When the tools and settings matters. Part 1 and Part 2

 When the tools and settings matters. Part 1

Here I present two models with exactly same source and target populations.

The first one is unscaled, and the second one is scaled.

As You can see the most significant change affect the EHG level which is 2.5 times higher in the unscaled.

You may wonder which one is the most correct. Well, the unscaled coordinates are the one that are produced by the smartpca in their unaltered form.

While the scaled coordinates are deliberately altered by an algorithm. I don't know exactly how this algorithm works.

But the main idea of scaling is too artificiality increase the distance for distant and drifted populations. For instance, in the East Asian populations but also the local drifted pops like CHG and Turkey_N. Those artificial changes alter the result in different ways. As You can see for Armenians it is creating a masking effect that hides the real EHG.

It must be noted the qpadm numbers are close to the unscaled numbers. But qpadm also has its own tips and secrets.

In any case questions like how much EHG, Levant or CHG do have an X population do not have a strict answer. They are rather ranges than just one correct answer.

When the tools and settings matters. Part 2

Here I add a modification to the models present in the first part. I am adding samples from South Caucasian farmers. Similar populations existed all over historic Armenia and north Mesopotamia. Here we use a generic term for them as Central farmers.

The addition of this new population changes once more the results in both unscaled (the first) and the scaled (the second). The EHG increases once more (average 5.5) but the difference between unscaled and scaled is now very low. You can also notice that the fits are improved, and the errors are reduced. Which means that those farmers are a better source for Armenians (and not only Armenians) than those four distal pops.

Why?

The reason of this is that modern Armenians and not only Armenians are not a real mixture of four West Asian distal populations.

Central farmers =//= Turkey_N + Kotias + Ganj Dareh + Natufian

Central farmers are only approximately similar to the addition to those four populations. But the real history of West Asia, which is not fully uncovered, most probably will show that the deep origins of Central farmers is different. That is something of the future but at this stage we must know that Central farmers are more basal than the four distal pops combined. The Turkey_N and the Kotias-CHG have a WHG related alleles which acts as a mask for the EHG. Thus, the addition of a basal population like Central farmers lacking this WHG causes an increase of EHG. While the difference between the scaled and the unscaled decrease because the model does not rely anymore on distal four populations whose coordinates are artificially changed.

Some remarks on a genetic shift that affected modern RoA in Iron Age.

Those are the possible events by their importance.

1. Politic of large population movements organized by the Urartian kings. This policy would decrease the Etiuni genetic profile in ancient RoA and increase new genetic profiles from other regions. It would result also in the apparition of Etiuni profile elsewhere.

Numbers in cuneiform texts are sufficient to explain this shift. But with the current paleogenetic data available this is not yet visible. At last not on a scale comparable to the claims of the kings. Out of 30 samples from 800-600 BC only two are from south. Most probably with more samples from Urartian cities like Teishebaini, Erebuni, Argishtihinili and others we will see them in the future. Another reason that could "hide" the newcomers is the practice of cremation. Even though it was limited to a subset of Urartians.

2. A theory exist that in its final period the Urartian kingdom elite moved to the modern Armenia. For instance mentions of last Rusa and king Sarduri son of Sarduri are found in Karmir Blur (Teishebaini) but not in Tushpa. It's possible that in its final periods the Biainili dinasty lost control of Tushpa and prefered to move to north. A similar event occured in last period of Assyria and other kingdoms. This theory is not widely accepted but there are some reasons to believe that it occured.

3. A new groups moved to Armenian heartland from more southern regions than Van basin. From historic Korduk and Nor Shirakan. Those groups are mentioned in Khorenatsi as Yervandians, Zarehians, Vahuni, Nersehians. They are mentioned as native but in cuneiform texts possible related names are found in the south. Their supposed arrival fits to late and post Urartian periods. It is probably associated to wider regional changes. Tribal names like Parnaki are attested in the most southern regions while later we see toponyms with it in more northern regions. Cawdek' (Ծաւդեք) in the south but also in Artsakh / Syunik. What triggered those migrations, are they really significant and how much impact they left is unknown.

4. A possible Persian and Medes impact. This sounds trivial given historic events but the direction of genetic shift in modern RoA contradict to the expected impact. There is no visible increase in Iran_Neo ancestry (Lazaridis and Hovhannisyan do not detect Iran_Neo increase). It would be also strange that ancient Medes and Persians had much lower steppe than what was already present in ancient Armenia. So it's possible that this event affected indirectly via the event number 3.

5. Transfer of capital to Armavir. This event is dated to 330BC but could have started earlier. Anyway it's very unlikely that it has left much impact.

Besides those points we also need to better understand the Middle Bronze Age Karmir-Berd culture which was an offshoot of Van-Urmia culture. It affected Araratian plain so this could have altered the Araratian plain Etiunians genetics. But the samples we have from Karmir Blur do not speak in favor of strong impact. Anyway more samples from Araratian plain are needed in Lchashen Metsamor period.

I think I mentioned all possible events that are responsible for this change. With more genetic data this puzzle will be solved. There is also need to review once more ancient texts for better understanding this situation. Combined with archaeology I hope all answers will be found

According to the link below this coin was minted by the satrap of Armenia Orontes ( Eruand ) who is mentioned in the Xenophon's Anabasis.

According to the link below this coin was minted by the satrap of Armenia Orontes ( Eruand ) who is mentioned in the Xenophon's Anabasis. He was "exiled" to Mysia where he minted these coins. Later he managed to return back to Armenia after organizing a rebellion against the Achaemenid king. The Pergamon inscription mentions him as son of Artašir. We have a thread about this inscription in this group. Links can be found in the comments.

See also

• About Yervanduni ( old Eruanduni , Greek Orontid ) origins. Part I

Koban culture 1200-400BC

This data was already published in a Russian paper, now it is corrected and translated in English.

Judging by their autosomes the Koban people were migrants from south. In most likelihood from western parts of southern Caucasus. Their Y DNA G2a1 also supports that idea. Other Y DNA found there is the R1b almost certainly a remnant from earlier periods.

Koban culture also had steppe rich people. One of them was from north Balkans. The authors think that it was a Scythian, but I have a feeling that with more sampling we will find other possible candidates. In any case sometimes after 600BC the area was gradually conquered by Scythians and few centuries later by Sarmatians and a new Iranic people formed there. The Alans.

Klin-Yar III:ID355 Lib2al Female 0.286153

Zayukovo-3:ID72 Lib7al Male 0.042127 G2a1a1a1b1

Zayukovo-3:ID79/1 Lib8al Male 0.449777

Zayukovo-3:ID80 Lib9al Male 0.016644 G2a1a1a

Zayukovo-3:ID82/1 Lib11al Male 0.017636 R1b1a1b

Bratskiye 1-ye Kurgany:ID1402 Lib40al Female 0.338059

Chalcolithic period cultures.

Chaff faced ware (4300-3500bc) was stretched from Cilicia to Caspian Sea. This cultural horizon is the common denominator of Minoan Y DNA and Maykop Y DNA. Their common ancestor.

One group moved to north from South Caucasus where a variant of this culture is known as Leila Tepe. In the north they participated to the formation of Maykop culture. While another group moved to Crete and Greek islands..From Aintab-Urfa region. It's also possible that CFW related groups moved to Central Asia.

This is the reason why we have similar haplotypes in both places. T1a3 and L2 both in Maykop and Greece. With more sampling from Maykop we will find more common haplotypes.

We have some aDNA from CFW period. It's Areni from Armenia and Azerbaijan LC. Both can be used for the modeling of Maykop in qpadm. See qpadm models in the comments.

As for Sioni-Adablur culture (5300-4300/4000bc) they were a different group who were adding grit to the pottery. We don't have ancient DNA from that period and sites.

The source 1. Sagona A. In: The Archaeology of the Caucasus: From Earliest Settlements to the Iron Age. Cambridge World Archaeology. Cambridge University Press; 2017:v-v.

Unexpected ancient DNA results from pre-Islamic Bahrain.

Unexpected ancient DNA results from pre-Islamic Bahrain. They are different from modern day Arabs living there and plot close to ancient Mesopotamian samples from Iraq. On the PCA they plot just in the vicinity of ancient samples from South Caucasus, North-West Iran and North Iraq LBA. In this group we use the term "Central farmers" for this type of ancestry.

Assuming those samples were not some kind random migrants then we can imagine that most of Mesopotamia was like this prior the arrival of Arabs.

This data gives us a hint what we can expect from more ancient inhabitants of Mesopotamia. Sumerians and Akkadians.

The island Bahrain is usually connected with the land Dilmun in ancient Mesopotamian texts. Although other opinions also exist on the location of Dilmun.

Below are some excerpts from the paper.

Lastly, we evaluate the ancestry of Bahrain Tylos individuals in a context of Near Eastern variation by estimating ancestry proportions using a previously published 12 three-way model with TUR_Pınarbaşı_EpiP, ISR_Natufian_EpiP and CHG as sources in a set of relevant ancient groups which can also be modelled in this way (Figure 3C) 12. In this model, the Bahrain_Tylos samples present similar ancestry proportions to AZE_ChL, Mesopotamia_PPN and IRQ_Nemrik9_LBA, IRN_Dinkha_Tepe_A, LBN_IA and to ARM_Aknashen_N. Accordingly, rank=0 qpAdm models show that Tylos-period Bahrainis form a clade with several of these ancient groups (p≥0.01; Table S6), suggesting that similar sources have contributed to their ancestry.

...

Tylos-Period Bahrainis are genetically closer to present-day Levantine populations than to present-day Arabians

Regarding affinities with present-day populations, the temporally aware model-based clustering analysis (Figure 1B) suggests that Tylos period Bahrain samples are more similar to present-day Levantine groups than to present-day Arabians or South Asians,

...

In order to gain further insights into the relationship of Tylos to present-day populations from the Arabian Peninsula and the Levant, we tested if the Bahraini samples form a clade with any modern population in our dataset using a set of reference populations (as outgroups) that can differentiate the different ancestries in the Near East. We found that Iraqis, Assyrians and Jewish groups from Iran, Georgia and Iraq could derive all their ancestries from Tylos-period Bahrainis (Table S8). Arabians such as Saudis, Emiratis and Yemenis have, in addition to ancestry from Tylos-period Bahrain, ancestry from East Africa, while Levantines such as Druze and Lebanese have additional Southeast European ancestry (Table S9)

See also

• The genetic profile of eastern Jews
• Origins of Sumerians

The genetic story of G2b

Thanks to Hovann Simonian we have a number of modern Armenian G2b on Yfull. Coupled with ancient DNA we can now have a better idea about the history of G2b.

G2b unlike his "brother" G2a was a minor Fertile Crescent lineage that formed in more eastern regions than Anatolia. It was absent in Anatolian and European Neolithic sites. The finding of 9200-year-old G2b in Zagros, West Iran confirms it's more eastern homeland. (See the map). G2b have three important branches, having an old common ancestor, who lived 20.000 years ago. He lived even prior farming was invented. Those three branches had different stories.

• G2b1-M377 - This branch apparently was a Copper Age lineage. It is popular in Ashkenazi Jews and Pashtos in Afghanistan. Both are result of Current Era founder effects. The common ancestor of Jewish and Pashto clusters lived some 5500 years ago, so it is hard to say its real origin given the absence of aDNA from this branch. An Armenian from Syunik is present on basal position in this branch having a 8700-year-old common ancestor. https://www.yfull.com/tree/G-M377/
• G2b2a-Z8022 - It was found in Wezmeh cave in West Iran in a Neolithic period. Later another sample was found in Kaps (Shirak) from Kura-Araxes period (more than 5000 years ago). And finally, a number of G2b2a were found from Teishebaini (Karmir Blur) in later LBA and Iron Age period. Etiuni people had preserved some Y DNA from Kura-Araxes culture so the G2b2a was one of them. In most likelihood G2b2a was present in South Caucasus since the Neolithic era. See the second picture. An Armenian from Urfa and a number of Turks are from this branch. Their common ancestor lived 3200 years ago so it's probably represented an old migration of KA to Anatolia and a secondary expansion in Iron Age. https://www.yfull.com/tree/G-Y37100/
• G2b2b-FT36238 - There are no ancient DNA from this branch. There is a young 2600-year-old branch which apparently is an Armenian branch given the presence of Armenians there. A very distant 19000 years parallel branch is found in Kuwait. https://www.yfull.com/tree/G-FT36238/