forum/threads/30466-Ancient-human-genomes-suggest-three-ancestral-populations-for-present-day-Europeans?highlight=Basal+Eurasians

If you read the supplement carefully, you'll see that Lazaridis tried to use far southern Bedouins as the reference population, but the problem is that they are recently SSA admixed, so it wasn't really satisfactory.

I think we're really just going to have to wait for some more ancient genomes. Problem is, the warmer the climate the less likely they survive.

Alright thanks. Then it's a sort of race against time. :-/

Mars
30-09-14, 18:03
You can read the paper that discusses the concept at David Reich's Harvard genetics website. I'd give you the link, except that I'm having trouble with my new computer. But just search under David Reich.
Thank you. I found something on facebook, a DNA tribes pdf about the Basal Eurasians, it seems pretty good
http://dnatribes.com/dnatribes-digest-2014-03-01.pdf

John Doe
30-09-14, 18:18
@Angela I was wondering, I used to check Dienekes for new studies, but he seems to be inactive, is there another blog that uploads the newest studies?

Angela
30-09-14, 19:29
EEF is estimated to have 44% Basal,plus or minus 10%.

As for Martin at DnaTribes that's just one speculation among many. It could all be shifted northward, and they could have been in Arabia all that time. The poster "Parasar" at Anthrogenica even holds out for a southeastern European refuge, although he's decidedly in the minority.

Far wiser to stick with Lazaridis, imo, and just say we don't know yet.

Even the details of the exodus from Africa posited by Dna Tribes are not universally accepted.
See: http://www.dienekes.blogspot.com/2014/09/an-archaeological-scenario-for-out-of.html

I personally take all the DnaTribes analyses with a lot of salt,forget a grain. Look at the hash he made with that first STR based ancestry tool. I am probably the only user for whom it actually worked.

As to where recent papers can be found, Dienekes still posts the ones that particularly interest him, but not as many as he used to do, and he no longer provides commentary.(The authors would sometimes get into the discussions as well, which was wonderful.) I know some schools and educators that were using it as a guide. It's a great pity it's so inactive.

Some are also posted at Anthrogenica, but it's such a confusing site to use...

Of course, you could always be a complete nerd like me and get news feeds about archaeology, genetics, psychology papers etc.:smile:

John Doe
30-09-14, 19:38
EEF is estimated to have 44% Basal,plus or minus 10%.

As for Martin at DnaTribes that's just one speculation among many. It could all be shifted northward, and they could have been in Arabia all that time. The poster "Parasar" at Anthrogenica even holds out for a southeastern European refuge, although he's decidedly in the minority.

Far wiser to stick with Lazaridis, imo, and just say we don't know yet.

Even the details of the exodus from Africa posited by Dna Tribes are not universally accepted.
See: http://www.dienekes.blogspot.com/2014/09/an-archaeological-scenario-for-out-of.html

I personally take all the DnaTribes analyses with a lot of salt,forget a grain. Look at the hash he made with that first STR based ancestry tool. I am probably the only user for whom it actually worked.

As to where recent papers can be found, Dienekes still posts the ones that particularly interest him, but not as many as he used to do, and he no longer provides commentary.(The authors would sometimes get into the discussions as well, which was wonderful.) I know some schools and educators that were using it as a guide. It's a great pity it's so inactive.

Some are also posted at Anthrogenica, but it's such a confusing site to use...

Of course, you could always be a complete nerd like me and get news feeds about archaeology, genetics, psychology papers etc.:smile:

Oh, it's 44% Basal Eurasian plus/minus 10%, pardon me. LOL, assuming I want to be a complete nerd, how will I start getting news feeds about archaeology, genetics etc? :-p

Angela
30-09-14, 21:09
Oh, it's 44% Basal Eurasian plus/minus 10%, pardon me. LOL, assuming I want to be a complete nerd, how will I start getting news feeds about archaeology, genetics etc? :-p

Well, there's Science Daily, for example, which provides a daily feed, or The National Geographic organization, or the Council of British Archaeology, or the one on Biblical Archaeology, or if you want it in audio, there's the Archaeology Channel. That's a good one, because you can listen as you do more mundane things. That's just for a start. Just google news feeds with your area of interest and things should pop up.

Then you can follow certain people on twitter, although I don't do that much, as it makes me feel like a stalker!

The problem is not access; the problem is the time to read and understand the papers. Then there's literature, and film and music, and most important, of course, family and friends. Then there's the little things like work, and cleaning and cooking and eating etc...It helps if you can multi-task...it also helps if you don't sleep much. :grin:

John Doe
01-10-14, 07:00
Well, there's Science Daily, for example, which provides a daily feed, or The National Geographic organization, or the Council of British Archaeology, or the one on Biblical Archaeology, or if you want it in audio, there's the Archaeology Channel. That's a good one, because you can listen as you do more mundane things. That's just for a start. Just google news feeds with your area of interest and things should pop up.

Then you can follow certain people on twitter, although I don't do that much, as it makes me feel like a stalker!

The problem is not access; the problem is the time to read and understand the papers. Then there's literature, and film and music, and most important, of course, family and friends. Then there's the little things like work, and cleaning and cooking and eating etc...It helps if you can multi-task...it also helps if you don't sleep much. :grin:

Lol thanks, I'll check those sites out. :)

Edit: Science daily fits me best, I just don't have enough time to daily check so many pages. :-P

joeyc
01-10-14, 14:50
Basal Eurasian peaks among Arabs. Israeli Beduins from the HGDP panel score 90% ENF and 10% East African.

John Doe
01-10-14, 14:57
Basal Eurasian peaks among Arabs. Israeli Beduins from the HGDP panel score 90% ENF and 10% East African.

Via which study/calculator? May I have a link? What do Ashkenazi Jews get according to HGDP?

My results for: Eurogenes_ANE K7 Admixture Proportions:

Revised 2014-Sep-12

Population
ANE 8.38%
ASE 1.83%
WHG-UHG 32.72%
East_Eurasian 0.14%
West_African 0.57%
East_African 0.91%
ENF 55.44%

joeyc
01-10-14, 17:01
Eurogenes ANE K7. You can find the spreadsheet on Polako's blog.

Have you got those results from Gedmatch? If yes they are wrong and you should use the software from Dodecad.

John Doe
01-10-14, 17:07
Eurogenes ANE K7. You can find the spreadsheet on Polako's blog.

Have you got those results from Gedmatch? If yes they are wrong and you should use the software from Dodecad.

Yeah I got those results from Gedmatch. Here are my manual results:


8.38% ANE
1.58% ASE
33.16% WHG-UHG
0.31% East_Eurasian
0.38% West_African
1.32% East_African
54.87% ENF


They aren't that different truth be told, but more accurate I guess.

Angela
17-10-14, 18:18
I'm sorry to revive an old thread, but questions were raised once again in the ancient British genomes threads about the three ancestral populations of Europe. I think to get into a detailed discussion there about this topic would have been hijacking those threads, so I am posting my thoughts here.

Questions concerning the amount of "WHG" in EEF keep being asked and again. For suggesting that it is a distraction in terms of the discussion of the peopling of Europe, a respected, published author has been attacked on another forum.

I will here speak only for myself. I get the distinct feeling at times that this obsession with quantifying the amount of "WHG" in EEF may, in some people, stem from an attempt to nail down exactly how "European" a group or a person is by taking that figure and adding it to the "regular" WHG in the figures given for modern populations in Lazaridis et al. Apparently, ANE is considered "European" enough not to raise concern, despite its eastern affinities. The short answer is that we are all 100% European, whether we come from France, or Finland, or southern Italy, and whether we can be modeled best with two or three of these ancestral EEF/WHG/ANE populations.

That undertone also is present, imo, in many of these discussions about how much hunter-gatherer is present in groups or individuals. This reflects a fundamental misunderstanding of human history. Everyone is 100% descended from hunter-gatherers as I've said repeatedly on many threads for many years, because all of those groups, Basal Eurasian, UHG, WHG, ANE, and all the others were hunter gatherers before they learned how to farm.

It seems to me that some people obsessed with these questions (of course, not those who merely seek to understand the issues), who are constantly, to use a phrase I'd like to borrow, "massaging" the data through calculators etc. are merely concerned with minimizing, as much as possible, any "Near Eastern" element in them or their groups.

I'm afraid that like it or not, most of EEF was Near Eastern.

Since apparently people forget it, here is the appropriate excerpt, I think, from Lazaridis et al.

"The amount of Near Eastern admixture estimated for Stuttgart can be seen in Table S10.2 and range between 61-98% with estimates increasing as the amount of estimated African admixture in BedouinBincreases.There are reasons to doubt both the lower estimates (near60%), since ALDER provides only a lower bound on African ancestry, but also the )higher estimates (near 100%) since there is direct evidence that Stuttgart has European hunter-gatherer ancestry (Fig. 1B and Table S10.1

Determining the precise levels of Near Eastern admixture in Stuttgart must await further ancient DNA studies from both Europe and the Near East, but we can at least reasonably claim that most of the sample’s ancestry was Near Eastern, consistent with the mtDNA evidence for the Linearbandkeramik, which demonstrated a strong Near Eastern influence3-5"


(So, in Stuttgart, the Near Eastern admixture, according to this excerpt , is somewhere between 60 and 98%. I may have erred in using the 25% figure for the non Near Eastern admixture in Stuttgart (whether you call it UHG or WHG or a combination or anything else) I believe that is the figure for Oetzi. Anyone is free to correct the percentage from the academic literature, not if you please, from amateur "calculators", some of which have already been proved to be unreliable. Regardless, that is why I stated elsewhere that the majority of EEF’s ancestry is from the Middle East.

If any of this is incorrect, in fact, please direct me to a quote from the paper to that effect.

If someone wants to dispute the general statement, then I would suggest that they contact Lazaridis and Reich and point out how their statistical ability is superior to that of the authors. Or, they might want to write a paper and submit it for peer review. )


I also want to make sure that we are comparing similar things. The calculations that were made in the paper as to EEF/WHG/ANE in modern populations were based, to the best of my recollection, on Stuttgart. They certainly were not based on the Gok farmer results. Therefore, it's irrelevant for this purpose that Gok farmers had more WHG than did Stuttgar. The calculator used in the paper is comparing the genomes of modern Europeans to Stuttgart. That is the source of the 50% figure that is used for the EEF level in English people. They are not being compared to the Gok famers Again, if I'm wrong, and the paper is using both Stuttgart and Oetzi, for example, please correctt the record. This shouldn't be all about ego; it should be about getting it right.

Perhaps I am, knowing the history of certain segments of the amateur community, seeing a problem where none exists, and if that is the case, I apologize, and I certainly don't mean to tar all people who ask these questions or discuss them with the same brush, but it seems to me that a related issue involves all of the discussions and data analysis around how much total UHG/WHG is present in certain populations and people. It sometimes seems to me that the underlying concern for some people is not to have Basal Eurasian. If that's the case, I don't even have the words to express how pathetic I think that is...

In terms of the Near Eastern farmers, I do not recollect that the authors of Lazaridis et al provided a figure for the BE in them. There is a figure for the amount of Basal Eurasian in Stuttgart of 44% plus or minus 10%. So, if anyone wants to figure out their percentage of Basal Eurasian, just, for a rough estimate, take 44% of your group's EEF and there you have it. Now, for those so inclined, you can have a contest over who has the least amount of it. Mazel Tov in advance.

As to the "source" of Basal Eurasian, this is what the authors of the paper have to say:
" The Near East was the staging point for the peopling of Eurasia by anatomicallymodern humans. As a result, it is entirely plausible that it harbored deep Eurasian ancestry which did not initially participate in the northward colonization of Europe, but was later brought into Europe by Near Eastern farmers. More speculatively, some basal Eurasian admixture in the Near East may reflect the early presence of anatomically modern humans7in the Levant, or the populations responsible for the appearance ofthe Nubian Complex in Arabia8, both of which date much earlier than the widespread dissemination of modern humans across Eurasia. Finally, it could reflect continuing more recent gene flows between the Near East and nearby Africa after the initial out-of-Africa dispersal, perhaps associated with the spread of Y-chromosome haplogroup E subclades from eastern Africa 9, 10into the Near East, which appeared at least 7,000 years ago into Neolithic Europe11. "

So far as I can see, the question is still open, and the answers must await further ancient dna and responsible modeling by academics.

To conclude, Jean Manco posted a synopsis of the peopling of Europe which is a model of clearsightedness and logic. I hope she doesn't mind my posting it here for those who don't check in to Anthrogenica occasionally.


"The import of the Lazaridis paper is that there were three migrations into Europe [my notes in brackets]:

1. From the Asian crossroads/Middle East in the Palaeolithic. [mtDNA U and Y-DNA IJ and F]
2. From the Middle Eastern Neolithic heartland in the Neolithic. [mtDNA U3, H, I, J, V etc and Y-DNA G, with a bit of E]
3. From the Asian steppe in the Copper Age. [Y-DNA R]

As each of the waves reached Europe it mixed with descendants of the previous wave(s). "

All of the other comments in this post are my own and not to be attributed to her.

John Doe
17-10-14, 19:08
I'm sorry to revive an old thread, but questions were raised once again in the ancient British genomes threads about the three ancestral populations of Europe. I think to get into a detailed discussion there about this topic would have been hijacking those threads, so I am posting my thoughts here.

Questions concerning the amount of "WHG" in EEF keep being asked and again. For suggesting that it is a distraction in terms of the discussion of the peopling of Europe, a respected, published author has been attacked on another forum.

I will here speak only for myself. I get the distinct feeling at times that this obsession with quantifying the amount of "WHG" in EEF may, in some people, stem from an attempt to nail down exactly how "European" a group or a person is by taking that figure and adding it to the "regular" WHG in the figures given for modern populations in Lazaridis et al. Apparently, ANE is considered "European" enough not to raise concern, despite its eastern affinities. The short answer is that we are all 100% European, whether we come from France, or Finland, or southern Italy, and whether we can be modeled best with two or three of these ancestral EEF/WHG/ANE populations.

That undertone also is present, imo, in many of these discussions about how much hunter-gatherer is present in groups or individuals. This reflects a fundamental misunderstanding of human history. Everyone is 100% descended from hunter-gatherers as I've said repeatedly on many threads for many years, because all of those groups, Basal Eurasian, UHG, WHG, ANE, and all the others were hunter gatherers before they learned how to farm.

It seems to me that some people obsessed with these questions (of course, not those who merely seek to understand the issues), who are constantly, to use a phrase I'd like to borrow, "massaging" the data through calculators etc. are merely concerned with minimizing, as much as possible, any "Near Eastern" element in them or their groups.

I'm afraid that like it or not, most of EEF was Near Eastern.

Since apparently people forget it, here is the appropriate excerpt, I think, from Lazaridis et al.

"The amount of Near Eastern admixture estimated for Stuttgart can be seen in Table S10.2 and range between 61-98% with estimates increasing as the amount of estimated African admixture in BedouinBincreases.There are reasons to doubt both the lower estimates (near60%), since ALDER provides only a lower bound on African ancestry, but also the )higher estimates (near 100%) since there is direct evidence that Stuttgart has European hunter-gatherer ancestry (Fig. 1B and Table S10.1

Determining the precise levels of Near Eastern admixture in Stuttgart must await further ancient DNA studies from both Europe and the Near East, but we can at least reasonably claim that most of the sample’s ancestry was Near Eastern, consistent with the mtDNA evidence for the Linearbandkeramik, which demonstrated a strong Near Eastern influence3-5"


(So, in Stuttgart, the Near Eastern admixture, according to this excerpt , is somewhere between 60 and 98%. I may have erred in using the 25% figure for the non Near Eastern admixture in Stuttgart (whether you call it UHG or WHG or a combination or anything else) I believe that is the figure for Oetzi. Anyone is free to correct the percentage from the academic literature, not if you please, from amateur "calculators", some of which have already been proved to be unreliable. Regardless, that is why I stated elsewhere that the majority of EEF’s ancestry is from the Middle East.

If any of this is incorrect, in fact, please direct me to a quote from the paper to that effect.

If someone wants to dispute the general statement, then I would suggest that they contact Lazaridis and Reich and point out how their statistical ability is superior to that of the authors. Or, they might want to write a paper and submit it for peer review. )


I also want to make sure that we are comparing similar things. The calculations that were made in the paper as to EEF/WHG/ANE in modern populations were based, to the best of my recollection, on Stuttgart. They certainly were not based on the Gok farmer results. Therefore, it's irrelevant for this purpose that Gok farmers had more WHG than did Stuttgar. The calculator used in the paper is comparing the genomes of modern Europeans to Stuttgart. That is the source of the 50% figure that is used for the EEF level in English people. They are not being compared to the Gok famers Again, if I'm wrong, and the paper is using both Stuttgart and Oetzi, for example, please correctt the record. This shouldn't be all about ego; it should be about getting it right.

Perhaps I am, knowing the history of certain segments of the amateur community, seeing a problem where none exists, and if that is the case, I apologize, and I certainly don't mean to tar all people who ask these questions or discuss them with the same brush, but it seems to me that a related issue involves all of the discussions and data analysis around how much total UHG/WHG is present in certain populations and people. It sometimes seems to me that the underlying concern for some people is not to have Basal Eurasian. If that's the case, I don't even have the words to express how pathetic I think that is...

In terms of the Near Eastern farmers, I do not recollect that the authors of Lazaridis et al provided a figure for the BE in them. There is a figure for the amount of Basal Eurasian in Stuttgart of 44% plus or minus 10%. So, if anyone wants to figure out their percentage of Basal Eurasian, just, for a rough estimate, take 44% of your group's EEF and there you have it. Now, for those so inclined, you can have a contest over who has the least amount of it. Mazel Tov in advance.

As to the "source" of Basal Eurasian, this is what the authors of the paper have to say:
" The Near East was the staging point for the peopling of Eurasia by anatomicallymodern humans. As a result, it is entirely plausible that it harbored deep Eurasian ancestry which did not initially participate in the northward colonization of Europe, but was later brought into Europe by Near Eastern farmers. More speculatively, some basal Eurasian admixture in the Near East may reflect the early presence of anatomically modern humans7in the Levant, or the populations responsible for the appearance ofthe Nubian Complex in Arabia8, both of which date much earlier than the widespread dissemination of modern humans across Eurasia. Finally, it could reflect continuing more recent gene flows between the Near East and nearby Africa after the initial out-of-Africa dispersal, perhaps associated with the spread of Y-chromosome haplogroup E subclades from eastern Africa 9, 10into the Near East, which appeared at least 7,000 years ago into Neolithic Europe11. "

So far as I can see, the question is still open, and the answers must await further ancient dna and responsible modeling by academics.

To conclude, Jean Manco posted a synopsis of the peopling of Europe which is a model of clearsightedness and logic. I hope she doesn't mind my posting it here for those who don't check in to Anthrogenica occasionally.


"The import of the Lazaridis paper is that there were three migrations into Europe [my notes in brackets]:

1. From the Asian crossroads/Middle East in the Palaeolithic. [mtDNA U and Y-DNA IJ and F]
2. From the Middle Eastern Neolithic heartland in the Neolithic. [mtDNA U3, H, I, J, V etc and Y-DNA G, with a bit of E]
3. From the Asian steppe in the Copper Age. [Y-DNA R]

As each of the waves reached Europe it mixed with descendants of the previous wave(s). "

All of the other comments in this post are my own and not to be attributed to her.

Thank you for the detailed explanation. I was really confused as to what it all meant, but now I understand (at least, as much as we currently know). Thanks. :)

So, let's see, as an Ashkenazi Jew according to Iosif I would be 93.1% EEF, so:
93.1-44%=52.1%
Interesting. :-P

Aberdeen
17-10-14, 19:16
That was an excellent summary, Angela, and it helped clarify some things for me. But I have a question. If we eventually have detailed information about the genetic history of North Africa, do you think it could reveal the possibility that "basal European" could be gene flow from North Africa during the Neolithic? Given that Neolithic people were apparently much better sailors than was once assumed, we have two probable access routes, one from what is now Libya and one from what is now Morocco. IMO, if "basal European" is a yet undiscovered "ghost population", the ghosts might be hiding in the one place nobody has yet looked.

John Doe
17-10-14, 19:30
Well, since the academics say over and over again that the ancient samples we have cluster with modern day Sardinians, I suppose they're the best candidate.

Here's the PCA from Lazaridis et al:
https://lh4.googleusercontent.com/-r4BFSXC2SnI/U52vsEP-ggI/AAAAAAAAAmM/jhLYu5dx88U/w350-h331-no/Ancient_human_genomes_suggest_three_ancestral_popu lations_Fig1b_small.png

It's too small an image, but if you enlarge it on your computer you can see what I mean.
Probably better to take a look at it in the paper.
http://www.nature.com/nature/journal/v513/n7518/full/nature13673.html

Or we can go with EEF levels:
6673

Ashkenazi 93%, Sicilians 90%, Sardinians 82%, Spanish 81%, Greeks 79% and down from there.

The Sicilians score higher because of additional "doses" they got later, probably mostly, although not only during the Metal Ages through mainland Greece and the Islands as vectors. (The Maltese would fit in here as well.)

The Ashkenazi are a special case. It's complicated. They may be preserving the genetic signal of the ancient Near East better than other populations.

Interesting. I suppose we wont know for sure until we'll get a Neolithic near eastern and a pre exile Jewish genome.

Angela
17-10-14, 19:45
That was an excellent summary, Angela, and it helped clarify some things for me. But I have a question. If we eventually have detailed information about the genetic history of North Africa, do you think it could reveal the possibility that "basal European" could be gene flow from North Africa during the Neolithic? Given that Neolithic people were apparently much better sailors than was once assumed, we have two probable access routes, one from what is now Libya and one from what is now Morocco. IMO, if "basal European" is a yet undiscovered "ghost population", the ghosts might be hiding in the one place nobody has yet looked.

Please don't assume quite yet that it's an excellent summary...the criticisms have yet to appear. :smile: I may have gotten some of it wrong, and if I did, I hope it is pointed out...civilly, of course!

As to your specific question about where Basal Eurasian was "hiding", if I may rephrase it that way, I really don't know. Lazaridis et al seem to be hinting toward Arabia, but the "Red Sea" area might be more precise? That would include the North African side of the Red Sea.

As for movement during the Neolithic, we don't have the genome of a Near Eastern farmer. However, we have a genome from the LBK farmer, and we are told she was 44% Basal Eurasian, plus or minus 10%. We also know from the yDna and mtDna and archaeology and papers like Paschou et al, that the Neolithic farmers moved from the Near East north and then north west into Europe.

They also, of course, moved east toward India, as one of the recent archaeology papers with very accurate dating pointed out. The prevailing opinion seems to be that they also spread west along the coast of North Africa and eventually deeper south into Africa itself as pastoralists.

Now, whether some of them also crossed the straits of Gibraltar into the Iberian peninsula, that argument has been made to explain some of the E-M81 in Spain, as I pointed out on the thread about Iberian genetics. I know that there has been some speculation that perhaps some R1b also made that trip. It's certainly possible, I would think, for something like R1b V88. Perhaps, some intrepid souls braving the currents in the Mediterranean also made the trip to Sicily or Sardinia directly from the coasts of North Africa, and that could explain the presence of that particular clade in those islands.

However, as to the P-312 in Europe, it seems to me that the current evidence is heavily in favor of that type of R1b being an ANE derived lineage that mixed with farmers and WHG/UHG somewhere to the east and then moved into Europe from there.

John Doe
17-10-14, 20:13
Please don't assume quite yet that it's an excellent summary...the criticisms have yet to appear. :smile: I may have gotten some of it wrong, and if I did, I hope it is pointed out...civilly, of course!

As to your specific question about where Basal Eurasian was "hiding", if I may rephrase it that way, I really don't know. Lazaridis et al seem to be hinting toward Arabia, but the "Red Sea" area might be more precise? That would include the North African side of the Red Sea.

As for movement during the Neolithic, we don't have the genome of a Near Eastern farmer. However, we have a genome from the LBK farmer, and we are told she was 44% Basal Eurasian, plus or minus 10%. We also know from the yDna and mtDna and archaeology and papers like Paschou et al, that the Neolithic farmers moved from the Near East north and then north west into Europe.

They also, of course, moved east toward India, as one of the recent archaeology papers with very accurate dating pointed out. The prevailing opinion seems to be that they also spread west along the coast of North Africa and eventually deeper south into Africa itself as pastoralists.

Now, whether some of them also crossed the straits of Gibraltar into the Iberian peninsula, that argument has been made to explain some of the E-M81 in Spain, as I pointed out on the thread about Iberian genetics. I know that there has been some speculation that perhaps some R1b also made that trip. It's certainly possible, I would think, for something like R1b V88. Perhaps, some intrepid souls braving the currents in the Mediterranean also made the trip to Sicily or Sardinia directly from the coasts of North Africa, and that could explain the presence of that particular clade in those islands.

However, as to the P-312 in Europe, it seems to me that the current evidence is heavily in favor of that type of R1b being an ANE derived lineage that mixed with farmers and WHG/UHG somewhere to the east and then moved into Europe from there.

Is LBK Stuttgart?

Angela
17-10-14, 20:13
Sorry, double post.

Angela
17-10-14, 20:20
Is LBK Stuttgart?

Stuttgart is a place in Germany where an LBK community was found. The bones of the inhabitants, one in particular, were analyzed. The genome of one of these LBK people from that site has been used as the model for EEF.

John Doe
17-10-14, 20:35
Stuttgart is a place in Germany where an LBK community was found. The bones of the inhabitants, one in particular, were analyzed. The genome of one of these LBK people from that site has been used as the model for EEF.
Oh, I see, when people say "Stuttgart" they're talking about LBK who was found in Stuttgart. Thanks. :)

Aberdeen
17-10-14, 21:27
......................

Now, whether some of them also crossed the straits of Gibraltar into the Iberian peninsula, that argument has been made to explain some of the E-M81 in Spain, as I pointed out on the thread about Iberian genetics. I know that there has been some speculation that perhaps some R1b also made that trip. It's certainly possible, I would think, for something like R1b V88. Perhaps, some intrepid souls braving the currents in the Mediterranean also made the trip to Sicily or Sardinia directly from the coasts of North Africa, and that could explain the presence of that particular clade in those islands.

However, as to the P-312 in Europe, it seems to me that the current evidence is heavily in favor of that type of R1b being an ANE derived lineage that mixed with farmers and WHG/UHG somewhere to the east and then moved into Europe from there.

That would certainly seem like a plausible theory, provided Basques and Sardinians have high levels of ANE, but they don't. I'm not personally convinced that the only R1b to migrate to Africa was V88. Perhaps whatever (possibly climate related) event pushed most of the V88 south pushed other R1b subclades into Europe. The problem is that Neolithic North African DNA seems to be pretty much unresearched at present, so there's no way to prove or disprove the idea.

Angela
17-10-14, 21:52
That would certainly seem like a plausible theory, provided Basques and Sardinians have high levels of ANE, but they don't. I'm not personally convinced that the only R1b to migrate to Africa was V88. Perhaps whatever (possibly climate related) event pushed most of the V88 south pushed other R1b subclades into Europe. The problem is that Neolithic North African DNA seems to be pretty much unresearched at present, so there's no way to prove or disprove the idea.

I agree with you that North African yDna has not been sampled extensively, but there are some pretty good studies, and the P-312 does not seem to show any kind of phylogenetic trail from the Middle East.

I think another thing to consider is that by the time the R1b got to places in the far south or southwest it might have been to a large degree rather de-coupled from the ANE autosomal component. We just need to look at the British for example, who have very high levels of R1b, and comparatively very low levels of ANE.

Also, the Basque do have some ANE...11% according to the chart in Lazaridis et al. It is the Sardinians who lack it, scoring under 1%, while having some R1b. My personal theory is that R1b in Sardinia is very recent, and mostly from the Italian mainland, where the levels are under 12% for ANE for the Tuscans, for example. I could see that getting diluted through progressive intermarriage with Sardinians in a very isolated setting, while the yDna would survive.

That's just a theory, though, and I am used, by now, to being surprised by ancient dna findings, so I'm certainly keeping an open mind.

Ed. Oh, one thing that I definitely think could have happened, is that some R1b L23 people, perhaps in the late Neolithic/Copper Age, as just an example, could have set sail from the eastern Mediterranean and gone across to Iberia, even perhaps stopping for some time on the coast of North Africa.

Mars
17-10-14, 22:06
I agree with Angela, many people on antro boards tend to minimize the near eastern identity of the early farmers, probably for some political agenda, I think. Political wannabeism and science always clash, genetics are not exception to this rule ;-) Leaving aside "hobby" calculators, according to Genographic and FamilyTreeDNA I'm around 16% "Asia minor". It's a trace of neolithic expansion from the Fertile Crescent into Europe according to them - and we know they're right - and the very most europeans have (variable) amounts of this component in their DNA. It's part of us since 8,000 years.
My MTDNA haplogroup is HV, genographic project associates it to neolithic expansion, too.

Aberdeen
17-10-14, 22:42
I agree with you that North African yDna has not been sampled extensively, but there are some pretty good studies, and the P-312 does not seem to show any kind of phylogenetic trail from the Middle East.

I think another thing to consider is that by the time the R1b got to places in the far south or southwest it might have been to a large degree rather de-coupled from the ANE autosomal component. We just need to look at the British for example, who have very high levels of R1b, and comparatively very low levels of ANE.

Also, the Basque do have some ANE...11% according to the chart in Lazaridis et al. It is the Sardinians who lack it, scoring under 1%, while having some R1b. My personal theory is that R1b in Sardinia is very recent, and mostly from the Italian mainland, where the levels are under 12% for ANE for the Tuscans, for example. I could see that getting diluted through progressive intermarriage with Sardinians in a very isolated setting, while the yDna would survive.

That's just a theory, though, and I am used, by now, to being surprised by ancient dna findings, so I'm certainly keeping an open mind.

Ed. Oh, one thing that I definitely think could have happened, is that some R1b L23 people, perhaps in the late Neolithic/Copper Age, as just an example, could have set sail from the eastern Mediterranean and gone across to Iberia, even perhaps stopping for some time on the coast of North Africa.

I agree that if R1b was originally ANE, that would have been diluted as it travelled west, but since Sardinia is nearly 20% R1b and well under 1% ANE, that's a lot of dilution, especially since the small amount of ANE could have come from other haplotypes. And I know of nothing that gives us an ANE connection to R1b of the kind we have for R1a. I can't find anything on line about an autosomal analysis of the two oldest R1b samples we have for Europe (which are also the only two Y DNA samples we have for Bell Beaker). It would be interesting to see whether such ancient R1b was ANE.

Angela
18-10-14, 17:08
[QUOTE=Aberdeen;442002]I agree that if R1b was originally ANE, that would have been diluted as it travelled west, but since Sardinia is nearly 20% R1b and well under 1% ANE, that's a lot of dilution, especially since the small amount of ANE could have come from other haplotypes. And I know of nothing that gives us an ANE connection to R1b of the kind we have for R1a. I can't find anything on line about an autosomal analysis of the two oldest R1b samples we have for Europe (which are also the only two Y DNA samples we have for Bell Beaker). It would be interesting to see whether such ancient R1b was ANE.[/QUOTI]

It certainly would, although, of course, they would be the product of admixtures along the way as well.

I suppose part of what underlies my reasoning is the finding that Mal'ta, who is by definition 100% ANE, was "R" or pre "R". Therefore, I guess it seems logical to me that both R1b and R1a are related to ANE.

I also think there's something to be said for the formulation of Jean Manco and others that this group then moved southwest (tracking micolith technology), with R1a perhaps further north and R1b further south.

The path that R1b took from there is an open question as far as I'm concerned.

I've seen some people speculate that R1b was the haplogroup of Maykop, or Cucuteni, for example, and got scattered when steppe invasions began in earnest. I've wondered if that's true, whether that could also have led to a migration west by sea.

I think the only way we're going to know is with lots and lots of ancient dna. As recent threads have shown, a few results don't answer all the questions.

Aberdeen
18-10-14, 17:21
[QUOTE=Aberdeen;442002]I agree that if R1b was originally ANE, that would have been diluted as it travelled west, but since Sardinia is nearly 20% R1b and well under 1% ANE, that's a lot of dilution, especially since the small amount of ANE could have come from other haplotypes. And I know of nothing that gives us an ANE connection to R1b of the kind we have for R1a. I can't find anything on line about an autosomal analysis of the two oldest R1b samples we have for Europe (which are also the only two Y DNA samples we have for Bell Beaker). It would be interesting to see whether such ancient R1b was ANE.[/QUOTI]

It certainly would, although, of course, they would be the product of admixtures along the way as well.

I suppose part of what underlies my reasoning is the finding that Mal'ta, who is by definition 100% ANE, was "R" or pre "R". Therefore, I guess it seems logical to me that both R1b and R1a are related to ANE.

I also think there's something to be said for the formulation of Jean Manco and others that this group then moved southwest (tracking micolith technology), with R1a perhaps further north and R1b further south.

The path that R1b took from there is an open question as far as I'm concerned.

I've seen some people speculate that R1b was the haplogroup of Maykop, or Cucuteni, for example, and got scattered when steppe invasions began in earnest. I've wondered if that's true, whether that could also have led to a migration west by sea.

I think the only way we're going to know is with lots and lots of ancient dna. As recent threads have shown, a few results don't answer all the questions.

I understand your point about Mal'ta Boy, and whatever surviving relatives of his became the ancestors of R1a and R1b people, but I haven't seen any data showing whether the ANE stayed strong in R1b or whether it was diluted to the point of disappearance, although it wouldn't surprise me if that was the case for the V-88 subclade. IMO, whether or not other subclades retained a strong ANE profile would depend on how they reached Europe. If R1b wasn't part of proto-IE but instead reached western Europe by way of Anatolia and from there further westward by sea, I wouldn't expect to see much of an ANE signature in the earliest examples of R1b in western Europe. And I wouldn't expect a high level of ANE if R1b took the Balkan route from Anatolia. However, if the earliest examples of R1b were high in ANE, I would assume R1b was likely part of the proto-IE population.

Silesian
18-10-14, 18:51
I agree that if R1b was originally ANE, that would have been diluted as it travelled west, but since Sardinia is nearly 20% R1b and well under 1% ANE, that's a lot of dilution, especially since the small amount of ANE could have come from other haplotypes. And I know of nothing that gives us an ANE connection to R1b of the kind we have for R1a. I can't find anything on line about an autosomal analysis of the two oldest R1b samples we have for Europe (which are also the only two Y DNA samples we have for Bell Beaker). It would be interesting to see whether such ancient R1b was ANE.

Same example could be made from R1a Shammar bedouins. By your logic they should have a fair amount of ANE, the Shimar sample carried two main haplogroups—J1 (at 52.3%) and R1a1 (at 42.8%)—with a small percentage of G2 (4.76%).
What about groups/regions like Lezgins/Tabassarans from where did they get there ANE J/R1a/G?

http://en.wikipedia.org/wiki/Y-DNA_haplogroups_by_ethnic_group

https://docs.google.com/spreadsheets/d/1v4zYizoWtsoW1MNBN7SUrLf8R62NHPbMRySUJ2J48_Q/edit?pli=1#gid=1410860471 (http://en.wikipedia.org/wiki/Y-DNA_haplogroups_by_ethnic_group)

Aberdeen
18-10-14, 19:22
Same example could be made from R1a Shammar bedouins. By your logic they should have a fair amount of ANE, the Shimar sample carried two main haplogroups—J1 (at 52.3%) and R1a1 (at 42.8%)—with a small percentage of G2 (4.76%).
What about groups/regions like Lezgins/Tabassarans from where did they get there ANE J/R1a/G?

http://en.wikipedia.org/wiki/Y-DNA_haplogroups_by_ethnic_group

https://docs.google.com/spreadsheets/d/1v4zYizoWtsoW1MNBN7SUrLf8R62NHPbMRySUJ2J48_Q/edit?pli=1#gid=1410860471


If we apply my logic concerning R1b and ANE to R1a, we could expect to find some modern R1a people with little or no noticeable ANE if they travelled a long way from Siberia a long time ago while repeatedly mixing with other people who aren't ANE, which I believe is the situation we have with modern Arab R1a types. But if other R1a types migrated westward from Siberia to Europe without much mixing with other people, we could expect to find that they have a strong ANE signature, which apparently was the case with the Corded Ware folk and may have been the case with the IE folk. Now do you understand? I don't know how much clearer I could make my explanation.

Angela
18-10-14, 20:12
I agree with Angela, many people on antro boards tend to minimize the near eastern identity of the early farmers, probably for some political agenda, I think. Political wannabeism and science always clash, genetics are not exception to this rule ;-) Leaving aside "hobby" calculators, according to Genographic and FamilyTreeDNA I'm around 16% "Asia minor". It's a trace of neolithic expansion from the Fertile Crescent into Europe according to them - and we know they're right - and the very most europeans have (variable) amounts of this component in their DNA. It's part of us since 8,000 years.
My MTDNA haplogroup is HV, genographic project associates it to neolithic expansion, too.

Sorry, I have to edit it

Hauteville
28-11-14, 18:21
Angela maltese are the europeans with higher neolithic farmer affinities (circa 93%) followed by Ashkenazi jewish. No samples from south and island Greece though in Lazaridis study.

Sile
28-11-14, 19:25
Have you guys read this ?

http://www.pnas.org/content/111/25/9211.abstract

Hauteville
28-11-14, 19:40
Yes but it is different from Lazaridis study however.

Angela
28-11-14, 20:07
Angela maltese are the europeans with higher neolithic farmer affinities (circa 93%) followed by Ashkenazi jewish. No samples from south and island Greece though in Lazaridis study.

As far as the Ashkenazim are concerned, I think that part of it may have to do with the fact that they have been mostly endogamous for the last approximately 2000 years, which means that they have preserved many autosomal (as well as uniparental)l signatures lost not only in Europe but in the Near East. The other, somewhat contradictory part of the equation is that I think the mercantile, coastal Mediterranean "Jewish" population of the Classical era which provided the "founder" groups of the non Near Eastern "Jewish" population was already pretty "mixed" away from its strictly Levantine roots. However, I don't want to derail the thread into a long discussion of Ashkenazi, in particular, ethnogenesis.

As to the Greeks, there is a dearth of samples. We don't know the origin of the samples in Dodecad. The Lazaridis study didn't use samples from the Peloponnese or the islands, to my knowledge, but their sample, which I believe is from far northern mainland Greece (Thessaly?), is 79% EEF.

The Paschou et al study does provide some academic samples for these areas, but doesn't provide an EEF/WHG/ANE analysis. As you say in your PM, looking at all their data and graphics it does seem to show that Sicilians are between the mainland and the island Greeks, so it's not unreasonable to speculate that island Greeks have more EEF, and mainland Greeks less than Sicilians. In those graphics, although a few mainlanders overlap with far southern Tuscans(probably the Thessaly group), most mainland Greeks are south of central Italians. The people of Firenze who provide the sample for the Tuscans are 75% EEF. Thessaly is 79%. By the time you get to Lazio I don't think it would be outlandish to speculate that you'd be close to the 83% levels you see in much of Spain. So I'd say that upwards of 83%, would be in the ballpark for most mainland Greeks and certainly for the Peloponnese. I wonder if they would be a more ANE shifted version of Campanians or Lucanians perhaps? However, someone should do a study on the Greeks which is careful to screen samples for long history in certain areas, at least to great grandparent level, especially given the population upheavals in Greek history in the last 1000 years and even very recently.

Hauteville
28-11-14, 20:59
As far as i know the samples of Lazaridis et al are from Thessaloniki.

oreo_cookie
29-11-14, 10:01
The Paschou et al study does provide some academic samples for these areas, but doesn't provide an EEF/WHG/ANE analysis. As you say in your PM, looking at all their data and graphics it does seem to show that Sicilians are between the mainland and the island Greeks, so it's not unreasonable to speculate that island Greeks have more EEF, and mainland Greeks less than Sicilians.

The islands sampled in that study are Cretans and Dodecanese, and from having seen many 23andme, and Gedmatch results for different Greek islanders it is likely that these Greeks have the most Near Eastern ancestry of all the islands, and other islanders seem to be more similar to the mainland, either due to proximity or due to the smaller pre-Greek populations as compared to Crete (which was heavily populated by Minoans).

Peloponnesians are very similar to other mainland Greeks. In fact some of them on the 23andme PCA plot fall near me, and I am half southern Italian, a quarter Polish and a quarter Portuguese. I suspect most mainland Greeks are a more Balto-Slavic influenced version of Abruzzese and Campanians.

Anyway, since the vast majority of the Greek population is mainland (and centered toward the north and center of the country), it makes most sense to represent Greece in studies with a mainland sample.

Angela
29-11-14, 16:31
The islands sampled in that study are Cretans and Dodecanese, and from having seen many 23andme, and Gedmatch results for different Greek islanders it is likely that these Greeks have the most Near Eastern ancestry of all the islands, and other islanders seem to be more similar to the mainland, either due to proximity or due to the smaller pre-Greek populations as compared to Crete (which was heavily populated by Minoans).

Peloponnesians are very similar to other mainland Greeks. In fact some of them on the 23andme PCA plot fall near me, and I am half southern Italian, a quarter Polish and a quarter Portuguese. I suspect most mainland Greeks are a more Balto-Slavic influenced version of Abruzzese and Campanians.

Anyway, since the vast majority of the Greek population is mainland (and centered toward the north and center of the country), it makes most sense to represent Greece in studies with a mainland sample.


Sorry, 23andme results, like the results of any private testing firm, are self-selected samples from people interested in the topic and with sufficient income to indulge their interest. Any analysis based on these results is therefore not dispositive. (The same thing happened with y Dna testing by the private companies, heavily skewed toward people of British Isles descent, which obscured the source and routes of migration of many R1b clades. Of course the results when properly understood have been very helpful in other ways.)

In addition, there is no way of knowing if any individual's "collection" of results is an "accurate" reflection of all 23andme results for a certain group as a whole. Of course, I'm excluding the situation where some hacker could have gotten into the 23andme data base, but in that case, such a person would be unlikely to present the date honestly any way, and ultimately the 23andme me samples are still not necessarily representative of any "national" group.

Therefore, only academic samples chosen using standard protocols should form the basis for any solid conclusions. Of course, such results then have to be analyzed carefully. There are academics, and then there are academics. None of their conclusions should be taken at face value. At least, however, we have scientifically selected samples most of the time as a start point.

Your decision to ignore Greek island samples is novel to say the least. Perhaps we should ignore Basque samples as well? How about the decision in Lazaridis et al to divide the Spanish sample into a "northern" group and a "southern" group? Was that a bad idea as well? Or, in a highly structured country like Italy, is it a bad idea to divide the samples into northern, Tuscan and southern Italian results?

The fact that modern Greeks (like modern Spaniards, or Italians, or anyone else) currently live in large urban areas with more economic opportunities is irrelevant for population genetics purposes. The purpose of this testing is to see if the results from "modern" populations can give us any clues about ancient migrations, which looks increasingly as if it is very problematic indeed. Unless, of course, your analysis has another purpose entirely, of which I'm unaware?

Also, you might want to refresh your recollection of Paschou et al. Samples from the Peloponnese were included in the study.

oreo_cookie
29-11-14, 19:48
Your decision to ignore Greek island samples is novel to say the least.

It's not "ignoring" it, :rolleyes2: Just stating that Crete and the Dodecanese might not be genetically representative of the islands in the North Aegean (like Lesbos) or Ionian islands (like Lefkada). And based on the differences in results I have seen for people in Crete and Dodecanese compared to other islands, they would not be representative as these are the most genetically outlying islands.

Hauteville
30-11-14, 10:38
I am curious to see what kind of look the neolithic farmers had. It's must be interesting.

Angela
30-11-14, 16:29
It's not "ignoring" it, :rolleyes2: Just stating that Crete and the Dodecanese might not be genetically representative of the islands in the North Aegean (like Lesbos) or Ionian islands (like Lefkada). And based on the differences in results I have seen for people in Crete and Dodecanese compared to other islands, they would not be representative as these are the most genetically outlying islands.

Let me rephrase: Your opinion that "it makes most sense to represent Greece in studies with a mainland sample" is novel to say the least. I've never before heard anyone interested in population genetics opine that characterizing the population of a highly genetically structured population by using one sample from one extreme of that spectrum (far northern Greece) is a good idea. I will also repeat: the population in all developed countries has moved to larger cities for work. However, in order to accurately represent the population structure of a country one must sample people from all areas. This is even more true if one is attempting to trace migration flows in order to answer questions about the peopling of Europe. However, perhaps your choices and focus are dictated by other motivations.

[QUOTE=Oreo Cookie: And based on the differences in results I have seen for people in Crete and Dodecanese compared to other islands, they would not be representative as these are the most genetically outlying islands.[/QUOTE]

That may or may not be the case. Perhaps I was unclear, so I will repeat. Any collection of results you may have assembled through sharing with people on 23andme, even if they are honestly presented, are not necessarily representative of the entire body of Greek results at 23andme, without even taking into consideration the fact that the samples at 23andme are not a scientifically chosen representative sample, so I'm afraid I find your conclusions to be on the level of anecdotal evidence.

When you are able to provide scientifically chosen samples from these areas that could be interpreted in such a way, I would, of course, be happy to discuss further what these would then say about migration flows and the peopling of Europe. I'm afraid I'm uninterested in anthrofora games on the level of who has the most North African, who has the most Near Eastern, who has the most SSA, and who has the most Asian ancestry in order to determine who is more "European" so I will not be participating in any such discussions.

oreo_cookie
30-11-14, 16:49
There was a y-dna study of the islands that showed that Crete was genetically distinct and that Chios and Lesbos were closer to the mainland; it doesn't directly translate into autosomal DNA but supports what I have seen so far, I can link you to it if you'd like.

Angela
30-11-14, 16:57
There was a y-dna study of the islands that showed that Crete was genetically distinct and that Chios and Lesbos were closer to the mainland; it doesn't directly translate into autosomal DNA but supports what I have seen so far, I can link you to it if you'd like.

I've read all the major studies about the dna of the Mediterranean so I doubt it's new to me. However, FYI, if you're going to make a claim based on a scientific study it's your responsibility to provide the link or at least the name of the study. Otherwise, I, at least, am not going to take it very seriously.

Also, as you say, we are discussing autosomal analysis here, and y Dna haplogroups are only very speculatively tied to autosomal "clusters".

Aberdeen
30-11-14, 20:11
If I was going to do a study of Greek genetics, I'd want to find out where they came from a few generations back, at least. After all, about 1.5 million people were transferred from Turkey to Greece as a result of the Chanak crisis of 1922 and that must have affected modern Greek genetics quite significantly. And of course people from all over rural Greece and nearby countries have been moving to Athens looking for jobs for several decades now, although the current economic crisis seems to be causing a small reversal of that trend. As for islands, some of them may have populations that have remained relatively stable for generations while others have had complete population turnovers, so understanding the history of the island whose population one studies would be quite important, I think.

Hauteville
30-11-14, 22:02
I always thought that the modern greeks who are more closer to ancient greeks are the maniotes. It's my opinion eh.

oreo_cookie
30-11-14, 22:13
I always thought that the modern greeks who are more closer to ancient greeks are the maniotes. It's my opinion eh.

Lakonia region? If so, it's between them and Cretans (or somewhat overlapping with both) that Sicilians plot on the study you mentioned earlier.

Hauteville
30-11-14, 22:21
A greek girl i know in my personal life (she is from Rhodes and she has studied here) said me that about maniotes. She thinks that maniotes descendent from ancient spartans and remained isolated. I also think that southern calabrians from Bovesia have manteined very good their greek genetic heritage.

oreo_cookie
01-12-14, 00:19
A greek girl i know in my personal life (she is from Rhodes and she has studied here) said me that about maniotes. She thinks that maniotes descendent from ancient spartans and remained isolated. I also think that southern calabrians from Bovesia have manteined very good their greek genetic heritage.

You'd have to see if southern Calabria and Mani plot together on a PCA plot. Calabria might end up more like Crete though.

Alan
01-12-14, 00:55
Alright, but from what I know one of the components that make up EEF is a Mesolithic component that is WHG like, please correct me if I'm wrong though.


EEF is basically ~75% Early Near Eastern Farmer and ~15 to 20% WHG like.


Sardinians come closest to Early European Farmers but perfect examples of early Near Eastern farmer don't exist anymore. But I would imagine something close to Cypriots. Since they have very low ANE (~7%) and almost no SSA (~2%) admixture.

Alan
01-12-14, 01:26
I will here speak only for myself. I get the distinct feeling at times that this obsession with quantifying the amount of "WHG" in EEF may, in some people, stem from an attempt to nail down exactly how "European" a group or a person is by taking that figure and adding it to the "regular" WHG in the figures given for modern populations in Lazaridis et al. Apparently, ANE is considered "European" enough not to raise concern, despite its eastern affinities. The short answer is that we are all 100% European, whether we come from France, or Finland, or southern Italy, and whether we can be modeled best with two or three of these ancestral EEF/WHG/ANE populations.



The funny thing. People questioning this want to be the least Near Eastern most WHG admixed but at the same time "lightest" of all, not knowing or ignoring the basic fact that genes for light skin were brought to Europe by farmers.

Greying Wanderer
05-12-14, 06:02
Questions concerning the amount of "WHG" in EEF keep being asked and again. For suggesting that it is a distraction in terms of the discussion of the peopling of Europe, a respected, published author has been attacked on another forum.

I will here speak only for myself. I get the distinct feeling at times that this obsession with quantifying the amount of "WHG" in EEF may, in some people, stem from an attempt to nail down exactly how "European" a group or a person is by taking that figure and adding it to the "regular" WHG in the figures given for modern populations in Lazaridis et al. Apparently, ANE is considered "European" enough not to raise concern, despite its eastern affinities. The short answer is that we are all 100% European, whether we come from France, or Finland, or southern Italy, and whether we can be modeled best with two or three of these ancestral EEF/WHG/ANE populations.



That may well be true but there is also another more fundamental historical reason for getting to the bottom of it imo i.e the two distinct paths East and West Asia took caused imo by the East Asian farmer expansion being more total.

The dominant theory until very recently was European replacement by neolithic farmers and that appears not to be the case probably (again imo) because the process was interrupted by the I-E. So East Asia had an almost complete farmer expansion (apart from a few refuge zones) whereas in Europe it was stalled. I'd say that was possibly quite a big deal in historical terms. For example the earlier spread of civilization in East Asia and southern Europe.

edit:

After reading through the rest of the comments

EEF is defined as 44% plus or minus 10% "Basal Eurasian". (for some reason I keep remembering it as 50 +/- 10)

Combining Basal and WHG this way and then comparing the composite to WHG separately, conceptually fits the neolithic expansion model better but when you separate the two components then it looks more like mesolithic survival so which one it actually is matters. If it's mesolithic survival (not necessarily directly but by cousin) then how come given the extent of the initial farmer expansion? The I-E are the most likely answer to how come but either way if the farmer expansion into Europe was stalled in the north did the slower arrival of farming (crop-centric version as opposed to herding version) to at least northern and central Europe have any significant consequences? I'd say the answer is likelyto be yes.

#

"Basal Eurasian peaks among Arabs. Israeli Beduins..."

If it's Bedouin then it's possibly so high because the desert was a refuge so that component could have originally been much more widespread i.e. Basal may have been in some parts of Europe (south and west) before the farmers as well as coming with the farmers.

#


"The import of the Lazaridis paper is that there were three migrations into Europe [my notes in brackets]:

1. From the Asian crossroads/Middle East in the Palaeolithic. [mtDNA U and Y-DNA IJ and F]
2. From the Middle Eastern Neolithic heartland in the Neolithic. [mtDNA U3, H, I, J, V etc and Y-DNA G, with a bit of E]
3. From the Asian steppe in the Copper Age. [Y-DNA R]"
(Jean Manco)

The following are just guesses for my own entertainment but personally I think E is likely to be or be connected to Basal, with a widespread coastal distribution including north Africa, southern and western Europe and Arabia and earlier than G - whether before or after IJ I guess time will tell although my gut feel is IJ are both the product of Basal + archaics.

I also think the fertile crescent was likely a big swamp before farmers drained it so the spread of neolithic farming was more likely from the surrounding highlands or possibly the coast.

There was probably a significant geographic / climactic feature that split R1b and R1a.

Aberdeen
05-12-14, 07:39
But was the East Asian farmer aspect the whole story prior to the Mongol expansion? If we look at the Y haplotypes among the Han Chinese, the presence of C, N and R1a might be explained solely by the 13th century Mongol expansion, but do we know that for sure? And Yong-Bin Zhao et al suggested that Q1a1 admixed into the Han Chinese about 3000 years ago. Dienekes mentioned that in his blog on August 21, 2014. And how do we explain the presence of Y haplotype J in China. It's possible that bronze may have entered China from the west, possibly associated with the Seima-Turbino Phenomenon.

arvistro
05-12-14, 09:01
The funny thing. People questioning this want to be the least Near Eastern most WHG admixed but at the same time "lightest" of all, not knowing or ignoring the basic fact that genes for light skin were brought to Europe by farmers.
I guess this is because these genes were most successful in WHG rich populations. It is needed for agricultural societies (low D vitamin) where there is not enough sun (difficult D vitamin without light skin), which in modern days happen to be the WHG peak land. If you chart WHG admixture and then light eyes, hair, skin, it surely looks like WHG folk "kidnapped" that EEF gene :)

So, am I correct? It was brought by EEFs. It was not selected as much in more Southern territories (more EEF adm in general), but got selected favorably in North (more WHG adm in general), creating this same modern paradox.

This article tells about why it is North Europe that is depigmented, Golf current is to be blamed for ensuring agriculture so far in North:
https://backintyme.wordpress.com/article/why-are-europeans-white-e1-k16kl3c2f2au-14/

Angela
05-12-14, 16:44
I think it's probably a bit more complicated than that. The mutations that are associated with depigmentation (one study does seem to show actual causation) in modern Europeans might have arisen numerous times in human history. They, like other mutations, expand or "sweep" in populations, when they are highly beneficial. Studies done on SLC24A5, a major skin lightening gene, show that it seems to radiate out of the Caucasus in all directions. A few cases of SLC42A5 showed up in far northeastern Europe, but it may have appeared in other places as well.

So far, the scientific papers seem to be in agreement that the sweep of these genes to virtual fixation in modern Europeans may be tied to the effects of agriculture in Vitamin D poor climates. I have a hunch it may also be related to the consumption of milk products.

We also know that the studies of ancient Dna using the modern predictors developed for law enforcement show that Stuttgart was "fairer" than Loschbour and LaBrana. Otzi was probably "fairer" than all of them, because he had two copies of both the major skin depigmentation genes. The Neolithic farmers in Gamba et al were fairer than the presumably "Mesolithic" farmer, and this is also the culture (100% EEF genetically) where the oldest light haired, light eyed and fair skinned sample has been found.

So, it seems to me that the scientists may indeed be on to something.

It should be remembered however, that it's possible that Mesolithic Europeans had some totally unknown skin lightening snps, and the new groups introduced a totally new set. However, I think that's highly unlikely given the extreme rapidity in evolutionary terms with which these snps spread in more northern populations, relatively speaking. I think the most logical explanation is that these snps must have provided some sort of extreme advantage in certain areas, particularly during the transition to farming perhaps, so it seems unlikely to me that they were "duplicates" so to speak.

Speaking on just a personal level, I find it both ironic and sad that something which especially in the last couple of centuries has been the cause of so much suffering and discord should come down to an adaptation to climate and diet.

Oh, and thanks for the link. Very interesting.

Alan
05-12-14, 16:53
So far, the scientific papers seem to be in agreement that the sweep of these genes to virtual fixation in modern Europeans may be tied to the effects of agriculture in Vitamin D poor climates. I have a hunch it may also be related to the consumption of milk products.



Yep thats what also went through my head when the first Blonde Bronze Age individuals to turn out in Europe( Hungary) where during a time when the first Haplogroup J2a* appeared.

The reason why this fascinated me is, because I connect the expansion of proto herders to Haplogroup J* from Zagros mountains. I think the first people to switch from classical farmers to herders were people of Haplogroup J*. Milk products can be the main reason why their was a even more lack of Vitamin D which caused for even lighter features.

I even assume this is how the "West Asian" component turned out to existence. farmers who crossed some ANE folks in mountainous regions and turned to herders. I have seen similar trend in the West Asian highlands and Kurdistan. The typical nomadic Kurdish herder has sligthly sunburned skin but usually lighter hair color, especially the children. The same is even the case among Bedouin herders. I don't know if the same is the case in other parts of the world.


Also werent there some rumors that Ötzi was probably more of a herder too? he probably took this technique over from BR2 like people from Hungary.

Whatever even if herders contributed in additional light features among Europeans or not. I think herders came to Europe with Haplogroup J*, R1a* and R1b*.

John Doe
05-12-14, 17:21
I think it's probably a bit more complicated than that. The mutations that are associated with depigmentation (one study does seem to show actual causation) in modern Europeans might have arisen numerous times in human history. They, like other mutations, expand or "sweep" in populations, when they are highly beneficial. Studies done on SLC24A5, a major skin lightening gene, show that it seems to radiate out of the Caucasus in all directions. A few cases of SLC42A5 showed up in far northeastern Europe, but it may have appeared in other places as well.

So far, the scientific papers seem to be in agreement that the sweep of these genes to virtual fixation in modern Europeans may be tied to the effects of agriculture in Vitamin D poor climates. I have a hunch it may also be related to the consumption of milk products.

We also know that the studies of ancient Dna using the modern predictors developed for law enforcement show that Stuttgart was "fairer" than Loschbour and LaBrana. Otzi was probably "fairer" than all of them, because he had two copies of both the major skin depigmentation genes. The Neolithic farmers in Gamba et al were fairer than the presumably "Mesolithic" farmer, and this is also the culture (100% EEF genetically) where the oldest light haired, light eyed and fair skinned sample has been found.

So, it seems to me that the scientists may indeed be on to something.

It should be remembered however, that it's possible that Mesolithic Europeans had some totally unknown skin lightening snps, and the new groups introduced a totally new set. However, I think that's highly unlikely given the extreme rapidity in evolutionary terms with which these snps spread in more northern populations, relatively speaking. I think the most logical explanation is that these snps must have provided some sort of extreme advantage in certain areas, particularly during the transition to farming perhaps, so it seems unlikely to me that they were "duplicates" so to speak.

Speaking on just a personal level, I find it both ironic and sad that something which especially in the last couple of centuries has been the cause of so much suffering and discord should come down to an adaptation to climate and diet.

Oh, and thanks for the link. Very interesting.

This would explain why I can be on one hand fully Ashkenazi Jewish but on the other hand be very fair, those light features were in west Asia all along! And since we don't really know how the Neolithic near eastern or even the iron age near eastern genetic landscape looked like, it's possible it was like that even when proto-Ashkenazis were still there.

John Doe
05-12-14, 17:22
Yep thats what also went through my head when the first Blonde Bronze Age individuals to turn out in Europe( Hungary) where during a time when the first Haplogroup J2a* appeared.

The reason why this fascinated me is, because I connect the expansion of proto herders to Haplogroup J* from Zagros mountains. I think the first people to switch from classical farmers to herders were people of Haplogroup J*. Milk products can be the main reason why their was a even more lack of Vitamin D which caused for even lighter features.

I even assume this is how the "West Asian" component turned out to existence. farmers who crossed some ANE folks in mountainous regions and turned to herders. I have seen similar trend in the West Asian highlands and Kurdistan. The typical nomadic Kurdish herder has sligthly sunburned skin but usually lighter hair color, especially the children. The same is even the case among Bedouin herders. I don't know if the same is the case in other parts of the world.


Also werent there some rumors that Ötzi was probably more of a herder too? he probably took this technique over from BR2 like people from Hungary.

Whatever even if herders contributed in additional light features among Europeans or not. I think herders came to Europe with Haplogroup J*, R1a* and R1b*.

Good point.

Greying Wanderer
07-12-14, 03:21
But was the East Asian farmer aspect the whole story prior to the Mongol expansion? If we look at the Y haplotypes among the Han Chinese, the presence of C, N and R1a might be explained solely by the 13th century Mongol expansion, but do we know that for sure? And Yong-Bin Zhao et al suggested that Q1a1 admixed into the Han Chinese about 3000 years ago. Dienekes mentioned that in his blog on August 21, 2014. And how do we explain the presence of Y haplotype J in China. It's possible that bronze may have entered China from the west, possibly associated with the Seima-Turbino Phenomenon.

Yes it gets complicated very fast - partly why I'm keen on the first two or three steps being fixed if at all possible i.e. is there a more OOA "Basal" component originally widespread but centered somewhere around the middle-east and an "ASE" component that back migrated from S/SE Asia.