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kostop
07-06-16, 09:48
A really interesting study carried out by the Univeristy of Mainz (Germany) in collaboration with the University of Thrace (Greece)

http://www.pnas.org/content/early/2016/06/01/1523951113/suppl/DCSupplemental

We have new data on neolithic individuals from Greece and Anatolia. G2a pops up again, strongly indicating a link between Aegean populations and the Iceman. mtDNA hgs mostly K1, nothing unusual here.

Closest modern populations are Sardinians, Greeks, and Italians, while modern Turkish inhabitants of Anatolia do not seem to be related to the neolithic population of the region.

Other data points to lactose intolerance, depigmented skin and dark eyes.

In general, the paper reinforces the theory that early European farmers spread from the Aegean.
It contains a wealth of information, it will take me a while to go through everything...

Angela
07-06-16, 22:06
Thanks Kostop.

We discussed some of this on a prior thread started by you. Here it is:
http://www.eupedia.com/forum/threads/31454-Ancient-DNA-from-Greece?highlight=Neolithic

I think this is the pre-print from late 2015.
http://biorxiv.org/content/biorxiv/early/2015/11/25/032763.full.pdf

This is the link to the final version, which contains the abstract:
http://www.pnas.org/content/early/2016/06/01/1523951113

"Farming and sedentism first appeared in southwestern Asia during the early Holocene and later spread to neighboring regions, including Europe, along multiple dispersal routes. Conspicuous uncertainties remain about the relative roles of migration, cultural diffusion, and admixture with local foragers in the early Neolithization of Europe. Here we present paleogenomic data for five Neolithic individuals from northern Greece and northwestern Turkey spanning the time and region of the earliest spread of farming into Europe. We use a novel approach to recalibrate raw reads and call genotypes from ancient DNA and observe striking genetic similarity both among Aegean early farmers and with those from across Europe. Our study demonstrates a direct genetic link between Mediterranean and Central European early farmers and those of Greece and Anatolia, extending the European Neolithic migratory chain all the way back to southwestern Asia."

Well, nothing very new about any of that.

Anyone have a link to the new full version beyond the abstract?

Ed. The samples were also discussed in this thread:
http://www.eupedia.com/forum/threads/31744-Neolithic-Greek-and-Anatolian-genomes

Angela
07-06-16, 23:31
I've been saying for a few years that CHG probably started to arrive in the western parts of Anatolia, at least, pretty early, and that therefore we could perhaps speculate that there was a later Neolithic wave into Europe that carried it, meaning that not all the CHG in Europe arrived after the Neolithic. I repeatedly wondered why someone didn't analyze the later samples to see if we could get a handle on this question, or some of the late Neolithic samples from the Balkans. For some strange reason, bloggers declined to do it.

Well, this team has done it, and indeed they have CHG and so do the later Neolithic samples from Greece. Now I suppose we'll have to hear from the academics again to find out what some mid-to-late Neolithic samples from the rest of the Balkans and Italy show.

Interesting also that the same group hinted in prior publications that there was very little change in Greece from the late Neolithic to the Bronze Age, although I think that was based only on mtDna? We'll have to wait for subsequent papers, and also to see if that was true more generally in southern Europe.

Ed. The Kuntempe sample is the Anatolian Neolithic sample to which I am referring, and not only this sample, but the later Greek Neolithic samples show the CHG.

Angela
08-06-16, 01:03
Perhaps the fact that among the Early European farmers only the samples from Hungary show some admixture with hunter-gatherers might have something to do with the large population of them around the Danube Gates, as many of us have speculated before?

"most other early Neolithic farmers also show the same ancestry componentwith no evidence of admixture with hunter-gatherers. The only exceptions are NE1, NE3 and NE4(data from Gamba et al. [81]). This result agrees with the f 4-statistic analysis (see SI7, TableS26), where the HungaryGamba EN group containing these samples also demonstrates an apparentsignal of admixture with hunter-gatherers."
(from the supplement, page 69)

I do think there is evidence for this second Neolithic wave:
"For K=3, all Neolithic samples demonstrated mixed ancestry withat least some CHG-defined component in addition to the WHG-defined component described about.Interestingly, the CHG cluster was found at a higher proportion in Aegeans than other Early Neolithicsamples, especially for Kumtepe4. The difference between Kumtepe4 and earlier Aegeans in termsof higher CHG influence was also observed using f -statistics (SI7)."

As for population continuity since the Neolithic for Greece and Turkey, this is what they have to say:

"Together, these results indicate that the ancient genomes are not sampled from a population continuouswith modern Greeks or Turks. However, genetic drift alone would still be able to explainthe differences seen between our ancient genomes and the modern populations samples if the ancientpopulations were very small."

Of course, total continuity from the earliest or even the later Neolithic is nothing I, at least, have ever proposed, but similarity is something different again. There are some interesting graphics in the paper about the areas in modern Europe where those similarities are the highest. Most of that information is in the Supplement.

Angela
08-06-16, 02:30
Goodness, it looks like I missed a lot of the fun, if you can call what's been going on, fun. I don't, but that's another issue.

The bone of contention seems to be the following graphic. I don't see what all the fuss is about, frankly. It does require one to read the paper in order to understand what the authors are getting at, but it seems that they're just trying to visually show the proportions of the various Neolithic samples in the modern populations of West Eurasia. The Loschbour "black" seems to be a sort of stand in for all the hunter-gatherer groups, certainly EHG, but also CHG, if the modern Turkish samples are any indication. Doesn't that make sense? I doubt the authors were trying to taint the sacred European-ness of the WHG by associating them with Mongoloids, but then I don't think academics approach this material with those kinds of concerns.

Or is it the lack of "Loschbour" in certain samples that is the problem? Poland certainly has less of the "Loschbour" black than one would expect.*

It also does seem a little odd that southern Germany and the border area between France and Germany have little to no "Loschbour". I expected that result for southern Italy, but the graphic would indicate it's also true of Macedonia and Albania? Sicily has more, but that might be from the settlement of the island by groups from northern Italy during the Middle Ages. In fact, the biggest difference between those two areas seems to be the tiny sliver of Yoruba in Sicily, which also shows up in some of the Iberian samples, although in Iberia it may be masked by what makes up North African since they have more of it than Sicily.

I need to check this against the formal stats.

Ed. * Had I read more carefully, I would have realized that the small graphic on the area of Poland is for the Ashkenazim. Also, the large circles refer to the ancient populations. In terms of modern Turkey, the "Loschbour" might also include East Asian/Turkic.

That this graphic is confusing is clear, but it still gives good information about the different Neolithic groups in modern populations, and of course this is only one part of this paper.

If the graphic is too small, follow this link:
https://www.researchgate.net/profile/David_Diez_del_Molino/publication/284727438/viewer/AS:[email protected]/background/6.png
https://4.bp.blogspot.com/-hWFcwkfIp6Q/V1YjP6VOzTI/AAAAAAAAEgc/_E_HUr-bdDYzqd2Pjwk2WGLMQ5p6-JnCgCLcB/s637/Nonsense.png

Fire Haired14
08-06-16, 06:47
@Angela,

Those ancestry percentages with Neo genomes and Loschbour are complete nonsense. Poor job by the authors. They used Ashkenazi Jews to represent Poland and didn't use an East Asian reference(hence high Loschbour score for East Asian-admixed groups). CHG isn't being replaced by WHG, the scores are just nonsense.

There's a spreadhseet in supp. info though where they model modern/ancient genomes as a mixture of modern genomes. It makes some sense but is really just a waste. The only part of this paper that is worth while is the formal stats, and there they don't even list the number of SNPs used in each run which is crucial information. If you use 10,000 SNPs for example the test result has to be ignored.

I really feel this whole study was a waste. I respect the skill and work of the authors but we already have genomes from Neolithic Anatolia. People have been studying the genetic origins of the European Neolithic with ancient DNA for years now. Their only samples that are of any use are the ones from Mesolithic Greece and those are the only ones they didn't get autosomal DNA from. Very disappointing. There's really no use for this study at all.

Tomenable
08-06-16, 07:08
They used Ashkenazi Jews to represent Poland

Oh, good to know. I already started wondering who killed our dear hunters...

BTW - pie charts for Syria, Lebanon and Cyprus look similar to Ashkenazi.

holderlin
08-06-16, 15:55
@Angela, Their only samples that are of any use are the ones from Mesolithic Greece and those are the only ones they didn't get autosomal DNA from.

Seriously. I was scouring the appendix and I didn't catch a clue until I read the methods.

lame

Angela
08-06-16, 17:03
Well, I'm sure some of the premier researchers in the world at premier institutions of higher learning will be devastated to learn that some one still in high school, or some blogger of unknown education or training thinks there was no point to this study. It may seem strange to you, but some of us are actually interested in knowing the different types of Neolithic immigrants and where their influence is stronger. We're also interested in how much change there was with the Copper and Bronze Age transitions in southern Europe, which this group will no doubt publish about relatively soon, one hopes.

How dare you or anyone else presume to judge what should interest other people? That's why I don't post on certain sites or threads. The major topic of conversation doesn't usually interest me very much. I don't, however, go on the site or thread and call people morons because they are interested in them, but then I'm a civilized person.

Some of us also read papers carefully, and are pretty good at reading comprehension, which through exposure to various posters and bloggers I can say is definitely not the case for them. Even I occasionally slip up. If I had read really carefully, I would have known that the pie chart on the area of Poland was for the Ashkenazim.

Perhaps that was the cause for the meltdown, total lack of professionalism, extraordinary bad manners, and foul language? Well, all is now clear. The hunter gatherer ancestry for the Poles is secure.

It would also be appropriate for you and certain bloggers to acknowledge that those of us who maintained that a later wave of the Neolithic, perhaps exemplified by Kumtepe, might have brought some CHG relatively early to western Anatolia, and perhaps to Europe before the Bronze Age might actually be correct. You do remember your insistence and that of others that all of the CHG in Europe absolutely came with the Bronze Age or indeed much later in the case of southern Europe, don't you? Or are you going to adopt the practice of certain people and never acknowledge mistakes in the hope that people will have forgotten them? I'm cursed with a very good memory so I don't forget.

You people make me tired. I've told you before, Fire-Haired. You're learning the wrong lessons from the wrong people; if you continue down this path you'll pay for it both professionally and personally. There, I'm sick of taking this mother role. Do as you wish.

berun
08-06-16, 18:53
Frankly I'm also somewhat puzzled with this paper:


Additionally, the analysis for K=2 to K=8 and the supervised analysis for K=3 (supervised for CHG, Motala and Anatolian) was repeated while including Yamnaya individuals, a group that are considered to be the descendants of a major hunter-gatherer migration from the east during late Neolithic [102].

err.... what???


Early Neolithic farmers again demonstrate almost no evidence of hunter-gatherer admixture, while it is still observed in the Middle Neolithic farmers. However, much of the Late Neolithic hunter-gatherer ancestry from the previous analysis is replaced by Yamnaya ancestry. These results are consistent with Haak et al. [102] who demonstrated a resurgence of hunter-gatherer ancestry followed by the establishment of eastern hunter-gatherer ancestry.

I don't believe much in admixture calculations because as with statistics you can do that they mean whichever thing you want; if the Aegean Neolithics had a faint HG percentage, and late Aegean neolithics received some CHG, we have the good licours to make the best cocktail: Yamnayans before Yamnayans in Neolithic Greece!! party must go on!! lets roll the rock!! [sorry for the irony, but as nobody hears the red alarms...]

Angela
08-06-16, 20:25
I don't believe much in admixture calculations because as with statistics you can do that they mean whichever thing you want; if the Aegean Neolithics had a faint HG percentage, and late Aegean neolithics received some CHG, we have the good licours to make the best cocktail: Yamnayans before Yamnayans in Neolithic Greece!! party must go on!! lets roll the rock!! [sorry for the irony, but as nobody hears the red alarms...]

I've posted some articles on this site to the effect that Admixture analyses are both over-interpreted and misinterpreted. However, interpreted correctly, they provide another tool for analysis of dna. You can use the search engine to find them if you're interested.

On your other point, I don't follow your logic. All later migrations into and around Europe are just admixtures of more ancient groups in different proportions. The Yamnaya steppe people can be modeled as half EHG and half CHG. That's a very far cry indeed from the people of Neolithic Greece who were overwhelmingly EEF.

berun
08-06-16, 23:27
The "logic" behind is like that:

1. Provide a base EEF
2. Give a litte admuxture of fresh WHG related to EHG
3. Some bubbling CHG in late neolitic
4. Shake it gently
5. Serve a late neolithic population with a Yamnaya elite or alike

Yetos
09-06-16, 01:37
I think that nearby future will be full of surprises,
for many theories.

holderlin
09-06-16, 04:40
Well, I'm sure some of the premier researchers in the world at premier institutions of higher learning will be devastated to learn that some one still in high school, or some blogger of unknown education or training thinks there was no point to this study. It may seem strange to you, but some of us are actually interested in knowing the different types of Neolithic immigrants and where their influence is stronger. We're also interested in how much change there was with the Copper and Bronze Age transitions in southern Europe, which this group will no doubt publish about relatively soon, one hopes.

How dare you or anyone else presume to judge what should interest other people? That's why I don't post on certain sites or threads. The major topic of conversation doesn't usually interest me very much. I don't, however, go on the site or thread and call people morons because they are interested in them, but then I'm a civilized person.

Some of us also read papers carefully, and are pretty good at reading comprehension, which through exposure to various posters and bloggers I can say is definitely not the case for them. Even I occasionally slip up. If I had read really carefully, I would have known that the pie chart on the area of Poland was for the Ashkenazim.

Perhaps that was the cause for the meltdown, total lack of professionalism, extraordinary bad manners, and foul language? Well, all is now clear. The hunter gatherer ancestry for the Poles is secure.

It would also be appropriate for you and certain bloggers to acknowledge that those of us who maintained that a later wave of the Neolithic, perhaps exemplified by Kumtepe, might have brought some CHG relatively early to western Anatolia, and perhaps to Europe before the Bronze Age might actually be correct. You do remember your insistence and that of others that all of the CHG in Europe absolutely came with the Bronze Age or indeed much later in the case of southern Europe, don't you? Or are you going to adopt the practice of certain people and never acknowledge mistakes in the hope that people will have forgotten them? I'm cursed with a very good memory so I don't forget.

You people make me tired. I've told you before, Fire-Haired. You're learning the wrong lessons from the wrong people; if you continue down this path you'll pay for it both professionally and personally. There, I'm sick of taking this mother role. Do as you wish.


I really hope you're not talking to me because I don't blog around with beta white supremacists.

It was sort of a lame paper. We're a bunch of spoiled dilettantes who want all the answers because we know they're only time, effort, and maybe a little diplomacy away.

I was actually really interested in the CHG because it supported my theory of a CHG mediated allele share between EEF and the Villabruna samples.

Fire Haired14
09-06-16, 10:18
Well, I'm sure some of the premier researchers in the world at premier institutions of higher learning will be devastated to learn that some one still in high school, or some blogger of unknown education or training thinks there was no point to this study.

This paper made mistakes and I pointed them out. My criteria doesn't change facts. My age and education doesn't change the fact they made mistakes. I overeacted that I was my only mistake. But really I didn't overeact very much. The paper isn't a total waste, but they did make bone headed mistakes and left out analysis that would have been interesting.


It may seem strange to you, but some of us are actually interested in knowing the different types of Neolithic immigrants and where their influence is stronger. We're also interested in how much change there was with the Copper and Bronze Age transitions in southern Europe, which this group will no doubt publish about relatively soon, one hopes.

I'm interested in that to. I never said I wasn't interested. It's just they made mistakes in their analysis that make scores in EEF subgroups unrelaible. They didn't include East Asian and ancient European ancestor references that aren't Loschbour or EEFs. No one is WHG+EEF. They should know this. The other mistake they made is using Ashkenazi Jews as their Polish reference. They should know better.


How dare you or anyone else presume to judge what should interest other people? That's why I don't post on certain sites or threads. The major topic of conversation doesn't usually interest me very much. I don't, however, go on the site or thread and call people morons because they are interested in them, but then I'm a civilized person.

I never said I wasn't interested in that.


It would also be appropriate for you and certain bloggers to acknowledge that those of us who maintained that a later wave of the Neolithic, perhaps exemplified by Kumtepe, might have brought some CHG relatively early to western Anatolia, and perhaps to Europe before the Bronze Age might actually be correct.

That's an interesting idea. I don't trust the D/F4-stats from this paper and so won't look at them as evidence or lack of evidence for this theory. I don't trust the D-stats from this paper Davidski got completely differnt results when he recreated some of the D-stats and because they don't list SNP-number.


You do remember your insistence and that of others that all of the CHG in Europe absolutely came with the Bronze Age or indeed much later in the case of southern Europe, don't you? Or are you going to adopt the practice of certain people and never acknowledge mistakes in the hope that people will have forgotten them? I'm cursed with a very good memory so I don't forget.

I'm not confident about any theory concerning CHG, outside of theories saying it is a popular type of ancestry in the Caucasus and Yamnaya. All I've looked at are D-stats and PCA. We only have one high coverage CHG genome. We need another one in order to determine how much CHG ancestry exists in modern populations. My guess is that most CHG in Southern Europe is of Steppe origin and that CHG ancestry is only important for Northern West Asians.

I've posted my opinion that peoples from West Asia(maybe they were part CHG), not CHG people, made a considerable genetic impact on Southern Europe after the Neolithic. I'd be happy to admit I'm wrong. I don't care. I just like learning. I haven't been proven wrong yet. All of the Neolithic Aegean genomes look like EEFs with maybe minor non-EEF admixture. Kum6 on PCA pulls pretty strongly away from EEF towards the Near East. I haven't read the paper thoroughly yet, so I don't have a definite opinion yet on this issue.

There are lots of holes in our data. No one provides a decent mtDNA/Y DNA database online. No one has sequenced enough full mito-genomes to create a good world-wide or continent or region wide database. The same is true for high coverage Y DNA. Almost all of our ancient DNA so far is from a handful of locations in Europe. Worthwhile data, like detailed analysis of autosomal or mtDNA/Y DNA, is hidden in hard to find studies online. Unless you keep track of blogs/forums online that are dedicated to the subject, you won't find any useful data.

Because of all the holes in our data I'm not confident of any theories that aren't based on ancient DNA. How Southern Europe changed from EEF to what it is today(Not saying it is a genetically-defined region because it isn't. Greeks share nothing in common with Spanish or Tuscans) is a mystery and we have too many holes in data to be confident of much. Data I've seen suggests there's Steppe and Near Eastern ancestry, but I don't have any theories about the fine details.


You people make me tired. I've told you before, Fire-Haired. You're learning the wrong lessons from the wrong people; if you continue down this path you'll pay for it both professionally and personally. There, I'm sick of taking this mother role. Do as you wish.

You're tired because I overreacted. Thanks for the advice you give anyways. I have learned from it. I think you might be too much of a perfectionist though.

Fire Haired14
09-06-16, 10:21
It was sort of a lame paper. We're a bunch of spoiled dilettantes who want all the answers because we know they're only time, effort, and maybe a little diplomacy away.


Very True.

Angela
09-06-16, 15:34
I really hope you're not talking to me because I don't blog around with beta white supremacists.

It was sort of a lame paper. We're a bunch of spoiled dilettantes who want all the answers because we know they're only time, effort, and maybe a little diplomacy away.

I was actually really interested in the CHG because it supported my theory of a CHG mediated allele share between EEF and the Villabruna samples.

No, Holderlin, of course I wasn't, and your idea is an interesting one.

Angela
09-06-16, 18:15
The "logic" behind is like that:

1. Provide a base EEF
2. Give a litte admuxture of fresh WHG related to EHG
3. Some bubbling CHG in late neolitic
4. Shake it gently
5. Serve a late neolithic population with a Yamnaya elite or alike

I don't think we can draw those sorts of conclusions from the data we have at hand.

The only thing that the data from the paper indicates is that around 4000 BC there was a spike in CHG in northwest Anatolia, although there was also some in earlier Neolithic migrants to Europe. Neither of those things should be a surprise, in my opinion. We have a J2a result in the Early Anatolian farmer samples, and uniparental data from many papers points to an eastern Anatolian or Caucasus source for J2a. From there it spread in many directions, one of which was to India with the Neolithic.

That CHG spike can also be seen in Europe. Years ago Dienekes ran Otzi's genome through his calculators, and he showed a Caucasus percentage of 22.3%, although let's be clear that this is different from "West Asian", which has a "Gedrosia" "component". (Might that be why he doesn't have a very typical EEF skull?). We also get J2 in Hungary in Sopot/Lengyel cultures. Those samples have also not been analyzed yet by the the internet posters, although they apparently have the ability to do it. I guess we'll have to wait and see what forthcoming academic papers have to say.
http://dienekes.blogspot.com/2012/04/first-look-at-dna-of-neolithic.html

As to the Kumtepe samples, is there anything in the archaeology to indicate that this is an "Indo-European" culture? Is that what some people are afraid of, that someone will try to resurrect the Out of Anatolia theory for the Indo-European languages? If anyone has some links about the Kumtepe culture that would be helpful, that would be great. I'll check our prior threads.

For my part I am totally persuaded that some of the Indo-European languages moved directly from the steppe into Europe. I'm keeping an open mind about the earliest branch, the "Anatolian" one. David Anthony of course maintains that it left the steppe early, moved down through the Balkans and then entered Anatolia from the west. That's certainly possible, although he proffers no archaeological evidence to support that, and although I've looked through as many papers as I could find, I came up with nothing. The other possibility is that it moved from the Caucasus south and then west. I don't see how we can tie that to Kumtepe however. If "Anatolian" did move from the steppe south through the Caucasus into Anatolia one would think it carried some EHG with it, and there's no indication of that from Kumtepe, although it may have happened later. If Anatolian was actually spoken in or just south of the Caucasus then it wouldn't necessarily have much or any EHG. Again, however, I don't know if there's any indicia of the "Indo-European" culture in Kumtepe.

There's nothing to say, of course, that the "Anatolian" speakers, if they came south from the Caucasus, weren't quite different from the steppe people who went to Europe. It's just that I don't think this sample has much to offer in terms of answering those kinds of questions.

Angela
09-06-16, 18:59
Fire-Haired:They didn't include East Asian and ancient European ancestor references that aren't Loschbour or EEFs. No one is WHG+EEF. They should know this. The other mistake they made is using Ashkenazi Jews as their Polish reference.

One graph is not an entire paper. Is this the best paper I've ever read? No. Is it confusing? Yes. This reaction you're parroting is totally over the top, though, besides obviously being inappropriately expressed. When people react like this there's something besides a disagreement over methodology or labeling on a graph going on: there's something emotional or an agenda behind it, and no, I'm not talking about you as the source of that.

Yes, the graph is confusing, but if you read the paper and the entire supplement and the explanations for the graphics carefully, which I also didn't do to a sufficient degree, you can figure out what they're trying to show. That chart only means to provide a visual for the places where the similarity to different Neolithic groups are the highest. Of course they understand everyone is not just a mixture of WHG and EEF, and that the Mongolian sample is not Loschbour plus Neolithic. If, instead of flying off the handle, you and others had actually gone through the entire Supplement you would have seen that they obviously didn't intend to imply that.* And for goodness sakes', they didn't use the Ashkenazi sample as the Polish reference sample. Stop repeating nonsense. They placed the Ashkenazi "pie" there in the region of Poland because if you're going to place them in Europe, that's approximately where they should be placed. That's where they lived and built their distinctive culture, there and in surrounding areas in Russia and Lithuania. It was confusing for a minute, but not if you went back and actually looked at everything carefully. This hysteria is borderline mad. Everybody knows that the Ashkenazi Poles and the Christian Poles are not the same people genetically. Even the popular press wouldn't get that wrong if that's the fear.


Greeks share nothing in common with Spanish or Tuscans)

How can you possibly write such a thing? Greeks and Spaniards and Tuscans share tons of Neolithic farmer ancestry. How can they have nothing in common with each other? There are dozens of analyses, admixture, IBD, PCA, etc., which show that some northern Greeks from Thessaly overlap the southernmost Tuscans, and the rest plot south and east of the Tuscans. Albanians and people from Kosovo are also very close to them autosomally. Now, what precise population movements created these similarities we don't know, and won't know until we get ancient dna, if then, but to say they have nothing in common with each other is just flat out wrong.


I think you might be too much of a perfectionist though.



Yes, well, so I've been told all my life. It takes all kinds to make a world, though, and perfectionists have their place too even if they're not always the easiest people to be or be around. They keep themselves and everybody else up to the mark.

*Ed. If people would just look in the supplement, they clearly model that Mongolian sample as 0% Loschbour. To imply that they meant anything else is deliberately misleading.

berun
09-06-16, 19:30
I don't think we can draw those sorts of conclusions from the data we have at hand.

From the Figure S32 of the paper:


Genomes from the Late Neolithic additionally demonstrate a substantial amount of ancestry from a group related to the people of the Yamnaya culture.

That's the sort of problem with Yamnaya, if someone finds shared auDNA between two populations then someone can think that one of them must be the ancestor of the other, and this case is a good example about how this statement is false as the "Yamnaya ancestry" might come from two different ancestors: EHG through the WHG substrate plus the late CHG arrival; Indoeuropeans or Yamnayans in Late Neolithic Aegean is plainly absurd at le linguistic and archaeological level.

Angela
09-06-16, 21:06
The first analysis of a Kumtepe sample was done in Omrak et al

We discussed it here:
http://www.eupedia.com/forum/threads/31842-Anatolia-is-the-source-of-the-European-Neolithic?highlight=Kumtepe

This is the link to the full Omrak et al paper...
http://www.cell.com/cms/attachment/2042476822/2055464038/mmc2.pdf

This is the link to the supplement.
http://www.cell.com/cms/attachment/2042476822/2055464037/mmc1.pdf..

I haven't yet read the complete paper or supplement, although I've seen a graphic or two, because I lost track of that thread. In the beginning, all we had was the abstract because it seemed the paper was behind a pay wall. I know that my initial reaction was that the results showed that the sample probably contained CHG admixture. It now appears that was correct. I also wondered whether the paper specifically didn't say that because that CHG sample hadn't yet come out. Once I get the time to read the data and supplement I'll see whether that was the case.

In the meantime, some quotes from that paper that were posted in our thread:

"The Anatolian Kum6 individual falls close to the early and middle Neolithic European farmers, showing a tendency toward modern-day Near Eastern populations. Interestingly, Kum6 does not group with any modern-day Anatolian populations. These results were confirmed by outgroup f3 statistics where, among modern-day groups, Kum6 shows the greatest genetic similarity to Sardinians, Greeks, and Cypriots, whereas modern-day Anatolian populations display lower levels of genetic affinity to Kum6 (Figure 2)."

I have to check if they included any southern Italian populations. I would think they might show the same kind of genetic similarity as do the Greeks.

"We computed D statistics [20] to further investigate additional genetic relationships between ancient Europeans with
sufficient sequencing coverage (>13) and Kum6. All proposed tree topologies where the Tyrolean Iceman [20] was included as one of the in-groups were rejected (2 < jZj < 4.6), suggesting gene flow or a more recent shared ancestry between Kum6 and the Tyrolean Iceman (Figure 4A). A similar tendency was observed with a Middle Neolithic Hungarian farmer [23], (co1), contemporary with the Tyrolean Iceman, resolution due to the low coverage of Kum6 and Co1. The observed genetic affinity between the Tyrolean Iceman and Kum6 could be interpreted as additional contacts between western Anatolia and Neolithic Europe at a later stage. This scenario is congruent with mitochondrial [29] and archaeozoological [30] studies, as well as the archaeological indications of multiple waves of contact between the Balkans and Anatolia. "

The paper under discussion shows the same thing.

Finally...
"the third component (green) is mostly found in the modern-day Near East and Caucasus, and the highest proportion of this third component among Neolithic individuals was observed in Kum6 (45% for K = 9). The notion that this component is West Asian is also supported by its presence in a Bronze Age Armenian sample (51%), which contains less than 2% of the orange component. Interestingly, this ‘‘West Asian’’ component (green) is not related to the potential genetic material brought to Europe by migration during the Bronze Age and recently connected to the Yamnaya culture [19, 24], visualized in Figure 3 as light blue, and it is observed in high frequency in modern-day people from southern Asia. The elevated ‘‘West Asian’’ affinity of Kum6 is likely to be the cause of the genetic differentiation observed between Kum6 and all other ancient farmers shown in the PCA plot (Figure 1B.). "

I don't know that I'd call it "West Asian" in Dodecad terms, but I'd certainly call it a Caucasus component.

Greying Wanderer
09-06-16, 22:59
@Angela


David Anthony of course maintains that it left the steppe early, moved down through the Balkans and then entered Anatolia from the west. That's certainly possible, although he proffers no archaeological evidence to support that

When I read about the Anatolian IE the consensus idea seemed to be they didn't conquer but arrived for some reason and then gradually took over from the inside.

To me that sounds more like invited artisans / traders / mercenaries than a tribal migration in which case they could have arrived by sea without a trail.

However that doesn't help with


one would think it carried some EHG with it

unless they were quite a small minority and we haven't found any Hittite bigwigs yet.

Angela
10-06-16, 04:26
Just to clarify, Omrak et al analyzed both Kumtepe 6, which they said was found in a Neolithic context and is dated to 5000-4500 BC., (4700 BC) and Kumtepe 4, dated 3500-2800 BC. However, the low coverage they got for Kumtepe 4 means that they used it only to confirm the patterns in Kumtepe 6. So, the quotes above from Omrak et al really are related to the older Kumtepe sample. Even at that early period, Omrak et al found that Kumtepe 6 included 45% of a "green" component which was found at 51% in the Armenian Bronze Age. The "European Neolithic" component was orange.

Kumtepe 4 is from the Early Bronze of Anatolia and is dated from 3500 to 2800 BC.

In the Hofmanova paper presently under discussion the Kumtepe sample is also labeled Kumtepe 6, is dated 4846 - 4618 BC and is said to be in a Chalcolithic context. Unless I'm missing something, this would seem to be the same sample that was analyzed in Omrak et al, despite the fact that they're calling it Chalcolithic. It's certainly not from 3500-2800 BC.

Even in the earlier period under discussion, this seems to have been an area that was heavily involved in dairy farming. Many of the pottery sherds seem to be from cheese strainers and butter churns.
https://www.academia.edu/714609/Patterns_of_Dairying_in_Coastal_Northwestern_Anato lia

A summary of the Anatolian Chalcolithic. There was a lot of regionalism and so there could have been a lot of genetic variation.
https://www.academia.edu/9491182/Anth.245_Ppt._lecture-4_Chalcolithic_Anatolia_Anth.245_Mediterranean_Are a_by_G._Mumford_

See also:
The Middle Chalcolithic Cultural Sequence of the Troad
https://www.academia.edu/14422493/The_Middle_Chalcolithic_Cultural_Sequence_of_the_T road_Northwest_Anatolia_Chronological_and_Interreg ional_Assessment._In_B._Horejs_M._Mehofer_eds._Wes tern_Anatolia_before_Troy._Proto-Urbanisation_in_the_4th_Millennium_BC_OREA_Orienta l_and_European_Archaeology_1_Vienna_2014_125_155

Fire Haired14
10-06-16, 09:50
How can you possibly write such a thing? Greeks and Spaniards and Tuscans share tons of Neolithic farmer ancestry. How can they have nothing in common with each other? There are dozens of analyses, admixture, IBD, PCA, etc., which show that some northern Greeks from Thessaly overlap the southernmost Tuscans, and the rest plot south and east of the Tuscans. Albanians and people from Kosovo are also very close to them autosomally.

The only thing they share in common genetically is similar proportions of ancestry from pre-historic West Eurasians, unless someone proves they have more recent connections(which is possible). They share as much in common as Ukrainians and Irish do. I was thinking of recent and ethnic connections which as far as we know Spain/Italy/Greece have none.

Fire Haired14
10-06-16, 09:51
Just to clarify, Omrak et al analyzed both Kumtepe 6, which they said was found in a Neolithic context and is dated to 5000-4500 BC., (4700 BC) and Kumtepe 4, dated 3500-2800 BC. However, the low coverage they got for Kumtepe 4 means that they used it only to confirm the patterns in Kumtepe 6. So, the quotes above from Omrak et al really are related to the older Kumtepe sample. Even at that early period, Omrak et al found that Kumtepe 6 included 45% of a "green" component which was found at 51% in the Armenian Bronze Age. The "European Neolithic" component was orange.

Kumtepe 4 is from the Early Bronze of Anatolia and is dated from 3500 to 2800 BC.

In the Hofmanova paper presently under discussion the Kumtepe sample is also labeled Kumtepe 6, is dated 4846 - 4618 BC and is said to be in a Chalcolithic context. Unless I'm missing something, this would seem to be the same sample that was analyzed in Omrak et al, despite the fact that they're calling it Chalcolithic. It's certainly not from 3500-2800 BC.

Even in the earlier period under discussion, this seems to have been an area that was heavily involved in dairy farming. Many of the pottery sherds seem to be from cheese strainers and butter churns.
https://www.academia.edu/714609/Patterns_of_Dairying_in_Coastal_Northwestern_Anato lia

A summary of the Anatolian Chalcolithic. There was a lot of regionalism and so there could have been a lot of genetic variation.
https://www.academia.edu/9491182/Anth.245_Ppt._lecture-4_Chalcolithic_Anatolia_Anth.245_Mediterranean_Are a_by_G._Mumford_

See also:
The Middle Chalcolithic Cultural Sequence of the Troad
https://www.academia.edu/14422493/The_Middle_Chalcolithic_Cultural_Sequence_of_the_T road_Northwest_Anatolia_Chronological_and_Interreg ional_Assessment._In_B._Horejs_M._Mehofer_eds._Wes tern_Anatolia_before_Troy._Proto-Urbanisation_in_the_4th_Millennium_BC_OREA_Orienta l_and_European_Archaeology_1_Vienna_2014_125_155

Thanks for the info. Because of the low coverage of Kum4 we can be sure of anything.

Angela
10-06-16, 16:36
[/COLOR]The only thing they share in common genetically is similar proportions of ancestry from pre-historic West Eurasians, unless someone proves they have more recent connections(which is possible). They share as much in common as Ukrainians and Irish do. I was thinking of recent and ethnic connections which as far as we know Spain/Italy/Greece have none.

Obviously, you understand that they do indeed have a lot in common, but that isn't what you wrote. Words matter, Fire-Haired. It's very important to use them properly to accurately convey meaning.


Thanks for the info. Because of the low coverage of Kum4 we can be sure of anything.




I'm assuming you meant to write "we can't be sure of anything". That isn't at all, however, the conclusion that can be properly drawn. Both papers seem to have analyzed Kumtepe 6, which is high coverage. The low coverage of Kumtepe 4 is therefore irrelevant to that analysis.

Unless, of course, you're saying that the Hofmanova paper analyzed the Bronze Age Kumtepe 4 sample. If that's the case, could you point me to where it says that in the paper?

holderlin
11-06-16, 05:06
@Angela



When I read about the Anatolian IE the consensus idea seemed to be they didn't conquer but arrived for some reason and then gradually took over from the inside.

To me that sounds more like invited artisans / traders / mercenaries than a tribal migration in which case they could have arrived by sea without a trail.

However that doesn't help with



unless they were quite a small minority and we haven't found any Hittite bigwigs yet.


This had to be a very early departure and not coincidentally it's the oldest historically attested IE language because it was the first to encounter a literate civilization. Hittite is about as archaic as they come among IE. This is actually why when I saw the Yamnaya samples at Z2103 it made perfect sense as the modern Z2103 distribution fits the range of Anatolian languages perfectly. I bet IE Anatolian was in Anatolia by 3000BC.

Remind me, is there any WHG in the bronze age Armenian at all? It doesnt matter though because I wouldn't be surprised by this admixture at all if the Y DNA line had been in the region for 1600 years among non IndoEuropean populations.