View Full Version : Brahui IBD Results
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.
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
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
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 ?
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