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Sunday, April 22, 2018

Likely Yamnaya incursion(s) into Northwestern Iran


Despite being stratigraphically dated to 5900-5500 BCE (ie. the Chalcolithic period), ancient sample Hajji_Firuz I2327 from Narasimhan et al. 2018, belongs to Y-haplogroup R1b-Z2103 and shows minor, but unambiguous, Yamnaya-related ancestry on the autosomes. Why is this a problem? Because both R1b-Z2103 and the Yamnaya culture are dated to the Bronze Age, and Yamnaya samples from Kalmykia and Samara are exceptionally rich in R1b-Z2103.

Hence, pending a successful radiocarbon (C14) dating analysis, it seems unlikely that Hajji_Firuz I2327 was alive during the Chalcolithic. Rather, it appears that he's partly of Yamnaya origin and has been wrongly dated. His remains are likely to be from a secondary burial from the Bronze Age that collapsed into the layer below, right into a Chalcolithic bin ossuary burial full of much older bones.

This scenario is strongly corroborated by data from two other ancient individuals from what is now Northwestern Iran:

- Hajji_Firuz_BA I4243 (also from Narasimhan et al. 2018 and from the same site as Hajji_Firuz I2327) was initially also stratigraphically dated to the Chalcolithic, but is now labeled as a Bronze Age sample after a radiocarbon (C14) analysis of the remains revealed a date of 2465-2286 calBCE. Moreover, this individual packs around 50% Yamnaya-related ancestry.

- Iran_IA F38 (from Broushaki et al. 2016) from an Iron Age burial at Tepe Hasanlu, which is just a few miles from Hajji Firuz, also belongs to Y-haplogroup R1b-Z2103 and harbors some sort of steppe ancestry on the autosomes (see here).

Below is a Principal Component Analysis (PCA) showing how this trio compare in terms of genome-wide ancestry to C14-dated Chalcolithic samples from Hajji Firuz and the nearby Seh Gabi. The relevant datasheet is available here.


Clearly, they're shifted "north" relative to the Chalcolithic group and thus closer to the Eneolithic/Bronze Age steppe cluster, suggesting that they carry steppe ancestry that was missing, or at least much less pronounced, in the region before the Bronze Age. I can use qpAdm and Global25/nMonte to double check this and also estimate more precisely their levels of Yamnaya-related admixture.

Hajji_Firuz_I2327
Afanasievo 0.172±0.033
Hajji_Firuz_ChL 0.313±0.156
Seh_Gabi_ChL 0.515±0.158
tail: 0.668410201 (full output)

Hajji_Firuz_BA_I4243
Hajji_Firuz_ChL 0.484±0.033
Yamnaya_Samara 0.516±0.033
tail: 0.26511852 (full output)

...

Hajji_Firuz_I2327
Afanasievo,17.4
Hajji_Firuz_ChL,42.8
Seh_Gabi_ChL,39.8
distance%=2.9435

Hajji_Firuz_BA_I4243
Hajji_Firuz_ChL,44
Yamnaya_Samara,56
distance%=2.8762

Considering the standard errors and statical fits, qpAdm and Global25/nMonte have produced very similar results for both samples, which cannot be explained away as coincidental outcomes. I think these are signals of a population movement or movements from the Pontic-Caspian steppe into the South Caspian region, probably across the Caucasus, and most likely during the Bronze Age rather than the Chalcolithic.

I don't have a clue who these people were. It's rather unlikely that they were the early Iranians, who probably arrived in the region from Central Asia during the Late Bronze Age or even Iron Age (for instance, see here). Perhaps they were the Hittites? Indeed, in his book In Search of the Indo-Europeans, archaeologist James Mallory suggested that the ancestors of the Hittites and other Anatolian-speakers entered the Near East via the Caucasus route:

Most arguments for an Indo-European invasion from the northeast concern the appearance of a new burial rite at the end of the fourth and through the third millennium BC. At that time, both north of the Black Sea and the Caucasus, burials on the Russian-Ukrainian steppe were typically placed in an underground shaft and covered with a mound (kurgan in Russian). Before 3000 BC there begin to appear in the territory of the indigenous Transcaucasian (Kuro-Araxes) culture somewhat similar burials such as the royal tomb of Uch-Tepe on the Milska steppe. As tumulus burials are previously unknown in this region, some would explain their appearance by an intrusion of steppe pastoralists who migrated through the Caucasus and subjugated the local Early Bronze Age culture. More importantly, a status burial inserted into a mound at the site of Korucu Tepe in eastern Anatolia has been compared with somewhat similar burials both in the Caucasus and the Russian steppe. The discovery of horse bones on several sites of east Anatolia such as Norsun Tepe and Tepecik are seen to confirm a steppe intrusion since, as mentioned earlier, the horse, long known in the Ukraine and south Russia, is not attested in Anatolia prior to the Bronze Age.

Another option, however, is that they belonged to some other extinct Indo-European group, such as the Gutians (see here). In any case, keep an eye out for more Bronze Age samples from this part of the world. I have a strong feeling that, unlike their Neolithic and Chalcolithic predecessors, they will be rich in steppe ancestry and R1b-Z2103.

See also...

Late PIE ground zero now obvious; location of PIE homeland still uncertain, but...

265 comments:

«Oldest   ‹Older   201 – 265 of 265
Anonymous said...

@epoch2013

The results are ready for them, as I understood completely. Here is only to publish they threaten already as year, but not publish. So it's their new "to be published soon" means nothing more than the past times.

Open Genomes said...

@David

Here's the 1240k file for the Egyptian JK2911, who is Y J2b1-M205:

http://www.open-genomes.org/genomes/Schuenemann%20(2017)/JK2911/genome_JK2911-1240k.zip

Somewhat low coverage:
SNPs read: 429533 percent covered: 35.84%

The other Egyptian, JK2134 has only SNPs read: 99709 percent covered: 8.32%.

I see a lot of high-coverage Canaanites / Phoenicians that I wasn't aware of from the study. I have to see what all of these are.

Davidski said...

@All

Egyptian_mummy_769-560calBCE:JK2911 is now in the Global25 and Basal-rich K7 datasheets.

Global25

Basal-rich K7

Sanuj said...

@Nirjhar

Thanks for the info. It was a bit evident from the article.

Samuel Andrews said...

@Anthro Survey,
"Yes, but where did GAC EEFs come from, then?"

Yeah, it is confusing. They must decend from Danbuian farmers. Still, I don't know how to explain the mtDNA mismatch between Hungary Neolithic and Globular Amphora.

Hungary Neolithic was rich in N1a1a. Andronovo did carry an N1a1a1 founder effect. This N1a1a1-sub clade also exists in Balts & Estonians & Finns today.

But, still I'm skeptical of big Danbuian influence in Globular Amphora or modern northern Europeans.

Davidski said...

@Sanuj

Rai told Nirjhar what he wanted to hear.

Santosh said...

I am surprised none of you are looking at the coorgis.
1) They have the highest Iran_N in India.
2) A lot of them are brachysephalic. The % of brachysephalism in people around Iran is high even today.
3) Coorgi's are dravidian by language.
4) Yet they have a high level of R1a, closer to upper castes.

Sanuj said...

@Davidski

No, it was also clear from the way that article was structured. The questions and quoted answers were sliced and diced. In any case, we should be getting the Shinde-Rai pre-print soon, that was the takeaway from that article.

old europe said...


@Samuel

"Yes, but where did GAC EEFs come from, then?"

May be this can be useful:


Globular_Amphora
Iberia_EN 58.3 %
LBK_EN 20.4 %
Ukraine_N 9.55 % + WHG:I1875 8.05 % + Romania_HG 3.7 %
((WHG:Rochedane 0 %
Loschbour:Loschbour 0 %
Latvia_HG 0 %
Narva_Lithuania 0 %
Narva_Lithuania:Kretuonas1 0 %
SHG 0 %))

Slumbery said...

Anthro Survey
"Oh, I doubt these samples belong to ancient Celts. We have to remember, though, that *Celt-like* groups probably existed around Czechia and Hungary(Late Rome's fringes, basically) circa when the Hunnic confederation made its mark."

Celtic substrate in 11th century Transylvanian toponyms was identified, so they reached quite east at some point.

capra internetensis said...

Thanks Davidski and OpenGenomes!

Richard Rocca said...

@OpenGenomes,

DA111 (Z373539) and DA119 (Z873665) are both throwing "kit not found" errors on Gedmatch.

Anthro Survey said...

@Matt

I don't think it's post-Roman in all cases because when I run the full set of Copper and Bronze Age Iberians as individuals using this scheme, a good number deviate from the Iberia_Chl-like EEF base, taking more WHG-poor EEF ancestry. The ones in Portugal do, for example. Also, if Roman Italy was the source, it'd be Southern Italy and such ancestry would be accompanied by an unambiguous Near East signal. Now, Andalusia does exhibit this. Unsurprising, ofc, since it was an urbanized, Hellenized area attracting "Greeks" from the Eastern Med and Roman colonies were likewise plentiful there.

So, for populations like Catalonia and Cantabria, I think it's mainly a result of pre-existing variation across the peninsula, some of which may be potentially be due to some I2a1-rich Remedello-like expansion b/ween 4500 and 3000BC Rob has hinted at once that ties in with the Jeunesse paper.

Anthro Survey said...

@Slumbery

Yes, their influence had a pretty wide reach. The thing is, was it accompanied by a significant demic shift so far to the east? I.E Were there French-like or Halberstadt_BA-like people situated there at one point?

Anthro Survey said...

Alright, here's an exploratory run of Anatolian Turks using the Medieval Karluk sample.

https://justpaste.it/5mrkh

It's still kinda messy and not everything should be taken at face value, but some trends are spot on. I figured the sample was going to be useful because its West/East Eurasian ratio is close to that derived using previous analyses. It also out-competed Altai_IA, which was strongly preferred by Monte before.

1)As expected, Pontic Turks(Trabzon) and Anatolian Greeks do not take the the Karluk, while Aydin and Balikesir take quite a bit. Pretty consistent with previous runs and history alike.

2)I included Macedonians to simulate a flow of Balkan Muslims taking place on the close of the Ottomans. The thing is, much of the signal is likely spurious, except in Istanbul and Balikesir, where it's significantly stronger. Popular muhajir destinations and Istanbul was relatively cosmopolitan anyway.

How can I change my modeling strategy to reduce this effect?

3)Stronger Levantine pull in Adana---the area is practically para-Syrian, though.

4)Adygei signal in Aydin----is this real or just an artifact? Did it have a large Circassian settlement? Can anyone confirm?

Matt said...

@Anthro Survey: Ah, OK, yeah, I see what you mean; there are some variations with the exact positions of the averages for Iberia_South_CA, Iberia_Central_CA, Iberia_Chl, Spain_LNCA, Portugal_LNCA samples, though whether this relates to geography or is just random sampling noise is harder for me to see. The variations in WHG between groups for the CA Iberian subdivisions are not larger here than within group.

For modeling Beakers in Iberia with steppe ancestry, what happens if you just use Beaker_Iberia_no_steppe samples?

The modern Spanish averages do seem too far beyond both the (limited number) Beaker_Iberia and all the geographically varied Chalcolithic samples though, to actually fit even allowing for geographical structure though, to me: https://imgur.com/a/Ki57xfd

Movements within the EEF CA are going to be very fine scale and hard to check out (unless they cause major disruptions in level of WHG). It seems quite likely to me that the late Neolithic / Copper Age prior to disruptions of steppe mass migrations was mostly characterized by isolation-by-distance (fight with and marry the next village across) type dynamics, at least averaged out of thousands of years of relatively slow movement.

Rob said...

@ Slumberry

“Celtic substrate in 11th century Transylvanian toponyms was identified, so they reached quite east at some point. ”

That would be surprising
Even Dacian is hard to demonstrate, let alone a substrate left behind by transient interlopers

Rob said...

@ ole Europe
I think you’re correct there. I get a similar result. It’s an interesting interplay between the old Danubian & Iberian type ancestry, with differential adstrata of local foragers. I think the Michelsberg culture will be interesting.
An mtDNA analysis by someone who knows what they’re doing would be useful

Carlos Aramayo said...

@Davidski,

You wrote: "The Indus Valley samples will be practically the same as the Indus Periphery samples. No Steppe-like ancestry".

But in a previous message, answering Rob, you commented that Dali-EBA ancestry is in Sarazm-Eneolithic and present in your graph in a node labelled ANI1 and you highlighted next that: "In other words, the Indus Periphery/Civilization population already had Dali-EBA-related ancestry".

Isn`t Dali`s sample ancestry, anyway, from the Steppes? Even though from a much earlier period (and not related to 2000-1500 BC movements through the "mountain corridor"). Maybe I missed some of your posts, but I would like a clarification on this issue.

Davidski said...

@Carlos Aramayo

Dali_EBA is from a site within the Inner Asian Mountain Corridor from Turan, not from the steppe, and there's no evidence that this type of ancestry arrived in the Indus Valley from the steppe, unless as part of admixture carried by Steppe_MLBA.

In fact, it's more likely that it was native to Central Asia, and that it mostly arrived in the Indus Valley with Neolithic farmers similar to Sarazm_Eneolithic.

The main type of steppe ancestry that exists in South Asia is derived from Steppe_MLBA. So when I say steppe-like in the context of South Asia and the Indus Valley, I mean very much like Steppe_MLBA.

And obviously, it's rather unlikely that there was any Steppe_MLBA ancestry among the Indus Valley Civilization peoples, because Steppe_MLBA only appeared in Asia after the expansions of the Sintashta and derived cultures from the Middle Bronze Age onwards.

Open Genomes said...

@David

I realize/remember that here are 5 ancient Lebanese now from the Haber (2017) study.
So far I know about ERS1790733 and ERS1790732, which are both male, and I'll get the accessions for the other three.

ERS1790733 is the Bronze Age J-FGC11 from Sidon:

The 1240k SNPs in 23andMe format:

http://www.open-genomes.org/genomes/Haber%20(2017)/ERS1790733/genome_ERS1790733-1240k.zip
SNPs read: 656835 percent covered: 54.81%

The problem with these is twofold:
1. There are multiple read files where each is about 6Gb. There is another general list with just one read file each. Are these separate runs that have more SNPs, or have they all been combined into one final file?
2. The files are in CRAM format. I already converted (one file?) from ERS1790733 to BAM in the past but I just need to figure out how to work with this in the latest version of samtools, which fully supports CRAM. I should be able to get that working ...

Once I get that, I can just convert the rest, and working with CRAM files should be transparent.

I'll investigate these several files for each sample. I have a suspicion that these others are just unaligned reads (FASTQs) in CRAM format. 55% sounds about right from the previous Y analysis for ERS1790733.

Davidski said...

@Samuel Andrews and Rob

Do not communicate with each other at this blog from now on.

Anthro Survey said...

@Matt

So, first, here is the full thing using Iberia_Chl+Remedello combination:

Ancient Iberian individuals using Beaker_Central_Europe
https://justpaste.it/1t4xi

Ancient Iberian individuals using Beaker DF27 average(a custom average of Beakers from a location associated with a DF7 individual in NW Europe)
https://justpaste.it/3zxfx

Modern Iberia using Beaker_Central_Europe
https://justpaste.it/75i05

Modern Iberia using Beaker DF27 ave
https://justpaste.it/4tm0p

Moor_Moz is a synthetic population using Dave's Mozabite model from a few threads back sans Yoruba.

Anthro Survey said...

@Matt

Now, here is a run of just Iberian Beakers using Beaker_no_steppe_ave in lieu of Iberia_Chl as you've suggested.
With Beaker_Central_Europe:
https://justpaste.it/3gogq

With Beaker_DF27 ave:
https://justpaste.it/2zqt1

The interesting part about the runs in the previous post is that 4/5 males who are I2a1 positive get a substantial Remedello shift.

Notice also how French_Basques and French_South have a clear Remedello_BA shift in their EEF preference which can't be explained by SE European influence.

Now, between the two runs, Catalans do show a small Aegean signal, but their preference for Remedello vs Iberia_Chl is too strong to be solely explained by Roman colonists or Circum-Aegean people.

Also, can you look more closely into Beaker_no_steppe_4229?

Karl_K said...

"@Samuel Andrews and Rob

Do not communicate with each other at this blog from now on."

I think I just heard a big round of applause.

Davidski said...

@All

Sidon_BA:ERS1790733 is now in the Global25 and Basal-rich K7 datasheets.

Global25

Basal-rich K7

RobertN said...

Question: Who are the ANF? I'm an occasionally visitor here and hadn't seen this designation before. I know of ANE, but ANF?

Davidski said...

@RobertN

ANF = Anatolian Neolithic Farmer.

Open Genomes said...

@David @Nick Patterson (Broad)

Don't worry, I found the link to the BAM files for the 5 Bronze Age Lebanese from Sidon, which do not have aligned reads (BAM or CRAM) in the ENA. :)

I'll extract them now in 1240k SNP 23andMe format as soon as I can download all of them.

@Dr. Patterson - do you want them in ANCESTRYMAP .geno format too, or is 23andMe format with your SNP names good enough? As I said the filter is QUAL>=10, because additional filtering basically doesn't change the principal components at all.

When I finish with these Bronze Age Canaanites / Amorites I'll continue with the high quality Eurasian Steppe samples.

Davidski said...

@Open Genomes

Nick Patterson didn't request the Canaanite genomes, I did. I'm guessing he's already got them on his system.

By the way, ERS1790733 worked just fine.

Anthro Survey said...

@Open Genomes

Would you be able to take a look at some of the better quality Guanche genomes in this study? Would make a good addition to G25.

https://www.ebi.ac.uk/ena/data/view/PRJEB86458

Open Genomes said...

@Richard Rocca,

DA111 R-P312 is now Gedmatch: Z302274 and
DA119 R-U106 is now Gedmatch: Z371280

The updated list is here:
https://docs.google.com/spreadsheets/d/1Rja6ZyjQrz3UK7_HTagkzczoOFjwcXOGdNOm9FC3Rik/edit?usp=sharing

Apologies, I had to get rid of some noise in the earlier uploads that crept in by mistake, but these as you can see are very "clean" at K15. This didn't affect the 1240k SNP files.

If you anyone find out anything about more specific Y haplogroups, I'll change the list. Right now I'm concentrating on those file that have >= 5 Gbases base counts. because these should produce the best results for Global 25. I listed the base counts for the high-coverage samples in a separate column.

(David if you want you can check the filtering parameters in the third line of the 23andMe file. The default has been QUAL=10, which works.)

Open Genomes said...

@Anthro Survey

The Guanche genomes are only in the NCBI Sequence Read archive, and they're
just unaligned reads.

You can see one example here, with no ability to download an individual chromosome:
https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=ERR2111946

You can check the others in the SRA as well.

These would need alignment, which is a very long and compute intensive process for a WGS.

That's really too bad, because the Guanches are in fact very important. I think that all researchers who publish should be required to submit alignments (BAM or CRAM) along with the indexes, so they can be accessed directly.

Open Genomes said...

@Anthro Survey

23 Gigabases of unaligned reads for a Guanche. Super-high coverage, but useless.
What's the point then?

https://trace.ncbi.nlm.nih.gov/Traces/sra/?view=run_browser&run=ERR2112083

Anthro Survey said...

@Open Genomes

Wow, what a shame. Definitely (would be) a good set of genomes to work with.

Well, what about those BAM files on the last page?

Open Genomes said...

@David

DA28 is a very high coverage genome, 12 Gigabases.

DA28 Y: C-Y4541 mtDNA: D4m2 Gedmatch: Z027433

The 1240k SNP file in 23andMe format:

http://www.open-genomes.org/genomes/Eurasian%20Steppe/DA28/genome_DA28-1240k.zip
SNPs read: 1105378 percent covered: 92.23%

K13 Oracle4:

Using 1 population approximation:
1 Oroqen @ 4.271263
2 Yakut @ 9.658758
3 Buryat @ 12.923331
4 Evenki @ 15.026437
5 Tuvinian @ 15.342115
6 Dolgan @ 16.464664
7 Evens @ 17.217066
8 Koryak @ 20.523249
9 Mongolian @ 24.595619
10 Altaian @ 24.858284
11 Chukchi @ 28.853518
12 Hakas @ 31.632706
13 Ket @ 31.975416
14 Selkup @ 34.520718
15 Shors @ 35.505188
16 Kirgiz @ 36.016872
17 Kazakh @ 38.337494
18 Hezhen @ 42.979336
19 Xibo @ 44.521709
20 East_Greenlander @ 50.748657

Using 2 populations approximation:
1 50% Oroqen +50% Yakut @ 3.312087

Using 3 populations approximation:
1 50% Evens +25% Hezhen +25% Yakut @ 1.728408

Using 4 populations approximation:
1 Buryat + Evens + Oroqen + Oroqen @ 1.639745
2 Evens + Evens + Hezhen + Yakut @ 1.728408
3 Buryat + Evenki + Oroqen + Oroqen @ 1.739571
4 Oroqen + Oroqen + Oroqen + Yakut @ 1.818324
5 Dolgan + Oroqen + Oroqen + Oroqen @ 1.908784
6 Evenki + Evenki + Evens + Hezhen @ 1.947259
7 Evens + Evens + Evens + Japanese @ 1.972052
8 Evenki + Evens + Hezhen + Yakut @ 2.016490
9 Evenki + Evenki + Evenki + Hezhen @ 2.096125
10 Evenki + Evens + Evens + Xibo @ 2.115335
11 Evenki + Evenki + Evens + Xibo @ 2.118041
12 Evens + Evens + Xibo + Yakut @ 2.122734
13 Evenki + Evens + Evens + Hezhen @ 2.125787
14 Evens + Evens + Evens + Xibo @ 2.367930
15 Evenki + Evenki + Evenki + Xibo @ 2.385466
16 Evens + Oroqen + Oroqen + Tuvinian @ 2.393740
17 Evenki + Oroqen + Oroqen + Oroqen @ 2.478726
18 Evenki + Evens + Xibo + Yakut @ 2.491940
19 Evenki + Evenki + Hezhen + Yakut @ 2.499138
20 Evenki + Evens + Evens + Japanese @ 2.505757

Extremely East Siberian. Is he a Manchu, or pre-Manchu Tungusic?

Open Genomes said...

@Anthro Survey

Which BAM files? The ones from Bronze Age Lebanon? I'm downloading the other 4 right now ...

Open Genomes said...

DA28 is here. Is this the "Jochid" C2 clade? (I remember that Mr. Kondratyev, a Cossac from Ukraine, is in this "Jochid" branch, and the Kondrat Banner of the Golden Horde were said to be "the most noble banner because they were all descended from Genghis Khan". In fact Jochi, Genghis' eldest son, was not his on, but the he was the son of the Merkit Chilger Boke who forcibly married Genghis' wife Borte Chino after she was kidnapped by the Merkit chieftain. "Merkit" means "hunter" so presumably they were hunter-gatherers.) It was the descendants of Jochi who became the Khans of the Golden Horde, and later many other Khans including the Khans of Crimea and Bukhara.
Members of the Kondrat Banner lineage also became the Polish noble Subritzky clan.

https://yfull.com/tree/C-Y4541/

I think DA28 is our very first real East Siberian ancient genome. Very important!

Anthro Survey said...

@Open Genomes

Well, most of those files are fastq, but it looks like pages 4 and 5 have BAM files for Guanche, after all. A couple of high-cov genomes among them. ERR2185283 on page 5 looks promising unless I've missed something.

Richard Rocca said...

@Anthro Survey, which are the 4/5 I2a1 samples?

Chetan said...

Does anyone have any info about what time and location those R1b M478 aka M73 samples in the steppe study belong to?

Open Genomes said...

@David

The long-awaited 4 remaining Bronze Age Levantine Amorite/Canaanite genomes are here.
You can decide which ones have enough coverage for Global 25:

ERS1790729:
http://www.open-genomes.org/genomes/Haber%20(2017)/ERS1790729/genome_ERS1790729-1240k.zip
SNPs read: 321718 percent covered: 26.84%

ERS1790730:
http://www.open-genomes.org/genomes/Haber%20(2017)/ERS1790730/genome_ERS1790730-1240k.zip
SNPs read: 703319 percent covered: 58.69%

ERS1790731:
http://www.open-genomes.org/genomes/Haber%20(2017)/ERS1790731/genome_ERS1790731-1240k.zip
SNPs read: 874175 percent covered: 72.94%

ERS1790732:
http://www.open-genomes.org/genomes/Haber%20(2017)/ERS1790732/genome_ERS1790732-1240k.zip
SNPs read: 810488 percent covered: 67.63%

Did a similar unsampled Amorite poputions (e.g. the Assyrians or Babylonians) provide any Levantine ancestry to the Iron Age Swat valley, who have many E-M123*s?

Open Genomes said...

@Nick Patterson (Broad)

The "trade secret" aligned BAM files from Haber et al. (2018) and the Welcome Trust. They should know better!

ftp://ngs.sanger.ac.uk/scratch/project/team19/Sidon_BA/

Joukowski Transform said...

@Onur Dincer

"He is too North European-admixed to be Central Asian Turkic. He is probably Uralic or Uralic-admixed or from some ancient population whose genetics we do not know."

How did those R1a Z94 Ashina look?

Onur Dincer said...

Thank you, Dave, for adding DA222 (medieval Karluk) to your Global 25 datasheets. I did Global 25 nMonte runs for the Kayseri Turkish and Aydin Turkish averages using the central Anatolian Greek, Cretan Greek and Armenian averages and the medieval Karluk sample as the input populations to characterize the genetics of eastern central Anatolian Turks and southwestern Anatolian Turks respectively and to quantify the genetic impact of the Oghuz/Turcoman incomers from the Kazakh Steppe of Central Asia in those regions of Anatolia. Here are the results:

Turkish_Kayseri

Armenian 58.1
Greek_Crete 27.0
Karluk_Medieval 14.8

distance%=0.4301 / distance=0.004301

Turkish_Aydin

Greek_Crete 39.2
Armenian 27.1
Karluk_Medieval 25.6
Greek_Central_Anatolia 8.2

distance%=0.7592 / distance=0.007592

The relatively high Karluk percentage of Aydin Turks is not unexpected since they show one of the highest levels of Oghuz/Turcoman incomer ancestry among modern Anatolian Turks.

Anthro Survey, I examined the individual results among those Aydin Turkish samples a few years ago. I did not find anyone likely to have Circassian ancestry among them. A few of them showed recent Balkan ancestry, but most looked native southwestern Anatolian Turk, and their genetic average also looks native southwestern Anatolian Turk. Nice analysis BTW.

Onur Dincer said...

@Joukowski Transform

How did those R1a Z94 Ashina look?

We do not have any ancient DNA samples specifically from the Ashina ruling clan of the medieval Turkic Khanate of Central/Inner Asia and as a result we do not know the autosomal makeup and haplogroups of the ruling house. But since they mostly lived in the eastern parts of the Turkic Khanate, I expect them mostly to have higher levels of Eastern Eurasian ancestry than the medieval Karluk sample.

Onur Dincer said...

@Anthro Survey

Oh, I doubt these samples belong to ancient Celts. We have to remember, though, that *Celt-like* groups probably existed around Czechia and Hungary(Late Rome's fringes, basically) circa when the Hunnic confederation made its mark.

There were already French-like genomes in what is now Hungary during the Late Bronze Age (look for LBA_Hungary in this PCA):

https://drive.google.com/file/d/0B9o3EYTdM8lQblFoT2dmNnJMYVU/view

Anthro Survey said...

@Onur Dincer

Yeah, I'm aware of this sample and the existence of others for the region and time period you've specified and was just envisioning parsimonious historical scenarios. We'll get to the bottom of it when the paper is published.

Re/Aydin: Could well be an artifact, sure. Anatolia and Caucasus do overlap quite a bit both in terms of deep and more recent ancestry. When I did a quick run of the individuals comprising the average, Ayddin18483 was somewhat of an outlier so that might be a reason, too.

One of the more interesting samples for me in the entire set, though, is Istanbul25098. It's basically a full-fledged Balkaner. Check it out.

Anthro Survey said...

@Richard Rocca

These males are I2a1 positive:
Beaker_Iberia_no_steppe:I4229
Iberia_ChL:atp002
Iberia_ChL:I1303
Portugal_LNCA:DolmenAnsiao96B

Iberia_Southwest_CA:I6601 is potentially I2a1, as well.

Of the following(WHG-poorer samples), 2 are females and one is a non-I2a1 male, but they are from the same same location as 1303:
Iberia_ChL:I0581
Iberia_ChL:I1272
Iberia_ChL:I1281

It's an interesting correlation, but I'm hesitant to make any definitive judgements about Copper Age expansions just yet. There may be nothing to this and we could just be looking at irregularities within the Iberian population. I2a1's presence in some regions may well be a holdover from Cardial times.

Matt said...

It might be noteworthy that although there are "French-like" LBA Hungarian samples, these samples to have a specific position with towards Slavic/modern Hungarian in G25 and Davidski's "North European specific" PCA (where populations from modern Eastern Europe are closer to Baltic BA). But DA111 and DA119 don't, for whatever reason.

(Although I don't really still know what the contexts of DA111 and DA119 are!).

FrankN said...

On Celts in the Danubian Basin, note
https://en.wikipedia.org/wiki/Gotini
https://en.wikipedia.org/wiki/Scordisci
https://en.wikipedia.org/wiki/Celts_in_Transylvania

The Tabula Peutingerania (ca. 375 AD) lists, a.o., the following Celtic place names:
- Brigantio (Komarno)
- Singidunum (Belgrade).

An older German PhD study suggests, based on archeological finds, two separate trajectories of Celtic (La Tene) eastward expansion:
The northern vector originated in the Saar-Mosel area, and went through Bohemia and Silesia into SE Poland. The southern expansion along the Danube originated in the W. Alps. Of course, afterwards both vectors interacted (not always peacefully) across the Carpathian mountains.

Rob said...

In fact, Celtic type finds can be seen all the way to the Black Sea. They are thought to be in part responsible for the demise of the scythian rule, and shifted the culture from Scythianoid forts to a series of La Tene influenced groups
However given this expansion occurred during a phase of cremation ritual, imaginably there aren’t many Eastern Celt finds to sample, but am keen to be pleasantly surprised

Samuel Andrews said...

Someone should do Y DNA analysis of Narasimhan 2018's genomes. Geneticker seems to be busy.

Nirjhar007 said...

Nice to see back Frank! :).

Onur Dincer said...

@Anthro Survey

Re/Aydin: Could well be an artifact, sure. Anatolia and Caucasus do overlap quite a bit both in terms of deep and more recent ancestry. When I did a quick run of the individuals comprising the average, Ayddin18483 was somewhat of an outlier so that might be a reason, too.

An artifact probably. Aydin18438 does not seem like an outlier to me. Even if he is an outlier (which I very much doubt), he is not an outlier in the direction towards Circassians.

One of the more interesting samples for me in the entire set, though, is Istanbul25098. It's basically a full-fledged Balkaner. Check it out.

Yes, I know that one. Probably fully descended from Balkan immigrants.

Anthro Survey said...

@Onur Dincer

When I use your Cretan-Armenian-Karluk setup w/Cherkes thrown in, the sample no longer has a particular affinity for them, but the Armenian signal is spiked instead relative to the others from Aydin. The fit didn't change much. So, not too sure. I wouldn't be surprised either way, though, because a cursory investigation yielded this:
https://en.wikipedia.org/wiki/%C3%87e%C5%9Ftepe

One individual that maintained a steady N. Caucasus pull was Adana23150.

Another interesting sample in that set is Istabul20040. Looks to have eastern Anatolian roots.

Anthro Survey said...

@Open Genomes

So, what's the verdict on the BAM file for that accession?

PF said...

The Canaanite genomes finally up! Thanks Open Genomes and Davidski.

Doing a very quick run here using older populations... yes, the Sidon samples are quite similar to the previous Ain Ghazal samples, as noted in the paper, but I do think there is some subtle substructure in the Levant at that time that can be picked up here. Sidon_BA pulls towards both Anatolian and Iranian farmers more, while Ain Ghazal pulls towards Natufians more. So some of the difference we see today between Lebanese and Jordanians/Palestinians existed well before Muslim expansions, and even before the Bronze Age Collapse.

(btw, perhaps change Levant_BA naming in the spreadsheet since now there are multiple BA samples from the Levant?)

[1] "1. CLOSEST SINGLE ITEM DISTANCE%"
Levant_N Barcin_N Natufian
5.568932 6.784771 9.824653
Ganj_Dareh_N WHG Iberomaurusian
11.276101 21.845137 22.378295

[1] "distance%=2.5873"

Sidon_BA:ERS1790733

Barcin_N,31.8
Levant_N,31.6
Ganj_Dareh_N,25.2
Natufian,11.4


[1] "1. CLOSEST SINGLE ITEM DISTANCE%"
Levant_N Natufian Barcin_N
4.275616 7.400732 8.463444
Ganj_Dareh_N Iberomaurusian WHG
12.570219 21.364120 21.953410

[1] "distance%=2.3887"

Levant_BA

Levant_N,62.2
Ganj_Dareh_N,19.4
Natufian,18.4

Anthro Survey said...

@PF

Indeed, and this substructure is not unexpected, to be frank. Southern Levant was always somewhat of a transitional zone between Arabia and Near East proper.

Couple of quick runs and consistent with what you're getting. Both were given an identical set of populations to choose from.

Sidon_BA
Armenia_EBA 39.8%
BedouinB 34.7%
Barcin_N 25.5%

Levant_BA
BedouinB 49%
Levant_N 29.4%
Armenia_EBA 21.6%


Here are modern Levantines. What's interesting is how results suggest that demographic influx into the Levant from the north didn't cease during Bronze Age times. What's more unexpected, though, is how Lebanese Muslims are not more Bedouin-shifted than Christians there. Ghassanid gene flow into Christians' ancestors? Muslim Armenian ancestry in the Shi'a?---Armenians are known to have had important roles in the Fatimid bureaucracy and military.

Lebanese_Christian
Sidon_BA 79.4%
Armenia_EBA 13.8%
BedouinB 4.6%
Iberomaurusian 1.8%
Dinka 0.4%

Distance 2.3474%

Lebanese_Muslim
Sidon_BA 68.2%
Armenia_EBA 24.4%
Iberomaurusian 2.6%
BedouinB 2.4%
Dinka 2.4%

Distance 2.1323%

Lebanese_Druze
Sidon_BA 69.8%
Armenia_EBA 24.2%
BedouinB 2.8%
Iberomaurusian 1.8%
Dinka 1.4%

Distance 2.1558%

Mher Ishkan said...

Aram and Me few years ago said that Z2103 come to Armenia,Iran from North and this gays was gutians ;)

An Idiot said...

This is probably why the big wigs see Kura-Araxes as the ultimate IE homeland, btw - this Z2103 just has to be from Kura-Araxes. It is the only expansion from the Caucasus Southwards during that time period, as Yamnaya never entered West Asia.

So, basically, they've likely found L23/Z2103 in the Southern Caucasus around the time of the K-A culture (as otherwise it would be absurd to place it as the ultimate IE homeland). Which is what I've been saying all along, but let's wait for definitive proof.

This is likely why the Areni sample has red hair, blue eyes and light skin; this is also why the Jordanian (practically Israeli based on its location) sample I1730 from the mid-late 3rd millenium BC also has red hair, blue eyes and light skin. Both are more CHG than anything else, with typically West Asian Y DNA. They picked up this pigmentation from R1b tribes.

Davidski said...

@An Idiot

Z2103 is native to the steppe and the Z2103 in Yamnaya isn't from Kura-Araxes, because Yamnaya doesn't have any Kura-Araxes (Armenia_EBA) ancestry.

See here...

Yamnaya: home-grown

An Idiot said...

@Davidksi Those two light-skinned, light-eyed red-headed samples, and these likely Bronze Age Z2103 samples from NW Iran fit perfectly with this:

http://www.pnas.org/content/pnas/112/30/9190/F1.large.jpg

The Zagrosian branch of the K-A culture would then be the Gutians.

This doesn't necessarily invalidate Z2103 from the Steppe (even though I personally think it wasn't), so it could still be the case that you're broadly correct (as K-A was trans-Caucasian, it could have picked up Z2103 from the Southern Steppe) but come on this fits wayyy too well to be coincidence. The only other way to explain those NW Iranian Z2103s is that they had been there for a while - no reasonable hypothesis permits a Yamnaya incursion. It's either Kura-Araxes or practically native.

Rip Bailey said...

The Hajji Firuz site is known for having well preserved archaeological layers on the grave-side of the burial mound. The R1b-M269 sample, labeled I2327, was found in the 'sub'-grave 'K10', which lied buried neatly under well documented layers we can date by looking at pottery and other finds in those layers. Besides, his grave lied in the same burial mound as graves 'F10' and 'F11', which were the graves with the J2b samples(and those 2 are C14 dated). Also, I2327, is not autosomally different from the other Neolithic samples as it too lacks Steppe Ancestry. I would expect it to have some Steppe Ancestry if it were a Bronze Age genome with R1b-Z2103; yet it doesn't. This makes it extremely probable the dating is correct. The chances that the current dating is false are low, close to 0%.

Davidski said...

@Rip Bailey

Also, I2327, is not autosomally different from the other Neolithic samples as it too lacks Steppe Ancestry.

The chances of this are 0%. Do you know why? Because of this...

Mbuti EHG Hajji_Firuz_ChL Hajji_Firuz_ChL_I2327 0.0151 3.737

Try pulling your head out of your ass. You might find it an enlightening experience.

And if you still don't understand what I said, then get in touch with the scientists from Harvard who sequenced this sample and link them to what I just said, maybe they'll understand it and can explain it to you.

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