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DMXX
03-01-2014, 01:46 AM
I frequently partake in population genetics discussions with other members of this forum. Some of the split-second investigations we carry out are at the very least thought-provoking.

This thread is open to all members to chip in and contribute in any desirable way on any population genetics topic. I imagine things will get pretty hectic with several discussions going on at once, but chaotic threads do carry a certain charm to them.

Out of sheer curiosity I decided to investigate which out of a select bunch of West and Central Asian populations share best with the Altaians of East-Central Asia overall using the Dodecad K12b Oracle program (http://dodecad.blogspot.co.uk/2012/01/k12b-and-k7b-calculators.html). The results are shown below.



> DodecadOracle(("Altai"), k=200)
[,1] [,2]
[23,] "Turkmens_Y" "54.751"
[38,] "Pathan" "67.1013"
[39,] "Turks" "67.2661"
[41,] "Turkish_D" "67.7791"
[44,] "Iranians" "68.2547"
[45,] "Iranian_D" "68.2551"
[50,] "Kurd_D" "68.6744"
[64,] "Kurds_Y" "70.4552"
[73,] "Lezgins" "71.311"
[74,] "Syrians" "71.3536"
[76,] "Jordanians" "71.5357"
[136,] "Assyrian_D" "77.0361"
[141,] "Armenian_D" "78.0794"
[150,] "Armenians" "80.0161"
[186,] "Georgians" "89.7722"


Some things are expected (e.g. Turks being closer to Altaians than Armenians), but there are quite a few interesting patterns which defied my expectations:
- Anatolian Turks being barely 1 GD closer than Iranians, with Kurds not being that far behind (1-3 GD)
- Assyrians being closer to Altaians than both Armenians and Georgians
- The great disparity between affinities to the Altai across the Caucasus (Lezgin @ 71 vs. Georgians @ 89)
- The Turkmen being quite a poor match with Altaians

For the record, my Altaian GD is 65.7027, which puts me second on that list!

Humanist
03-01-2014, 03:14 AM
Thanks, DMXX. Interesting.

What do you make of the Jordanian and Syrian distances? They appear to defy what one would expect based on geography (i.e. they are the western most populations included in the comparison).

ZephyrousMandaru
03-01-2014, 03:57 AM
There's something I've noticed, when comparing Semitic-speaking ethnic minorities such as Assyrians, Iraqi Jews and Iranian Jews and Indo-European speaking populations, such as Kurds and Iranians. It appears that the latter are closer to European populations, with the exception of a few compared to the Semitic speakers. Examples.

Assyrian_D's Genetic Distances From Southern Europeans, Eastern Europeans, Western Europeans and Northern Europeans.


Southern Europe

[36,] "Sicilian_D" "32.2557"
[35,] "S_Italian_Sicilian_D" "34.6742"
[39,] "Greek_D" "35.1138"
[43,] "C_Italian_D" "39.9133"
[44,] "O_Italian_D" "42.9096"
[45,] "Tuscan" "43.6826"
[53,] "N_Italian_D" "52.1462"

Balkan Peninsula/Eastern Europe

[49,] "Bulgarian_D" "47.0993"
[50,] "Bulgarians_Y" "48.0956"
[51,] "Romanians" "49.2816"
[70,] "Hungarians" "65.6512"
[116,] "Mixed_Slav_D" "78.6059"
[121,] "Polish_D" "78.8829"
[127,] "Russian_B" "80.1493"
129,] "Russian_D" "80.8675"
[132,] "Russian" "81.3741"
[133,] "Belorussian" "81.5795"




Western Europe

[62,] "Baleares_1KG" "62.3089"
[63,] "Canarias_1KG" "62.3843"
[64,] "Extremadura_1KG" "63.5765"
[65,] "Galicia_1KG" "63.8424"
[66,] "Murcia_1KG" "63.8835"
[67,] "Andalucia_1KG" "63.918"
[68,] "Portuguese_D" "64.0746"
[71,] "Castilla_Y_Leon_1KG" "66.2981"
[73,] "Spaniards" "66.8452"
[77,] "Spanish_D" "67.7777"
[79,] "Cataluna_1KG" "67.8948"
[80,] "Castilla_La_Mancha_1KG" "68.1328"
[84,] "French" "69.0942"
[85,] "French_D" "69.2952"
[87,] "Aragon_1KG" "69.9363"

Northern Europe

[88,] "German_D" "70.7069"
[89,] "Mixed_Germanic_D" "72.1028"
[94,] "Dutch_D" "74.3005"
[99,] "Kent_1KG" "75.2648"
[101,] "CEU30" "75.7456"
[102,] "English_D" "75.7768"
[104,] "Cornwall_1KG" "76.4861"
[107,] "British_D" "77.1899"
[110,] "British_Isles_D" "77.6151"
[114,] "Irish_D" "78.4311"
[117,] "Orcadian" "78.7126"
[122,] "Orkney_1KG" "78.9392"
[135,] "Swedish_D" "81.9087"
[136,] "Norwegian_D" "82.2559"
[150,] "Lithuanian_D" "87.8936"

Iranian_D's Genetic Distances To Eastern, Western, Southern and Northern Europeans


Southern Europe


[35,] "S_Italian_Sicilian_D" "34.6742"
[38,] "Sicilian_D" "35.6347"
[39,] "Greek_D" "37.1997"
[45,] "C_Italian_D" "40.686"
[47,] "O_Italian_D" "41.4614"
[49,] "Tuscan" "43.7955"
[59,] "N_Italian_D" "49.8412"
[63,] "North_Italian" "51.8252"

Balkan Peninsula/Eastern Europe

[51,] "Bulgarian_D" "44.2811"
[53,] "Bulgarians_Y" "45.8989"
[54,] "Romanians" "46.0278"
[73,] "Hungarians" "59.5671"
[113,] "Ukranians_Y" "68.8692"
[120,] "Mordovians_Y" "70.2077"
[127,] "Mixed_Slav_D" "71.7778"
[128,] "Polish_D" "72.301"
[131,] "Russian_B" "73.2014"
[132,] "Russian" "73.4701"
[133,] "Russian_D" "73.4857"
[140,] "Belorussian" "74.9109"

Western Europe

[69,] "Canarias_1KG" "58.9493"
[71,] "Baleares_1KG" "59.2375"
[72,] "Extremadura_1KG" "59.567"
[74,] "Portuguese_D" "60.0362"
[75,] "Galicia_1KG" "60.2369"
[78,] "Murcia_1KG" "60.7933"
[79,] "Andalucia_1KG" "60.8409"
[81,] "Castilla_Y_Leon_1KG" "62.7214"
[83,] "Spaniards" "63.3067"
[88,] "Cataluna_1KG" "63.7279"
[89,] "Spanish_D" "63.9909"
[92,] "Castilla_La_Mancha_1KG" "64.5548"
[99,] "Cantabria_1KG" "66.0308"
[103,] "Aragon_1KG" "66.4317"

Northern Europe

[82,] "French" "63.2942"
[84,] "French_D" "63.3378"
[87,] "German_D" "63.6913"
[94,] "Mixed_Germanic_D" "64.5806"
[105,] "Dutch_D" "66.8214"
[107,] "Kent_1KG" "67.8433"
[111,] "English_D" "68.2306"
[114,] "Cornwall_1KG" "68.9556"
[118,] "British_D" "69.5832"
[121,] "British_Isles_D" "70.2342"
[122,] "Irish_D" "70.5024"
[123,] "Orcadian" "70.7141"
[124,] "Orkney_1KG" "70.9044"
[136,] "Swedish_D" "73.8264"
[137,] "Norwegian_D" "74.1943"

My explanation for this, is that Iranians have more shared ancestry in common with Europeans both in terms of their Y-DNA and Autosomal DNA via their North European component. Whereas Assyrians are more dissimilar due lacking Northern European admixture, high amounts of R1a and also being more Southwest Asian shifted than Iranians. Although Assyrians are closer to certain Southeastern European populations than Iranians are, Iranians are closer to all other European populations than Assyrians are.

Dr_McNinja
03-01-2014, 04:04 AM
That's kind of strange. In my experimentation with admixture I've noticed the Turkmens are almost entirely West Caucasian (Georgian, Abhkasian) rather than North/East (Lezgins, etc). They do have high (single digits to high teens) Altaic admixture though.

Palisto
03-01-2014, 07:26 AM
There's something I've noticed, when comparing Semitic-speaking ethnic minorities such as Assyrians, Iraqi Jews and Iranian Jews and Indo-European speaking populations, such as Kurds and Iranians. It appears that the latter are closer to European populations, with the exception of a few compared to the Semitic speakers. Examples.

Assyrian_D's Genetic Distances From Southern Europeans, Eastern Europeans, Western Europeans and Northern Europeans.


Southern Europe

[36,] "Sicilian_D" "32.2557"
[35,] "S_Italian_Sicilian_D" "34.6742"
[39,] "Greek_D" "35.1138"
[43,] "C_Italian_D" "39.9133"
[44,] "O_Italian_D" "42.9096"
[45,] "Tuscan" "43.6826"
[53,] "N_Italian_D" "52.1462"

Balkan Peninsula/Eastern Europe

[49,] "Bulgarian_D" "47.0993"
[50,] "Bulgarians_Y" "48.0956"
[51,] "Romanians" "49.2816"
[70,] "Hungarians" "65.6512"
[116,] "Mixed_Slav_D" "78.6059"
[121,] "Polish_D" "78.8829"
[127,] "Russian_B" "80.1493"
129,] "Russian_D" "80.8675"
[132,] "Russian" "81.3741"
[133,] "Belorussian" "81.5795"




Western Europe

[62,] "Baleares_1KG" "62.3089"
[63,] "Canarias_1KG" "62.3843"
[64,] "Extremadura_1KG" "63.5765"
[65,] "Galicia_1KG" "63.8424"
[66,] "Murcia_1KG" "63.8835"
[67,] "Andalucia_1KG" "63.918"
[68,] "Portuguese_D" "64.0746"
[71,] "Castilla_Y_Leon_1KG" "66.2981"
[73,] "Spaniards" "66.8452"
[77,] "Spanish_D" "67.7777"
[79,] "Cataluna_1KG" "67.8948"
[80,] "Castilla_La_Mancha_1KG" "68.1328"
[84,] "French" "69.0942"
[85,] "French_D" "69.2952"
[87,] "Aragon_1KG" "69.9363"

Northern Europe

[88,] "German_D" "70.7069"
[89,] "Mixed_Germanic_D" "72.1028"
[94,] "Dutch_D" "74.3005"
[99,] "Kent_1KG" "75.2648"
[101,] "CEU30" "75.7456"
[102,] "English_D" "75.7768"
[104,] "Cornwall_1KG" "76.4861"
[107,] "British_D" "77.1899"
[110,] "British_Isles_D" "77.6151"
[114,] "Irish_D" "78.4311"
[117,] "Orcadian" "78.7126"
[122,] "Orkney_1KG" "78.9392"
[135,] "Swedish_D" "81.9087"
[136,] "Norwegian_D" "82.2559"
[150,] "Lithuanian_D" "87.8936"

Iranian_D's Genetic Distances To Eastern, Western, Southern and Northern Europeans


Southern Europe


[35,] "S_Italian_Sicilian_D" "34.6742"
[38,] "Sicilian_D" "35.6347"
[39,] "Greek_D" "37.1997"
[45,] "C_Italian_D" "40.686"
[47,] "O_Italian_D" "41.4614"
[49,] "Tuscan" "43.7955"
[59,] "N_Italian_D" "49.8412"
[63,] "North_Italian" "51.8252"

Balkan Peninsula/Eastern Europe

[51,] "Bulgarian_D" "44.2811"
[53,] "Bulgarians_Y" "45.8989"
[54,] "Romanians" "46.0278"
[73,] "Hungarians" "59.5671"
[113,] "Ukranians_Y" "68.8692"
[120,] "Mordovians_Y" "70.2077"
[127,] "Mixed_Slav_D" "71.7778"
[128,] "Polish_D" "72.301"
[131,] "Russian_B" "73.2014"
[132,] "Russian" "73.4701"
[133,] "Russian_D" "73.4857"
[140,] "Belorussian" "74.9109"

Western Europe

[69,] "Canarias_1KG" "58.9493"
[71,] "Baleares_1KG" "59.2375"
[72,] "Extremadura_1KG" "59.567"
[74,] "Portuguese_D" "60.0362"
[75,] "Galicia_1KG" "60.2369"
[78,] "Murcia_1KG" "60.7933"
[79,] "Andalucia_1KG" "60.8409"
[81,] "Castilla_Y_Leon_1KG" "62.7214"
[83,] "Spaniards" "63.3067"
[88,] "Cataluna_1KG" "63.7279"
[89,] "Spanish_D" "63.9909"
[92,] "Castilla_La_Mancha_1KG" "64.5548"
[99,] "Cantabria_1KG" "66.0308"
[103,] "Aragon_1KG" "66.4317"

Northern Europe

[82,] "French" "63.2942"
[84,] "French_D" "63.3378"
[87,] "German_D" "63.6913"
[94,] "Mixed_Germanic_D" "64.5806"
[105,] "Dutch_D" "66.8214"
[107,] "Kent_1KG" "67.8433"
[111,] "English_D" "68.2306"
[114,] "Cornwall_1KG" "68.9556"
[118,] "British_D" "69.5832"
[121,] "British_Isles_D" "70.2342"
[122,] "Irish_D" "70.5024"
[123,] "Orcadian" "70.7141"
[124,] "Orkney_1KG" "70.9044"
[136,] "Swedish_D" "73.8264"
[137,] "Norwegian_D" "74.1943"

My explanation for this, is that Iranians have more shared ancestry in common with Europeans both in terms of their Y-DNA and Autosomal DNA via their North European component. Whereas Assyrians are more dissimilar due lacking Northern European admixture, high amounts of R1a and also being more Southwest Asian shifted than Iranians. Although Assyrians are closer to certain Southeastern European populations than Iranians are, Iranians are closer to all other European populations than Assyrians are.

I think that your observed pattern reflects an calculator effect: heterogeneous populations appear to be closer to other heterogeneous populations.

Example:
K=6
Population 1: 100% Component A
Population 2: 100% Component B
Population 3: 50% Component C + 50% Component D
Population 4: 50% Component E + 50% Component F

In this example you can see that Population 1 does not share any component with Populations 2-4, however, based on the calculated distance Population 1 is most distance to Population 2.

Population 1 vs. Population 2: 141.4 [= ((100-0)^2+(0-100)^2+(0-0)^2+(0-0)^2+(0-0)^2+(0-0)^2)^0.5]
Population 1 vs. Population 3: 122.5 [= ((100-0)^2+(0-0)^2+(0-50)^2+(0-50)^2+(0-0)^2+(0-0)^2)^0.5]
Population 1 vs. Population 4: 122.5 [= ((100-0)^2+(0-0)^2+(0-0)^2+(0-0)^2+(0-50)^2+(0-50)^2)^0.5]

The two heterogeneous populations 3 and 4 are closer to each other than to the homogenous populations 1 and 2.

Population 3 vs. Population 4: 100.0 [= ((0-0)^2+(0-0)^2+(50-0)^2+(50-0)^2+(0-50)^2+(0-50)^2)^0.5]

mnd
03-01-2014, 12:01 PM
When I put in the values for Turks from SW Turkey (http://dienekes.blogspot.co.uk/2012/02/first-look-at-turkish-and-kyrgyz-data.html) (Behar's Turks are from Cappadocia, deep in central Anatolia) excluding those with evident Balkan and non-local ancestry, the distance Oracle K12b gave me from Altaians was:

[95,] "Altai" "57.0335"

Which is almost the same distance as the Turkmen. What I personally would infer from this is that the population which Turkified Anatolia was notably more “East Eurasian” than modern-day Turkmen.

DMXX
03-01-2014, 02:04 PM
What do you make of the Jordanian and Syrian distances? They appear to defy what one would expect based on geography (i.e. they are the western most populations included in the comparison).

I don't have a satisfactory explanation for this. It is a rather peculiar result. I'm not even sure population-specific genetic diversity can account for it. Perhaps it's a feature of some sort of calculator effect as Palisto's suggested (bearing in mind this will be different from "the" calculator effect (http://dodecad.blogspot.co.uk/2012/08/on-so-called-calculator-effect.html)).


When I put in the values for Turks from SW Turkey (http://dienekes.blogspot.co.uk/2012/02/first-look-at-turkish-and-kyrgyz-data.html) (Behar's Turks are from Cappadocia, deep in central Anatolia) excluding those with evident Balkan and non-local ancestry, the distance Oracle K12b gave me from Altaians was:

[95,] "Altai" "57.0335"

Which is almost the same distance as the Turkmen. What I personally would infer from this is that the population which Turkified Anatolia was notably more “East Eurasian” than modern-day Turkmen.

Is the slightly greater GD of SW Anatolian Turks to Altaians compared with the Turkmen not indication that the population was in fact slightly less East Eurasian by the time they reached Anatolia?

Returning to my response to Humanist's post, there is a possibility that intra-population sampling and/or diversity differences is distorting these results to some degree. Both Turkish_D and Iranian_D are composed of individuals from across their respective regions, giving us only a broad impression of where the affinities lie. Having said this, Iranian_D and the Behar Iranians scored nearly identically, despite the latter possibly originating from a fixed location in southern-central Iran.

mnd
03-01-2014, 08:37 PM
Is the slightly greater GD of SW Anatolian Turks to Altaians compared with the Turkmen not indication that the population was in fact slightly less East Eurasian by the time they reached Anatolia?
I’m not sure what you mean. My assumption was that the Byzantine population outnumbered the Turkic newcomers (not an unreasonable one, I don’t think). In order for the incoming Turkic population to have absorbed the majority pre-existing population, they would have to have been significantly more East Eurasian than modern Turkmen in order to end up at a similar distance from Altaians, given Altaians are mostly East Eurasian.


Returning to my response to Humanist's post, there is a possibility that intra-population sampling and/or diversity differences is distorting these results to some degree.
I agree with this. I think for populations spread over a large area, sampling from one particular location may give a distorted impression of intra-population diversity and overall affinities (in Europe, the French come to mind).

everest59
03-01-2014, 08:40 PM
On a different board, someone of Turkish background wanted to know the date of Northern European admixture in Turks. What I did was, I assumed Turks as a population admixed between Lithuanians and Armenians. So, here is what I get per chromosome:
# CHR SNPs Estimated_date
1 3875.000000 86.778447
2 3690.000000 103.627590
3 3160.000000 86.093392
4 2936.000000 89.582869
5 2915.000000 90.876377
6 2864.000000 80.381578
7 2574.000000 83.501766
8 2450.000000 71.497939
9 2262.000000 93.641811
10 2527.000000 95.673814
11 2334.000000 80.772786
12 2400.000000 100.221010
13 1776.000000 72.646021
14 1614.000000 82.036064
15 1548.000000 104.728590
16 1689.000000 79.586757
17 1599.000000 100.153620
18 1603.000000 81.175334
19 1251.000000 87.328374
20 1415.000000 100.133750
21 808.000000 98.061568
22 873.000000 81.431495

Another file gives mean estimate for the date as follows:

Number of iterations to convergence: 0
Achieved convergence tolerance: 2.032e-06

mean (generations): 87.742415

Assuming 27 years in a generation, I get 87.74*27 or admixture date of 2368.98 years ago.

Now, there's another file that gives mean estimate of 69 with a standard error of a whooping 48. This file may have some issues though, as I had to modify the file the software came with.

Dr_McNinja
03-01-2014, 10:04 PM
From my recent playing around with ADMIXTURE, I would be wary of comparing admixture with individuals with high Northeast European components as it's possible a good chunk of East Eurasian admixture is being subsumed within that. I would figure the Turks in or near Anatolia would be one such group as opposed to Turkmens and other groups who probably show higher East Eurasian admixture (and perhaps artificially inflated NE-Euro numbers).

DMXX
03-01-2014, 10:31 PM
I’m not sure what you mean. My assumption was that the Byzantine population outnumbered the Turkic newcomers (not an unreasonable one, I don’t think). In order for the incoming Turkic population to have absorbed the majority pre-existing population, they would have to have been significantly more East Eurasian than modern Turkmen in order to end up at a similar distance from Altaians, given Altaians are mostly East Eurasian.


Ah, we're both viewing this from different perspectives but are arriving at the same point. Thank you for clarifying your earlier post.

The question I attempted to pose was framed through the common assumption on genetics forums among some is that the early Turks became more West Eurasian as their culture, language and way of life traversed across Asia.

The thrust of my message was that the Turkmen are still closer to the Altaians than SW Anatolian Turks are, which is in line with geography. But, for the difference to be as slight as it is, that could well mean the Turkish contribution to the aboriginal populations of Anatolia and West-Central Asia wasn't too different in character.

If that's the case, it supports a conclusion reached through your point, which is that the East Eurasian admixture in Anatolian Turks represents most of the contribution by the first Oghuz Turks.

everest59
03-01-2014, 11:41 PM
From my recent playing around with ADMIXTURE, I would be wary of comparing admixture with individuals with high Northeast European components as it's possible a good chunk of East Eurasian admixture is being subsumed within that. I would figure the Turks in or near Anatolia would be one such group as opposed to Turkmens and other groups who probably show higher East Eurasian admixture (and perhaps artificially inflated NE-Euro numbers).

Well, these programs seem to work well. Using Turks as the admixed population, and Han and Armenians as the reference population (Uzbeks was giving some issues, perhaps I needed to prune the data a little bit), I got the following result:

DATA: failure (warning: decay rates inconsistent) 2.7e-06 Turks Han Armenians 4.69 5.45 -1.75 77% 33.88 +/- 6.73 0.00013865 +/- 0.00002955 34.90 +/- 6.14 0.00012520 +/- 0.00002297 75.97 +/- 21.60 -0.00000351 +/- 0.00000201

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

Certainly, I got a decay inconsistent warning, but a 2-ref decay is at 33 generations, which is 33*27 or about 900 years ago.

So it seems to me that these softwares do a good job of separating out East Asian from Northern European. For the Northern European, I got 87 generations (max of >100 generations if you look at the chromosome number). For the east asian admixture, I got 33 generations.

DMXX
03-02-2014, 02:33 AM
I was curious to see what the distribution of the South Asian component outside of the Indian Subcontinent and South-Central Asia would look like if it is isolated from Dodecad's Gedrosia component. Referring to the Dodecad K12b spreadsheet (https://docs.google.com/spreadsheet/ccc?key=0ArJDEoCgzRKedEY4Y3lTUVBaaFp0bC1zZlBDcTZEY lE#gid=0), I've outlined populations in the Middle-East and the Caucasus below, in order of decreasing South Asian frequency. I have also included the Gedrosian component scores to determine whether any correlation exists.



Population Source N South_Asian Gedrosia
Iranians Behar 19 4.2 30.9
Iranian_D Dodecad 8 3.6 28.8
Yemenese Behar 8 2.4 5.9
Syrians Behar 15 1.3 11.4
Kurd_D Dodecad 9 1.1 28.7
Turkish_D Dodecad 27 1 13.4
Turks Behar 19 0.9 15.5
Kurds_Y Yunus 6 0.8 28.2
Druze HGDP 32 0.7 8.9
Nogais_Y Yunus 14 0.7 12.9
Palestinian HGDP 31 0.6 6.8
Armenians_15_Y Yunus 13 0.4 18
Kumyks_Y Yunus 13 0.4 20
Saudis Behar 20 0.3 3.6
Adygei HGDP 16 0.2 17.2
Armenians Behar 18 0.2 15.8
Jordanians Behar 20 0.2 9.6
Assyrian_D Dodecad 13 0.1 18.3
Balkars_Y Yunus 17 0.1 15.8
Iraq_Jews Behar 10 0.1 16.8
Abhkasians_Y Yunus 14 0 17.2
Armenian_D Dodecad 32 0 16.8
Bedouin HGDP 33 0 5
Chechens_Y Yunus 14 0 21.8
Georgia_Jews Behar 4 0 16.9
Georgians Behar 16 0 16.9
Iranian_Jews Behar 4 0 18.8
Lebanese Behar 7 0 10.8
Lezgins Behar 16 0 27.8
Nth_Ossetians_Y Yunus 12 0 16.5
Samaritians Behar 2 0 3.7
Yemen_Jews Behar 14 0 0.2


Comments:
- The South Asian component drops off fairly significantly anywhere west of Iran. The only exception seems to be Yemen to an extent, although maintained contacts with the distal Arabian peninsula societies with South Asia for centuries (e.g. pearl diving slave trade) probably accounts for this. If the United Arab Emirates was included as a sample site, I imagine they'd have a couple percent South Asian more than the Saudis and Bedounis (who have practically none).
- Kurds have a South Asian score comparable to Anatolian Turks rather than to Iranians. Of course, the inverse is true with Gedrosian.
- No linear correlation between South Asian and Gedrosian in either the Middle-East or the Caucasus. It is therefore likely an independent phenomenon (except for when regional histories allow perhaps, e.g. Iran).
- Most of the Middle-Eastern minority groups have 0% South Asian, indicating its' influx in the region happened sometime after at least the reign of the Neo-Assyrian empire.
- Although not included in this comparison, Central Asian groups (e.g. Hazara, Tajiks) have a significant frequency (>5%) of South Asian. The Silk Road may be part of the reason why Iran in particular has a higher frequency.

Humanist
03-02-2014, 03:00 AM
- Most of the Middle-Eastern minority groups have 0% South Asian, indicating its' influx in the region happened sometime after at least the reign of the Neo-Assyrian empire.

This comment reminded me of the Iranian Jewish thread ("Reconciling Autosomal DNA and Physical Appearance") (http://www.anthrogenica.com/showthread.php?1772-Iranian-Jews-Reconciling-Autosomal-DNA-and-Physical-Appearance) I created several weeks back. Although the difference is minuscule, it is interesting that the Iranian Jews record even less "South Asian" than Assyrians (0% v. 0.1%).

everest59
03-02-2014, 03:23 AM
This comment reminded me of the Iranian Jewish thread ("Reconciling Autosomal DNA and Physical Appearance") (http://www.anthrogenica.com/showthread.php?1772-Iranian-Jews-Reconciling-Autosomal-DNA-and-Physical-Appearance) I created several weeks back. Although the difference is minuscule, it is interesting that the Iranian Jews record even less "South Asian" than Assyrians (0% v. 0.1%).

Well, the Lazairidis paper listed f3 ratios for various populations, including for Iranian Jews, and it suggests real South Asian ancestry in them--actually higher South Asian in them than WHG and ANE admixture. Now, the f3 ratio is greater than -4, so it's probably not that significant, but it's there. Other populations who have some South Asian ancestry are Georgians as well as Armenians. These populations don't show any in ADMIXTURE runs.
The lowest f3 statistic for these populations is f3(population;gujarati3, stuttgart).
Check out extended table 1.
http://arxiv.org/pdf/1312.6639.pdf

(Big file above)

Humanist
03-02-2014, 03:28 AM
Well, the Lazairidis paper listed f3 ratios for various populations, including for Iranian Jews, and it suggests real South Asian ancestry in them--actually higher South Asian in them than WHG and ANE admixture. Now, the f3 ratio is greater than -4, so it's probably not that significant, but it's there. Other populations who have some South Asian ancestry are Georgians as well as Armenians. These populations don't show any in ADMIXTURE runs.
The lowest f3 statistic for these populations is f3(population;gujarati3, stuttgart).
Check out extended table 1.
http://arxiv.org/pdf/1312.6639.pdf

(Big file above)

I do not doubt that. If you have ever had the opportunity to read my posts on Assyrian mtDNA, you would find several references to Assyrian and Indian mtDNA similarities.

ZephyrousMandaru
03-02-2014, 07:20 AM
I don't think we're currently in any position to readily preclude the possibility of South Asian admixture in any Middle Eastern minority groups. We have to remember that these components are not 100%, unadulterated compositions of allele frequencies. Many of these components conceal archaic Non-West Eurasian admixture, and I believe that Gedrosia does in fact, subsume some of the ASI. My reasons for thinking this, are how Gedrosia drifts eastwards toward ASI.

Which may manifests itself at lower Ks, just as East African alleles in Southwest Asian/Red Sea/Arabian does at lower Ks in the Pagani et al K2-10 test. At lower Ks, Iraqi Jews have around 4% East African on average, but once you increase the K value that disappears and in place of it, is the Red Sea/Arabian component which is found at around 40% in Iraqi Jews. Also, Iraqi Jews exhibit East Eurasian admixture at lower Ks as well, as do other Middle Eastern groups. I believe this East Eurasian admixture may be ASI related. ADMIXTURE doesn't detect everything, minor percentages are often obscured by being allocated into other components, usually ones that are related to it in some way.

Humanist
03-02-2014, 07:49 AM
I don't think we're currently in any position to readily preclude the possibility of South Asian admixture in any Middle Eastern minority groups.

I do not believe that South Asian admixture is lacking in ME minorities. But, I do not believe it is of recent origin. If it was fairly recent, I do believe you would see it appear in ADMIXTURE results.

See: mtDNA from the Early Bronze Age to the Roman Period Suggests a Genetic Link between the Indian Subcontinent and Mesopotamian Cradle of Civilization (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0073682)

Witas et al. (2013)


We anticipate that the analysed remains from Mesopotamia belonged to people with genetic affinity to the Indian subcontinent since the distribution of identified ancient haplotypes indicates solid link with populations from the region of South Asia-Tibet (Trans-Himalaya).

newtoboard
03-07-2014, 01:57 PM
- Although not included in this comparison, Central Asian groups (e.g. Hazara, Tajiks) have a significant frequency (>5%) of South Asian. The Silk Road may be part of the reason why Iran in particular has a higher frequency.

What do you think of the South Asian ancestry in Central Asia? Do you think it is pre-Neolithic or much more recent? I wasn't aware of West Eurasian populations in Central Asia prior to the Neolithic although Keltiminar and Botai are always possibilities (but I don't think they left much ancestry in West or South Central Asia). I guess there is always the possibility that populations high in R2 and L populations existed prior to the Neolithic too.

newtoboard
03-07-2014, 02:00 PM
I do not believe that South Asian admixture is lacking in ME minorities. But, I do not believe it is of recent origin. If it was fairly recent, I do believe you would see it appear in ADMIXTURE results.

See: mtDNA from the Early Bronze Age to the Roman Period Suggests a Genetic Link between the Indian Subcontinent and Mesopotamian Cradle of Civilization (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0073682)

Witas et al. (2013)

I disagree. I think most South Asian admixture in West Asia is very recent and connected to two events. namely the collpase of the IVC and the movement of IE speakers from Central Asia to West Asia (who probably picked up a small South Asian component). None the mtDNA links in that article persist (there is no mtDNA M in modern Syria and these were likely the result of South Asian trading populations who moved West rather than a common link).

DMXX
02-24-2015, 06:58 PM
What do you think of the South Asian ancestry in Central Asia? Do you think it is pre-Neolithic or much more recent? I wasn't aware of West Eurasian populations in Central Asia prior to the Neolithic although Keltiminar and Botai are always possibilities (but I don't think they left much ancestry in West or South Central Asia). I guess there is always the possibility that populations high in R2 and L populations existed prior to the Neolithic too.

My current (weak) opinion on this topic is that South Asian (xGedrosian) admixture in Central Asians is the result of mutual shared ancestry rather than a Subcontinental contribution to that region. I've done some cursory reading recently on proto-Dravidian and am surprised at how many linguists have proposed that the swathe of territory from eastern Iran onwards was the Dravidian urheimat. Have no idea what the lingustic evidence for this is (isn't explicitly stated in the papers I read) or when it was first proposed. A part of me perceives the issue of Dravidian to be treated as an afterthought in a discipline that is still rather "IE-centric".

It is tempting to correlate the two, but I realise the evidence is so weak (or non-existent?) that even mild assertions are tantamount to special pleading. So, I wouldn't be surprised if this South Asian (xGedrosian) admixture in Central Asia ends up being an early Neolithic connection between Central Asia and the Subcontinent via Dravidian, but place no firm stock in the idea.