November 03, 2012

rolloff and ALDER analysis of Turks

I carried out rolloff analysis of the Behar et al. (2010) sample of Turks together with the sample of Uzbeks from the same, and the Yunusbayev et al. (2011) sample of Armenians. A --geno 0.03 flag was applied for merging and SNPs available in the Rutgers recombination map for Illumina chips were used.

The exponential decay can be seen below:

The signal of admixture seems pretty clear and extends up to several cM. Of course, as always, this does not mean that exactly these two populations mixed to form the Turks sample, but it does mean that they are reasonable standins.

The jackknife gives an admixture time estimate of 27.622 +/- 5.348 generations or 800 +/- 160 years, which of course makes perfect historical sense as it is a date between the first arrival of the Seljuks in Anatolia and the final consolidation of power by the Ottomans. Note also that this probably applies principally to this particular sample (which I believe is from Cappadoccia) and there were perhaps different admixture dynamics elsewhere.

I had started this analysis before the announcement of ALDER, but since it is very fast, I decided to give it a go as well. Below is the raw output:




                    *** Admixture test summary ***

Weighted LD curves are fit starting at 1.45 cM

Pre-test: Does Turks have a 1-ref weighted LD curve with Armenians_Y?
   1-ref decay z-score:    0.09
   1-ref amp_exp z-score: -0.01
                                  NO: curve is not significant

Pre-test: Does Turks have a 1-ref weighted LD curve with Uzbeks?
   1-ref decay z-score:    6.56
   1-ref amp_exp z-score:  5.02
                                  YES: curve is significant

Does Turks have a 2-ref weighted LD curve with Armenians_Y and Uzbeks?
   2-ref decay z-score:    5.61
   2-ref amp_exp z-score:  5.58
                                  YES: curve is significant

Do 2-ref and 1-ref curves have consistent decay rates?
   1-ref Armenians_Y - 2-ref z-score:                  0.01   ( 13%)
   1-ref Uzbeks - 2-ref z-score:                       0.69   ( 11%)
   1-ref Uzbeks - 1-ref Armenians_Y z-score:          -0.00   ( -1%)
                                  YES: decay rates are consistent

Test FAILS (z=5.58, p=2.4e-08) for Turks with {Armenians_Y, Uzbeks} weights

DATA: failure 2.4e-08 Turks Armenians_Y Uzbeks 5.58 -0.01 5.02 13% 23.92 +/- 4.26 0.00002930 +/- 0.00000525 27.18 +/- 302.36 -0.00000082 +/- 0.00013129 26.84 +/- 4.09 0.00002316 +/- 0.00000461

DATA: test status p-value test pop ref A ref B 2-ref z-score 1-ref z-score A 1-ref z-score B max decay diff % 2-ref decay 2-ref amp_exp 1-ref decay A 1-ref amp_exp A 1-ref decay B 1-ref amp_exp B



The age estimate appears to be very similar, and most curves appear to be significant, except the one with Armenians_Y. This makes good sense. From Loh et al. (2012):
Also, if a reference A' shares some of the same admixture history as C or is simply very closely related to C, the pre-test will typically identify long-range correlated LD and deem A' an unsuitable reference to use for testing admixture.
In our case, A'=Armenians and C=Turks. We can be fairly sure that Armenians lack the same admixture history as Turks (because they were not affected by Central Asian Turkic invasions), but we can try a 1-ref analysis of Armenians with Uzbeks to substantiate it. The admixture lower bound estimate is a huge interval 7.6 +/- 88.2 and the jackknife is unable to estimate the admixture time. Thus, more plausibly, the second explanation applies, and because Armenians_Y are very closely related to Turks, they are deemed as an inappropriate reference to test admixture.

Finally, the lower bound of the admixture fraction for Turks with an Uzbek reference is estimated as:

Mixture fraction % lower bound (assuming admixture): 29.8 +/- 4.0

This is a very interesting number. We can be fairly sure that Central Asian Turkic people who invaded Anatolia carried with them an East Eurasian component, but in what proportion to their West Eurasian one? The East Eurasian element in Turks has been rather consistently estimated at ~5-7% with various methods, so perhaps this formed the minority element in the Turkic people who arrived in Anatolia. 

On the other hand, this case is rather muddled by the occurrence of by-directional gene flow: Uzbeks may have West Eurasian ancestry of ultimate West Asian origin, just as Turks have Central Asian ancestry. And, indeed, when we estimate the admixture fraction of Uzbeks with the Turks as a reference, we obtain:

Mixture fraction % lower bound (assuming admixture): 46.7 +/- 2.4

The age estimate for this is ~16 +/- 2 generations = 460 +/- 60 years. Very similar time estimates appear when Armenians are used as a West Eurasian reference. So, this might indicate that the Uzbek population was formed by admixture after the Anatolian Turks were so formed.

I see no easy way to solve the problem of estimating admixture proportions when both extant populations have been both donors and recipients of gene flow, but in any case, these numbers are something to think about.

Analysis of Turks with a variety of Turkic and East Asian populations

I subsequently formed a new dataset by merging the sample of Turks with a variety of Turkic and East Asian populations (same procedure for SNP choice).


For the calendar year calculation, I arbitrarily set the birthdate of the modern sampled individuals at 1980; I have no idea on the age profile of the individuals comprising the Behar et al. sample of Turks. I have also used a mindis=0.5cM which facilitated the convenient automated extraction of the dates from the ALDER output and also gave a level playing field for all the reference populations. The age picked by ALDER using its own adaptive threshold did not usually differ from the reported one by more than a few generations.

The results indicate two things:

  • The % of admixture depends on the choice of population, with highest amount using Uzbeks  as a reference, and lowest using the far Asian populations from China. This indicates our uncertainty regarding the East/West Eurasian-ness of the people who settled in Anatolia.
  • Admixture times, on the other hand appear to be fairly constant and appear to frame an important watershed moment of Anatolian history, the Battle of Manzikert which paved the way for the eventual Turkification of the peninsula. The Turkmen sample appears as an outlier in this respect, which might indicate that limited migration of Turkmen tribes may have occurred at a later date.

23 comments:

Anatolian Turkmen said...

Dienekes these results may suggest Turkmens mixed heavily in Turkmenistan after 1071

Can you do a roll off using :
1. Uzbeks and Iranians in a 2 way admix to estimate Turkmens
2. Uzbeks and Greeks to analyze Aydin Turks
3. Turkmens and Greeks to analyze Aydin Turks
4. Turkmens, Iranians, Greeks to analyze Aydin Turks
5. Turkmens, Uzbeks and Greeks to analyze Aydin Turks
6. Turkmens and Armenians to analyze Kayseri Turks
7. Uzbeks and Armenians for Kayseri Turks
8. Uzbeks, Greeks and Armenians for Istanbul Turks
9. Turkmens, Greeks and Armenians for Istanbul Turks

libya said...

I think you should use Salars instead of Turkmens
Turkmens are heavily mixed (perhaps 80% Iranian 20% Turkic) with the original Iranian population of Dahae&Gorgan (what is nowadays Turkmenistan)

On the other hand Salars are Oghuz speakers Turks (same as Turks and Turkmens) and did not mix much with original Iranian population of Turkmenistan because they very rapidly migrated to China where due to the religion barrier (budhist vs muslim) they did not mix either with Hans

So Salars are the most accurate proxy to use in order to determine the Turkic admixture in Anatolian Turks

Also I think that a part of east Asian admixture amongst Turkey, Iran, India and other west Asian countries could very well be pre Turkic and connected to the east Asian admixture present amongst all the eastern&northern Eurasian populations (such as Russia, Swede, Ukraine...)

Anatolian Turkmen said...

There are 100,000 Salars in the world many of whom mixed with Chinese. There are 25 million Uzbeks and 5 million Turkmens to 70 million Turks. (maybe 60 if you exclude Kurds)

Either Turkmen or Uzbek makes sense as Turkish source but Salar makes no sense

Anatolian Turkmen said...

There is a caveat here Dienekes:

We know of no Armenian/Anatolian/Iranian migration to Uzbekistan in the last 500 years. However we know of a Turkic migration to Anatolia in the last 1000 years.

The fact that using Uzbeks as a source population gives us a time around Manzikert +200 years or so expansion time is quite amazing.

I'd say the more weird thing is the result regarding Turkmens. I wonder if this is so because Turkmens are more similar to Anatolians and the software assigns a much more recent admixture time and as a result a smaller admixture ratio.

I think that is what is going on. I think one way admixture between Turkmens and Turks may yield results that would make using Turkmens as a source for Turks not appropriate.

If you look even Altaians have a higher genetic impact on Turks of Anatolia which simply can not be true.

I think Turkmens and Turks of Turkey are way too similar for ALDER.

Valikhan said...

460 years for Uzbeks' admixture makes sense. The end of 15th - beginning of 16th century is the time of big migration of Qipchak (Turkic) tribes from what now Astrakhan oblast of Russia, West Kazakhstan, Central Kazakhstan south to modern Uzbekistan. From historical point of view, there should more admixture events for Uzbeks, one of them from Arabs from 8-9 century AD.

libya said...

Salar did not mix with Chinese because Islam prohbits marriage with non Muslim for women and for non Muslim-Jew-Christian for men; Salars are Muslims and Hans are budhists

Anyway only with a Salar sample one could verify that

I dont understand what the numbers are supposed to mean

Uzbeks and Turkmens could not make sense as a source for Anatolian Turks because Uzbeks and Turkmens are the result of near 1000 years of mixing between Turk newcomers and the much more crowded Iranian locals, a comparing look to sex chromosomes of Iran, Armenia, Turkey, Turkmenistan, Uzbekistan (and very possibly Salars too) show that there is no matching between the sex chromosomes makeup of Turkmens/Uzbeks and the one of Turkey's Turks

libya said...

I would like to add that Uzbeks are not a homogeonous group, there are the:
1/until recently nomadic uzbeks wich are markedly mongoloid and speak a kipchakic Turkic
2/sart uzbeks wich are more caucasoid than "real" uzbeks and speak a chaghtaic Turkic
3/many of the Uzbeks are Iranic speaking Tadjiks (who are the most caucasoid Uzbeks) who choose to declare themselves to be ethnic Uzbeks (according to wikipedia as much as 10-20% of Uzbeks are Tadjiks that declare themselves Uzbek,so The used Uzbek sample could very well be Sart or Tadjik

Please see below
http://www.state.gov/j/drl/rls/hrrpt/1999/369.htm
Government statistics dating from 1992 show that the population of approximately 23 million is about 71 percent Uzbeks, 8 percent Russians, 5 percent Tajiks, 4 percent Tatars, and 3 percent Kazakhs, with many other ethnic groups represented. The statistics may underestimate the actual number of ethnic Tajiks. The figures also do not include many ethnic Tajiks whose mother tongue was Uzbek. Moreover, some Tajiks choose for a variety of reasons to declare themselves to be ethnic Uzbeks.

Anatolian Turkmen said...

Libya are you also called onur?

libya said...

No, I have only 1 username and I am not the user called Onur
You may ask the blog administrator to check that

Anatolian Turkmen said...

Anatolian Turks are as much Siberian as Turkmenistan Turkmens in Aydin and about half in Istanbul. Rolloff and Alder pick up a migration wave between 1070 and 1270 and then a continuous migration until late 1500's. A rapid migration would be confined to a military conquest. However there is more East Asian mtDNA in Anatolia than there is East Asian y-DNA suggesting Turkic families migrated to Anatolia not Turkic men.

Uzbeks are 40+% Siberian and East Asian. They have picked up not only West Asian in Uzbekistan but also additional East Asian, too.

Using them as a proxy for incoming Anatolian Turkomans was up until this day acceptable to you, Dienekes and everyone else as it was proving Anatolia was 1/7 Turkic.

Now that rolloff and alder suggest at the minimum a 30% Uzbek like Turkic group entered Anatolia in the 11th through 13th centuries somehow now makes Uzbeks not acceptable. I don't get this. I think it is useless to attack the Turkishness of Anatolia this much.

It is clear that the Turkification of Anatolia at least in the pre 1500 regions of Anatolia happened via population admixture of a huge incoming Turkic immigrant wave. I believe this percentage to be closer to 50% in areas such as Aydin, 30-50% in Central and Mediterranean Anatolia, 30% or so in Istanbul and Northern Balkans (Northern Greece, Bulgaria) but 10-20% in Southern Greece and Northeastern Anatolia. This one can understand by looking at Siberian percentages in these areas.

Southeastern Anatolia is a different story. We lost the Turkish population there to Iran.

Why fight rolloff and alder only in the case of Turks but no one else.

Science can dig deeper to the question of Turkic migrations but some things are clear:

1. You can not infer the Turkic migrations to Anatolia from Y-DNA and mtDNA. My great aunt who has H mtDNA is 10+% Far Asian, more than Turkmens and my grandpa who is about 10% Siberian is I1*.

2. You can not infer Turkic migrations to Anatolia by comparing Anatolian Turks to Kirgiz. Oghuz Turks have mixed with West Asians for a long time. Uzbeks, Turkmens as well as Azeri, Anatolian, Balkan and other Ottoman Turks trace roots to Oghuz. Incoming Turkic tribes came to Anatolia from Iran, Turkmenistan. Assuming an Uzbek like incoming population in 1070 is an over estimation of their Siberian content.

3. A 200 year migration period of Uzbek like Turks suggests a 30% Turkic immigration to Anatolia. If we model a small immigration per year but a steady one we might get even a higher % of Turkic immigrants.

Dienekes said...

Using them as a proxy for incoming Anatolian Turkomans was up until this day acceptable to you, Dienekes and everyone else as it was proving Anatolia was 1/7 Turkic.

Now that rolloff and alder suggest at the minimum a 30% Uzbek like Turkic group entered Anatolia in the 11th through 13th centuries somehow now makes Uzbeks not acceptable. I don't get this. I think it is useless to attack the Turkishness of Anatolia this much.


I have no interest in "attacking" anything. I could turn your argument on its head, and say that until I posted this experiment you always complained that I shouldn't be using Uzbeks and I should be using Turkmen. Now that the admixture using an Uzbek sample is higher than that using a Turkmen one, you apparently have decided that the admixture proportion using Uzbeks is more reliable than using Turkmen.

I post all experiments as they are, and they can be repeated or re-interpreted by anyone interested to do so.

With respect to the substantive part of the issue, I have also posted evidence that Uzbeks have recent West Eurasian admixture, which took place a few centuries after the Seljuqs arrived in Anatolia. In fact, most Altaic populations that I experimented on seem to have that type of admixture.

This means that when the Seljuqs arrived in Anatolia, the various Altaic populations living in Central Asia had not yet been formed in their current form by mixing with West Eurasians, and, consequently, they were more East Eurasian than they are today.

libya said...

@AT
1/as you know a population of Armenian or Greek origin could become Turk through devshirmizing or language shift or through sexual intercourse with Turkicized Iranians without it's sex chromsomes changing
There are, for example many Slavs who have retained their local autochtonous sex chromsomes yet they have up to 10% east asian admixture

We could track the Turk input only by looking to east asian Y-DNA
and mt-DNA

2/by the years 900-1000 Turkic was still 1 language (see the book
"history of Turkic languages") and did not bifurcate yet to
Oghuz/Kipchak/Chaghtai and The Turks did have the same Mongoloid
stock and nomadic siberian culture and far eastern sex chromosomes
because they were still not beginning mixing heavily with Muslim Iranian local populations of Central Asia and the incoming Turk
tribes to Iran and Anatolia came very rapidly at once from the west
Kazakstan stepps and were surely very higly east asian autosomally
speaking (perhaps up to 90-100%) and carriying east asian sex
chromosomes

3/The Turkic migration was not steady but did came basically in
only 2 waves (Seljuq then Timurid) and nowadays Uzbeks could not be
a proxy of year 1070 Turks since Uzbeks mostly descend from
original Iranic population of central Asia with a minority of
Turkic input and that's why Uzbeks are closer to Iranic Tadjiks and
Pashtuns and Persians than they are to Anatolian Turks

Onur said...

Libya are you also called onur?

No, as is clear from my writings, I am not libya. libya = lars = ashraf = aynakom bilibyanalanamihan = Van Hooijdonk = Colin Wilson = pier van lancaster (some of these user accounts may have fallen into disuse or deleted). My sole username is Onur (it is also my real name). It was previously written with a lowercase initial letter, but I later converted the initial letter to an uppercase letter.

Anatolian Turkmen,

You keep repeating your step-by-step (first into Greater Iran and after several centuries of mixing there into Anatolia) and centuries-long Turkic migration theory, which lacks historical support. In reality, Anatolia was colonized by the Turkic migrants concurrently with Greater Iran (including what is now Turkmenistan and Uzbekistan) from what is now the middle parts of Kazakhstan (from around the Aral Sea area) during the late 11th and early 12th centuries at the height of the Great Seljuq rule in Greater Iran and the northern Arabic-speaking lands. Turkmens of today cannot be used as a proxy for the Turkic colonizers of Anatolia due to the centuries-long mixing of the Turkic colonizers of what is now Turkmenistan with the Iranic-speaking natives during the last about 1000 years after the Turkic colonization of Anatolia. The ADMIXTURE component distribution of Turkmens too does not support the use of them as a proxy for the Turkic colonizers of Anatolia, as ADMIXTURE component distributions of Turks and Turkmens have no order between each other so that there is no way to derive Turks from the admixture of a Turkmen-like population with a Greek or Armenian-like population (or with an Iranian-like population BTW). As for Uzbeks and Uyghurs, their ALDER analysis results show that a substantial part of their Caucasoid ancestry comes from mixing with non-Turkic natives of Central Asia during the post-Seljuqid centuries. It seems that during the Seljuqid period the Turkic populations of Central Asia had more Mongoloid ancestry than they have today. This is quite undestandable, as back then many parts of Central Asia, especially those in the south, were populated by Iranic-speaking populations.

apostateimpressions said...

It would be interesting to test for flow into Italians from Greeks and Anatolians. Also for flow into Northern Cypriots from Southern Cypriots and Turks.

aspromavro said...

Dienekes, any chance you could run this analysis with the Balkans and other parts of Europe + Anatolia + Caucasus?

Anatolian Turkmen said...

There is a significant problem in your inference that major admixture happened in Central Asia after Turks arrived in Anatolia.

The Alder and rolloff analysis suggests a roughly 12.6% Altaian admixture in Anatolia but only 10.8% Turkmen admixture in Anatolia.

How is this possible?

If admixture happened in Central Asia post 1100's did this not happen in Turkmenistan?

How come the Turkmen admixture is smaller than Altaian admixture?

And what about Uyghur admixture being 23.5% and Uzbek 30%.

Are you seriously claiming that whatever admixture happened in Central Asia did affect only Uzbeks and Uyghurs and that this admix had common roots with Anatolia but that this somehow skipped Turkmenistan?

This is non sense.

Dienekes said...

If admixture happened in Central Asia post 1100's did this not happen in Turkmenistan?

The Turkmens_Y are a recently East/West Eurasian mixed population, over the last 600 years or so.

Test SUCCEEDS (z=5.59, p=2.2e-08) for Turkmens_Y with {Sardinian, Dai} weights

DATA: success (warning: decay rates inconsistent) 2.2e-08 Turkmens_Y Sardinian Dai 5.59 2.84 5.31 54% 21.44 +/- 3.83 0.00025207 +/- 0.00002698 12.37 +/- 4.35 0.00002338 +/- 0.00000373 19.82 +/- 3.73 0.00015816 +/- 0.00001678

DATA: test status p-value test pop ref A ref B 2-ref z-score 1-ref z-score A 1-ref z-score B max decay diff % 2-ref decay 2-ref amp_exp 1-ref decay A 1-ref amp_exp A 1-ref decay B 1-ref amp_exp B


In general, there are no good references for the Central Asian ancestors of the Anatolian Turks; all extant Altaic groups of Central Asia/Siberia show evidence of more recent admixture.

Onur said...

In general, there are no good references for the Central Asian ancestors of the Anatolian Turks; all extant Altaic groups of Central Asia/Siberia show evidence of more recent admixture.

Has that recent admixture in the extant Altaic groups of Central Asia/Siberia rendered them more Caucasoid or more Mongoloid than they were during the Seljuqid times and before?

Also, which extant population do you think is the best reference for the Central Asian ancestors of Anatolian Turks?

Dienekes said...

Has that recent admixture in the extant Altaic groups of Central Asia/Siberia rendered them more Caucasoid or more Mongoloid than they were during the Seljuqid times and before?

That is hard to tell, but given that the expansion of Turkic languages followed an east-west trajectory, I'd think that the main trend would be increasing West Eurasian admixture.

Onur said...

That is hard to tell, but given that the expansion of Turkic languages followed an east-west trajectory, I'd think that the main trend would be increasing West Eurasian admixture.

There is also the recent north-south trajectory (towards then Indo-European - mainly Iranic - lands), which also must have increased the Caucasoid admixture in many Altaic groups of Central Asia during the last 1000 years.

Anatolian Turkmen said...

These effects make another question an important one:

-If there was indeed a change of genetic characteristic in Central Asia could this have been more Asiatic in nature rather than Caucasian?

What we see is the following:

-Turks, Azeris, Turkmens are very Caucasoid and Uzbeks and Anatolian Turks are very closely related, as Rolloff/Alder indicates a minimum of 30% Uzbek input in Anatolian Turks (given certain caveats, obviously)

There is however an important mystery. According to Wells et al. (2001) Kazakh males are 66% Y-DNA C.

1/54 = 1.9 D-M174
5/54 = 9.3 C-M130(xC3c-M48)
31/54 = 57.4 C3c-M48
36/54 = 66.7 C-M130 total

http://en.wikipedia.org/wiki/Haplogroup_C-M217_(Y-DNA)

The question to answer is then the following:

Is it possible that, whatever immigration happened in Central Asia, after the Turkic invasion of Anatolia could have been Asiatic in nature, via the Mongols? And is it then possible to say that Turkic peoples had long had lower Asiatic genetic input?

I think this is a question that needs to be considered and if the answer is yes, then the minimum 30% Uzbek input calculated by Rolloff may even be more in terms of the Turkic genetic input in Anatolia.

Onur said...

Is it possible that, whatever immigration happened in Central Asia, after the Turkic invasion of Anatolia could have been Asiatic in nature, via the Mongols? And is it then possible to say that Turkic peoples had long had lower Asiatic genetic input?

I think this is a question that needs to be considered and if the answer is yes, then the minimum 30% Uzbek input calculated by Rolloff may even be more in terms of the Turkic genetic input in Anatolia.


Above I asked Dienekes whether the recent admixture in the extant Altaic groups of Central Asia/Siberia has rendered them more Caucasoid or more Mongoloid than they were during the Seljuqid times and before, and he replied by saying "that is hard to tell, but given that the expansion of Turkic languages followed an east-west trajectory, I'd think that the main trend would be increasing West Eurasian admixture." Then I drew attention to the fact that most of the southern half of Central Asia was Turkicized only during the last 1000 years, which must have increased the Caucasoid admixture in many Turkic groups of Central Asia during the last 1000 years. Of course, possible future analyses of ancient DNAs from Central Asia will probably give the most conclusive answers on the genetic history of Central Asia.

Rabatli said...

Poor Turks here. Just trying to stick to any explanation, how implausible or irrational it may be, just so not to have to conclude that 'proto-turks' were mongoloid, which would mean that they and their ancestors are NOT.

You people make me sick.

Bow down for science and swallow it.