Planet Earth

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

Gene ExpressionBy Razib KhanDec 12, 2012 4:25 PM
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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 issimilar. 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).

PopulationGenetic distance from DanStandardized distance

Brahui0.25381.268

Burusho0.25782.736

Razib's Mother0.25882.783

CEU0.25882.993

Burusho0.25883.024

CEU0.2683.547

Sakilli0.2683.555

Brahui0.26183.831

Brahui0.26183.857

GIH0.26183.955

CEU0.26183.972

CEU0.26183.985

CEU0.26284.043

North Kannadi0.26284.169

CEU0.26284.207

CEU0.26284.318

CEU0.26284.33

CEU0.26384.391

Paniya0.26384.408

CEU0.26384.437

CEU0.26384.445

CEU0.26384.488

CEU0.26384.606

CEU0.26384.609

CEU0.26484.691

Brahui0.26484.709

CEU0.26484.752

CEU0.26484.764

Brahui0.26484.822

GIH0.26484.826

Burusho0.26484.841

CEU0.26484.898

CEU0.26484.975

North Kannadi0.26484.992

CEU0.26585.087

Paniya0.26585.212

CEU0.26585.226

CEU0.26585.25

CEU0.26585.25

CEU0.26585.278

CEU0.26585.299

North Kannadi0.26585.3

Burusho0.26585.309

Burusho0.26685.328

CEU0.26685.363

CEU0.26685.409

North Kannadi0.26685.412

CEU0.26685.436

Burusho0.26685.446

Bene Israel0.26685.508

CEU0.26685.521

GIH0.26685.618

GIH0.26785.661

CEU0.26785.696

CEU0.26785.722

CEU0.26785.732

Brahui0.26785.777

GIH0.26785.793

CEU0.26785.799

CEU0.26785.816

Cochin Jews0.26785.85

CEU0.26785.943

Brahui0.26885.996

CEU0.26886.005

Cochin Jews0.26886.011

CEU0.26886.08

CEU0.26886.115

CEU0.26886.18

GIH0.26886.229

Cochin Jews0.26886.234

CEU0.26886.244

Burusho0.26886.265

CEU0.26886.277

CEU0.26886.278

CEU0.26986.288

CEU0.26986.291

CEU0.26986.318

CEU0.26986.325

CEU0.26986.326

GIH0.26986.327

CEU0.26986.329

CEU0.26986.354

CEU0.26986.387

CEU0.26986.463

CEU0.26986.515

CEU0.26986.517

CEU0.26986.55

CEU0.2786.609

Paniya0.2786.682

CEU0.2786.687

CEU0.2786.696

CEU0.2786.717

CEU0.2786.733

Sakilli0.2786.74

CEU0.2786.866

Malayan0.2786.879

North Kannadi0.2786.883

CEU0.27186.937

Brahui0.27186.952

Burusho0.27186.956

CEU0.27186.957

CEU0.27186.977

North Kannadi0.27186.995

GIH0.27187.018

CEU0.27187.042

CEU0.27187.066

CEU0.27187.07

Brahui0.27187.09

Bene Israel0.27187.094

Sakilli0.27187.141

CEU0.27187.2

CEU0.27187.24

North Kannadi0.27287.253

CEU0.27287.297

Burusho0.27287.307

CEU0.27287.327

GIH0.27287.353

CEU0.27287.355

Cochin Jews0.27287.381

CEU0.27287.384

CEU0.27287.5

CEU0.27287.535

CEU0.27387.594

Malayan0.27387.676

CEU0.27387.702

CEU0.27387.741

Burusho0.27387.806

CEU0.27387.846

Cambodians0.27487.932

North Kannadi0.27487.951

CEU0.27487.951

Burusho0.27488.03

CEU0.27488.047

CEU0.27488.081

CEU0.27488.089

CEU0.27488.101

CEU0.27488.179

CEU0.27488.19

North Kannadi0.27588.243

CEU0.27588.32

GIH0.27588.325

CEU0.27588.349

Brahui0.27588.393

CEU0.27588.402

CEU0.27588.457

Bene Israel0.27688.552

CEU0.27688.577

CEU0.27688.603

CEU0.27688.647

CEU0.27688.7

CEU0.27688.729

CEU0.27688.814

CEU0.27688.85

Brahui0.27688.855

CEU0.27788.923

GIH0.27788.99

Paniya0.27789.082

CEU0.27789.118

CEU0.27789.15

CEU0.27789.151

CEU0.27789.17

CEU0.27889.184

Cambodians0.27889.208

Cambodians0.27889.233

Cambodians0.27889.383

CEU0.27889.45

CEU0.27889.493

Cambodians0.27989.522

CEU0.27989.595

CEU0.27989.679

CEU0.27989.753

CEU0.27989.762

CEU0.27989.807

Cambodians0.2889.942

GIH0.2890.085

CEU0.28190.178

Brahui0.28190.364

Cambodians0.28290.543

Cambodians0.28290.559

Cambodians0.28290.77

Cambodians0.28390.898

CEU0.28390.956

CEU0.28491.316

CHD0.28992.952

Sakilli0.2993.103

Bene Israel0.2993.122

CHD0.29193.619

CHD0.29193.663

CHD0.29394.125

CHD0.29394.248

CHD0.29494.451

CHD0.29494.629

CHD0.29694.965

CHD0.29695.279

Yorubas0.29795.298

CHD0.29795.368

CHD0.29795.438

CHD0.29795.441

Yorubas0.29795.567

CHD0.29895.678

CHD0.29895.828

CHD0.29996.032

CHD0.29996.127

CHD0.396.349

CHD0.396.403

CHD0.396.443

CHD0.396.508

CHD0.396.523

CHD0.396.533

CHD0.30196.575

CHD0.30196.598

CHD0.30196.624

CHD0.30196.625

CHD0.30196.738

CHD0.30196.758

CHD0.30196.869

Yorubas0.30297.106

CHD0.30397.37

CHD0.30397.41

Yorubas0.30497.681

CHD0.30497.713

CHD0.30497.747

Yorubas0.30497.829

CHD0.30497.838

CHD0.30598.106

CHD0.30698.309

Yorubas0.30798.499

CHD0.30798.546

CHD0.30798.547

CHD0.30798.606

CHD0.30798.764

CHD0.30798.78

CHD0.30798.803

Yorubas0.30898.947

Yorubas0.30899.03

Yorubas0.30999.411

Yorubas0.30999.417

CHD0.30999.452

CHD0.3199.624

Yorubas0.311100

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