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Thursday, November 26, 2015

First Neolithic genomes from Greece


Just in at bioRxiv: Hofmanová et al., Early farmers from across Europe directly descended from Neolithic Aegeans

The main focus of the preprint are five Neolithic genomes from north-central Greece and northwestern Turkey. They're very similar to previously published Neolithic European and Anatolian samples, and strikingly different from present-day Greeks and Turks, pointing to major genetic turnovers in the Aegean region since the Neolithic.

The manuscript also reveals that, somewhat unexpectedly, two Mesolithic individuals from Thessaly, central Greece, belong to mtDNA haplogroup K1c. This is not a marker typical of other Mesolithic Europeans. It's a pity their genome-wide structure wasn't analyzed.

By the way, the key to Figure 2 lists Lithuanians and Mordovians as "Slavic", which is an oversight and needs to be corrected.

A bigger problem, however, is the mixture analysis presented in Figure 3. Loschbour-related ancestry is obviously inflated by East Asian admixture, hence it peaks among such groups as the Nogais of the North Caspian steppe, even though in reality they have very little Western European hunter-gatherer ancestry, if any.

Also, it seems to me that Ashkenazi Jews are used to represent Poles in the mixture analysis, because there's a slither of Yourba admixture in the pie-chart sitting over Poland. If so, that's a bit silly.

62 comments:

Shaikorth said...

I looked over ancient mtDNA catalogued at the Ancestral Journeys site, and these two mesolithic Greeks appear to be the only K1c to predate Bronze Age. According to the lists there it is found in German Bell Beakers and BA Hungarians but not in Neolithic farmers.

Davidski said...

Fair enough, I'll change it to "this is not a marker typical of Mesolithic Europeans".

Krefter said...

Quote from paper.
"The dissimilarity and lack of continuity of the Early Neolithic Aegean genomes to modern
Turkish and Levantine populations, in contrast to those of early central and southwestern
European farmer and modern Mediterraneans, is best explained by subsequent gene-flow into
Anatolia from yet unknown sources. "

We were in the same situation with North Europe. Then we learned Steppe is the source. CHG could at least partially be the source for a shift in West Asia and SE Europe. That's what one abstract suggested.

Ponto said...

Ancient Levantine farmers or hunter/gathers were not tested, so the study erred in its claim of a discontinuity with modern Levantine populations. With modern Anatolian populations who are genetically tied to Turkic populations in Central Asia, the claim of a discontinuity is a no brainer.

Pity the Mesolithic Greek samples were too dna poor to do more extensive genome testing.

With the inclusion of the Yoruba as an proxy ancient African sample, the report would have done better with the older Ethiopian caveman sample.

Krefter said...

@Pontus,
"With modern Anatolian populations who are genetically tied to Turkic populations in Central Asia"

You're assuming Turks from Central Asia were similar to people in Turkey today. Despite Turkish being among modern people most similar to neighboring non-Turks in West Asia. And we know the first Turks were from Siberia and probably similar to modern Siberians. We have to assume even if Turks mixed with West Asians then came to Anatolia, that in Anatolia there was already a genetic shift since the Early Neolithic.

Davidski said...

Ha. You just called him Pontus.

Karl_K said...

Pontus! Classic!

Simon_W said...

I hope people will start to realise that more LNBA samples are needed. EN farmers were roughly the same all over Europe. In the case of Greece a few samples from the classic era would be interesting too, to really see the degree of continuity or discontinuity to modern Greeks. We don't want to rely on inference from linkage disequilibrum in modern DNA all the time...

Grey said...

Thinking aloud again but... the Hyksos might seem too late to be connected to any of this but on the other hand Egypt may have been the last stop on the line from wherever the Hyksos started?

Onur said...

With modern Anatolian populations who are genetically tied to Turkic populations in Central Asia, the claim of a discontinuity is a no brainer.

The discontinuity in Anatolia cannot be explained only or largely by the Turkic migration to Anatolia since all the populations of Anatolia and the nearby regions show a similar discontinuity. That is largely because of post-Neolithic CHG admixture in Anatolia and the nearby regions. Modern populations of Anatolia, Armenia, the South Caucasus, Cyprus and Iran more or less fall on a cline between Anatolian Neolithic farmers and the Caucasus hunter-gatherers (CHG):

https://drive.google.com/file/d/0B9n4j3PQ81RcQ0lsOGJEMEVyUVU/view?usp=sharing

Kristiina said...

It looks like K1c is almost completely European. Moreover, K1c has not been identified in ancient farmer samples as if K1c reached Europe before farming:
K1c1 Northern Europe, Italy
K1c 16224C! Iberia
K1c152C! Poland, Ireland
K1c1a Italy
K1c1c Finland, Russia
K1c1b North Western Europe
K1c1d Germany
K1c1g Great Britain, USA
K1c1f Slovak, Germany, Finland
K1c1e Russia, Poland, Romania
K1c2 North Western Europe

K1 root has been found in Europe, Georgia and in an Azeri.

Did you notice that there is no H in Neolithic Greece in this analysis. There was not so much H in Barcin and Menteşe either: T2b, J1c11/J1/J1c, K1a2, K1a3a, K1a4, K1a4, K1a2, K1a/ K1a1, K1a/ K1a6, K1a-C150T, K1b1b1, H/ H5-C16192T, H5, N1b1a, N1a1a1a, N1a1a1, N1a1a1a, N1a1a1, U3, U3, U8b1b1, W1-T119C, X2m2, X2d2.
In Barcin and Menteşe only 7.7% is H and it may all fall in H5. Mesolithic K1c has not been found in Turkey (instead, K1a and K1b are found) and Neolithic X2b either. It looks like the oldest branches of X2b are today found in France, Spain and Morocco. In Portalón there was H3 and H3c and the oldest mtDNAs were K1a2b, J1c1b1 and X2c.

The new paper concludes that “Aegean Neolithic populations can be considered the root for all early European farmers and their colonization routes. A key remaining question is whether this unbroken trail of ancestry and migration extends all the way back to southeastern Anatolia and the Fertile Crescent, where the earliest Neolithic sites in the world are found. Regardless of whether the Aegean early farmers were ultimately descended from western or central Anatolian, or even Levantine hunter-gatherer, the differences between the ancient genomes presented here and those from the Caucasus indicates that there was considerable structuring of forager populations in southwest Asia prior to the transition to farming.”

IMO, the route of different H clades into Europe is interesting and the question still remains unresolved. It looks like several “Neolithic” mtDNA lines reached Mediterranean early and even before farming.

Jean said...

"The manuscript also reveals that, somewhat unexpectedly, two Mesolithic individuals from Thessaly, central Greece, belong to mtDNA haplogroup K1c. This is not a marker typical of other Mesolithic Europeans."

It is not entirely unexpected. A member of this team lectured (in Greek) on the Mesolithic and Neolithic mtDNA results from Greece in this project back in 2012. None was U. http://dienekes.blogspot.it/2012/12/talk-by-christina-papageorgopoulou-on.html

This actually makes sense as the few Mesolithic sites in Greece tend to be coastal and similar to the Natufian in the Levant i.e. it looks as though a few Near Eastern hunter-gatherers followed the coast northwards and westwards as far as Greece as the climate improved.

Krefter said...

@Kristiina,

K1c is defined by HVR2 mutations that are rarely tested. It's one of those haplogroups we don't much about it's distribution.

Europe is a man made location. Eurasia is a contious pieace of land. So, Greece, Anatolia, bla bla, doesn't matter. It's all the same area. Greece is closer to Anatolia than top Hungary. To treat Greece and Hungary as being in the same region as opposed to Anatolia doesn't make sense.

If anything the K1c from Mesolithic Greece suggests they were not WHG and had "Near Eastern" ancestry.

Rob said...
This comment has been removed by the author.
Ponto said...

@Kefter

No, I made no such assumption, but you did in your reply. Central Asia is a zone of admixture where the original Turkic speakers from nearby modern Mongolia and of similar appearance, admixed with all the other ethnic groups that had moved to Central Asia. However you cannot deny the genetic effects of both the Seljuk and Ottoman Turks on the population of Anatolia. As to the post Neolithic change in Anatolia is concerned more evidence is needed from ancient dna from Anatolia, the Levant, and Arabia. Otherwise everyone is running off half cocked.

What definitely is needed is dna from the ghosts, the Basal Eurasians, it is not proven that two Caucasian hunter/gatherers were those ghosts.

Ponto is actually a Tolkien name for Hobbit men.

Kristiina said...

Krefter, there is one very good academic paper that analyzes also the distribution of different K clades. I would not dismiss that paper in this context. Researchers concluded that K1c1 probably arose in Europe: “Haplogroup K arose within haplogroup U8~36 ka, in Europe or the Near East, with the MINOR subclades K1b, K1c and K2 all most likely arising in Europe, between the last glacial period and the Neolithic (Fig. 1; Supplementary Note 1; Supplementary Data 1–3; Supplementary Figs S1–S3; Supplementary Tables S1–S3). K1a expanded from ~20 ka onwards, both in the Near East and Europe, with its major subclade, K1a1b1 (Fig. 2), mainly restricted to Europe (with a few instances in North Africa), arriving from the Near East by ~11.5 ka, the beginning of the Holocene”

(http://www.nature.com/ncomms/2013/131008/ncomms3543/full/ncomms3543.html)

Among Barcin and Menteşe haplotypes, there is one haplotype, K1b1b1, that could go back to K1b1 which according to the paper most likely arose in Europe. The others fall into typical Near Eastern subclades such as K1a3 and K1a4 or typical Druze subclades such as K1a6.

In Kleitos Greece we find the same haplotype as in Barcin Turkey K1a2.

A detailed phylogenetic tree of U8’K is available here http://www.nature.com/ncomms/2013/131008/ncomms3543/full/ncomms3543.html#supplementary-information

Rob said...

Kristiina

Thanks
So 'K' is U8. Makes sense , but U groups were widespread in Eurasia.

Kristiina said...

Yes, the archetypal Near Eastern haplogroup K is a U haplogroup, and it could indeed be an indication that the Near Eastern component(s) carry Kostenki ancestry as Kostenki was U2. U8 and U2 both belong to U2'3'4'7'8'9 which forms a clade to the exclusion of U1, U5 and U6. We know that WHG is closely connected with U5.

ryukendo kendow said...

@Kristiina,

I am very bad with mtDNA haplogroups, could you describe the structure of haplogroup U a bit more? Would love to know what it suggests about the movements of western crown eurasian populations, which it seems associated with.

Onur said...

@Ponto

However you cannot deny the genetic effects of both the Seljuk and Ottoman Turks on the population of Anatolia. As to the post Neolithic change in Anatolia is concerned more evidence is needed from ancient dna from Anatolia, the Levant, and Arabia. Otherwise everyone is running off half cocked.

Anatolian Greeks and Armenians show no sign of Turkic admixture yet they are similarly shifted towards Caucasus hunter-gatherers (CHG) away from Early Neolithic Anatolians as Anatolian Turks are. Just wait for the publication of the paper that documents the genetic change of Anatolia beginning from about 5,000 BC (Late Neolithic) from the EEF-type structure to a more Caucasus-like structure that Krefter mentioned in the qpAdm tour thread, which is also consistent with the craniometric changes in Anatolia during the same times from the dolichocephal Mediterranid and Pontid types to the brachycephal Anadolid, Armenid, Taurid and Asian Alpinid types. You can find the abstract of that paper on this thread (the first abstract):

http://eurogenes.blogspot.com.au/2015/07/a-little-more-on-genome-wide-affinities.html

Kristiina said...

U2'3'4'7'8'9
Haplogroup U2 is most common in South Asia but is also found in low frequency in Central and West Asia, as well as in Europe as U2e. U3a is found in the Near East, the Caucasus and northern Africa and Europe and U3b is widespread across the Middle East and the Caucasus. Coalescence age for U3a is estimated as 18,000 to 26,000-years-ago while the coalescence age for U3b is estimated as 18,000 to 24,000-years-ago. U7 is considered a West Eurasian-specific mtDNA haplogroup, believed to have originated in the Black Sea area approximately 30,000-years-ago peaking in Iranians. U4 dates to approximately 25,000 years ago, and has been found in all Siberian and Fennoscandian hunter gatherer cultures and, apart from its expansion to Eastern and Northern Europe and West Asia, it is an autochthonous haplogroup of Nganasans, Mansi, Ket and Kalash. Haplogroup U9 is a rare clade in mtDNA phylogeny, characterized only recently in a few populations of Pakistan. Its presence in Ethiopia and Yemen points to gene flow along the coast of the Arabian Sea. Haplogroups U9 and U4 share two common mutations at the root of their phylogeny.

The distribution of U8 is availale here http://www.nature.com/ncomms/2013/131008/ncomms3543/extref/ncomms3543-s1.pdf

U5
Molecular dating suggests that the coalescence time estimate for the U5 is ∼25–30 thousand years (ky), and ∼16–20 and ∼20–24 ky for its subhaplogroups U5a and U5b, respectively. Phylogeographic analysis reveals that expansions of U5 subclusters started earlier in central and southern Europe, than in eastern Europe.

U6
Our own estimate of the time to the most recent common ancestor (TMRCA) for U6, using the current enlarged set of complete sequences, is 35.3 (24.6 - 46.4) ky. This period coincides with the Early Upper Paleolithic (EUP) period, prior to the Last Glacial Maximum, but cold and dry enough to force a North African coastal route.
U1

Haplogroup U1 is found more often in eastern Europe, Anatolia and the Near East. It is also found at low frequencies in India. U1 is an ancient haplogroup, with an estimated age of about 32,000 years. U1 was found in at about 4% frequency in Svanetia (Georgia, Caucasus).

According to this paper (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4166928/), U5 and U6 split is 50 kya and U2'3'4'7'8'9 is somewhat older than U5.

Both U8 and U5 have been found in ancient remains in Dolni Vestonice, Czech Republic, 31 kya. U2'3'4'7'8'9 has been found in ancient remains in Pagliacci Cave, Italy c.11 kya. By 11 kya, U2'3'4'7'8'9 clades were already diverged so I wonder if this specimen was U8. Considering that U8 has been found in Czech Republic and Italy, it is not impossible that K arose in the Mediterranean Europe.

Kristiina said...

To sum up, U subclades could be ordered as follows: U2 in India, U1, U3 and U7 in the Near East, U4 and U9 in Central Asia, U6 in Africa and U8 and U5 in Europe.

Rob said...

Kristiina

Thanks (!) for that summary
I read somewhere, however, that K reaches peak highs in some Caucasus groups (eg Daghestani) ?

hesychius said...

I inferred from reading the paper that the genetic discontinuity between Neolithic Aegeans and modern Mediterraneans (i.e., Italians, Greeks, etc.) was mainly caused by genetic drift instead of "genetic turnovers" (not that I dispute any proof of genetic/biological upheavals). Figure 2 on page 5 shows modern Mediterranean populations clustering together and being closer to Early Neolithic samples/clusters than other modern Indo-European population clusters. Also, the authors state on page 8 that "...each Aegean Neolithic genome closely corresponds genetically to modern Mediterraneans, and in particular Sardinians...with few substantial contributions from elsewhere." So the genetic discontinuity described for the Aegean appears to be quite different from the type of genetic discontinuity between Early Neolithic farmers and modern Turks and Levantines (see page 12). Hopefully, future studies will have even greater samples of ancient DNA that will provide a clearer picture of the past.

Great post Davidski and thanks for letting me leave a comment.

Davidski said...

Random genetic drift can't explain the genetic shifts in the eastern Mediterranean, because the changes are too big and affect many different populations in similar, but always not always the same, ways.

So admixture is the main cause. I'd say Greeks have about 30% ancestry from western Anatolian and Greek Neolithic farmers. The rest came to Greece after the late Neolithic from West Asia, the steppe and Northern/Eastern Europe. On the other hand, Sicilians have much less "recent" ancestry from Northern/Eastern Europe and more from North Africa.

Kristiina said...

This paper was published yesterday http://www.nature.com/jhg/journal/vaop/ncurrent/full/jhg2015132a.html
“Coevolution of genes and languages and high levels of population structure among the highland populations of Daghestan” (I somehow managed to see the supplementary information for free!)

I would not say that the frequencies are specifically high everywhere: the highest frequencies are in Godoberi 5/31 (Nakh Daghestanian/Avar-Andic) and Kumyk 5/62 (Altaic/Turkic/Kypchak). In this new paper, Avar (Nakh-Daghestanian/Avar-Andic) frequency is 3/85. The frequencies of H, X and T are higher than K frequency.
In a previous paper there were the following frequencies: Avars 8/61, Dargins 13/110, Adyge 13/155, North Ossetians 12/138, Georgians 3/76.

By way of comparison, Wikipedia tells us that “the average of European K frequency is 5.6%. K appears to be highest in the Morbihan (17.5%) and Périgord-Limousin (15.3%) regions of France, and in Norway and Bulgaria (13.3%). The level is 12.5% in Belgium, 11% in Georgia and 10% in Austria and Great Britain”.

Krefter said...

@Davidski,

How did you come up with 30%?

Davidski said...

Just a rough guess.

It can't be much more than that, considering the position of Greek Neolithic farmers and modern Greeks on PCA, and the fact that many of the populations moving into Greece after the Neolithic already had Anatolian/EEF-type Neolithic admixture themselves.

hesychius said...

Interesting point Davidski, but if genetic shifts in the Eastern Mediterranean were attributed mainly to genetic admixture, then the modern Mediterranean cluster in Figure 2 would have been even more distant from the Early Neolithic samples and have heavy overlap with non-Mediterranean Indo-European populations with hunter-gatherer admixture. Also, genetic drift can have as much of a significant impact on a population as genetic admixture especially in areas such as the Aegean where the inhabitants adapted to alterations in their standard of living and even survived natural cataclysms (see "The Early Bronze Age in Greece" by Daniel Pullen). This is not to say that admixture doesn't occur or that it's unimportant in the study of past and present populations. However, it's no accident that the authors mention the close genetic correspondence between Neolithic Aegean populations and modern Mediterraneans and make no mention of any significant foreign/unknown gene-flow to the Aegean as the primary cause for the genetic discontinuity between the Neolithic Aegean and modern Mediterraneans. If the Italians and Greeks, for example, were genetically distant from their Neolithic predecessors as the Turks and Levantines based strictly on foreign/unknown admixture, then the authors would have lumped the former groups in with the latter groups on page 12. Ultimately, the genetic data-analysis submitted by the authors doesn't exclusively rule out genetic drift as a significant cause for genetic discontinuity in the Aegean.

Thanks for letting me respond.

P.S. I think your estimate of 30% is off. According to Kalevi Wiik ("Where Did European Men Come From?"), the Greeks have 48.6% ancestry from Early Farmer population groups (see Table 1 on page 38). I don't know how accurate Wiik's percentage is, but I do know that it does confirm the fact that the spread of farming from Asia Minor to Greece was predominantly a demic phenomenon.

Roy King said...

@hesychius,
I think that Davidski is more or less correct--what you don't understand is that Mediterranean Europeans, like Cypriots have a huge influx of CHG to the initial Neolithic substratum. This would include Sicilians, some Greeks, and S Italians and is way beyond the steppe admixture--see Srkz's IBD plot of CHG-Yamnaya. Even late Neolithic Kumtepe apparently will have a large CHG input. So the Cyclades, the Cretans and likely S Italy and part of mainland Greece received a Late Neolithic to Late Bronze input from Anatolia.

Davidski said...

hesychius,

You don't seem to know how drift works and the effect it can potentially have on these types of analyses.

Sardinians are actually one of the most highly genetically drifted populations in Europe, and the Sardinian sample from the HGDP is the only population that clusters with early European and Anatolian farmers.

The reason they cluster with these early farmers, despite their heavy genetic drift, is because they have been shielded from significant admixture events since the Neolithic, and drift doesn't affect broad (eg. West Eurasian-wide) ancestral components.

In fact, it's because of these Sardinians that early European and Anatolian farmers are said to be similar to present-day Mediterraneans.

Greeks, southern Italians and Sicilians carry significant levels of admixtures that aren't shared with early Neolithic farmers, and the reason they carry them is not because of parallel drift processes with, say, West Asians, North Africans, and North/East Europeans, but because they have significant post-Neolithic admixtures from these groups.

There are lots more ancient samples on the way from Greece, so you'll eventually see how various populations contributed to the genetic makeup of present-day Greeks. The genetic shifts you'll see will be massive, and these will be due to admixture not drift.

Ponto said...

I can tell you that as far as Maltese Islanders are concerned, they have a lot of North African ancestry, mostly Berbers with little sub Saharan ancestry. The North Africans were the chief source of slaves, and were freed on becoming Christians.

The other groups West Asians and North/East Europeans are negligible as admixture. I only know of one post Norman Arab family that chose to become Christians due to their wealth, but they eventually died out due to marriages between uncles and their nieces. All Maltese Islanders are related because they come from the same founder population, and if male descendants of Mehmed II arrived in Malta from Italy and Sicily in the 15th century, every Maltese Islander is related to those men. That is what happens in small islands.

Krefter said...

BTW, West Asian admixture in SE Europe probably predates historical records.

@Ponto,

Davidski is speaking of pre-historic or undocumented North Europe/West Asia ancestry. The Slavs obviously made an impact on non-Slavic speaking SE Europeans, including some Greeks. Slavs in Early Middle Ages settled in Balkans mixed with locals. Then those locals(eg, Bulgarians) mix with Greeks.

jparada said...

krefter, slavic tribes settled as far south as the peloponessus. So admixture from Bulgarians and such is likely not the only source of Slavic ancestry in Greeks.

Arch Hades said...

"So admixture is the main cause. I'd say Greeks have about 30% ancestry from western Anatolian and Greek Neolithic farmers"

I'd say that's way too low an estimate. That's more accurate for a place like Britian.

Why were Greeks modeled by Haak et all as being 67% descended from EEFs? Since EEFs are 90% Neolithic Anatolian, Greeks should at least be 60% Anatolian-'Greek' Neolithic farmer, no?

Davidski said...

The question isn't how much admixture Greeks have from Neolithic Anatolia or Fertile Crescent. The question is how much admixture Greeks have from Neolithic Greece.

My figure of ~30% is based on the assumption that many of the groups moving into Greece after the Neolithic already had high levels of Neolithic Anatolian admixture.

Why wouldn't they? Think about it, even the various Eastern European invaders would've had double digits of the stuff.

Also, Haak's Yamnaya/EEF modeling didn't include CHG, so the 67% for Greeks is no longer valid. How can it be? And how did you not pick this up?

Arch Hades said...

"The question isn't how much admixture Greeks have from Neolithic Anatolia or Fertile Crescent. The question is how much admixture Greeks have from Neolithic Greece."

I see,

Well then that's possible, it's pretty difficult to tell either way I guess.


Also, Haak's Yamnaya/EEF modeling didn't include CHG, so the 67% for Greeks is no longer valid. How can it be? And how did you not pick this up?

I did think of this, but didn't mention it because I figured most CHG in Greeks is from Yamnaya dispersals. You think this is wrong? Yamnaya is 50% CHG as you know. If CHG made it's way to Greece before Yamnaya/Indo-European dispersals, then we're looking at a pretty narrow window of time, since the 4,000 BC farmers in Greece are identical to the 6,300 BC farmers. What do you think 2,500 BC populations were like in Greece?

There is of course hypotheticals of Greeks receiving more than trivial geneflow from the Near East in historical times, but then again Haak had a model which included modern Levantines and Greeks showed no admixture from these guys [unlike Sicilians].

Davidski said...

Greeks have a lot of admixture from post-Neolithic Anatolia. This is not a hypothetical. That's where most of their CHG comes from, and it was being picked up in part as ANE/Yamnaya in earlier papers, because CHG has a similar eastern shift.

Sicilians have admixture from the Levant and North Africa, that's why they get better fits in Haak when modeled as partly Bedouin.

This will all become clear with more ancient DNA. Greek ancestry is as complex as anything in Europe. Anyone who doesn't realize this yet must have had their brains rotted away by reading Dienekes.

James said...

Haak's purple BedouinB component is also in Sardinians - about the same amount Greeks have, and half the amount that's in Sicilians/south Italians. So some of it is in fact shared with Neolithic farmers, since Sardinians are identical to early European and Anatolian farmers.

Davidski said...

I wasn't talking about the Admixture run, but the f4 models. Admixture isn't a formal mixture test, unlike the f4 ratio test.

And Sardinians aren't identical to Neolithic European farmers, although some are very similar.

Ponto said...

@Kefter

I am European by birth, I do not need an Australian Pole or an admixed American to tell me about Europe's history. Don't teach your grandfather how to suck eggs. Davidski does not need you to hold his prick when he pisses.

A lot of Admixture studies are flawed due to assumptions made by the researchers. With far Southern Europeans it must be the Middle East where admixture comes from, hence the usage of Africanized Middle Eastern Bedawi tribes by the researchers, while ignoring the obvious which is North Africa. The Spanish, the Sardinians, the Southern Italians and the Maltese all have North African admixture. For a long time researchers fixated on the Mongol Urdu as contributors of Mongolian like ancestry in Northern Europeans. Now we know about the ANE, the Baikal boy and the man who liked like Captain Picard of the Enterprise. With Southern European they could have used a purer source of West Asian ancestry in the Cypriots, but no, it has to be the Bedawi.

Krefter said...

@Ponto,

"I am European by birth, I do not need an Australian Pole or an admixed American to tell me about Europe's history."

Actually Americans are unique in this way. We have parents who have little common ancestry since the Bronze age.

Where is this coming from? When did I ever claim to know more about Europe? The fact is Europeans, and probably everyone in the world, are very mixed. People from outside of Europe and within Europe constantly move and mix with each other.

Our oral history is very limited. Our knowledge of geography and history was always small before school. No one knew what was European or non-European or what was native to certain region or their own genetic history. People just moved around mindlessly and mated with whoever they wanted to. You shouldn't have this attitude that "I'm Mr. European in genetics and culture" and admit you don't know who your ancestors were, that you're mixed, and your ancestors constantly moved from place to place.

You're wrong and I'm pointing out how you're wrong, it's as simple as that. Nothing personal, I'm not attacking you. You just not understanding the data. The data is giving a clear message. There's only one way to interpret it. Your only argument against me is the methods used to get the data is inaccurate.

North African admixture in South Italy, Iberia, Sardinia, Malta, and where ever else is minor. There's a clear pull towards West Asia in SE Europeans and a lesser extent Iberians.

I dis agree with Davidski that this admixture came in historical times. IMO, it came in the Bronze age. No one remembers when Corded Ware stormed half of Europe. Just as no one remembers when there were large migrations of West Asians into the Balkans and Italy.

Arch Hades said...

In Haak's ADMIXTURE run, at K=18 a very small percentage of that purple component is found in Stuttgart farmer. Though it's not found at all in Oetzi or LBK farmers. Either way it looks pretty minimal in Southern Europe.


"There's a clear pull towards West Asia in SE Europeans and a lesser extent Iberians."

Well even Northern Europeans have that pull. Look how much further east they are than WHGs and EEFs. They just plot much more North, which is explained by their significantly less EEF. So CHG and ANE can all be the main factors pulling SE Europeans east towards West Asia. The Levantine/purple component plays a role in SE Europe but it looks pretty minimal to me.

James said...

True. Even Gamba, Ust-Ishim and SwedenHG have some purple; Kostenki has a ton. No reason to think all or most of it in SE is recent.

In all of the PCA's from the latest studies, South Euros look like a Farmer-Yamnaya/CHG mix with more Farmer. No strong "Bedouin" affinity.

http://dienekes.blogspot.com/2015/11/neolithic-farmers-from-greece-and.html

http://dienekes.blogspot.com/2015/11/westasian-in-flesh-hunter-gatherers.html

Davidski said...

Here's what it says in Haak on page 124.

Figure S9.27: Adding BedouinB as a 5th reference population improves residuals for Maltese, Sicilians, Ashkenazi Jews, and Spanish.

This is strong formal statistical evidence of recent (ie. post-Yamnaya) gene flow from the Near East to southern Europe.

Rob said...

Dave
How certain can we be that's it's recent and not archaic stuff whicj never made its way into temperate Europe ?

Davidski said...

There's IBD sharing between southern Euros and Middle Easterners/North Africans that can't date back to more than the Iron Age, because the segments are too big.

But even if we assume that there's something wrong with the IBD stats, like the direction of gene flow being mixed up, then clearly many southern European populations still have Bedouin-related admixture from somewhere. If it's really ancient, then I wonder why Neolithic Anatolian farmers lack it?

Rob said...

Thanks
I guess its distribution exclusively along the Mediterranean littoral also speaks in favour of it

Arch Hades said...

In Haak, It's only found in Sicily and 'Spain'. Northern Spain, Tuscany, Northern Italy, and all the Balkan samples including Greeks and Albanians [SE Europe] didn't have the Levantine/'Bedouin' admixture. My guess Greek Cypriots would have a lot of it though.

But yeah, it looks to be something that arrived in Europe after 3-4,000 BC. Maybe some of it came from Phoenician colonization or something. I don't know what 'Bronze age' expansions Krefter is thinking of. There is Roman and medieval era as well.

Krefter said...

@Arch Hades,
"I don't know what 'Bronze age' expansions Krefter is thinking of."

I'm not referring to any historical or archaeological record of migration. I think it came in the Bronze age, because what's inbetween 3000 BC and the begging of historical age: Bronze age.

Rob said...

Arch
That's what i recalled
So I wonder if the BA shift in SEE was caused by something other- like a direct CHG-like input, with minor additional EHG in more recent periods (eg with Slavs etc)

Krefter

The Bronze Age in Europe is dated differently depending on sub region: In the Balkans; the true Bronze Age begin c.2250 BC (prior to this is a sort of "proto-Bronze age" from 3000-2300 BC. )

In Central Europe, it begins even later - 1800 BC

Ariele Iacopo Maggi said...

"I wasn't talking about the Admixture run, but the f4 models. Admixture isn't a formal mixture test, unlike the f4 ratio test."

cherry picking

Davidski said...

No, you fool, formal statistics override ADMIXTURE results.

James said...

It's known already that Sicilian and Spanish have some Moorish admixture, but not more than a few percentages. That must be what the f4 models are detecting, and why none is detected in Sardinia, North Italy and the Balkans. So a little of the purple is recent, but most is not.

Sicilians still cluster with Greeks, and Spanish still cluster with North Italians, so their ancestries can't be all that different.

Davidski said...

Well at least now you're thinking.

But you didn't consider the possibility that most southern Euros have CHG ancestry above what they acquired from the steppe.

If this is so, and it does look plausible, then the question is did this extra CHG arrive with the Bedouin-related signal, or is it a separate issue?

See, that's what I'm saying here; we haven't yet got much of an idea of what happened in the Med area. That's probably coming next year.

Karl_K said...

"If this is so, and it does look plausible, then the question is did this extra CHG arrive with the Bedouin-related signal, or is it a separate issue?"

"Maltese, Sicilians, Ashkenazi Jews, and Spanish."

Ashkenazi Jews most likely came into Europe through Southern Italy, or at least they are most similar (but that could because of a shared source population).

So why couldn't they have been a small part of a larger migration that just happened to stay more culturally and therefore genetically isolated?

If that was true, it would narrow down the timeline of BedouinB admixture.



Karl_K said...

Some great quotes in this thread:

Krefter:
"People just moved around mindlessly and mated with whoever they wanted to."

"Europe is a man made location."

Davidski:
"No, you fool, formal statistics override ADMIXTURE results."

Pontus:
"Don't teach your grandfather how to suck eggs. Davidski does not need you to hold his prick when he pisses."

All classics!

Simon_W said...

@ Rob

Well, how do you define the "true Bronze Age"? In the German terminology it starts when tin Bronze occurs more often than very rarely, though isn't yet predominant either, a state which in central Europe is reached in c. 2200 BC. But the terminology that seems to win in the DNA camp already calls the preceding era with predominant copper and arsenic Bronze the "early Bronze Age". And if you prefer to wait for the era when tin Bronze predominates, that started in central Europe with the classical Unetice c. 1900 BC.

Rob said...

Simon
Yes definitely after 2500 BC in SEE,
As for Central Europe; I'm not fussed on picking between 2200 or 1900
Btw; have a look at the question I asked you in the next thread up

Simon_W said...

Rob

Do you mean this question: "I'm not sure I'd make much of some 4% in the odd Iberian Chalcolithic sample. How's this shaped your perspective on the spread of R1b-L51 west ?" It's in the thread after the next thread.

I think this post of mine had addressed your point:

"If the Basques had their 8% EHG from a population like the German Bell Beakers who had 25%, then they needed about 1/3 German Bell Beaker ancstry. Seems like a lot, but not impossible imho.
This would have given them about 7% CHG from German Bell Beakers (who had 21%). So since Basques have 22% CHG, they must have 15% independent CHG admixture. = less than the German Bell Beaker admixture. So there is still good reason to believe that their R1b is from the latter, not the independent CHGs.
It's true, there really is quite some J2 in southwestern and even northern Europe, too, so that is reasonably associated with the independent CHG influence. But probably also with some rare variants of R1b, like found on Sardinia."

Arch Hades said...

J2 was found in Neolithic Anatolian right? They were 60% G2, but did have some J2 as well IIRC.

Onur said...

@Arch

J2 was found in Neolithic Anatolian right? They were 60% G2, but did have some J2 as well IIRC.

Yes, one of the northwestern Anatolian Early Neolithic samples was found to be J2a. It was one of the Barcin samples. So certainly J2 existed among Early Neolithic Anatolians, but in much lower frequency than G2a.