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Friday, July 22, 2016

The Basal-rich K7


Update 28/11/2016: The Basal-rich K7 is now available to personal genomics customers. For a small fee. See here and here.

...

I've got a new test. Currently I'm only using it to explore ancient genomes, but at some point I'll make another version available to personal genomics customers, one way or another. However, that might take a little bit of work and time to mitigate the effects of the calculator effect and so on.

Below is a spreadsheet featuring a wide range of ancient and present-day samples from recent papers. A table with the Fst genetic distances between the seven ancestral populations is available here.


Please note that the Basal-rich component is unlikely to be a perfect representation of the hypothetical Basal Eurasian population. At the same time, it's likely that the two hunter-gatherer components, Ancient North Eurasian (or AG3-related) and Villabruna-related, contain some Basal Eurasian admixture.

Here's a Principal Component Analysis (PCA) of the West Eurasian populations based on their K7 ancestry proportions. It captures all of the main features of West Eurasian genetic diversity, including the two parallel clines made up of Europeans and Near Easterners, and the intermediate position of South Central Asians between the ancient samples from Neolithic Iran and Bronze Age Europe.


An extra large version of the same PCA, with the samples labeled individually, can be downloaded here.

Also, using the K7 ancestry proportions, I modeled the ancient ancestry of a few present-day populations from the Near east, Northern Europe and South Central Asia with the nMonte R script. Bronze Age steppe admixture in groups from the latter two regions is usually inferred at 40-50% with tools based on formal stats, such as qpAdm and TreeMix, so I wanted to check if I could reproduce such results.

Iranian_Mazandarani
Iran_Chalcolithic 42.05
Iran_IA:F38 31.35
Iran_Neolithic 14.95
Andronovo_Kytmanovo 7.6
Yamnaya-Catacomb_Ulan 1.95
Han 1.35
Andamanese_Onge 0.75
Papuan 0

distance%=0.285 / distance=0.00285

Iranian_Zoroastrian
Iran_Chalcolithic 40.95
Iran_IA:F38 38.25
Yamnaya-Catacomb_Ulan 11.25
Iran_Neolithic 6.45
Andronovo_Kytmanovo 2.8
Andamanese_Onge 0.15
Han 0.15
Papuan 0

distance%=0.2979 / distance=0.002979

Kurdish
Iran_IA:F38 96.3
Andronovo_Kytmanovo 2.35
Han 0.6
Andamanese_Onge 0.55
Papuan 0.2
Iran_Chalcolithic 0
Iran_Neolithic 0
Yamnaya-Catacomb_Ulan 0

distance%=1.3845 / distance=0.013845

Latvian
Yamnaya_Peshany 44
Loschbour 30.65
Sweden_MN:Gokhem4 25.35
Barcin_Neolithic 0
Ulchi 0

distance%=1.2569 / distance=0.012569

Polish
Sweden_MN:Gokhem4 39.4
Yamnaya_Peshany 39
Loschbour 21.6
Barcin_Neolithic 0
Ulchi 0

distance%=0.5208 / distance=0.005208

Swedish
Sweden_MN:Gokhem4 42.15
Yamnaya_Peshany 36.55
Loschbour 21.3
Barcin_Neolithic 0
Ulchi 0

distance%=0.939 / distance=0.00939

Kalash
Iran_Neolithic 54.05
Yamnaya-Catacomb_Ulan 25.5
Andronovo_Kytmanovo 9.35
Han 7.6
Andamanese_Onge 1.95
Papuan 1.55

distance%=0.4592 / distance=0.004592

Pashtun_Afghanistan
Iran_Neolithic 54.8
Andronovo_Kytmanovo 31
Han 7.5
Yamnaya-Catacomb_Ulan 3.5
Andamanese_Onge 1.75
Papuan 1.45

distance%=0.4921 / distance=0.004921

Pathan
Iran_Neolithic 55.25
Yamnaya-Catacomb_Ulan 19.1
Andronovo_Kytmanovo 12.3
Han 8.45
Andamanese_Onge 3.4
Papuan 1.5

distance%=0.4848 / distance=0.004848

Tajik_Pomiri
Iran_Neolithic 41.7
Andronovo_Kytmanovo 30.65
Yamnaya-Catacomb_Ulan 19.15
Han 6.95
Andamanese_Onge 1.05
Papuan 0.5

distance%=0.5318 / distance=0.005318

Admittedly, these estimates look very conservative, but certainly not out of the ballpark. I suspect that I'll be able to improve the models and statistical fits as new Bronze Age steppe samples become available. Indeed, I'll be updating the spreadsheet above regularly.

369 comments:

«Oldest   ‹Older   201 – 369 of 369
Kurd said...

"But that wont help in properly capturing the relevant ancient components."

I agree, I was just trying to see if I can use ADMIXTURE to calculate Iran N vs CHG in W Asians vs Iranians and S Asians. You have a point with not needing an Iran N cluster as well as MA1/AG3


"I should also add that Anatolia_N, Levant_N and the Natufians look like populations on the same cline."

Yes, I am seeing that too especially with Natufian - Levant N - One of the Levant BA samples

Chad Rohlfsen said...

Alright. I am trying to improve on the model left in Lazaridis et al (2016), where Anatolia was modeled as about 34% WHG, 31% Levantine, 35% Iranian. That run with their outgroups only had a chi-square of like 9, with a fit of .005. I am getting up to around 80%. I will post those shortly.

About my test. I do have WHG (more western, with WHG having minor North Eurasian), North Eurasian( peaking in MA1 99.9%, getting about 75-80% in EHG (like the paper)), Iran_EN (maxed in Iran_EN, fitting CHG as about 85% of this now), Natufian (working on those numbers), South Eurasian (peaking in Onge 99.9%, Paniya around 55%, Papuan 62%), SE Asian (peaking in Ami at 99.9% for now), Sub-Saharan (maxing out in some Esan and Yoruba), San (maxing in Ju hoan North).

Open Genomes said...

David, here are the plink files for WC1.
I was actually able to extract all the SNPs, not just the ones in the VCF that are different from the Build37 Reference Sequence.

The Affymetrix Axiom Human Origins Array plink files:
http://www.open-genomes.org/genomes/Broushaki%20(2016)/WC1/plink/Human_Origins_Array/

The Illumina Human OmniExpess-24 (the same chip used by 23andMe v4, FF, and Ancestry) plink files:
http://www.open-genomes.org/genomes/Broushaki%20(2016)/WC1/plink/OmniExpress-24/

I also uploaded WC1 to Gedmatch:
M197341 (951408 SNPs, compatible with 23andMe v2, v3 and the above chips)

Here are the autosomal data files, including 23andMe-formatted .txt files for the above chips, and the consolidated set of SNPs from commercial tests:
http://www.open-genomes.org/genomes/Broushaki%20(2016)/WC1/

Davidski said...

Thanks, I'll try and run it now.

Btw Chad, how much ANE are you seeing in Amerindians in your test, and any Onge? In my latest version I've got Karitiana at 45% ANE with 0.17% Onge.

Chad Rohlfsen said...

The Karitiana are at 39-42%, with an average a bit over 41%. I don't have Onge in them, but I haven't tweaked the SE Asian cluster yet. I'm still tinkering with Natufian and Iranian. Once I have that set, I'll move onto Asians.

ryukendo kendow said...
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Gioiello said...

DEDICATED TO THE THEORIST OF THE BALTIC REFUGIUM

Sample ID HG 5190993
YF05343 J-P56 A
YF04883 J-P56 A
The mutation from T to A is present in the Sardinian samples from Francalacci 2015 763, 764, 765, which are negative for P56, thus the mutation is at the level of J-L136 but of the Sardinian-Italian cluster and not of the J-L136 which generated J-P58 and all the subclades.
Thus, once more, Italy gets the most varied and oldest haplotypes also of hg. J1.
We are waiting that www.yseq.net complets the J1 pack upon David Noone, from an Italian father very likely from the mountaineous zones of Abruzzi, which could be the oldest sample of J1 found so far, older also than the samples from Caucasus (see Satsurblia), thus I expect that also J1 is found in Palaeolitic Italy with R1b1a of Villabruna.

YF05343 J-P56
12 24 14 10 12 18 10 15 11 13 11 30 18.2 8 9 11 11 xx 14 20 xx 13 13 15 16 10 10 xx xx 15 14 17 21 xx xx 13 10 9 8 15 15 8 11 11 8 10 9 12 xx xx 23 10 12 xx 17 8 12 28.g 22 15 xx xx xx xx 12 12 xx
YF04883 J-P56
12 24 14 10 12 18 10 15 11 13 11 29 18.2 8 9 11 11 xx 14 20 28 13 13 15 16 11 10 xx xx 15 14 18 21 xx xx 13 10 9 8 15 15 8 11 11 8 10 9 12 xx xx 21 10 12 xx 17 8 13 28.g 22 15 xx 11 xx xx 12 12 11

The presence of J1-P56 so old in Arabia would be strange, in fact J1 and J2 are very recent in Middle East, not older than 5000 years, in fact the haplotype is of Italian origin, as the close haplotype of Mantegna, from Italy, demonstrates: Ysearch BGFVN.

Matt said...

I should also add that Anatolia_N, Levant_N and the Natufians look like populations on the same cline.

I broadly agree from what I've seen (PCA fit and ADMIXTURE both support this, it's only really the relatedness to outgroups that seems to vary from it).

Though I would qualify that with Anatolia_EN farmers should have a degree drifting uniquely of Levant_Neolithic and WHG, as IRC, the populations that are have lowest D(Mbuti,Pop)(Anatolia_Neolithic,Levant_Neolithic) are not the same as the lowest D(Mbuti,Pop)(WHG,Levant_Neolithic).

Same for Natufian in place of Levant_Neolithic.

Like you know how D(Mbuti,Pop)(Spain_MN,Anatolia_Neolithic) basically identifies the lowest populations as WHG rich populations, modern Lithuanians, etc, because the drift between Spain_MN and Anatolia_EN mainly is WHG.

But that doesn't, IRC, happen with D(Mbuti,Pop)(Anatolia_Neolithic,Levant_Neolithic), and instead lowest populations are Mediterranean, so the difference between Anatolia_Neolithic and Levant_Neolithic is somehow different to WHG alone.

(Btw, one tangent thought: I wonder whether at some point worth replicating Fu et al's analyses showing Villabruna cluster closer to the Near East, with the new ancient near samples that are different than EEF, to see if this pattern is still consistent or reduced.)

ryukendo kendow said...
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Matt said...

The Levant_N version is on page of 75 of the supplement, although only with ancient populations. I can't see a Natufian version, so may be misremembering it.

Rob said...

Simon W

Yep, though the date is more like 2200/1800 BC for central & Western Europe (although goodluck convincing the 'cowboys' that theirs was originally actually some kind of NW Caucasian language). ;)

Have a gander at "Heyd V. Europe 2500 to 2200 BC: Between Expiring Ideologies and Emerging Complexity"

It pre-empts what we're seeing

ryukendo kendow said...
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Davidski said...

Open Genomes,

West Eurasian PCA plot with WC1 (red dot)

https://drive.google.com/file/d/0B9o3EYTdM8lQTUhFT09pMDBLems/view?usp=sharing

Global PCA datasheet (look for Iran_Neolithic2)

https://drive.google.com/file/d/0B9o3EYTdM8lQUTVOVWJibFFzMVU/view?usp=sharing

rk,

The non-MA1 type of forager ancestry in Iran_Hotu appears to be Southeast Asian-like and Onge-like, but perhaps only very distantly, and reference samples from ancient Central Asia would be a much better fit.

Rob said...

Ryu

No Probs, my comments about language were partly tongue-in-cheek, but I would still shy away from notions that BB & CWC were pan- & exclusively- IE, esp for the former, which was possibly largely non-IE in the southern & western aspect, and whilst the latter spoke possibly very early, now extinct IE forms, with Germanic & Balto-Slavic forming a little later.

Heyd did a follow -up paper, looking specifically at the post-2200 BC situation in southern Germany. He concludes that there was more or less continuity with BB times, whilst other areas show more profound change (eg Unetice) - whether through dynamism or sheer necessity.

I think it's important not to arrive at the early bronze Age and then leave it at that. Many more changes occurred after the Yamnaya period, as the paper above (& many others illustrate). Yamnaya appears to have receded deeply, back to the steppe (east of the Dniester-Dniepr interfluvial) as it transformed into Katakombnaya. The western and SW areas of CWC were occupied by BB and Unetice-like groups, resp, whilst in the east it continued on as cultures which can certainly be seen as its derivatives.

But I think, lest this upcoming paper shows something surprising, for most of Europe (excepting Mediterranean islands and the Uralic northeast), its "genetic stock' was made by 2500 BC, with the rest being local adjustments and cultural / ideological shiftings, etc. I think with, and subsequent to the 4.2 kya, the pre-forms of what became the 'great' (as in large) European-IE families emerged (which is what Anthony suggested in his book: at 2500 BC, we'd have seen still mostly just 'islands' of IE speakers in central Europe).

Im happy to see you agree now also that Yamnaya and CWC appear to have been 'egalitarian' at least *from within*- that is if you happened to be one of the CWC males, then you were equals, more or less. but there must have been tensions/ competition/ conflict with other macro-'cultures' which co-existed - as we see from Eulau in Germany, as well as the mosaic in Poland, as well as some very good studies in Scandinavia (eg TRB blocking off the best flint sources from CWC, whilst the latter cut off the Amber supply from TRB, each occupyiing mutually exclusive land- see K Kristiansen).
But i think the era of domination, heirarchy, and coercion, really began post-2200 BC, which is when the real Bronze Age began, and probably when lineage and language dominance set in.

ryukendo kendow said...
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Aram said...

Oh that WC1 looks very Southern. The idea of Open Genomes about the Paleolithic Mesopotamia looks plausible. But wasn't Mesopotamia a dry desert during LGM?

Roy King said...

WC1 does look quite southern. I would argue that WC1 is a local Neolithic phenomena, perhaps with an small adstrate of immigrants from the western Fertile Crescent bringing in some knowledge of grain cultivation (or even a separate origin of grain cultivation in the central Zagros). The lithics of the Neolithic central Zagros are quite different from the concurrent PPNB of the Levant and middle to upper Euphrates.

Roy King said...

There appears to be a large indirect connection between PPNB and the Anatolian Neolithic, while the connection between PPNB and the Iranian Neolithic seems modest at best.

ryukendo kendow said...
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Rob said...

AH2 from same paper is even older *82. - 7.7 ky BP).
Have we looked at that ?

Davidski said...

rk,

It looks like the Anatolian farmers have less complex ancestry than the early Neolithic Iranians, who appear to be less homogeneous and probably also mixtures of more highly divergent components that help to define the two dimensions.

Btw, WC1 is the most basal of the Iranian farmers. That's why he's so southern, both in my PCA and the one in the paper.

ryukendo kendow said...
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Chad Rohlfsen said...

Okay. Here is their result in qpAdm, same pops and out-groups.

left pops:
Anatolia_EN
WHG
Levant_EN
Iran_EN

right pops:
Ust_Ishim
Kostenki14
MA1
Han
Papuan
Onge
Chukchi
Karitiana
Mbuti

best coefficients: 0.316 0.337 0.347

std. errors: 0.039 0.150 0.167

fixed pat wt dof chisq tail prob
000 0 6 13.502 0.0357176

Chad Rohlfsen said...

Adding EHG to out-groups

Anatolia_EN
WHG
Levant_EN
Iran_EN

right pops:
Ust_Ishim
Kostenki14
MA1
Han
Papuan
Onge
Chukchi
Karitiana
Mbuti
EHG

best coefficients: 0.299 0.331 0.370

std. errors: 0.026 0.141 0.135

fixed pat wt dof chisq tail prob
000 0 7 15.453 0.0306077 0.299 0.331 0.370

Chad Rohlfsen said...

Adding Natufian and Iran_HG to outgroups

WHG
Levant_EN
Iran_EN

best coefficients: 0.217 0.747 0.036

std. errors: 0.051 0.067 0.069

fixed pat wt dof chisq tail prob
000 0 9 11.080 0.270274

Chad Rohlfsen said...

Adding a second WHG group (Bichon, Villabruna) and ElMiron to outgroups.

WHG
Levant_EN
Iran_EN

best coefficients: 0.100 0.760 0.140

Jackknife mean: 0.101302171 0.753828387 0.144869441
std. errors: 0.025 0.077 0.067

fixed pat wt dof chisq tail prob
000 0 11 17.168 0.103006 0.100 0.760 0.140

Chad Rohlfsen said...

Trading out Iran EN for CHG, just for geographic proximity and chance that Iran EN has unusual admixture not found in CHG, other than excess BE.

WHG
Levant_EN
CHG

best coefficients: 0.067 0.696 0.238

std. errors: 0.024 0.071 0.075

fixed pat wt dof chisq tail prob
000 0 11 11.655 0.390125

Chad Rohlfsen said...

Swapping out WHG groups in pleft and pright, also adding GoyetQ116-1 for potential extra Aurignacian in West Asia.

WHG2
Levant_EN
CHG
GoyetQ116-1

best coefficients: 0.083 0.646 0.236 0.034

std. errors: 0.030 0.069 0.079 0.069

fixed pat wt dof chisq tail prob
0000 0 10 8.650 0.565587

Chad Rohlfsen said...

Removing EHG from pright and placing them in pleft, just in case EHG spread into West Asia before they became as BE as CHG, or extra EHG entrance to West Asia between Kotias and the Early Neolithic.

WHG2
Levant_EN
CHG
GoyetQ116-1
EHG

best coefficients: 0.053 0.711 0.103 0.047 0.085

std. errors: 0.037 0.089 0.135 0.068 0.067

fixed pat wt dof chisq tail prob
00000 0 8 6.251 0.619136

Chad Rohlfsen said...

Added Iran_EN to outgroups, just to be safe.

WHG2
Levant_EN
CHG
GoyetQ116-1
EHG

best coefficients: 0.053 0.705 0.142 0.031 0.068

std. errors: 0.040 0.083 0.116 0.069 0.065

fixed pat wt dof chisq tail prob
00000 0 9 7.893 0.544982

Open Genomes said...

Here is the interactive 3-D Global9 PCA plot including the new Broushaki (2016) and Lazaridis (2016) ancient DNA samples, with Iranians, Armenians, CHGs, Levantines, and Anatolians highlighted:

http://www.open-genomes.org/analysis/PCA/Eurogenes_Broushaki_(2016)_and_Lazaridis_(2016)_Iran_and_Near_East_aDNA_PC_plot_1-2-3.html

The Gedmatch IDs to compare IBD and run calculators:

M041601 Natufian Epipaleolithic (merge) (most derived: E1b1b1-PF1871*) 11840–9760 BCE
M677694 Satsurblia CHG Epipaleolithic J1b-Y6305 11430-11180 BCE

M967114 I1290 Iran Early Neolithic Ganj Dareh 8179–7613 BCE

M603839 Kotias CHG Epipaleolithic J2a1b-Y12379 7940-7600 BCE

M197341 WC1 Iran Neolithic Wezmeh Cave G2b2a-Z8022 7455-7082 BCE
M115616 I0867 Levantine PPNB Motza H2-M282 7300–6750 BCE
M897077 I0707 Anatolian Neolithic Barcin 6500-6200 BCE
M936428 I0709 Anatolian Neolithic Barcin H2-M282 6500-6200 BCE
M754279 I0746 Anatolian Neolithic Barcin G2a2b2a1a1c-CTS342 6500-6200 BCE
M411713 I1583 Anatolian Neolithic Barcin G2a2a1a2a2-FGC2315 6500-6200 BCE

M937770 I1671/SG2 Iran Late Neolithic Seh Gabi G2a1a-Z6553* 5837-5659 BCE

M124870 I1661/SG16 Iran Chalcolithic Seh Gabi 4696–4491 BCE
M926386 I1631 Armenian Chalcolithic Areni-1 4250–4050 BC
M169040 I1665/SG19 Iran Chalcolithic Seh Gabi 3956–3796 BCE
M091434 I1584 Anatolian Chalcolithic Barcin 3943–3708 BCE

M536324 I1658 Armenian Early Bronze Age Talin (Kura-Araxes) 3347–3092 BCE
M291439 I1706 Levantine Eary Bronze Age 'Ain Ghazal 2490–2300 BCE
M182163 I1656 Armenian Middle-Late Bronze Age Katnaghbiur Kurgan 1501–1402 BCE

M122475 F38 Iran Iron Age Tepe Hasanlu Lake Van R1b1a1a2a2a-Y:24376846 971–832 BCE

Matt said...

@ Chad, interesting to see all the different models that work for Anatolia_Neolithic. Hard to tell which ones are best because its so uncertain as to how valid qpAdm models are with close relatives in the right.
Based on location, doesn't seem unreasonable to model Anatolia_Neolithic as 70% Levant_EN, 10% CHG, then the remaining 20% as a composite of ancestry from mostly European Paleolithic clade that doesn't fit exactly any single population (which is what the fractions of WHG, Goyet, EHG should mostly be). That said, also seems like Levant_EN and CHG are themselves admixed with ancestry from the European Paleolithic set.

@ Davidski, how goes it with the test?

Davidski said...

The test is done. But it'll take me a while to put together the results and upload them.

By the way, I ran some TreeMix graphs of WC1 and friends. As expected, WC1 looks like a more basal Iran Neolithic farmer.

Also, Anatolia N looks like a sister clade of Levant N. I can't find anything suggesting direct links between Anatolia N and Iran N.

https://drive.google.com/file/d/0B9o3EYTdM8lQcDRpUGVxalFiVDg/view?usp=sharing

ryukendo kendow said...
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Kurd Dgk said...

@ David

Did you get the values you posted with only a few component references and one or two test samples, or are you doing them with the usual full complement of about 1000 samples?

I am getting about 10% less ANE and 10% more basal for both WC1 and Iran LN, than Ganj Dareh, and about 6% SSA for Papuans, at K=5, , which is very likely Denisovan related, but I am using the full complement, and the test seems to need quite a bit more tweaking.

Davidski said...

I'm using over 1000 samples, including 80 synthetic samples that trigger the seven clusters listed above.

The ancestry proportions will be different in the new test that I'll describe when I update the post. It's hard to say which proportions are correct; it depends on what you're testing exactly, and that will vary with each test.

My main focus is describing the key patterns of ancestry in ancient West Eurasia.

Davidski said...

I'm putting together the results now, but here's an interesting tit bit. AG3-MA1 affinity shows up in western Anatolia in a big way during the Chalcolithic. However, it was already present there in the guy with Y-HG J2a, probably via CHG admixture.

Pop Anatolia_Neolithic Anatolia_Neolithic Anatolia_Chalcolithic
ID I0709 I0708 I1584
AG3-MA1 0 0.61 14.14
Andamanese 0 0 0
Basal-rich 54.76 54.23 53.36
Oceanian 0.05 0.07 0
Southeast_Asian 0 0.02 0
Sub-Saharan 0.16 0.27 0.27
Villabruna 45.02 44.79 32.23

Kurd Dgk said...

I an about 30 runs into the test, and have so far been able to get by with just adding and subtracting pops, but am at the point where I will have to start adding clones (which I assume you refer to as synthetics) because my ANE is too high in W and S Asians.

Chad Rohlfsen said...

Ryu,

The rest is mostly SE Asian. There's about 5% SSA, which I'd imagine is the Denisovan. They're also getting a couple percent in Iran and Natufian, which will be cleaned up eventually. I haven't gotten to the SE Asian cluster yet.

Tesmos said...

David, will you create DIY files or will you send the files of the calculator to Gedmatch?

Davidski said...

Probably. Chad is also making a test for GEDmatch. But both tests will take a while.

Alberto said...

Was someone able to replicate the D-stats involving WC1 and Mota in the Broushaki paper?

WC1 EHG Mota Chimp 0.0789 13.644
WC1 Anatolia_Neolithic Mota Chimp 0.0628 12.748

The do look suspicious, but maybe worth checking if there is something to it.

Davidski said...

I can check that out later. I haven't yet merged WC1 into my formal stats dataset.

Btw, Iberia Bronze Age ATP9 does have steppe ancestry. It shows up as a weak AG3-MA1 signal in this test, but it's not noise. Nothing like this shows in any of the earlier Iberians.

Pop Iberia_BA
ID ATP9
AG3-MA1 3.26
Andamanese 0.24
Basal-rich 32.95
Oceanian 0.29
Southeast_Asian 0
Sub-Saharan 0.96
Villabruna 62.29

Rob said...

Dave
That's the one from 1700 BC ?
Where'd all that whopping Villabruna -like stuff come from ?
(not that I doubt yr calculations, but are you sure about 63%?)

ryukendo kendow said...
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Rob said...

Ah, yes of course . Thanks

Davidski said...

rk,

I have run Chromopainter before but it almost melted my laptop, so I can't run it again. See here...

http://eurogenes.blogspot.com.au/2012/01/eurogenes-north-euro-clusters-phase-2.html

Btw, I didn't especially like the CHG/EEF/EHG/WHG test because it assumed that EHG was an unadmixed pop, and I always knew that was a lost cause. Chad's updated version was better anyway, and I couldn't be bothered updating the post, so I took it down. You should ask him for the output from that analysis.

Rob,

I don't know the precise date of the Bronze Age Iberian off hand, but it's the one that was published in the Gunther et al. paper. Its ancestry proportions, including the estimate of Villabruna-related ancestry, put it between the Chalcolithic Iberians and modern Iberians, so the result makes sense.

This new test looks pretty solid. It captures all of the main features of West Eurasian genetic structure, and a PCA run with the output looks exactly like a genotype PCA, without me having to do any corrections based on Fst.

ryukendo kendow said...
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ryukendo kendow said...
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Davidski said...

Technically infeasible at the moment, due to the lack of appropriate high coverage true diploid ancient genomes.

Shaikorth said...

Broushaki et al. chromopainter runs have WHG, Iranian Neolithic, European and Anatolian Neolithic, Kotias, Mota and Ust-Ishim represented and besides those there's just Irish Bronze Age&Neolithic and BR2 that would have high enough coverage IIRC.

Samuel Andrews said...

Bronze age Spainard ATP is from 3,700–3,568 C14 cal yBP.

http://eurogenes.blogspot.com.au/2015/09/steppe-related-admixture-in-bronze-age.html

There's also confirmation of Steppe admixture in Croatia by the Bronze age and we know it was in Ireland by 2000 BC.

Rob said...

Thanks Krefter
I wasn't aware we have a Bronze Age Croatian sample ? (unless you're referring to the Pinhasi abstract)
We do have evidence of E.E. admixture in Hungary by middle Bronze Age (2200 BC), and Montenegro (1200 BC).

Samuel Andrews said...

@Matt,

Info was posted about an unpublished paper with Neo/Bronze age Croatian genomes a few months ago. They gave a picture of a PCA with the ancient Croatians. The Neolithic ones clustered with other Neolithic Europeans and the Bronze age one by modern SouthEast/Central Europeans. All the genomes were put on the PCA with less than 10,000 SNPs and the Bronze age one had the most SNPs.

Bronze age Genomes from SouthEast Europe in the upcoming paper David has told us about will be the very interesting, because they faced immigration from the North and East. Also, because they have low amounts of R1b-L151 and R1a-M417 but high amounts of Steppe ancestry(20-30%). While Western and Northern Europe received Steppe ancestry via Bell Beaker(R1b-L151) and Corded Ware-like(R1a-M417) groups from the Central Europe, SouthEast Europe might have received Steppe ancestry independently from maybe R1b(xL51) groups.

Rob said...

I imagine that future BA Balkans will cluster with modern Spaniards & (north) Italians, as the couple we already have appear to (with 10-20 % 'steppe' admixture)
The type of R1b in SEEs is a mixture (probably a layering effect), but if i had to guess the predominant type in the Bronze Age will be Z2103 (i.e. the type found in (eastern) Yamnaya)

Open Genomes said...

David and all, here are another two ancient whole genome sequences in 23andMe and in plink format:

Bar31 Anatolian Neolithic, Barcin, 6419-6238 BCE (8429-8248 ybp) Y-DNA: G2a2b-L30* mtDNA: X2m

Gedmatch: M072869

http://www.open-genomes.org/genomes/Hofmanova%20(2016)/Bar31/
http://www.open-genomes.org/genomes/Hofmanova%20(2016)/Bar31/plink/Human_Origins_Array/
http://www.open-genomes.org/genomes/Hofmanova%20(2016)/Bar31/plink/OmniExpress-24/

Klei10 is the only Late Neolithic Balkan sample available, and he still looks very much like an Early European Farmer combined with some additional (later?) CHG, but with no sign of EHG or Steppe admixture:

Klei10 Kleitos 10, Late Neolithic Greece, 4230-3995 calBCE (6240-6005 BP) Y-DNA: G2a2a1a2-L91* mtDNA: K1a2

Gedmatch: M822045

http://www.open-genomes.org/genomes/Hofmanova%20(2016)/Klei10/
http://www.open-genomes.org/genomes/Hofmanova%20(2016)/Klei10/plink/Human_Origins_Array/
http://www.open-genomes.org/genomes/Hofmanova%20(2016)/Klei10/plink/OmniExpress-24/

Open Genomes said...

The following ancient samples are also mtDNA X2 along with Bar31 from the Anatolian Neolithic, Barcin, 6419-6238 BCE (8429-8248 ybp) who was mtDNA X2m. These are only a few of a much larger set.
What could all these mtDNA X2's have in common?

X2b Rev5 Early Greek Neolithic, Revenia,6438–6264 calBCE (8448-8274 BP)
X2 I1290/GD13A Early Iranian Neolithic from Ganj Dareh 8179-7613 calBCE (10189-9623 BP)
X2m2 I0723 Late Anatolian Neolithic, Menteşe 6400-5600 BCE (8410-7610 BP) G2a2a1-PF3177 (ancestral for G2a2a1a1-FGC6669)
(X2 subclade unspecified) BAM13 Starčevo, Alsónyék-Bátaszék Hungary 5660-5570 BCE (7670-7580 BCE) G2b2a-L30 (subclade untested)
X2b-T226C I1499/HUNG86, NE3 Early Neolithic Bukk Culture, Garadna Hungary, 5210-5010 calBCE (7220-7020)
X2c CB14 Cardial Cova Bonica, Vallirana (Barcelona) Spain, c. 7100 BCE (5100 BP)
X2d1 I0821/HAL24 LBK, Halberstadt 5201-4850 calBCE (7211-6860 BP) G2a2a1-PF3148
(X2 subclade untested) 4 samples Treilles Cave, Aveyron, France c. 3000 BCE) G2a-P15 (subclade untested)
X2b4 I0049/ESP22 Corded Ware Germany 2464-2210 calBCE (4474-4220 BP)
X2f I1635 / KA1/12 Early Bronze Age Armenia / Kura-Araxes (Kalavan) 2619-2465 calBCE (4629-4475 BP) R1b1a1b-CTS3187 (earlier in R1b than Villabruna)
RISE489/T65 Late Neolithic/Chalcolithic Remedello Italy 2908-2578 calBCE (4918-4588 BP)
X2m I1706/AG98_2 Early Bronze Age Levant ('Ain Ghazal) 2490-2300 BCE (4500-4310 BP)

Also a Mesolithic hunter-gatherer from Francithi Cave in Greece was some kind of X (probably X2), and a Minoan (#8) from Ayios Charalambos, Crete (2390-1690 BCE /4400-3700 BP) was possibly X2j.

For more ancient mtDNA X2's, see here:
https://docs.google.com/spreadsheets/d/1HcAhe7QvggT792VruuoZX6IsTg4LhWXV-Z_ZfTk2KGA/edit#gid=1957623828
and here:
http://www.ancestraljourneys.org/europeanneolithicdna.shtml
http://www.ancestraljourneys.org/copperbronzeagedna.shtml

Open Genomes said...

mtDNA X2m today:
http://www.ianlogan.co.uk/sequences_by_group/x2m_genbank_sequences.htm

mtDNA X2 may seem mostly European and Druze (with some Native North Americans, of course), but it's also found in Iran, Egypt, Morocco, and South Asia, too:

http://www.ianlogan.co.uk/sequences_by_group/x2e_genbank_sequences.htmhttp://www.ianlogan.co.uk/sequences_by_group/x2j_genbank_sequences.htm

http://www.ianlogan.co.uk/sequences_by_group/x2b_genbank_sequences.htm

http://www.ianlogan.co.uk/sequences_by_group/x2p_genbank_sequences.htm

MfA said...

Open Genomes

M122475 doesn't work.

batman said...

Seems some need to rerun Mota, as well:

http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3621.html

Gioiello said...

@ Open Genomes
"X2f I1635 / KA1/12 Early Bronze Age Armenia / Kura-Araxes (Kalavan) 2619-2465 calBCE (4629-4475 BP) R1b1a1b-CTS3187 (earlier in R1b than Villabruna)"

What does it mean "earlier"? Not certainly older or ancestral or origin, because having found an "earlier" sample in the Caucasus 10000 years later than Villabruna from Italy is as having found R1b1-L278* in India and Central Asia, which, being L389-, aren't surely the ancestors of the R1b1 subclades, like the J1* from Satsurblia of 13000 years ago has much less probability to be the ancestor of the J1 subclades all over the world than Sardinian ERS256732/J1-L136* and of the haplotype of David Noone (from an Italian father) who seems J1-L620* and perhaps directly ancestor of the Sardinian haplotype, which could mean that Italy was the refugium not only of R1b1 (V88, L389, M335) but also of J1-P58* and many other hgs.

Open Genomes said...

@MfA - I didn't upload M122475 (F38 / Lake Van Hasanlu). It seems that many of these other Gedmatch uploads have disappeared ... is there a comprehensive list of working aDNA Gedmatch IDs?

@Gioiello - I meant "a phylogenetically earlier branch", but I made a mistake, Villabruna is R1b1a-L754, and so is I0122/SVP35 from Khvalynsk, Samara 5200-4000 BCE (L389-, V88- except for one SNP which may be DNA damage).

The question here is, what do representatives of phylogenetically early branches look like in their autosomal DNA, and so they share anything at all with their more derived relatives?

This is especially important for Bar31 and WC1, who are both G2-P287.
The common ancestor of G2-P287 lived during or just after the LGM, c. 23,000-18,000 ybp, not 47,000 years ago:
https://yfull.com/tree/G-P287/

These two populations, the Anatolian Neolithic and the Iranian Early Neolithic individual WC1 should have something in common. If the Anatolian Neolithic, the Levantine Neolithic, and the Natufians all appear to be populations on the same cline (and therefore share ancestry), then there should be something that connects them to WC1.

What is it?

Gioiello said...

Ted, I discussed a lot about Villabruna with Sergey Malyshev (smal) who put him just under R-L754 in his tree at FTDNA R1b basal subclades, because Genetiker found him poositive for two SNPs at the P297 level and it seemed to me that he were not tested for V88, L389. P297 etc. What do you think about those two SNPs (PF6401 and PF6412 if I remember well) thought unreliable from the Anthrogenicians?
I'll study your case about hg. G and I'll let you know my opinion. Unfortunately I haven't the programs and the knowledge for reading the BAM files and I have to use smal or YFull...

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


G-P287 CTS1900/PF2931/M3506 * PF2883/F1189/M3267/V1943 * CTS120/PF2781/M3443+86 SNPs formed 26600 ybp, TMRCA 20800 ybp info
G-P287*
G-M3115 M3194 * M3116 * FGC32392/Y12295+98 SNPs formed 20800 ybp, TMRCA 9000 ybp info
G-M3115*
id:YF05605 LBN [LB-JA]
G-Y12297 Y12312 * SK1168/Y12300 * M3111+28 SNPs formed 9000 ybp, TMRCA 5500 ybp info
G-Y12297*
G-M283 M283
id:HG02789 PJL
G-Y12975 FGC32414/Y12984 * BY1301/FGC32411/Y12982 * FGC32403/Y12977+28 SNPs formed 5500 ybp, TMRCA 1250 ybp info
G-Y12975*
G-Y15861 Y15861 formed 1250 ybp, TMRCA 1100 ybp info
G-Y15861*
G-Y15563 Y15563 * Y15564 * Y15862+1 SNPs formed 1100 ybp, TMRCA 450 ybp info
id:YF03534 LTU [LT-KU]
id:YF02993 LTU [LT-KU]
G-Y16169 Z37831/Y16169 formed 1100 ybp, TMRCA 900 ybp info
id:YF03777 ROU [RO-BT]
id:YF03059 UKR [UA-46]
G-Y14600 FGC32413/Y14600 formed 1250 ybp, TMRCA 1200 ybp info
G-Y14600*
id:YF04090
G-Y14601 FGC32409/Y14601 formed 1200 ybp, TMRCA 1150 ybp info
G-Y14601*
id:YF03699
id:YF03254
G-FGC32397 FGC35735 * FGC32397 formed 1150 ybp, TMRCA 1150 ybp info
id:YF03859
id:YF03292 UNK
We have discussed a lot about your haplogroup, and unfortunately I continue to be banned from everywhere and not having access to the YFull groups (except very few), where you and all the others of FTDNA are administrators, thus how may I say to you more than in the past? Your Jewish Ashkenazi subclade has a MRCA 1100 years ago, and nothing may make us think that it were old amongst Jews, but if some data, also of the aDNA, will come out I may change my opinion. To think, as you said above, to convince yourself that, as there was a link between Natufians, Iranians and Anatolians (what didn't seem from their autosome) about a possible old origin in Middle East has no support so far. The solution could be to get same samples at the level of G-Y12975* and G-Y15861*, and you, who have access to all the data I haven't to, may give the answer to me and not ask me for that.
These two SNPs have also an FGC number (35728 and 35913), thus someone has been tested at FGC, and also with Big Y (there is also some BY SNP), thus you should search home...

Chad Rohlfsen said...

Gioiello,

Would you please stop flooding this place with your Italian Refugia, STR, and anti-ME roots of Jews stuff. It's very tiring and you have no basis to any of your claims. Enough is enough.

Gioiello said...

@ Chad Rohlfsen

I answered a question that Ted Kandell did to me. If he or the owner of the blog ask me that I delete my post, I'll be glad to do that.

Chad Rohlfsen said...

@Open,

I'm pretty certain Anatolia and Levant EN have CHG/Iran-like admixture. Lazaridis found it to be about 40% in Anatolians, but I'm seeing closer to 15% with extra outgroups. I get much higher fits with that too. I think about 15% CHG in Anatolia is perfectly fine. That would only be about 4-5% ANE. Totally plausible with CHG being close to 30% and a neighbor for at least 7000 years. I'm pretty sure ANE appears in clines rather than steep drop offs to zero.

Davidski said...

It's more complex than that. I'll try and write it up properly after I put up all the stuff about this new test.

But basically it's like this, all ancient Near Easterners share ancestry from at least one ghost population that was rich in Basal Eurasian, but not purely Basal, with its other components probably more or less related to the MA1 and Villabruna clusters.

Also, there was probably a population in the northern Levant that was more or less intermediate between the Neolithic Anatolians, CHG and Neolithic Iranians, and it interacted with all of them from the Middle Neolithic onwards.

The Anatolians do have a lot of ANE-like ancestry, but almost all of this comes from their Villabruna-related admixture. Only some of the Anatolians have minor CHG ancestry, and hence some more recent ANE.

I think this scenario fits well with uniparental marker data, but I don't see how it would be possible to show it with something like qpAdm.

Open Genomes said...

David, it's interesting that you're finding such a "ghost population" that connects all three groups, the Anatolian, Levantine, and Iranian Neolithic.

Would anyone like to speculate about how such a population relates to the radiocarbon dated sites and cultures found on these maps?

Late Natufian - Trialetian - Zawi Chemi 10,000-9,500 calBCE:
http://context-database.uni-koeln.de/img/P2A.png

PPNA - Nemrikian - M'lefaatian 9,500-8,800 calBCE:
http://context-database.uni-koeln.de/img/P2B.png

Early PPNB => Cypriot Early Pre-Pottery Neolithic & Early Central Anatolian I - Nemrikian - M'lefaatian 8,800-8,200 calBCE:
http://context-database.uni-koeln.de/img/P3A.png

batman said...

@ OG

The spread of the first, post-glacial populations in the eastern Med, reaching Crete and Cypros, were obviously sea-borne. Thus we need a 'maritime culture' to explain their spread.

The spread of the vebry first domesticated plants and animals - of the smaller kinds - seem to be connected to the same population(s).

http://www.nature.com/news/2001/010508/full/news010510-4.html

According to present knowledge the origins of the pottery that was introduced to Anatolia and the levant, during the cultural transition of the mesolithic/neolithic, can be traced north of the Black Sea - to both Russia and the Balkan. Thus we know that the first Levantine and Anatolian populations received cultural and economical impulses from the glacial populations north of the Black Sea.

http://www.visual-arts-cork.com/prehistoric/vela-spila-pottery.htm
http://www.visual-arts-cork.com/prehistoric/amur-river-pottery.htm

Since the dating of Gobekli Tepe it's obvious that these pioneers - just as their later relatives in Europe - were already able to construct substantial megaliths as well.

Today the cultural connection between the northern and southern areas of paleolithic/mesolithic Eurasia is pretty well documented - as the idols (figures) and symbols found in and around "The Fertile Crescent" are echoed in the Baltics as well as mesolithic Russia.

http://siberiantimes.com/other/others/news/n0376-shigir-idol-is-oldest-wooden-sculpture-monument-in-the-world-say-scientists/

This seems to imply that there was sufficent contact - in terms of culture - across wide areas. Which may imply that the genetic relationships formed by the descendants of a (post-glacial?) y-dna C/CF - would be joined by the knowledge a known common origin, cultural heritage and historical counsciousness ("identity").

The various cultures/dynasties that can be recognized in the patrilinear genetics of post-glacial Eurasia (y-dna F->G,H, I, J, K/etc.) seem to be found across the entire northern side of the Meds, as well as eastwards on to India and China.

Consequently we may associate hg G to the first, seaborne Mediterranean culture ('minoan'), familiar with both domestication and megalithic architecture. Seemingly, it's brotherline hg I spread (mainly) north of the Alps, producing much of the same culture.

Their fellow brother-lines hg H and J seems to have appeared simultaniously, building their respective cultures, dynaties and etnicities further east. Hf H seem to be the oldest, main dynasty of mainland India, while hg J obviously halted to their north and west, producing the (first) Iranian (aryan) and Indo-Iranian (indo-aryan) dynasties.

For SOME reason the spread of these mesolithic/neolithic dynasties congruate with the sperad of the Indo-European (centum/satem) and the Uralian languages (centum+satem) - bordering the ancient toungues of Chineese, Austro-Asian, Dravidian and African languages. Thus the Afro-Asiatic languages may be a 'creole' - as an early result of travel, trade and (later) migrations across the southern shores of Iran and Arabia.

One such migration seem to have happened during the middle of bronze-age - as an outlier of hg J2 west of the Suleiman mountains, etsblishing itself within ancient Sumeria. I wonder if this could be an origin of hg J1 - or some of its extant derivates, as well as the extant derivates of J2 across the ME and Europe...

Rob said...

Open Gen (?Terry)

If both the Samara sample & Villabruna are 'pre-M297', then the connecting 'autosomal' thread is the ANE -like component, which is to say, it's more like a brother Clade which split off the pre-Afantova-Mal'ta cluster prior the LGM, and then re-expanded from the Black Sea
(As a tentative guess)

Samuel Andrews said...

@Rob,

Samara HG was pre-R1b-M73. M73 is a brother to M269 and is under M297.

Rob said...

Sam
I know. But different people are making different calls. OG just stated he thinks it's L754*.
Either way, I don't think it changes the overall impression im getting

batman said...

@ Rob

The Malta-population, together with most (north) Eurasian populations, went extinct during the LGM. Implying it can't be ancestral to any present R1a/b.


The few populations of larger mammals - humans included - known to have survived the LGM were located in the milder parts of northern Eurasia, such as the Atlantic facade.

Though, most of them seem to have died out during the next cold-dip, known as the 'extinction event' of the Younger Dryas.

Which explains the (ca) 12.000 year old bottle-neck visible in the genetic material of the present Eurasians.

Rob said...

Batman

The Black Sea refuge isn't in Siberia. You can use google or Wikipedia to search where it is.
And yes, some some lineages survived in the Atlantic facade. But overall, this was a small minority. Most other lines came from other areas.

batman said...

You have to differ between the number of known human populations ('refugias') surviving the LGM, 25-17.000 years ago - and the possible refugia(s) surviving the even colder Younger Dryas as of 12.900 - 11.800 yrs BP, as of lately called the "Late Glacial Maxima".

We know of several possible refugias from the first cold-vawe - such as the transit Solutrean-Magdalenien/Cresswell, etc.

But - so far - there are NO known refugia located during The Younger Dryas. Not in and around the Black Sea. Not in Anatolia. Not in Greece or it's islands. Not in Italy. Not in Iberia. Not even in the stable and favorable climate of Guernsey, where the last sites disspear just as the Younger Dryas starts. Thus we're left - so far - with the Scanian refugia - that did - to most people surprise - endure the Younger Dryas.

We have just about been getting the evidence clarified that - indeed - there was ONE such refugia around the shores of Scania, that didn't only survive the coldest climate-period on record - but even had the ability to start spreading by sea and land, establishing several outliers in arctic Europe, as soon as the climated soared back to its present level.

The first suspricions of such a refugia were discussed already 2005, at a conference in Greifswald - thanks to the compilation made by professor-in-spe Tomas T. et al:
https://www.researchgate.net/publication/267641747_From_the_first_humans_to_the_Mesolithic_hunters_in_the_Northern_German_Lowlands_-_current_results_and_trends


So far the 'Hasselberga-collective', dating 12.500 yr BP, is the only Younger Dryas-refugia known, proven by hands-on archaeology and consequent datings. AFAIK.

That does obviously not exclude any other refugia surviving the YD north of the African coast, but so far it's the only proven one. Wheter we like it or not.

Thus my point is that any genetic analyzis concerning the Eurasian genomes must take this plain fact into account, wether one likes it or not...

---

Addendum:

Causes and dates for the extra-ordinary cold-dip of the YD, resulting in an Eurasian and N-American 'extinction event':
http://www.nature.com/nature/journal/v464/n7289/full/nature08954.html

According to this study the final bottleneck of the present, Eurasian y-dna happened just about the same time, some 10.000+ yrs ago. :

https://www.researchgate.net/publication/273631580_A_recent_bottleneck_of_Y_chromosome_diversity_coincides_with_a_global_change_in_culture

Late-Paleolithic temperatures of northern Europe: (See BTW, fig 3:)
https://www.researchgate.net/publication/262379520_Persistent_intermediate_water_warming_during_cold_stadials_in_southern_Nordic_seas_during_the_past_65_ky

Another relevant study to determine the possible location(s) of a 'glacial refugium' that made a survival possible - at the brink of extinction:
https://www.researchgate.net/publication/273631580_A_recent_bottleneck_of_Y_chromosome_diversity_coincides_with_a_global_change_in_culture

Pinhasi's bottleneck, with comments:
http://eurogenes.blogspot.no/2015/03/european-foragers-almost-wiped-out-by.html

---

Since I seem to be uninformed, could you please clearify what "Black Sea Refugia" you refer to?

Is this known and proven to have been existing during BOTH the LGM as well as the Younger Dryas?

Or do you simply refer to the 'estimates' made by geneticians - describing hypothetical refugias based on median values from the present distribution of mtDNA and what Maju substantiate with "common sense"?

Gioiello said...

@ batman
"But - so far - there are NO known refugia located during The Younger Dryas. Not in and around the Black Sea. Not in Anatolia. Not in Greece or it's islands. Not in Italy. Not in Iberia".

Are you sure? Not only I hypothesized an Younger Dryas refugium in Northern Italy (Northern Europe has no R-L389*, R-V88*, R-M335* etc.), but also a Southern Italian Mesolithic Refugium is supposed from scholars for the presence of mt hg. HV etc (already found in aDNA from Favignana, Sicily).
Of course the answer will be only in aDNA, also about Scania.

ryukendo kendow said...
This comment has been removed by the author.
Alberto said...

@batman

You really need to get acquainted with the data that has been surfacing from ancient DNA in the last few years instead of repeating this nonsense again and again.

We have a sample referred to as Satsurblia which is pre-YD and another one from the same place (Kotias) which is post-YD. They are the same population, and they are very near the Black Sea.

This is only an example. We have from several other populations. We have WHGs (Villabruna clade) from before and after the YD, and they are the same population. We have Afontova Gora samples from Siberia that are pre-YD and we have Karelia_HG which is post-YD, and largely descended from AG. We have Natufians, Anatolians, Iranians... All distinct populations. They ALL survived the YD in different places.

Please read the papers of the last few years regarding ancient DNA.

@Gioiello, you would also greatly benefit from reading those papers and understanding them.

Rob said...

Batman
You're incorrect
During the younger Dryas, Northern Europe was again depopulated, with its population again moving south or becoming extinct. It's been known archaeologically for years, and it's also been recently been shown (Posth, Fu) by genetic replacement. There was definite continuity in EE, southern France, Italy, the Balkans.
We've been through this before.
Your Scanian refuge theory is even more crazy than Gio's "everything came from Italy" theory.

Davidski said...

Almost there, but I'm running behind with stuff this week, so I'll need until tomorrow. Meantime, another little teaser; a model with nMonte using Ulan IV and WC1.

Kalash_HGDP00285
Iran_Neolithic_WC1 50
Yamnaya-Catacomb_Ulan 39.9
Han 7.2
Andamanese_Onge 1.7
Papuan 1.2

[1] distance%=1.2006 / distance=0.012006

Generally, the estimates of steppe ancestry with the K7 and nMonte seem a bit too low. I suspect it's because with this method I really need to have the perfect references to nail the scores. Then again, maybe the truth is somewhere in the middle between K7/nMonte and TreeMix/qpAdm?

Kurd said...

David,

Estimates with ADMIXTURE are not as accurate as with qpAdm, mainly because the allele frequencies for a component are never 100% based on those for the component maximizing samples.Other samples in the cluster skew those a little. This of course is minimized when there are many samples of the component references, but in most cases the samples are limited.

Clones are useful for component definition only, but as you know they have to be very carefully used as they introduce other types of problems, such as lowering the diversity in the allele frequencies for the references, so they are a somewhat poor substitute for the real thing. This manifests itself when you see that the non references all score under 20%.

Building hybrid synthetics is preferable to clones, but that takes alot of time.

Davidski said...

It's often easy to produce good fits with qpAdm with models that don't look plausible. It's also easy to blow out ancestry proportions. I managed to get the Kalash at around 60% Yamnaya-Catacomb using qpAdm and TreeMix, which seems very high.

So there's no perfect way to estimate fine scale and/or ancient admixture. There are always margins of error and some mystery.

But in any case, what I wanted to show with my model above was that the K7/nMonte combo can reproduce rather faithfully the patterns established with formal stats.

batman said...

@ rk

Karmin et al starts at a hypothetical Out-of-Africa, presuming that:

"non-African populations was shaped primarily by an out-of-Africa dispersal 50-100 thousand yr ago (kya)."

Moreover they "detect a cluster of major non-African founder haplogroups in a narrow time interval at 47-52 kya".


Base on this time-line they prognose a mutation-rate before an after a second bottle-neck, condensed in their main statement:

"In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky."

If you interpret any of the above dates as absolutes I'm afraid we're getting into fundamentalistic waters...

Which is exactly why I re-phrased their statement, to adjust to earlier repports on bottlenecks, as well as the climatological and archaeological evidence I refered to (above). Here's one more:

http://www.sciencedirect.com/science/article/pii/S1040618210004180

Since most prior repports on the time of extictions and bottle-necks of Eurasian mammals are linked to the very same time-frame. Thus it's rather obvious that the major bottlenecks of extant arctic mammals, such as the Eurasian humans, were contemporary to the extinctions of some 45 terrestial species - such as the European mammoths, elks, lions and cave-bears - all disapearing by the onset of the "Younger Dryas Extinction Event".

http://pidba.org/anderson/cv/Anderson%20et%20al%202011%20QI.pdf
http://www.sciencedirect.com/science/article/pii/S1040618211002333

To avoid a senseless discussion about the nitty-gritties i hope we may agree that the age given by Karmin et al, based on alledged mutation-rates - is hard to adhere to any known reality - unless we understand their dating as an "inference" - i.e. an assesment based on an interpretation - rather than a clear-cut, mathematical fact based on physical measurements.

Consequently we need to adress the time of their bottleneck to some hands-on historical facts - which leads to nothing but the YD. If you want to prove otherwise you have to constuct some new and completely unknown event during early Holocene to explain the bottleneck. Which doesn't only contradict the basic facts of the mamalian life-forms, but also the basic prinicples of scientific methodology.

ryukendo kendow said...
This comment has been removed by the author.
FrankN said...

On Refugia and the NE UP/Mesolithic
unsorted, but as hopefully helpful background to the discussion here:

1. Dave: Also, there was probably a population in the northern Levant that was more or less intermediate between the Neolithic Anatolians, CHG and Neolithic Iranians, and it interacted with all of them from the Middle Neolithic onwards.

Actually, the interaction started earlier, as can be traced on the following Obsidian trade maps:
http://www.archatlas.org/ObsidianRoutes/ObsidianRoutes.php

Already 14-12 ka BC, a trade networks between Cappadocian sources and the Northern Levante, had developed. In the Natufian period, this network reached the Red Sea and beyond. I suppose Red Sea salt as countertrade, which would imply early cattle domestication or at least intensive herd Management in NW Mesopotamia.
In parallel, a second network developed from the Bingöl sources near the Upper Tigris that during PPN A (9500-8500 BC)reached the
Middle Zagros. Transhumance?
Around 9000 BC, both Networks interlinked around Aleppo, with Bingöl Obsidian also finding its way towards the Red Sea (Jericho).

2. The eastern Central Zagros foothills have been demonstrated as LGM Refugium for various species, including the walnut, pistacchio, and several moths feeding on steppe plants (plantago lancelota etc.). At least for these moths, the Zagros seems to have formed a migration barrier towards Mesopotamis during the LGM. Note also that no evidence for walnut gathering has been found in Satsurblia and Kotias, even though walnuts today are a central ingredient in Georgian cuisine.
Therefore, I deem it quite likely that the Zagros during the LGM has also significantly affected human population exchange between Mesopotamia and Western Iran.

3. The Likhis mountains separating West and East Georgia, i.e. the Kura and Rioni basins,can be passed at around 1000 m asl. LGM glaciation of the Caucasus is paleoclimatically modelled to have reached down to 500-1000 m asl. This means that there may have been glacial periods when West and East Caucasians/ South Caspians were isolated, but interstzadials, maybe even warm LGM summers, should have allowed for human communication. As such, the genetic similarity of HotuIIIB and Satsurblia/Kotias doesn't come as much of a surprise, and may already date back to the Late UP.

4. The South Caspian coast bears evidence of early seaworthy boats. The Gobustan rock engravings in Azerbeijan depict large boats manned by 10 persons or more. Their context (hunters, Gazelles, Aurochs etc., no goat/sheep yet) dates them into the early Holocene (10-7 ka BC).
http://www.rockartscandinavia.com/images/articles/malahat_a11.pdf
Note also that the earliest Mesolithic layer from Hotu Cave points at a predominantly maritime nutrition, especially based on seals.
Mesolithic Gobustan is tentatively assigned to the Zarzian, which would imply connection across the Iranian Plateau between the Central Zagros and the southern Caspian coast (but I am not sure whether such connection existed during the LGM).

5. During the Early Holocene, the Caspian Sea would have been much larger than today for all the meltwater collected from the Caucasus, Alborz, Pamirs/ Hindukush (via Amur Daya), Urals and the Volga Basin (see map in link below), reaching up to Volgograd, and forming a several km wide inlet towards Samara. With seaworthy boats available, a parsimonous communication channel between CHG and EHG (wherever their glacial refugium was) already (and especially) during the early Holocene.
https://www.quora.com/Ancient-History-When-did-shipping-begin-in-the-Caspian-Sea-In-other-words-when-were-people-goods-first-transported-across-the-Caspian-on-a-regular-Basis

tbc

batman said...

@ Alberto

Nothing of the facts you refer to contradict what I've been saying. The samples from Alleroed/YD are NOT proving otherwise, like you seem to b-e-l-i-e-v-e.

"We have a sample referred to as Satsurblia which is pre-YD and another one from the same place (Kotias) which is post-YD. They are the same population..."

Regarding Satsurblia Cave. The dates given, just about 13.000 yrs BP, is very close to the YD - and thus somewhat problematic, due to the reservoir-effect - which tends to protect the decay of C-14 and thus give dates a bit to high. Which may inflict the measurement of samples like Satsurblia to 'look' older than it is.

However, the sample shows a y-dna J1. Genetiker calls it "pre-J1b-Y6304". Its mt-dna is K3.

The 5000 years younger Kotias is stated to be "J2a". Genetiker calls it "pre-J2a-Y12378". Its mt-dna is given H13c.

Different y-dna, different mt-dna.

And still you claim that Satsurblia is ancstral to Kotias?
Is that a proven fact, or a mere opinion?

@ Alberto:
"and they are very near the Black Sea."

Launching the principle of "Guilt by Association" as "Common Sense"?

What then about the contemporary sample from Carelia, 7.500 yrs BP, showing y-dna J and mt-dna U4?

Are they also descendants of Satsurblia and no-one else?

The calls show that the Grotte du Bichon hunter-gatherer belonged to Y haplogroup pre-I2a1a2a1-L1287. This is the same haplogroup that was found in the Mesolithic Swedish hunter-gatherer Motala 9, the three Swedish hunter-gatherers Ajvide 52, 58, and 70 of the Pitted Ware culture, and the two Hungarian samples KO1 and NE7, from the Neolithic Körös and Lengyel cultures.

@ Alberto:

"We have from several other populations. We have WHGs (Villabruna clade) from before and after the YD, and they are the same population."

I think the sample from Villabruna in Tirol, dated to 13.700-14.00 BP is enigmatic, showing R1b and U5b - both normally associated with northern Europe, early cattle-farming, lactose-persistance and diaries. Thus, again, we have to clearify if the samples dated have been exposed to said "reservoir-effect" (see wiki: C-14.dating).

Now there's already proof of Oat-growing from Paglicci dated to 19.000 yrs BP, which means that northern Italy may have been an area of paleolithic pioneers within cattle-farming.

AJ gives Villabruna R1b1. Genetiker specifes this to R1b1a-L754.
Next known R1b is dated some 6.500 yrs later, at El Trocs (R1b1c) and Samara (R1b1a).

So what post-glacial dna from Villabruna are you refering to - as "The Villabruna clade"?

@ Alberto:

"We have Afontova Gora samples from Siberia that are pre-YD and we have Karelia_HG which is post-YD, and largely descended from AG."

Aha.

AG2 came out of the LGM carrying mt-dna R*/R2. No y-dna given, afaik.

The dna from Carelia - taken from the neighbours of the first Carelian farmers - shows y-dna R1a and J, besides mt-dna U2/U4/U4a and C1g. Possibly also H.

So what's the imediate proof of a direct descendancy - accept "by association"?


@ Alberto:

"We have Natufians, Anatolians, Iranians... All distinct populations. They ALL survived the YD in different places."

So where are these 'refugias' - and where are the archaeological evidence of continuation throughout The Late Glacial Maximum (YD)- in ALL these places.

Unless you're able to locate the various refugia you claim existed - with a due, proven time-line througout the Dryas-periods - your statements are nothing but an expression of the very same kind of nonsense you accuse others of providing.

Please think about that for a while.

Chad Rohlfsen said...

WHG didn't come from Scandinavia. The first settlers were descended from Madalenians, which were still in Northern Germany at the time of Bichon and Villabruna. It's not until later that the Germans cluster with them. WHG is a ghost pop mixed with ANE, which later mixed with Magdalenians. They're likely from the Eastern half of Europe and not Scandinavia. This is pretty clear by looking at the samples.

batman said...

@ Rob

"During the younger Dryas, Northern Europe was again depopulated, with its population again moving south or becoming extinct."

That is NOT the conclusions from the discoveries and discussions during the last 10 years, within the archaeological, geological and biological professions. ALL of them have now given proof of paleolithic refugias existing in Scandinavia. Throughout the LGM as well as the YD.

I'll already been providing you with links to some of the core-material, above. It's somewhat surprising that you haven't even bothered to open the links.

If you can't respond to new facts and point-of-view, unless you get it via BBC, you may have a hard time gaining new insights by discussing the roots and history of The European Genome as science actualy proceed.

@ Rob:

"You're incorrect".

That's a clear-cut statement. But why can't you provide ANY evidence to prove it?

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

@batman

And still you claim that Satsurblia is ancstral to Kotias?
Is that a proven fact, or a mere opinion?


Satsurblia is not the father, let alone the mother, of Kotias if that's what you're trying to say. But that he belongs to the same population ancestral to Kotias is indeed a proven fact. And that's the problem here. We have hard facts that disprove your hypothesis. We have them for years. But you don't know them because you didn't read anything of what has been published in the last few years (or you didn't understand it).

Kotias didn't come from Sweden to Georgia and morphed into a clone of Satsublia by some magic. You really have to get acquainted with basic genetic facts that here everyone knows except you and Gioiello. There is a world outside uniparental markers. Get acquainted with it and you will understand by yourself why what you're saying is nonsense. It's really not that hard to learn it, especially if you are interested in the subject, as you seem to be.

batman said...

@ Alberto

"We have hard facts that disprove your hypothesis"

The "Scanian refugia" thoughout YD is not an hypothesis. It's a conclusion drawn from validated facts.

Moreover - what facts are you actually refering to, to contradict that?

A 'ghost population' surviving "somewhere" around the Black Sea?

batman said...

@ Rob:

"Ok . All humans came from from a refuge in Scania c. 12 ky BP.
Now you play in your looney farm, the rest of us are going back to reality"

Misquotes and Ad hominems never make you anything but looking silly and sounding nasty.

Thus your arrogance is nothing but a lame cover for blunt ignorance.

@ Gioello

"Are you sure?"

Yes - I'm sure there are no KNOWN YD refugias documented from the penninsulas of the Northern Meds.

Not even in the Levant, where the pre-Natufian sites seems depopulated during YD.

The reason seems to be the steep plunge in the middle temperature - of some 8-10 degrees Celsius - that hit also these areas. Perhaps the registered impact across southern Europe, as well as some volcanos erupting, are to be blamed.

https://wattsupwiththat.com/2014/08/29/younger-dryas-climate-event-solved-via-nanodiamonds-it-was-a-planetary-impact-event/

http://phys.org/news/2015-07-cataclysmic-event-age.html

As mentioned above, the cultures that populated Cypros and built Gobekli Tepe - at 11.600 years ago - had several things in common with the populations that crossed the seas to populate Scandianvia and the Brittish isles, as well as the lowlands and rivers beteen the Baltic, Balkan and Siberia...

Moeover - s the aDNA have shown - the male part of all these populations were descendants of a paleolithic hg CF, thus producing mesolithic 'dynasties' of hg I in the north-west, hg G down south-west, hg H south-east and hg J some east/south-east.

For some reason there is - also - an outright overlap between the distribution of these mesolithic y-lines and the known spread of the I-E languages.

--

That said - we may still find sites demonstrating the same kind of continuity as the Scanian population; througout the Last Glacial Maximum AND the Late Glacial Maxima. In that case the milder areas of the western Med should be the more sensible option.

Samuel Andrews said...

@Chad,
"WHG is a ghost pop mixed with ANE"

BTW, according to D-stats, ANE admixture in WHG can't be very high(not saying you claimed it was), because WHG closeness to ANE is about the same as in earlier Europeans. However I did say the same about CHG admixture in modern SouthWest Asians but I didn't know there were once populations in the Middle East who were much more distant from CHG than EEF was and much more distant from EEF than CHG was. So, maybe there were populations in Europe who were much more distant from ANE than Paleo Euros were.

"They're likely from the Eastern half of Europe and not Scandinavia. This is pretty clear by looking at the samples."

This makes sense. We shouldn't have assumed they were descended of Paleo settlers of Western Europe because our WHG genomes were all under 15,000 years old. WHG cluster is very drifted is it not? And it probably had been for well over 20,000 years.

WHG being from Paleolithic(Pre-Ice age?) Eastern Europe makes sense because of WHG-like ancestry in EHG and ancient/modern Middle Easterners. How WHG mostly replaced the Beligium-Paleo Western Europeans is a mystery but they obviously did and it started at least 19,000 years ago.

Olympus Mons said...

@Davidsky.
See, how I am keeping abay of all of these?! - However when one starts to talk about a ghost population and I am the one that keeps on mentioning the "ghost pop" that were the Aratashen-Shulaveri-Shomu and moved away at the start of the 5th millennia ( and later show up in Merimde/ElOmari)... man, it becomes difficult.

A note: Remember spelt. being an Hybridization of emmer wheat and bread wheat, it really show up first in early 6th millenia in Shulaveri land, them in Merimde then iberia and being later a trade mark of the bell beaker. However... there is a doubt if an earlier samples was not found in the Carpathians. So story would run from here to South Caucasus and them Nile Delta. Maybe that is the route of the "ghost Pop". Who knows.

Chad Rohlfsen said...

The Dstat with WHG being equally close to ANE was the red flag to start it all. If WHG had no ANE and 20k years of extra drift from the split of West Eurasians, they would've been significantly further from ANE, ENA, and Native Americans. Of course, the opposite is true. BTW, all WHG samples are significantly closer to NAs and ENA than UPs, so no one has zero. Just using Bichon as a baseline made Loschbour, LaBrana, and KO1 about 4-5% ANE or 6% EHG.

I can get into this more later, but I'm thinking WHG is more like 10-15% ANE.

Alberto said...

@Olympus Mons

Do you have any reference for a burial in Iberia with Palmela points that is securely dated to before 2400 BC? I was searching through all the literature in Spanish and couldn't find anything predating 2400 BC (most of it being from 2200 BC or later). Maybe you know something in Portuguese?

Or if not Palmela points, something that looks unambiguously Bell Beaker (not mixed with pre-Bell Beaker material, etc...)?

FrankN said...

7. Rob/Batman "Black Sea Refugium". Speculative, and also terminologically vague:
- We have a documented SE Black Sea Refugium that comprises West Georgia (CHG) and most likely stretched westwards up to Sinope. Lower Black Sea Water Levels would have brought up a quite sizeable coastal plain between Sinope and Samsum with adequate temperatures and precipitation to support Boreal trees. The SE Pontic is generally believed to be the origin of plum and cherry cultivation, which most likely means a glacial refugium of ist wild progenitors.
- For the NE Black Sea, Romanian hydrological research has demonstrated LGM water levels some 140 m lower than today. This would have exposed a huge coastal plain, with the coast approximately having run along the line Burgas-Sebastopol. Of course, that glacial plain hasn't yet been screened paleontologically and archeologically, so we don't have any proof of it acting as a Refugium. To my knowöedge, it also hasn't yet been included in paleoclimatic models, which means we have little idea about temperatures and precipitation. Especially the latter may be an issue for the Balkans' and Carpathians' rain shadow.
I personally think that Danube and Dniestr are unlikely to have seasonally fallen dry during the LGM, so at least their floodplains should most likely have provided refugia for ungulates, and consequently also humans. But that is a personal opinion and ultimately speculative.

8. In any case, the East Carpathians, i.e. Transylvania and NW Moldova, have been documented as refugium for various large mammals including Brown Bear (link 1), Lynx (link 2) and boar (various papers on boar/pig aDNA). If those animals found refugium in the Carpathians, humans most likely did so as well. Gioiello, forgive me - but my bet is that one day we will find R1b in the Carpathians that is even older than Villabruna, because when I triangulate between Villabruna, Samara and those "unspecified R" finds from Elbe-Saale MN, that's where I end up.

https://www.researchgate.net/publication/230033071_The_recolonization_of_Europe_by_brown_bears_Ursus_actos_Linneaus_1758_after_the_Last_Glacial_Maximum
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0093675

9. The Lynx paper identifies three more Eurasian refugia: The Caucasus, Central Asia, and Eastern Siberia, but doesn't see any signs of a Beringian Refugium.

10. Moving south: Paleoclimatic research for SEA still has ample room for development, but it has become clear over the last years that the area has been affected more severely during and after the LGM than originally thought. Lower sea levels, and consequently smaller oceans, combined with less evaporation due to lower temperatures substentially weakened Monsoon rains during the LGM. From 18 ka BC on, the SE Monsoon appears to have completely vanished. The linked paper discusses consequences for Anopheles mosquitos, which had to withdraw to two, seperated refugia in Northern Bengal and SW China/ N. Vietnam (check Fig. 7!).
Well, mosquitos are not humans. But they feed on them or potential hunting game (gazelles, monkeys etc.), and depend on sufficient sweetwater availability for breeding. As such, the fact that mosquitos were forced into specific LGM refugia in mainland SEA could provide some hint on the respective human faith.
http://www.intechopen.com/books/anopheles-mosquitoes-new-insights-into-malaria-vectors/understanding-anopheles-diversity-in-southeast-asia-and-its-applications-for-malaria-control

tbc

Davidski said...

My Villabruna cluster is about 15% ANE, which means all European Mesolithic foragers and West Eurasian early farmers have ANE as well, but it's basically masked.

Rob said...

@FrankN

Insofar as humans go, I wouldn't separate the Black Sea areas, in fact I'd group them even bigger with Moldovia, the north Balkans & Carpathian (Moravia; Hungary) into an east-central Eurpean Epigravettian technocolplex; chatacterized by significant mobility and complex chain of population shifts; which we can piece together from various sources (but no overall synthesis yet exists).
I think that explains the R1b in Villabruna (NE Italy)

Rob said...

^^^
Also Frank, Georgia wasn't an LGM refugium
It was abandoned during the LGM, and re-occupied from c. 18ky BP, from both south (BE; Zarzian, hg J) and north ("Villabruna", Epigravettian, ? hg I or R1?)

Samuel Andrews said...

@Chad,
"If WHG had no ANE and 20k years of extra drift from the split of West Eurasians, they would've been significantly further from ANE, ENA, and Native Americans. "

This makes sense but then why are Onge slightly closer to West Eurasians than Ust Ishim was?

"Just using Bichon as a baseline made Loschbour, LaBrana, and KO1 about 4-5% ANE or 6% EHG."

That's believable. K01 is definitely our most admixed WHG. Using D-stats best model for K01 was 54% Loschbour, 36% Motala HG, 10% Anatolia Neolithic. All Early Neolithic German/Hungary's best HG reference is K01 and when Loschbour is uses they need EHG admixture.

Olympus Mons said...

@Alberto,
Not to the context you want.
Bell beaker in Portugal starts 2800bc to 2600 bc . All campaniforme or Bell beaker in Portugal is widespread Extremadura and north portugal by the sea at those dates. Bear in mind that the earliest Bell beaker pottery found was actually in Porto Torrão, in south in these huge city, not in here north of Tagus river (there is always a twist). Anyway, a lot of people in zambujal were actually BORN in south in alentejo (most likely Porto torrão) and vice versa.

What you are looking for is the “warrior” bell beaker context. That is scarce and is by those dates you mentioned. That is the important fact. Bell beaker became more elite as it moved way from Portugal and not at its origins.
Bell beaker say in Leceia (actually just miles from where I live) , actually were a people that lived alongside the not bell beaker people. See, for over 700 year in some huts it was beaker (always) and on the other near by Huts they never, never get to be bell beaker. So, different people most likely.
This is the reason why the stories people here as in other places like to fantasied about a super elite from the steppe or whatever that became Bell beaker… does not pan out. They were normal folks, living alongside other normal folks for centuries and centuries before becoming the elite, warrior, that moved way into Europe…

By 2600/2500bc something arise and it became more warrior like, more Horselike, more elite (by 2600/2500bc) and it shows. Most notably at that point they moved massively south…. To occupy again the sites that once were more “warrior like” as per my description in my thesis like Porto carretas. But by then it was already a mixed of all types of Iberia bell beaker. Those guys by 2400bc were really a network, as it shows the diferent styles in south Portugal of all Iberia bell beaker types.

Alberto said...

@Olympus Mons

Yes, this is exactly the impression I get. The Bell Beaker phenomenon in Iberia has been mixed with pre-Bell Beaker cultures. Or if you prefer to call Bell Beaker to the first one then the second one would need a different name. It's not the name that matters, but they were 2 different people and cultures. One starts ca. 3000-2800 BC. The other one ca. 2400-2200 BC.

The one that they call in the rest of Europe Bell Beaker culture is the one that in Iberia starts ca. 2400-2200 BC. So I think it's better to call Bell Beaker to this second one and rename the first one instead to something else (though we have names already like VNSP, Los Millares... so probably it's better to stick to those).

I think that DNA will show this distinction quite clearly. Before 2400 BC there will be one kind of people (probably like Iberia Chalcolithic ones), and after 2400-2200 BC we'll start to find a different kind (that will probably cluster with modern Basques, or maybe modern Frenchmen) in those burials that you refer to as more warrior like.

Olympus Mons said...

Alberto,
This is where I disagree with you. There is no way a certain “kind” of people would get out of Iberia as campaniforme/ Ciempozuelos and a couple centuries later a different (even slightest) “kind” of people would come back as Bell beaker warriors but keeping so much of the original? - It does not exist in the real world. :)

For people that try to measure the lives of hundreds of thousands of people that lived 5000 years ago by a couple DNA alelles, found in one or two inhumations, it might make sense in that kind of “Westeros” land. Iberia chalcolithic was comprised of lots of different people (imo coming bundle up trough north Africa).
Its much more plausible that, if Iberia was “invaded” by hundreds, Hundreds of thousands of people in chalcolithic times, those were composed of very different people and that it took a while to have that elite differentiation show up. If one goes DNA way, them lets sample a lot in different places.
See how the DNA in Anatolia/Middle east/Caucasus is coming back much more complex than anyone ever previously thought.


Alberto said...

Olympus,

I never said or suggested that anyone went out of Iberia and then returned back. What I'm saying is that there are 2 different phases in Iberian cultures that have been loosely referred to as Bell Beaker, but only the second one is true Bell Beaker (or call it European Bell Beaker or however you prefer).

That second phase marks the arrival of new people from Central Europe, around 2400-2200 BC.

In the previous Chalcolithic phase, there are indeed increased contacts with North Africa, mostly via trade, but I guess they could imply some degree of gene flow too. Maybe these North African people ultimately came or had some relationship with Shulaveri culture, I have no idea about that. But they should not be expected to be Yamnaya-like, for obvious reasons. They could look "North African", though.

DNA will tell us soon enough, but I think there'll be not much mystery there (pity, I expected to find something solid from before 2400 BC to make the story interesting, but I couldn't).

Olympus Mons said...

@Alberto,

“That second phase marks the arrival of new people from Central Europe, around 2400-2200 BC.” - ----- That is my point...You do expect that Yamnaya type of people arrived in Iberia by 2400 bc HAVING THE SAME (OR IN LARGE PART) TRAITS as the Campaniforme people that originally arise from Iberia itself and departed Iberia in or around 2500BC ?? - How does that make sense?

Regarding North Africa,
Why do so many keep on thinking that after the havoc, and we all agree now by the latest posts here that transition from neolithic to chalcolithic in Anatolia/levant/Caucasus/iran was a leveling event of admixture and population replacement and that implied a lot of running havoc people, right? Again way to people think that the movement of people has done by they deliberate choosing crossing mountains, lakes and or by sea with boats nobody finds , crossing full mountains ranges of rough Europe…. Instead of strolling along the green grass plains of North Africa? I can’t figure out why people would think that. North Africa by 5000BC to 3900 bc was a strolling heaven for Cattle and farming people! Why would people not choose it?

I can’t say this times enough. It will be a surprise when aDna or even Y dna pops out of Nile Delta:
• Between 4800BC and 4000BC there was a very “Armenoid/Caucasian” people in Merimde/elomari in Delta Nile Egypt that shares traits (loads) with chalcolithic Iberia. These highly mesocephalic, tallish and sturdy people also shares lots of traits with neolithic Caucasus/Anatolia/levant. Prior (Natufians) and Later people around (Israel, levant, etc) were not morphological like them. I found 1960 references that they were at least in the vicinity of 30 thousand just in the delta. The ones that stood in the mix with Maadi were called the Giza people and were very Caucasoid.

• For whatever reason Nile Delta was abandoned by 4000BC and that Caucasoid people disappeared. At the same time it started the 5.9 kiloyear event when Hundreds of thousands of people disappeared from north Africa at that millennia (along side with Merimde and el-omari), at the same time that hundreds of thousands of people show up in Iberia peninsula (coming from where in 3500bc?). Why in heavens would one think that it’s not the same populations (see the plural) that was crossing over? Some went to Nile (pharaonic Egypt) some cross to Iberia and in fact some of those were the Caucasoid people of Merimde that later up even popped up King Tut as R1b-M269. That Different people was actually the campaniforme that lived along side the other north African population and mixed with local neolithic population but for instance in Leceia never never the bell beakers contaminate culturarly the others or vice versa.

• So, Finding a couple guys hidden in a cave in the “other side” of the mountains range in Atapuerta (probably the best hidden place in iberia to avoid “the others”) and thinking that their DNA represents the Iberia chalcolithic and copper age Iberia…. Is just wrong!


Alberto said...

@Olympus

If by those traits you mean a more complex society, becoming more hierarchical, less egalitarian, with increased importance to power and control, richness,... Yes, I completely agree that this is not something invented in the steppe or by Indo-Europeans. This is a general and natural trait of any society that reaches a certain level of development. Indo-Europeans just participated in this trend, but it was not invented or exclusive to them as once thought (for example, Marija Gimbutas in her original Kurgan hypothesis, where she already saw a first wave of steppe invaders around 4400 BC around Europe, when we now know that what she was seeing were autochthonous social changes happening at that time).

So yes, one should not put those traits into meaning one single population was responsible for spreading them. That's why it's important to try to check for specific traits that can really identify a population and not general ones. The general ones already started in Iberia in the Chalcolithic. But some specific ones that identify Bell Beakers specifically only appear ca. 2400-2200.

For the rest I can't agree much. There are too many problems in what you're proposing. But I'm glad to be surprised by ancient DNA, so I'll wait for those Yamnaya-like samples to show up in North Africa and Chalcolithic Iberia and I'll congratulate you if that happens for being the only one being able to figure it out.

Olympus Mons said...

@alberto,
Yes, Yamnaya like but with much less EHG and much ore CHG. :)

We will see. Wouldn't it be a blast?

One question. Do you know how long usually it takes from Collecting DNA samples and publishing a paper? I know the french got Shulaveri samples in late 2013 but so far no news!

Alberto said...

No idea, it depends on too many factors. Sometimes the samples are ready for a year or more before they get published. Sometimes the samples don't yield enough DNA to be useful and the process fails altogether. So it's quite unpredictable.

But it will all come sooner or later. Hopefully this second half of the year we'll see at least the Bell Beaker study and a few other interesting things.

Olympus Mons said...

@alberto,
I have dozens of these. Just found this today


"Possibly, SPANISH spelt originates from ASIA, rather than from Western Europe,and evolved independently from Bavarian spelt for along time."
- Analysis of Intraspecific Divergence of Hexaploid Wheat Triticum spelta L. by C-Banding of Chromosomes


You know spelt is a trademark of bell beakers right?
We have Spelt in south span near Gibraltar by 2800 bc, North Portugal by 3000 bc.... man, am i Just crazy?
Spanish Spelt is the same spelt of the one found in Shulaveri and nobody finds it strange. Shall we talk about pressure lever blade making? :)

Alberto said...

@Olympus

I haven't looked at the case of spelt, but for what you say it might have been introduced from North Africa. The contacts between Iberia and North Africa in the Chalcolithic are there, no doubt.

But if that spelt is different from the one the Bell Beakers had in Central Europe, wouldn't that mean that the Bell Beakers from Central Europe didn't come from Iberia but from the east?

Taking you hypothesis to a genetic level, I think you have a good case for showing that North African admixture in Iberia comes from the Chalcolithic and not (just) from Medieval times. Though I'm afraid that's not what you're interested in trying to prove.

The Yamnaya-like admixture and R1b-L51 coming from North Africa is a quantum leap you're making that no one here is going to buy before we see the samples. And that's because there are many reasons why it doesn't make sense.

But as you've stated, everyone just listens to his own pet theory, and hold to it until proven wrong (and then some people even keep repeating it for years after being proved wrong). So let's just wait to see the samples and everything will be clear.

Olympus Mons said...

@ Alberto,
I agree with most of your premises... except in the context.
You seem to have the impression that I think R1b-M269-L51 "lived" in North Africa but is not entirely correct.

What I say is the route was from North Africa into Iberia. Something West Asian popped up in Iberia by 3500 BC. What I say is Either Merimde/El omari or some population within them (meaning they might be P297, V88 in there) was R1b-M269 and even might be L51 and whatever made those 30,000 people move, some moved east, south or stayed but part moved west in the most of worst of times ever, because the 3900 bc Kiloyear event was kick starting and that climatic event saw the desapearence of hundreds of thousands of people in North Africa and the appearance of those same amounts in Iberia. Arrows and carenated Poterry if you wanted. Its not the same is it?
In that vast amount of people were the R1b-M269. So, lets sample Zambujal and early bell beaker and leceia and so forth and see what comes up.





Open Genomes said...

The complete set of known Y SNP calls for Bon001:

Bon001 Y-DNA SNP calls Epipaleolithic Central Anatolia Boncuklu
8300-7500 BCE (10310-9510 BP) G2a2b2b1a-PF3422


I1314 and his relative I1314 from the Iberian Chalcolithic 2880-2630 BCE were G2a2b2b1a1-PF3378.

G2a2b2b-PF3146 is found in two HGDP Palestinians, and one 1K Genomes CEU, but it's most common in Sardinia and it's found in about 1% of Dutch samples. It's also found in one Armenian from Iskenderun Turkey, an Iranian Arab family of Iraqi origin, and a single Han Chinese from Ningxia from Yan et al. (2014). There are other scattered G-M485's (G-L30's) who are M406- P303- and so in fact may be G-PF3359.
These were found in Crete, Nea Nikomedia, Greece, Hungary, and among Kabardinians, Mordvins, and non-Ashkenazi Jews.

Here is an individual from the Rhineland-Pfalz in Germany who is G2a2b2b1a1a-PF3415 from just 25.5 km south of the LBK type site of Flomborn:

Map of G-PF2420 from Altleiningen, Rhineland-Pfalz, Germany

Davidski said...

I updated the post!!!

Matt said...

@ Davidski, thanks for uploading this. Not sure if you want us to comment here, or on a less populated thread but:

Used the datasheet to run a quick couple of PCA myself:

With Basal Rich+Villabruna+AG3-MA>80% gives the neatest fit to Lazaridis and other PCA - http://imgur.com/a/y8jlM

If you use the full set of samples, including South and Central Asian then MA1 is displaced quite far "south" to compensate for position of those: http://imgur.com/5PxfLJR / http://imgur.com/UgTv6TI (the SCA drag MA1 away from Villabruna)

That continues if you remove all other components than BR, V and A-M and have them sum to 100%: http://imgur.com/yEQdx8F / http://imgur.com/wiWFEGM

If I take all the averages, then split the Basal Rich into 0.5 actual Basal and 0.5 that merges in which Villabruna, then you get a distribution like this: http://imgur.com/If2N3mK .

I think that conforms a bit more nicely to most PCA (as the positions with its "Fateful Triangle" seems to be more in line with the genotype PCA). A benefit of that is that the implied Basal Eurasian matches fairly well with the results from the paper, and goes only from 27% Anatolia_Neolithic to 18% Iberian_Chalcolithic to 7% Yamnaya, with recent Europeans intermediate (Lithuania 9%, Polish 11%, English 13%, Spanish 17%), and Levant_Neolithic at 34% and Iran_Neolithic at 31%.

Removing an additional 10% of the AG3-MA1 would also help to even out the Basal levels (Yamnaya then go to 12% Basal, Lithuania to 11%), even Basal Level between Iran and Levant Neolithic at 34% and would not change the PCA much. More in line with the paper, but not really necessary.

But this all is a bit of messing with the numbers.

Davidski said...

I'll start a new thread on a related topic tomorrow. Till then let's keep things here.

I'm still totally stumped that I can't make the Steppe_EMBA samples look more southern in this analysis. They just don't like the Basal-rich component. They're almost allergic to it.

Really not sure what to make of that, but I have a feeling that the formal stats-based tests are often bloating some ancestry proportions, perhaps due to a lack of the perfect outgroups, and giving good fits nonetheless.

Btw, Iran_Hotu is certainly less basal than Iran_N, and especially WC1. And based on this exercise, the Natufians do look the most basal, although still nowhere near 100%.

Matt said...

@ Davidski, yes. Formal stats could somehow be bloating the Basal level in some populations. I think that could be so. It seems not so likely to me that their methods are underweighting the Basal in most populations by a substantial amount, but I still think could be confusing ANE for Basal perhaps for some reason, so overweighting it in other places. Kind of hard to see why exactly as the outgroups should distinguish, but that seems like the only way to reconcile with these kind of measures.

Btw, when looking at the ratios of AG3-MA1:Basal Rich:Villabruna in the populations, one thing I do notice is that the more ASI heavy populations have a combination of AG3-MA1:Basal Rich:Villabruna that is out beyond what can be created by combining Iran_Neolithic with steppe:

http://imgur.com/a/l41nN

You can get roughly to the ratios of AG3-MA1:Basal_Rich:Villabruna in Kalash (44:42:14) by combining Iran_Neolithic (41:60:0) and Yamnaya (48:16:36). But to get to the Chenchu (50:48:2) or Chamar's ratios (51:45:4), they have a higher AG3-MA1:Basal-rich ratio than Iran_Neolithic, so that you can't use that, and steppe can't contribute either, because that has a high portion of Villabruna cluster. These seem to place on a point beyond a Basal_Rich->Iran_Neolithic cline (as also Iran_Hotu seems to be, but not quite enough).

Also seems like Mansi should be almost straight EHG plus Siberian East Asian here from the ratios (69:2:29).

(Neighbour joining all the ratios forms a fairly neat dendrogram http://imgur.com/a/txKRU)

idurar said...

Any change for the Eurasian part of Northwest Africans? Is there - unlike what was
initially assumed - a significant deviation from the Basal Eurasian-WHG cline (towards the Eurasian steppes or Neolithic Iran)?

Chad Rohlfsen said...

Matt,

Iran is about equally WHG and ANE. Mbuti Test WHG ANE is about equal in CHG and Iran.

Matt said...

That's the D-stats? That's hard to reconcile with Iran_Neolithic scoring 39% ANE, 56% Basal_Rich and neglible others here, including 0% Villabruna. Unless Basal_Rich is like 70% Villabruna, and that goes to 39% ANE, 17% Basal, 39% Villabruna. The FST distances suggest Basal_Rich is more like 30% Villabruna if anything though. I can't see how the D-stat being equal can match with this...

Davidski said...

@Matt

We might be missing a reference pop roughly on the Iran_HG/Steppe_EMBA cline that is important for South Asians, especially Dravidians. If so, this might make things interesting from a linguistic point of view.

@Chad

I can't see Iran_Neolithic being as much WHG as AG3/MA1.

There has to be a problem, like the stats being confounded by AG3/MA1 admixture in WHG, and we might not yet have the right reference samples for the AG3/MA1-related stuff in Iran_Neolithic to run successful formal stats.

This was also a bit of problem for EHG back in the day, until AG3 came along. AG3 does OK for Iran_Neolithic too, considering the poor quality of AG3, but I reckon Iran_Neolithic needs something from Central Asia.

Mbuti.DG Iran_Neolithic Villabruna AfontovaGora3 0.0174 Z 2.536 SNPs 226210

Davidski said...

Here are some more results. Substructure, probably via admixture, seems to be confounding the stats.

Mbuti.DG Iran_Neolithic Villabruna AfontovaGora3 0.0174 2.536 226210
Mbuti.DG Iran_Neolithic LaBrana1 AfontovaGora3 0.0157 2.253 230541
Mbuti.DG Iran_Neolithic Loschbour AfontovaGora3 0.0137 1.995 234022
Mbuti.DG Iran_Neolithic Bichon AfontovaGora3 0.0141 1.956 236671
Mbuti.DG Iran_Neolithic Hungary_HG AfontovaGora3 0.0055 0.759 214729
Mbuti.DG Iran_Neolithic Motala_HG AfontovaGora3 -0.0004 -0.06 233239

Chad Rohlfsen said...

Villabrunas 5% Neandertal screws with that one. Bichon shows there isn't any preference for ANE. CHG with a 10% more BE and a little ENA should make Iranians. If they're 46% BE, 30% ANE might be the max.

Davidski said...

But there's a clear pattern, and the LaBrana1 stat is high as well (2.253). The Bichon stat also shows a preference by Iran_Neolithic for AG3.

Mbuti.DG Iran_Neolithic Bichon AfontovaGora3 0.0141 1.956 236671

Just because the stat isn't over Z 3 doesn't mean you can argue that Iran_Neolithic has as much WHG as AG3 related ancestry.

It was argued in the recent Key et al. paper that Hungary_EN had more WHG ancestry than Stuttgart based on a similar stat, and the sequences they used were much higher quality and more relevant.

Interestingly, NE1 and Stuttgart are equally close to present-day European populations, but NE1 is slightly closer (not significantly) to the hunter gatherer than Stuttgart is (based on D-statistics, Z score=1.93, Supplementary Table 1 and PCA, Supplementary Fig. 24; see also Supplementary Note 2). This is consistent with gene flow between the populations of Loschbour and NE1. Like Stuttgart, NE1 has fewer alleles from the DAnc genic European tail than Loschbour (Supplementary Fig. 25), although the difference between the two genomes is not significant, consistent with Loschbour-to-NE1 gene flow.

Like I say, we probably don't yet have any good references for the AG3-related admixture in Iran_Neolithic, at least not for formal stats.

There's no way that Iran_Neolithic has as much WHG-related ancestry as other, more easterly forager admixtures.

Davidski said...

Transversions only. Pity about the lack of markers.

Mbuti.DG Iran_Neolithic Villabruna AfontovaGora3 0.0224 1.612 42112
Mbuti.DG Iran_Neolithic LaBrana1 AfontovaGora3 0.0286 2.141 42963
Mbuti.DG Iran_Neolithic Loschbour AfontovaGora3 0.0234 1.967 43794
Mbuti.DG Iran_Neolithic Bichon AfontovaGora3 0.0189 1.39 44145
Mbuti.DG Iran_Neolithic Hungary_HG AfontovaGora3 0.02 1.398 39743
Mbuti.DG Iran_Neolithic Motala_HG AfontovaGora3 0.0098 0.883 43511

Seinundzeit said...

David,

In general terms, this is the most robust ADMIXTURE analysis I have ever seen. It probably can't get better than this, with the sampling that we have. Everything makes sense.

Do you think there will ever be a point at which personal genotype data (23andMe, etc) will be usable in this test?

Davidski said...

At the moment it takes something ridiculous like 40 minutes to run a handful of samples. I'll try and get something together later this week that does the same job in a few minutes.

Davidski said...

idurar,

This test isn't all that great for Africans, because it only has one African-specific cluster, so it often compensates with things like Southeast Asian. But the North African results look OK, considering.

K7 Algerian_Algerian43A21
AG3-MA1 2.56
Andamanese 0.85
Basal-rich 54.63
Oceanian 1.07
Southeast_Asian 2.12
Sub-Saharan 11.45
Villabruna 27.33

K7 Libyan_LIB18
AG3-MA1 3.26
Andamanese 1.13
Basal-rich 63.17
Oceanian 0.26
Southeast_Asian 1.74
Sub-Saharan 7.86
Villabruna 22.59

K7 Moroccan_MCA37
AG3-MA1 0.68
Andamanese 0.56
Basal-rich 57
Oceanian 1.27
Southeast_Asian 2.11
Sub-Saharan 10.2
Villabruna 28.17

K7 Tunisian_Tunisian20B4
AG3-MA1 3.58
Andamanese 0.77
Basal-rich 58.03
Oceanian 0.81
Southeast_Asian 1.89
Sub-Saharan 8.73
Villabruna 26.2

Davidski said...

Getting almost Z=3 with Yoruba as outgroup. LaBrana1 is now on top.

Yoruba Iran_Neolithic LaBrana1 AfontovaGora3 0.0193 2.874 230555
Yoruba Iran_Neolithic Villabruna AfontovaGora3 0.0183 2.827 226222
Yoruba Iran_Neolithic Loschbour AfontovaGora3 0.0134 2.083 234035
Yoruba Iran_Neolithic Bichon AfontovaGora3 0.0136 2.058 236685
Yoruba Iran_Neolithic Hungary_HG AfontovaGora3 0.0026 0.383 214741
Yoruba Iran_Neolithic Motala_HG AfontovaGora3 0 0.003 233252

So getting too far out with the outgroup might be an issue as well.

Matt said...

@ Davidski, be interesting to have those samples, though anything clinal from Iran_Hotu towards the most AG3-MA1 Steppe samples would get a bit too Villabruna rich before it gets enough AG3-MA1:

http://imgur.com/CUFRI8K

Just looks like you need something pretty much exactly like Iran_HG, but with a touch more AG3-MA1 and a touch less Basal-rich.

Lots of the low caste / South Indian / Dravidian populations seem to basically lack all but a trace of Villabruna here. So should lack EHG, and then lack all but a trace of Steppe. Different from Laz 2016, but I don't think they did, or perhaps could not, use the Iran_HG in their mixture models.

Samuel Andrews said...

@Davidski, Matt, Chad, Ryuk, Rob, Kurd.

What are your thoughts on how related the WHG and ANE-type ancestry in ancient Middle Easterners really is to Western European WHG and Siberian ANE? Has any method, with relavnt outgroups(WHG and ANE-heavy outgroups), been able to model them as largely ANE and WHG with a good fit? As far as I know none have.

Davidski said...

The qpGraph model in Broushaki et al. has Iran Neolithic WC1 modeled as basically Basal/ANE 60/40.

Apparently it works OK, not sure why though exactly, as obviously that's not WC1 is, and it actually has the highest level of Villabruna-related stuff out of all the Early Neolithic Iranians, thanks to its high level of the Basal-rich component.

Davidski said...

Almost nailed those D-stats with Yoruba as outgroup and transversions only. This is somewhat frustrating, because it appears to be a game of the right samples + enough quality markers.

Yoruba Iran_Neolithic Loschbour AfontovaGora3 0.0305 2.745 43801
Yoruba Iran_Neolithic LaBrana1 AfontovaGora3 0.0332 2.572 42970
Yoruba Iran_Neolithic Bichon AfontovaGora3 0.0247 2.013 44152
Yoruba Iran_Neolithic Villabruna AfontovaGora3 0.0246 1.915 42118
Yoruba Iran_Neolithic Hungary_HG AfontovaGora3 0.023 1.769 39750
Yoruba Iran_Neolithic Motala_HG AfontovaGora3 0.0174 1.654 43518

By the way, in regards to how similar the unknown West Asian foragers were to Villabruna and Loschbour; they were almost identical, or so it seems to me.

Samuel Andrews said...

@Davidski,
"By the way, in regards to how similar the unknown West Asian foragers were to Villabruna and Loschbour; they were almost identical, or so it seems to me."

It's interesting you think that. I doubt it but I'm open to the possibility, because of the strange results we got from Natufians and Iran_Neolithic, which revealed so much was true that I didn't think was true.

The WHG ancestor of ElMiron and EHG wasn't the same as Villbruna or Loschbour. Wouldn't you agree? WHG looks like an old family with internal diversity.

Davidski said...

ElMiron didn't have any WHG ancestors per se. ElMiron is from a sister clade of WHG, or the Villabruna cluster rather, which developed into WHG.

Yeah, I know the graph from Q Fu et al. but it doesn't look entirely accurate to me.

In any case, keep in mind, the Villabruna cluster inc.WHG shows high affinity to CHG, EHG and all present-day Near Easterners.

So it has to be from the Balkans and/or the Black Sea littoral region close to Anatolia. Its sister clades probably inhabited Anatolia and the Levant and mixed with Basal Eurasians there, possibly during and/or just after the LGM peak (Ice Age).

Gioiello said...

@ Samuel Andrews
"WHG looks like an old family with internal diversity"
Of course. Franco-Cantabrian "El Miron" went extinct, and Villabruna peopled Europe and Middle East after the Younger Dryas (hgs. R, J, G and perhaps others).

@ Davidski
"So it has to be from the Balkans and/or the Black Sea littoral region close to Anatolia. Its sister clades probably inhabited Anatolia and the Levant and mixed with Basal Eurasians there, possibly during and/or just after the LGM peak (Ice Age)".
Agamemnon said the same on Anthrogenica, and I've already written about him...

Anyway Villabruna was in Italy at least 14000 years ago. Next aDNA will resolve also this question.

Davidski said...

Well, either Villabruna sister clades inhabited Anatolia and the Levant, or there were some very serious population movements of foragers from the Balkans into the Near East.

It has to be one or the other, or both, considering the high affinity of all ancient and modern Near Easterners to Villabruna.

Conversely, Villabruna came from the Near East. Take your pick.

Samuel Andrews said...

@Gioiello,
"Of course. Franco-Cantabrian "El Miron" went extinct, and Villabruna peopled Europe and Middle East after the Younger Dryas (hgs. R, J, G and perhaps others)."

Y DNA J yes. Y DNA R definitly not. Y DNA I existed Paleolithic Europe 30,0000 years ago, in close relatives of WHG, while R has been found in Paleolithic Siberia with ANE. This is old information everyone on this blog understands now.

Gioiello said...

@ Samuel Andrews

"Y DNA R definitly not. Y DNA I existed Paleolithic Europe 30,0000 years ago, in close relatives of WHG, while R has been found in Paleolithic Siberia with ANE. This is old information everyone on this blog understands now".

Of course R1b1-L389- was in Asia, but I, with my rough means, demonstrated just that Italy has the highest presence and variance of R-V88, R-L389+, and R-M335... thus my idea is that in the clan Villabruna, with hg. J and G, were also all the oldest R. Again, only aDNA will prove or disprove that.

Davidski said...

Matt,

What would be the ancestry proportions in this latest K7 for a sample that was 0.568/0.432 mixture of Karelia_HG and Iran_Chalcolithic:average?

Matt said...

@ Davidski, I feel a bit like this is to demonstrate something and I'm not sure what (or else you'd have just shown the result ;) ) but...

0.568Karelia:0.432Iran_Chal

AG3-MA1: 42.50
Andamanese: 0.38
Basal-rich: 27.51
Oceanian: 0.05
Southeast_Asian: 2.10
Subsaharan: 0.40
Villabruna: 27.07

Here's some contrasts in levels, above is vs most AG3-MA1 populations, below is against populations with the least root sum of squares difference :

http://imgur.com/3oHvxZB

It seems like Tajiks are the closest match. Steppe is close but seems too rich is Villabruna (so in that sense this is contradicting Laz, if that's where the 0.568 EHG : 0.432 Iran_Chal formula is from).

Just looks at the ratios, 0.568Karelia:0.432Iran_Chal has ratio AG3-MA1:Basal-Rich:Villabruna of 43.8 : 28.3 : 27.9.

http://imgur.com/Kx3ltEK

It seems like the Tajiks are still best match for that combination, though Uyghur climbs up the ranks when looking ratios of the West Eurasian 3 rather than all components.

Same method (root of sum of square of differences) to see which population closest matches ratios in Chamar:

http://imgur.com/XqZqzJh

Pretty much like Hotu cave or Satsurblia really, but with a little extra ANE.

Davidski said...

Thanks, so this is where Steppe_EMBA would cluster in my K7 PCA if it were a 0.568/0.432 mixture of EHG and Iran_ChL.

https://drive.google.com/file/d/0B9o3EYTdM8lQaGQwTjVMYUdmbFE/view?usp=sharing

The PCA from Laz et al. showing the positions of the actual vs inferred Steppe_EMBA looks similar, although the effect is more exaggerated on the K7 plot.

https://drive.google.com/file/d/0B9o3EYTdM8lQdHI3aDNPVS1GOU0/view?usp=sharing

Rafs said...

It's interesting how the Bronze Age Iberian, ATP9, is now showing some evidence of ANE admixture, which had escaped previous calculators. From some time now, Genetiker's K13 runs, too, have been showing steppe admixture in 7 of the 8 El Portalón samples, especially in ATP9 and the supposedly R1b-M269-carrying ATP3. I wonder if you can you confirm if ATP3 has ANE admixture?

Davidski said...

None of the Chalcolithic Iberians that I have show any steppe admixture. I don't have ATP3. It's too low quality to run in any of my analyses.

ATP9 is from the Late Bronze Age, so it post dates the main expansions from the steppe, and it was obvious for a while now from formal stats that it was showing an eastern shift, probably caused by steppe admixture.

duge_buwembo said...

Can you tell me what Basal means in regards to dna and the genome? Where do I need to go to learn this stuff as a primer.

Davidski said...

This blog has everything covered pretty well, especially for beginners. You just have to take a bit of time to check out the posts and comments.

Davidski said...

I updated the post above and the K7 spreadsheet.

I'll be doing this regularly.

TheNewPossibility said...

Hi Davidski,
I see you don't have any Coptic reference population. I believe it should be interesting to include and test Coptic raw data as well in your new calculator. If interested I can provide you with the Coptic genome of the Coptic/Ethnic Egyptian Christian in the R1a project here https://www.familytreedna.com/public/R1a?iframe=yresults And here https://www.yfull.com/tree/R-YP1272/(new Ytree version will put a much older date to it in the order of 7600 bpy or so).He's bearer of R1a-YP1272* (R1a1b). Please let me know how I can provide you with the data. Thanks.

MaxT said...

Davidski, can you please include Samara_HG as well? I could not find it on spreadsheet.

Davidski said...

Samara_HG is almost identical to Karelia_HG, just a little more noisy, with minor <1% Sub-Saharan admix due to its lower quality (that's why it's not in the datasheet).

MaxT said...

Davidski, it would still be helpful as Samara_HG has higher ANE (around 70s%) than Karelia_HG's ANE (around 50s%). They do seem different on that aspect.

Mathieson et al (2015) notes that "First dilution of Ancient North Eurasian ancestry" occurred in Samara_Eneolithic. study link: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4918750/#SD3

It's an important ancient sample, would be nice to see it included in K7. Thank you. :)

Davidski said...

Nope, they're the same, with around 55% ANE in the K7, which means 70% ANE overall, because the Villabruna cluster is about 15% ANE.

They form a very tight clade in formal stats in all papers published to date, including Mathieson et al.

So maybe you're confusing Samara_HG with Samara_Eneolithic? But as per the quote you posted, Samara_Eneolithic has less ANE than Samara_HG and Karelia_HG due to dilution from admixture with a more southern population.

MaxT said...

Thank you, Davidski. It is under "Extended Data Table 2".

He notes regrading Samara_Eneolithic & Yamnaya_Samara.

"First dilution of Ancient North Eurasian ancestry (prior to the Bronze Age Yamnaya culture)"

In same "Extended Data Table 2" he notes regrading late Yamnaya_Samara & Yamnaya_Kalmykia

"Contribution of Near Eastern ancestry to the Bronze Age Yamnaya culture."

He seems to say that that first dilution of ANE took place with (WHG) folks in Samara prior to Yamnaya culture. Near-eastern ancestry contribution comes during Late Yamnaya_Samara, Yamnaya_Kalmykia and Yamnaya culture.

What is your take on this? I would still like to see Samara_HG included just to test his theory. Thank you. :)

Davidski said...

Samara_Eneolithic refers to Copper Age Khvalynsk samples, not the Samara Hunter-Gatherer.

Samara_HG and Karelia_HG form the Eastern_HG clade in respect to all other ancient samples, which means that their ancestry proportions are basically the same. This is what all papers to date show and it's what my new K7 shows (apart from some minor noise in Samara_HG due to low quality DNA).

So the first dilution of ANE on the steppe occurred with the migration of southern people to the Samara region, and admixture between Samara_HG people and these newcomers from the south. The result of this mixture was Samara_Eneolithic, with less ANE than Samara_HG.

That's what the Mathieson et al. paper is arguing in the stuff you quoted.

MaxT said...

Thank you for explaining, I thought Samara_HG and Samara_Eneolithic were alike when i came across them.

"So the first dilution of ANE on the steppe occurred with the migration of southern people to the Samara region, and admixture between Samara_HG people and these newcomers from the south. The result of this mixture was Samara_Eneolithic, with less ANE than Samara_HG."

Indeed, Samara_HG is important sample in understanding steppe population. Would like to see it included, Thank you. :)

MaxT said...

@Davidski

Can you please add Native-Australians to your K7 spreadsheet?

blogmaster said...

My concern with some of the related studies, is that the sampling for "Neolithic Anatolian" is restricted to samples from the far west of Turkey; at one extreme of an interaction zone that stretched eastwards to it's polar end in Iran. In contrast to some assertions, the data does not support that West Anatolians were a unique ancestral source (as is more clearly the case with Iran Neolithics, WHG, EGH, or Levantine). Instead, the westward Anatolian samples, can easily be described as some proportion of WHG to Levantine, and smaller though significant amounts of Iran Neolithic. However, by the contrasting PCA positions of later populations; Chalolithic Anatolians and modern Europeans, who are clearly on a vector between WHG and Iran Neolithic, versus the earliest European farmers, one is forced into imagining scenarios which, ultimately, involve a considerable amount of genetic input from the Iranian plateau. This occurred not mainly through single migratory events into Europe, but through reciprocal gene flow, between early and later neolithic communities which spanned between Turkey and Iran, and the expansion of farming into Europe. Of course, later bronze age migrations from the Western Steppe, account for some of this Iranian influence, as well.

Davidski said...

There's absolutely no evidence of any admixture from Iran on the Bronze Age steppe.

Simon said...

ANE influence appears inflated in the graph from an FST point of view. Am I right if I say that the PCA would more accurately describe the FST genetic differance between samples and clusters if the sides of the triangle were adjusted to correspond to the FST differences between ANE, Basal-rich and Villabruna-related?

Davidski said...

If you mean the triangle plot, that's rotated to fit geography. That's why it's skewed, with PC2 longer than PC1, and ANE looking so dominant.

The reason I rotated it to fit geography, is because this makes it easier to grasp the key population shifts, like the migrations from the steppe.

Simon said...

The skewed projection is very intuitive for illustrating population shifts. But as you say, the x axis is disproportionately longer, therefore a vector between two given sample points in the chart will not proportionally reflect genetic distance. For example, Yamnaya appears to be equally distant from Sintashta and Iran_Neolithic if you don't understand the diagram, while if the length of PC2 is adjusted so the sides of the triangle more accurately represent the FST distances between ANE, Villabruna-related and Basal-rich, Yamnaya will appear to be equidistant from Basques and Iran_Neolithic, who in turn are equidistant from Jordan_EBA (?), which is much closer to the truth.

Davidski said...

You might find this version of the plot more informative in terms of true genetic distances.

https://drive.google.com/file/d/0B9o3EYTdM8lQSFVnTDZkT0RURjQ/view?usp=sharing

This is the datasheet I use for plotting the K7 results.

https://drive.google.com/file/d/0B9o3EYTdM8lQMXIxc2Q1cjYybWc/view?usp=sharing

You can plot it with the freely available Past3 software.

http://folk.uio.no/ohammer/past/

Simon said...

Thanks, I've seen it. Would you say that the 'true genetic distances version' could be faithfully superimposed on a grid representing FST distance between any of the data points?

Davidski said...

I don't know.

It's very difficult as a rule to show true genetic distances on two dimensional graphs or plots, because genetic structure is multi-dimensional.

Simon said...

It ought to be fairly accurate, within some confidence interval, as long as all populations can be modelled as wholly ANE-WHG-Basal-rich. Since the distance between these three may be accurately visualized as a triangle.

I realize of course that this is not the case.

Nezih Seven said...

How can I do this basal k7 test? Where should I send the money and DNA data?

Davidski said...

The instructions for ordering the Basal-rich K7 are here...

http://eurogenes.blogspot.com.au/2016/11/fund-raising-offer-basal-rich-k7-andor.html

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