A lighter shade of brown: the Dan MacArthur chronicles, not a Romani

By Razib Khan | December 12, 2012 11:25 am

Pakistani honor guard

A few days ago I suggested that Dr. Daniel MacArthur might have South Asian ancestry. Now, when confronted with surprise the best option is to stick with your prior assumption, unless that surprise is powerful enough for you to “update” your model. After a few days of further analysis I will update: I do think Dan MacArthur has South Asian ancestry. Dienekes dug further, and noticed that there are hallmarks of “Ancestral South Indian” ancestry along the first 2/3 or so of chromosome 10. Now, you do have to remember that this genomic region is only half South Asian. The other half is European.

But in any case, one question that some people brought up: perhaps MacArthur has Romani heritage? I’m skeptical of this partly because:

1) there weren’t that many Romani in Britain in the 19th century

2) The British Romani are already very highly admixed

Another friend, who is a population genomicist himself, expressed some skepticism that such a long segment wasn’t broken up by recombination over the generations. My only moderately informed answer is this: we’d only notice the long segments, because if a very small region of ‘exotic’ ancestry was embedded within the dominant ancestral component it probably would not show up on some of these tests (or, we’d assume it was noise). Dan has another segment of South Asian ancestry, but much smaller in size. It may be there are other regions which we could find if we used better reference populations.

Here’s what I tentatively want to do with Dan’s data now. First, take the 80 MB or so which has South Asian ancestry, and phase it. That way I’d have a South Asian chromosome and a European one, and we could look for matches for only the South Asian one. But being busy I didn’t have time to do this. What I did have time to do was reduce the chromosomal region under consideration, and then run an IBS distance analysis in a private data set I have. This is a crude, but not always uninformative analysis. But by looking at the relationships I can now conclude that Dan MacArthur probably does not have Romani ancestry. Why? Because the Romani are of Northwest Indian heritage, and MacArthur’s match pattern using the diploid genotype (so South Asian + European) does not match what I expect would emerge from such a combination.

The full table is below, but to me the fact that he has so many matches with Northwest Indian populations is evidence that his ancestry was not Northwest Indian. Otherwise, he would be matching more Utah white (CEU samples) more often. Rather, someone with a mix of more conventional South Asian ancestry and European ancestry often resembles some of the less South Asian populations of South Asia (e.g., Brahui) in these crude measures. In fact, one of the closest matches to Dan’s IBS profile’s is that of my own mother. She is a rather vanilla ethnic Bengali, so I think there is a strong chance that his Indian ancestry is similar. This weak genetic data isn’t really the primary reason. The British East India company operated out of Bengal for much of its history, and there are simply a lot of Bengalis.

There’s a lot more that can be done here. Since I don’t have time, here’s the pedigree file if anyone wants to play with them (Dan is DGM001).

Population Genetic distance from Dan Standardized distance
Brahui 0.253 81.268
Burusho 0.257 82.736
Razib’s Mother 0.258 82.783
CEU 0.258 82.993
Burusho 0.258 83.024
CEU 0.26 83.547
Sakilli 0.26 83.555
Brahui 0.261 83.831
Brahui 0.261 83.857
GIH 0.261 83.955
CEU 0.261 83.972
CEU 0.261 83.985
CEU 0.262 84.043
North Kannadi 0.262 84.169
CEU 0.262 84.207
CEU 0.262 84.318
CEU 0.262 84.33
CEU 0.263 84.391
Paniya 0.263 84.408
CEU 0.263 84.437
CEU 0.263 84.445
CEU 0.263 84.488
CEU 0.263 84.606
CEU 0.263 84.609
CEU 0.264 84.691
Brahui 0.264 84.709
CEU 0.264 84.752
CEU 0.264 84.764
Brahui 0.264 84.822
GIH 0.264 84.826
Burusho 0.264 84.841
CEU 0.264 84.898
CEU 0.264 84.975
North Kannadi 0.264 84.992
CEU 0.265 85.087
Paniya 0.265 85.212
CEU 0.265 85.226
CEU 0.265 85.25
CEU 0.265 85.25
CEU 0.265 85.278
CEU 0.265 85.299
North Kannadi 0.265 85.3
Burusho 0.265 85.309
Burusho 0.266 85.328
CEU 0.266 85.363
CEU 0.266 85.409
North Kannadi 0.266 85.412
CEU 0.266 85.436
Burusho 0.266 85.446
Bene Israel 0.266 85.508
CEU 0.266 85.521
GIH 0.266 85.618
GIH 0.267 85.661
CEU 0.267 85.696
CEU 0.267 85.722
CEU 0.267 85.732
Brahui 0.267 85.777
GIH 0.267 85.793
CEU 0.267 85.799
CEU 0.267 85.816
Cochin Jews 0.267 85.85
CEU 0.267 85.943
Brahui 0.268 85.996
CEU 0.268 86.005
Cochin Jews 0.268 86.011
CEU 0.268 86.08
CEU 0.268 86.115
CEU 0.268 86.18
GIH 0.268 86.229
Cochin Jews 0.268 86.234
CEU 0.268 86.244
Burusho 0.268 86.265
CEU 0.268 86.277
CEU 0.268 86.278
CEU 0.269 86.288
CEU 0.269 86.291
CEU 0.269 86.318
CEU 0.269 86.325
CEU 0.269 86.326
GIH 0.269 86.327
CEU 0.269 86.329
CEU 0.269 86.354
CEU 0.269 86.387
CEU 0.269 86.463
CEU 0.269 86.515
CEU 0.269 86.517
CEU 0.269 86.55
CEU 0.27 86.609
Paniya 0.27 86.682
CEU 0.27 86.687
CEU 0.27 86.696
CEU 0.27 86.717
CEU 0.27 86.733
Sakilli 0.27 86.74
CEU 0.27 86.866
Malayan 0.27 86.879
North Kannadi 0.27 86.883
CEU 0.271 86.937
Brahui 0.271 86.952
Burusho 0.271 86.956
CEU 0.271 86.957
CEU 0.271 86.977
North Kannadi 0.271 86.995
GIH 0.271 87.018
CEU 0.271 87.042
CEU 0.271 87.066
CEU 0.271 87.07
Brahui 0.271 87.09
Bene Israel 0.271 87.094
Sakilli 0.271 87.141
CEU 0.271 87.2
CEU 0.271 87.24
North Kannadi 0.272 87.253
CEU 0.272 87.297
Burusho 0.272 87.307
CEU 0.272 87.327
GIH 0.272 87.353
CEU 0.272 87.355
Cochin Jews 0.272 87.381
CEU 0.272 87.384
CEU 0.272 87.5
CEU 0.272 87.535
CEU 0.273 87.594
Malayan 0.273 87.676
CEU 0.273 87.702
CEU 0.273 87.741
Burusho 0.273 87.806
CEU 0.273 87.846
Cambodians 0.274 87.932
North Kannadi 0.274 87.951
CEU 0.274 87.951
Burusho 0.274 88.03
CEU 0.274 88.047
CEU 0.274 88.081
CEU 0.274 88.089
CEU 0.274 88.101
CEU 0.274 88.179
CEU 0.274 88.19
North Kannadi 0.275 88.243
CEU 0.275 88.32
GIH 0.275 88.325
CEU 0.275 88.349
Brahui 0.275 88.393
CEU 0.275 88.402
CEU 0.275 88.457
Bene Israel 0.276 88.552
CEU 0.276 88.577
CEU 0.276 88.603
CEU 0.276 88.647
CEU 0.276 88.7
CEU 0.276 88.729
CEU 0.276 88.814
CEU 0.276 88.85
Brahui 0.276 88.855
CEU 0.277 88.923
GIH 0.277 88.99
Paniya 0.277 89.082
CEU 0.277 89.118
CEU 0.277 89.15
CEU 0.277 89.151
CEU 0.277 89.17
CEU 0.278 89.184
Cambodians 0.278 89.208
Cambodians 0.278 89.233
Cambodians 0.278 89.383
CEU 0.278 89.45
CEU 0.278 89.493
Cambodians 0.279 89.522
CEU 0.279 89.595
CEU 0.279 89.679
CEU 0.279 89.753
CEU 0.279 89.762
CEU 0.279 89.807
Cambodians 0.28 89.942
GIH 0.28 90.085
CEU 0.281 90.178
Brahui 0.281 90.364
Cambodians 0.282 90.543
Cambodians 0.282 90.559
Cambodians 0.282 90.77
Cambodians 0.283 90.898
CEU 0.283 90.956
CEU 0.284 91.316
CHD 0.289 92.952
Sakilli 0.29 93.103
Bene Israel 0.29 93.122
CHD 0.291 93.619
CHD 0.291 93.663
CHD 0.293 94.125
CHD 0.293 94.248
CHD 0.294 94.451
CHD 0.294 94.629
CHD 0.296 94.965
CHD 0.296 95.279
Yorubas 0.297 95.298
CHD 0.297 95.368
CHD 0.297 95.438
CHD 0.297 95.441
Yorubas 0.297 95.567
CHD 0.298 95.678
CHD 0.298 95.828
CHD 0.299 96.032
CHD 0.299 96.127
CHD 0.3 96.349
CHD 0.3 96.403
CHD 0.3 96.443
CHD 0.3 96.508
CHD 0.3 96.523
CHD 0.3 96.533
CHD 0.301 96.575
CHD 0.301 96.598
CHD 0.301 96.624
CHD 0.301 96.625
CHD 0.301 96.738
CHD 0.301 96.758
CHD 0.301 96.869
Yorubas 0.302 97.106
CHD 0.303 97.37
CHD 0.303 97.41
Yorubas 0.304 97.681
CHD 0.304 97.713
CHD 0.304 97.747
Yorubas 0.304 97.829
CHD 0.304 97.838
CHD 0.305 98.106
CHD 0.306 98.309
Yorubas 0.307 98.499
CHD 0.307 98.546
CHD 0.307 98.547
CHD 0.307 98.606
CHD 0.307 98.764
CHD 0.307 98.78
CHD 0.307 98.803
Yorubas 0.308 98.947
Yorubas 0.308 99.03
Yorubas 0.309 99.411
Yorubas 0.309 99.417
CHD 0.309 99.452
CHD 0.31 99.624
Yorubas 0.311 100
MORE ABOUT: Daniel MacArthur

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This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at http://www.razib.com

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