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Kurd
01-05-2017, 06:16 AM
To further the understanding of the genetic relationship between Brahuis and W Asians such as Kurds and Iranians, I did an IBD run using about a dozen HGDP Brahui samples. Previous studies I had conducted comparing Kurds and Brahuis using Dstats had shown them to be a near clade, and so I wanted to see whether this could be corroborated with IBD.

Conspiracy theorists (ie the couple of users here who are well known, who try their best to slander yours truly, believe that I manipulate results because of some hidden personal agenda) will likely be disappointed to say the least, because this is another piece of scientific evidence that disproves their baseless (scientifically) held personal beliefs that Baloch and Brahui have no recent genetic relationship with Kurds and other NW Iranians, and that Baloch and Brahui have been living in their present locations since the Neolithic. Well to them I say wake up and smell the coffee, and stop living in denial.

I used Beagle's FastIBD for this purpose. Beagle is a powerful software used primarily for imputing missing calls (genotype likelihood), and for IBD analysis using plink files.

The fastIBD method is based on estimating frequencies of shared haplotypes. Haplotype frequency is critical because a shared common haplotype is unlikely to reflect recent IBD, whereas a shared haplotype that is very rare is likely to be identical by descent. The fastIBD method allows for uncertain haplotype phase by sampling multiple realizations of haplotype phase given the data, then allowing for some switching between alternative phasings; there is, however, a switch penalty to prevent excessive switching. The extent of haplotype sharing is measured by a score that is the frequency of the shared haplotype modified by the penalties assessed at each switch between alternate phasings. Thus, a small score (close to zero) for a pair indicates that the two individuals share a low-frequency haplotype and are thus likely to be identical by descent.

FastIBD is a quick method of sifting through dozens of genomes.


Browning, B. L., & Browning, S. R. (2011). A Fast, Powerful Method for Detecting Identity by Descent. American Journal of Human Genetics, 88(2), 173–182. http://doi.org/10.1016/j.ajhg.2011.01.010
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035716/


Edit: Results 143 - 5000 were dropped because they did not make my self imposed filter (smaller segments and/or lower IBD scores). That included a couple of S Europeans.

Kurd
01-05-2017, 06:27 AM
The fastIBD output file has five columns. The first two columns list the two sample identifiers for the shared haplotype described on each line. The next two columns list the starting (inclusive) and ending (exclusive) marker indices for the shared haplotype. The first marker has index 0. The last column gives the fastIBD score for the shared haplotype. A fastIBD score < 10 -10 provides strong evidence that the shared haplotype is IBD if the length of the shared haplotype length is ≥ 1 cM.

I used a more stringent criteria by dropping all outputs with a fastIBD score <1E-11. I also dropped any results with segments <100 SNPs.

The results show that Iranians and Kurds are high up in the table, which should not have been the case if Brahuis have been in their present locations since the Neolithic, because otherwise, nothing but S Asians and SC Asians such as Pashtuns should have dominated the top rankings, and Kurds and Iranians should have been all the way in the bottom, if they even made the table at all. I have highlighted S Asians in brown, and Pashtuns in purple to help visualize their rankings.

The fact that Iranians and Kurds are so high up in the table is evidence of the close genetic relationship between them and Brahuis, and that the separation of the 2 can't have been too long ago.



NO.
S1
S2
START
END
FastIBD Score
SNPs


1
.Zara
BrahuiHGDP00037
37505
37744
3.95E-26
239


2
.Zara
BrahuiHGDP00033
37505
37746
3.95E-26
241


3
.Kurd_SE
BrahuiHGDP00043
107189
107449
1.26E-23
260


4
.Kurd_SE
BrahuiHGDP00003
104720
105053
1.28E-20
333


5
.Kurd_SE
BrahuiHGDP00025
106682
106949
2.04E-20
267


6
.Kurd_SE
BrahuiHGDP00039
108155
108385
1.38E-19
230


7
.Kurd_SE
BrahuiHGDP00017
47811
48076
2.40E-19
265


8
.Kurd_SE
BrahuiHGDP00035
105155
105382
6.50E-19
227


9
.Zara
BrahuiHGDP00043
59725
59873
1.30E-18
148


10
.Kurd_SE
BrahuiHGDP00049
99938
100109
2.39E-18
171


11
.Farid
BrahuiHGDP00035
8527
8872
2.78E-18
345


12
.Kurd_SE
BrahuiHGDP00005
52820
53015
3.35E-18
195


13
.Kurd_SE
BrahuiHGDP00021
93057
93268
7.27E-18
211


14
.Zara
BrahuiHGDP00001
43282
43502
3.83E-17
220


15
.Kurd_F2
BrahuiHGDP00037
44336
44478
2.75E-16
142


16
.Kurd_SE
BrahuiHGDP00021
108170
108351
4.36E-16
181


17
.Bol_Nat
BrahuiHGDP00031
39618
39800
4.87E-16
182


18
.Kurd_SE
BrahuiHGDP00031
59331
59609
1.03E-15
278


19
.Kurd_SE
BrahuiHGDP00021
105056
105315
2.12E-15
259


20
.Kurd_SE
BrahuiHGDP00005
68052
68198
2.57E-15
146


21
.McNinja
BrahuiHGDP00027
45733
45896
4.26E-15
163


22
.Kurd_SE
BrahuiHGDP00043
101189
101382
4.35E-15
193


23
.Kurd_F6
BrahuiHGDP00047
97968
98182
4.58E-15
214


24
.Kurd_SE
BrahuiHGDP00001
105144
105334
5.38E-15
190


25
.NK19191
BrahuiHGDP00019
44341
44454
8.15E-15
113


26
.Zara
BrahuiHGDP00017
50535
50708
2.50E-14
173


27
.Kurd_SE
BrahuiHGDP00015
47344
47486
3.44E-14
142


28
.Kurd_SE
BrahuiHGDP00003
63645
63859
3.58E-14
214


29
.Pak_Gujjar
BrahuiHGDP00025
102194
102343
3.96E-14
149


30
.Farid
BrahuiHGDP00045
8548
8762
4.64E-14
214


31
.Sein
BrahuiHGDP00033
71937
72108
4.84E-14
171


32
.Melif
BrahuiHGDP00047
44314
44472
7.62E-14
158


33
.Jesus
BrahuiHGDP00011
25773
25921
1.14E-13
148


34
.Farid
BrahuiHGDP00047
8277
8479
1.33E-13
202


35
.Kurd_SE
BrahuiHGDP00045
67695
67893
2.26E-13
198


36
.Rukha
BrahuiHGDP00023
12789
12933
2.34E-13
144


37
.Kurd_SE
BrahuiHGDP00037
52789
52957
2.78E-13
168


38
.Farid
BrahuiHGDP00027
24983
25147
2.85E-13
164


39
.McNinja
BrahuiHGDP00037
45772
45896
3.18E-13
124


40
.Kurd_SE
BrahuiHGDP00007
67678
67929
3.25E-13
251


41
.Kurd_SE
BrahuiHGDP00003
13651
13925
3.48E-13
274


42
.Kurd_SE
BrahuiHGDP00045
114756
114987
3.61E-13
231


43
.Sein
BrahuiHGDP00001
20861
21019
3.77E-13
158


44
.Sapporo
BrahuiHGDP00017
62867
63054
3.86E-13
187


45
.Kurd_SE
BrahuiHGDP00047
60235
60413
3.89E-13
178


46
.Kurd_SE
BrahuiHGDP00003
23454
23591
4.90E-13
137


47
.Zara
BrahuiHGDP00025
61777
61932
5.58E-13
155


48
.Bored
BrahuiHGDP00007
15621
15797
6.54E-13
176


49
.Punjabi_Rajput
BrahuiHGDP00047
44335
44485
6.57E-13
150


50
.Punjabi_Rajput
BrahuiHGDP00039
57718
57866
7.21E-13
148


51
.Kurd_SE
BrahuiHGDP00033
67678
67893
7.73E-13
215


52
.Jesus
BrahuiHGDP00043
25819
25993
8.17E-13
174


53
.Kurd_C1
BrahuiHGDP00003
93144
93361
1.08E-12
217


54
.Jatt_Har393
BrahuiHGDP00023
107604
107843
1.16E-12
239


55
.Khana
BrahuiHGDP00033
65493
65715
1.36E-12
222


56
.Kenji
BrahuiHGDP00003
65499
65604
1.41E-12
105


57
.Zara
BrahuiHGDP00037
23938
24077
1.59E-12
139


58
.Pashtun_Afg
BrahuiHGDP00035
40254
40418
1.63E-12
164


59
.Kurd_F7
BrahuiHGDP00031
101655
101769
1.93E-12
114


60
.Melif
BrahuiHGDP00001
42327
42452
1.98E-12
125


61
.Sein
BrahuiHGDP00039
18558
18819
1.99E-12
261


62
.Kurd_F3
BrahuiHGDP00007
32454
32564
2.20E-12
110


63
.Khana
BrahuiHGDP00017
81315
81506
2.46E-12
191


64
.Hanna
BrahuiHGDP00045
97508
97613
2.55E-12
105


65
.Punjabi_Rajput
BrahuiHGDP00005
37946
38139
2.63E-12
193


66
.Varun
BrahuiHGDP00007
69325
69470
3.19E-12
145


67
.Mfa
BrahuiHGDP00047
74193
74374
3.52E-12
181


68
.Bol_Nat
BrahuiHGDP00027
31449
31620
4.49E-12
171


69
.Kurd_C1
BrahuiHGDP00007
26785
26890
4.50E-12
105


70
.Jesus
BrahuiHGDP00007
51787
51939
4.60E-12
152


71
.Pak_Gujjar
BrahuiHGDP00043
12439
12569
4.88E-12
130


72
.Zara
BrahuiHGDP00027
114348
114490
5.51E-12
142


73
.Punjabi_Rajput
BrahuiHGDP00003
102204
102341
6.02E-12
137


74
.Parasar
BrahuiHGDP00011
84251
84451
6.22E-12
200

Kurd
01-05-2017, 06:27 AM
75
.Znertu
BrahuiHGDP00015
56088
56215
6.24E-12
127


76
.Khana
BrahuiHGDP00047
44321
44458
6.31E-12
137


77
.Jesus
BrahuiHGDP00005
44314
44431
6.88E-12
117


78
.Zara
BrahuiHGDP00015
40526
40751
7.81E-12
225


79
.Jatt2016
BrahuiHGDP00011
103908
104067
8.01E-12
159


80
.Kenji
BrahuiHGDP00039
91547
91757
8.47E-12
210


81
.Kurd_C1
BrahuiHGDP00015
81463
81607
8.61E-12
144


82
.Kaido
BrahuiHGDP00039
81404
81555
9.08E-12
151


83
.Farid
BrahuiHGDP00047
110261
110377
9.13E-12
116


84
.Kurd_C2
BrahuiHGDP00047
77539
77639
9.20E-12
100


85
.Varun
BrahuiHGDP00025
6816
6936
1.01E-11
120


86
.Bol_Nat
BrahuiHGDP00035
5922
6031
1.10E-11
109


87
.Sein
BrahuiHGDP00049
44144
44377
1.23E-11
233


88
.Kurd_F8
BrahuiHGDP00043
62397
62498
1.24E-11
101


89
.Bored
BrahuiHGDP00025
40253
40356
1.28E-11
103


90
.Zara
BrahuiHGDP00021
15500
15601
1.29E-11
101


91
.Parasar
BrahuiHGDP00015
107672
107873
1.45E-11
201


92
.Pak_Gujjar
BrahuiHGDP00005
101448
101548
1.49E-11
100


93
.Kenji
BrahuiHGDP00001
768
904
1.56E-11
136


94
.Farid
BrahuiHGDP00017
52018
52147
1.57E-11
129


95
.Kurd_F3
BrahuiHGDP00047
81101
81205
1.64E-11
104


96
.Jatt_Har393
BrahuiHGDP00033
29734
29972
1.65E-11
238


97
.Humanist
BrahuiHGDP00025
108016
108217
1.68E-11
201


98
.Pashtun_Afg
BrahuiHGDP00001
16298
16437
2.00E-11
139


99
.Zara
BrahuiHGDP00015
46077
46248
2.04E-11
171


100
.Dluffy
BrahuiHGDP00047
45197
45328
2.12E-11
131


101
.Farid
BrahuiHGDP00027
113811
113925
2.16E-11
114


102
.Kurd_F5
BrahuiHGDP00011
62030
62139
2.22E-11
109


103
.Jatt2016
BrahuiHGDP00025
28392
28512
2.23E-11
120


104
.Sapporo
BrahuiHGDP00019
72234
72428
2.34E-11
194


105
.Kurd_F3
BrahuiHGDP00035
66855
67018
2.50E-11
163


106
.Mfa
BrahuiHGDP00031
7699
7807
2.52E-11
108


107
.Kurd_F6
BrahuiHGDP00027
31479
31653
2.69E-11
174


108
.Farid
BrahuiHGDP00037
18787
18970
2.99E-11
183


109
.Rukha
BrahuiHGDP00021
107544
107658
3.00E-11
114


110
.Pak_Gujjar
BrahuiHGDP00037
99495
99692
3.03E-11
197


111
.NK19191
BrahuiHGDP00037
46337
46487
3.07E-11
150


112
.Rukha
BrahuiHGDP00011
65379
65556
3.08E-11
177


113
.McNinja
BrahuiHGDP00021
60187
60358
3.25E-11
171


114
.Kaido
BrahuiHGDP00043
51203
51378
3.44E-11
175


115
.Kurd_C3
BrahuiHGDP00003
93127
93267
3.69E-11
140


116
.Zara
BrahuiHGDP00019
84221
84322
3.87E-11
101


117
.Reza1
BrahuiHGDP00019
84230
84346
4.17E-11
116


118
.Pak_Gujjar
BrahuiHGDP00015
104655
104767
4.40E-11
112


119
.Zephyrous
BrahuiHGDP00039
99075
99217
4.55E-11
142


120
.Pashtun_Afg
BrahuiHGDP00049
61710
61866
4.87E-11
156


121
.Bol_Nat
BrahuiHGDP00049
15453
15574
5.19E-11
121


122
.Farid
BrahuiHGDP00003
62754
62929
5.25E-11
175


123
.Kurd_F6
BrahuiHGDP00047
27557
27824
5.33E-11
267


124
.Sapporo
BrahuiHGDP00037
22718
22858
5.52E-11
140


125
.Dluffy
BrahuiHGDP00003
14645
14788
5.60E-11
143


126
.Kurd_F6
BrahuiHGDP00049
72159
72317
5.61E-11
158


127
.Melif
BrahuiHGDP00043
55417
55581
5.75E-11
164


128
.Kurd_F5
BrahuiHGDP00045
63688
63857
5.77E-11
169


129
.Kurd_F2
BrahuiHGDP00027
109062
109194
6.03E-11
132


130
.Zara
BrahuiHGDP00005
23490
23638
6.09E-11
148


131
.Khana
BrahuiHGDP00035
104976
105129
6.34E-11
153


132
.Jatt2016
BrahuiHGDP00015
81369
81500
6.61E-11
131


133
.Varun
BrahuiHGDP00031
83895
84032
6.71E-11
137


134
.Farid
BrahuiHGDP00003
78079
78288
6.79E-11
209


135
.Kurd_F3
BrahuiHGDP00031
55508
55617
6.94E-11
109


136
.Kurd_F6
BrahuiHGDP00015
102979
103084
7.25E-11
105


137
.Kurd_F7
BrahuiHGDP00017
104831
104952
7.31E-11
121


138
.Farid
BrahuiHGDP00043
31683
31807
7.32E-11
124


139
.Sapporo
BrahuiHGDP00005
76030
76185
7.47E-11
155


140
.McNinja
BrahuiHGDP00043
38015
38215
7.99E-11
200


141
.Kurd_Ezidi
BrahuiHGDP00049
97053
97247
8.65E-11
194


142
.Jesus
BrahuiHGDP00039
52071
52177
9.45E-11
106

Ciro
01-05-2017, 12:59 PM
What about Pashtuns?

arbaloch
09-28-2017, 08:58 PM
Great work sir, very informative.

Gravetto-Danubian
09-28-2017, 09:41 PM
What does this inform about relations of Iranian speakers, Brahui and the origins of Dravidian ?