search this blog

Saturday, August 13, 2016

PCA: Neolithic Central Anatolians


Note that the individuals from the earlier site of Boncuklu basically cluster with early Neolithic Europeans, while those from Tepecik-Ciftlik are shifted south and east, suggesting an influx of admixture into central Anatolia from perhaps eastern Anatolia and the Levant after the early Neolithic. This is in accordance with the findings of Kılınç et al. who published these genomes.


I also tested the same samples with the Basal-rich K7 (refer to the spreadsheet here). Their results appear to correlate very nicely with the PCA. However, I deleted Tep001 from the PCA plot because his PCA and Basal-rich K7 outcomes didn't match, suggesting that either one or the other, or both, were spurious. This isn't surprising, however, since Tep001 only has a coverage of 0.023x.

Citation...

Gülşah Merve Kılınç et al., The Demographic Development of the First Farmers in Anatolia, Current Biology, August 8, 2016, DOI: http://dx.doi.org/10.1016/j.cub.2016.07.057

Update 15/08/2016: Below are a few admixture f3-stats from an analysis involving the new Anatolian samples. Please note, the more negative the Z score, the more likely that the target is admixed. Also, I had to use transversion SNPs to make this work, so the Z scores aren't as imposing as they might have been with more markers behind them. I'm posting all of the outcomes with Z scores lower than -1, but it might be best to ignore anything above -2.

Boncuklu_EN + Levant_N > Barcin_N f3 -0.005525 Z -2.62 SNPs 48620
Boncuklu_EN + Natufian > Barcin_N f3 -0.004252 Z -1.34 SNPs 28893

Boncuklu_EN + Natufian > Tepecik-Ciftlik_N f3 -0.013262 Z -1.566 SNPs 4384

Barcin_N + Villabruna > LBK_EN f3 -0.003652 Z -2.685 SNPs 49325
Barcin_N + LaBrana1 > LBK_EN f3 -0.003382 Z -2.462 SNPs 53537
Barcin_N + Motala_HG > LBK_EN f3 -0.002539 Z -2.388 SNPs 57533
Barcin_N + Loschbour > LBK_EN f3 -0.003089 Z -2.272 SNPs 48728
Tepecik-Ciftlik_N + Villabruna > LBK_EN f3 -0.004176 Z -1.452 SNPs 34905
Barcin_N + Hungary_HG > LBK_EN f3 -0.001939 Z -1.32 SNPs 41610
Boncuklu_EN + Levant_N > LBK_EN f3 -0.003035 Z -1.221 SNPs 40815

Barcin_N + Loschbour > Iberia_EN f3 -0.002457 Z -1.171 SNPs 38141
Tepecik-Ciftlik_N + Hungary_HG > Iberia_EN f3 -0.004022 Z -1.039 SNPs 21848

Barcin_N + Villabruna > Hungary_N f3 -0.006408 Z -4.28 SNPs 44545
Barcin_N + Hungary_HG > Hungary_N f3 -0.005216 Z -3.355 SNPs 39808
Barcin_N + Bichon > Hungary_N f3 -0.002554 Z -1.667 SNPs 48500
Barcin_N + Motala_HG > Hungary_N f3 -0.001559 Z -1.298 SNPs 51052
Tepecik-Ciftlik_N + Villabruna > Hungary_N f3 -0.003929 Z -1.239 SNPs 31535
Tepecik-Ciftlik_N + Hungary_HG > Hungary_N f3 -0.003897 Z -1.192 SNPs 28472
Barcin_N + LaBrana1 > Hungary_N f3 -0.00179 Z -1.083 SNPs 46955

25 comments:

Nirjhar007 said...

Impressive data.

BTW this may interest you-
https://arxiv.org/ftp/arxiv/papers/1608/1608.02038.pdf

Gioiello said...

And which would be the mt introgressed in Europe? They were rich above all of mt N1a1a1, present in Central Europe Neolithic but to-day practically at very low frequency in Europe. Perhaps there was a migration to Central Europe, but Western Europe had another history.
Starčevo
Hungary
Alsónyék-Bátaszék [BAM22]
F
5670-5570 BC
N1a1a
16086c 16147A 16172c 16223t 16248t 16320t 16355t T16086C A16129G C16147a T16172C T16187C C16189T G16230A C16248T T16278C C16311T C16320T C16355T
Szécsényi-Nagy 2014

Starčevo
Hungary
Alsónyék-Bátaszék [I0174/BAM 25]
M
5710-5550 BC
231,471
H2
L281+ and markers for F: (P142+, P145+, P138+, P316+, P14+, P159+) Reported as F* in Szécsényi-Nagy
N1a1a1
16147A 16172c 16193t 16223t 16248t 16355t A16129G C16147a T16172C T16187C C16189T C16193T G16230A C16248T T16278C C16311T C16355T
Szécsényi-Nagy 2014; Haak 2015; Mathieson 2015; Lazaridis 2016

But we have mt N1a1a1 also in Iberia

Spain
Els Trocs [I0412 / Troc 5]
M
5310-5206 BC
1,025,420
I2a1b1
L161+, CTS1293+,
N1a1a1

Haak 2015; Mathieson 2015; Lazaridis 2016

but also N1a, N1a1, N1a1a3, N1a1a1a1, N1a1a1a2, N1a1a1a3 in 7000 YBP Hungary and Germany and France, thus only a deep exam could say who came from whom.

Perhaps some N1a1a1a my continue a woman of them:
N1a1a1 5736.8 3244.3
N1a1a1a 3662.9 2518.5
(Behar 2012b)

Nirjhar007 said...

Dottore,
Good I caught you here , Can you tell me something about the Basal y-dna R2 mutations in Italy?.

TIA.

Gioiello said...

K1a12a is diffused to-day from Italy to Middle East to Caucasus and is old
K1a12a 12982.6 +/- 3913.4
but K1a12* is found only in Italy and Western Europe
K1a12 15097.1 +/- 4353.9
1. JQ703323 Behar K1a12 07-APR-2012 A73G T195C A263G 315.1C C497T 523.1C 523.2A 523.3C 523.4A A750G T1189C A1438G A1811G A2706G A3480G A4769G G5460A C7028T A8860G G9055A T9698C A10398G A10550G T11299C A11467G G11719A A12308G G12372A C14167T C14766T T14798C A15326G T16093C T16224C T16311C A16343G T16519C
2. JX153006(Italy) Raule K1a12 10-JAN-2014 A73G T146C A263G 315.1C C497T 523.1C 523.2A A750G T1189C A1438G A1811G A2706G A3480G A4769G A5123C G5460A C7028T A8860G G9055A G9196A G9575A T9698C A10398G A10550G C11170T T11299C A11467G G11719A A11923G A12308G G12372A C14167T C14766T T14798C A15244G A15326G T16093C T16224C T16311C C16527T
User ID HVR1 Mutations
HVR2 Mutations
GFBDS 093C, 224C, 311C, 343G, 519C
Not Tested
295T6 093C, 224C, 311C, 343G, 519C
073G, 195C, 263G, 315.1C, 497T, 524.1C, 524.2A, 524.3C, 524.4A
CBHWK 093C, 224C, 311C, 343G, 519C
073G, 195C, 263G, 315.1C, 497T, 523.1C, 523.2A, 523.3C, 523.4A
CS8F3 093C, 224C, 311C, 343G, 519C
073G, 195C, 263G, 315.1C, 497T, 524.1C, 524.2A, 524.3C, 524.4A

Gioiello said...

@ Nirjhar0007

I never said that R2 came from Italy or Western Europe, but I may study it and let you know, I have Always thought that it was diffused from India, but it seems perhaps from Iran now...

Gioiello said...

From YFull Italian samples are old but not the oldest ones:
R-Y1280 Y1281 * Y1284 * Y1283+4 SNPs formed 7900 ybp, TMRCA 7100 ybp info
R-Y1280*
id:YF02834 ITA [IT-AV]

R-Y1288 Z29162 * Y1288
R-Y1288*
R-M3349 YP5338 * PF7502 * V4082+12 SNPs
R-M3349*
id:HG03856 STU
R-YP5340YP5340 * YP5341 * YP5349
id:ERS256937 ITA [IT-CA]
id:ERS256934 ITA [IT-CA]

Davidski said...

What if some Italians with these "old" mtDNA lineages a hundred years from now settle on Mars and the earth explodes. Will that mean their mtDNA lineages originated on Mars?

Gioiello said...

After the explosion of the Earth those people on Mars wouldl be the unique people survived and the "history" would be that that they tell.
History is always written from the winners.
But mine isn't the winner one... at least so far.

Nirjhar007 said...

I may study it and let you know

Thanks. I will wait eagerly.

Gioiello said...

@ Nirjhar007

I have already answered your question above, but I may complete my answer also for Davidski: why R2 cannot be born in Italy or Western Europe? Because the oldest samples separated from sister clades 7100 years ago, and, even though very likely it is wrong to think that they came recently with Gypsies or others but may be in Italy from neolithic, there is no witness that their origin could be here, and I'd say neither in India, because the oldest samples are around the Persian Gulf and India retains younger samples. If we add that R2 has been found in aDNA from Iran, to think to Iran rather thatn India is reasonable. The same for all the other haplogroups I studied: the reasoning is Always the same.

Nirjhar007 said...

But S Asia, if I'm not wrong also demonstrates basal clades of R2.

I think the problem is, since the population is huge , you need equally large nos of sampling to get to a good concluding position. Sooner or later that will be proven.

Gioiello said...

About R2 it isn't true that India gets some old basal haplotypes. The oldest is this
R-Y5080 FGC17612/Y5079 * FGC17619/Y5082 * FGC17617/Y5089+26 SNPs formed 9300 ybp, TMRCA 6300 ybp info
R-Y5080*
id:HG03794
id:HG02657 PJL
with a MRCA at only 6300 YBP
whereas these samples, even though with a MRCA at 4900 years, formed 16600 ya:
R-Y23194 FGC50368 * FGC50281 * FGC50297+88 SNPs formed 16600 ybp, TMRCA 4900 ybp info
id:YF06605 new
id:YF05544
Unfortunately I have no access to the YFull R2 group for seeing where they come from, but I think it is more likely an Arab country than India. Anyway if they did come from India, I might change my opinion.
About the samples tested, you are right (think that Italy has only 5 Y from aDNA whereas other countries have hundreds) and aDNA from India will be interesting, but India, like Tuscany, had the lucky having many samples in the 1KGP, thus, as Tuscany had many indications about hgs. J1 and J2 beyond hg R, India, if had had some interesting old R2, it would have come out. But it seems there was nothing.

bellbeakerblogger said...

There's a paper just published at Nature on a female Zargos farmer GD13a. Gallegos, Pinhasi, Connelly

Davidski said...

There was a preprint about that...

http://eurogenes.blogspot.com.au/2016/06/genetics-of-early-neolithic-pastoralist.html

bellbeakerblogger said...

Crap.

Nirjhar007 said...

Dottore,

India is under sampled by large large large.....

Aram said...

Gioiello
R2 can't come from Iran. R2 most probably splited from other Rs in Central Asia and moved to South Asia quite early. Perhaps in Paleolithic/Mesolithic bringing the first (?) wave ANE there. Some of this early R2s rushed into Near East. Later this R2s joined the local Zagros G2/J2 farmers. And they give them the ANE like component. R2 story is similar to I2 story in Anatolian Neolithic.
Gypsies in Europe have very little R2. Practically inexistant.

Aram said...

Here are the countries where genuine R2* M207+ M479+ M124-
Kazakhstan
Tajikistan
Pakistan

Gioiello said...

@ Aram

Of course it is possible that you are right about the oldest R2*, which, before the M479 SNP, were interpreted, wrongly, as R1*, but it doesn't seem that Indian R2 came from Central Asia rather than Iran... but, as Nirjhar007 said, India is a very little tested, thus let's wait...

Olympus Mons said...

@gioiello,aram and @Nirjhar
... What i really want to know is where those L1a guys at chalcolithic Armenia could come from... Isnt that a Hgroup common in north india and Pakistan?

Nirjhar007 said...

Yes its frequent in India .

Aram said...

Olympos

The Areni cave L1a-M27 is frequent in South Asia. But that samples were M27*. They had negative calls for SNPs present in SA. So they were neither ancestral to or descendant from S Asian L1a.

Aram said...

In Iran two pops have high level of L1 M27. It is the Bandaris and Baluchis. Both showed high affinities to Iran_N.



https://www.yfull.com/tree/L-M27/

Roy King said...

@Davidski,
Very nice PC plots! can you tell us which samples are which of the Tep and Bon samples? you already did this on the plot for Tep003 and Bon002.

Davidski said...

Roy,

https://drive.google.com/file/d/0B9o3EYTdM8lQTjYwU0pkblh0QTA/view?usp=sharing