December 13, 2012

Daniel MacArthur's chromosome 10

In a previous post I confirmed Razib's observation on the South Asian ancestry of part of Dan MacArthur's chromosome 10. Razib has a new post up in which he argues that this type of ancestry is not of Romani origin. I figured it was my turn to continue the series of gratis ancestry analysis, with two goals in mind: (i) to let people know that if you put your genome online, you may find interesting things about it, and (ii) to indeed figure out what is going on with this interesting case of unexpected admixture.

I used Beagle/fastIBD with default parameters and with the HapMap recombination map to figure out the mean IBD sharing between Dan's chr10 and a number of different populations, including most of my available South Asian references. I also included YRI as an appropriate outgroup, as well as CEU30 and the 1000 Genomes British populations, given that Dr. MacArthur is Australian and has a Scottish surname, so it's a good bet that he has plenty of British-type ancestry.

The mean chr10 sharing is plotted below:



Now, it's cool that the top-2 matches are Argyll and Orkney, both of which are part of Scotland. But, what is interesting, is that North_Kannadi squeezes in ahead of CEU, with a very respectable mean of 1.4cM, and a number of other Indian populations are not far behind, while most of the ones from Pakistan are not. I'd say this looks consistent with an "Indian" origin of this type of ancestry.

A useful control is to repeat this experiment with a different chromosome, the similar-sized chr9 which lacks evidence for South Asian ancestry:

It is now visually clear that the difference between the British populations and the South Asian ones is greatly diminished. And, while the North Kannadi were near the top of the order for chr10, they are near the bottom for chr9, even lower than the YRI outgroup at the "noise left end" of the spectrum. Even the highest ranked South Asian population has about 1/3 estimated IBD sharing as the British ones. 

Moreover, whereas in chr10 the top-ranked South Asian populations were often from the south, in chr9 the situation is reversed, with most of the top-ranked ones being from Pakistan. Again, this suggests that there is no real South Asian admixture here, but just some low-level sharing with the (more West Eurasian) populations of the northern part of South Asia.

So, to make a long story short, it does look to me like an excellent suggestion that there is some type of peninsular or even south Indian ancestry in the chr10 in question.

15 comments:

MOCKBA said...

But the Romani thread may be more difficult to rule out, because, even though they generally have roots in NW India, their chromosomal variation is shaped in great part by drift. Drift could have randomlu enhanced South-Indianness of some stretches of the Romani chromosomes.

Also, 1500 or so years ago when the Romani trek West started, their ancestral populations might have possessed somewhat stronger affinity to South India than it does today.

Wouldn't it be better to address the question directly with the Romani datasets of Mendizabal et al.?

Annie Mouse said...

Wow, that is a a powerful distinction to be able to make for a segment, between north indian and south indian. I would assume Romany would paint as ANI not ASI.

So I guess he should be looking for a colonial indian connection, or something through his aboriginal lines.

Mark D said...

Dienekes, have you thought of turning this into a for-fee service? I know I'd be interested. The commercial products today are sorely lacking your in-deph analysis.

Razib said...

MOCKBA, the best evidence that the segment isn't romani *is that it presents as a south asian segment* romani admixture is highly likely to have presented with a more recombined component.

"or something through his aboriginal lines."

please check previous posts before speculation.

1) dienekes had australasian reference sets, they don't match

2) also, u don't know this, but dan's parents were born in the UK. he's not an australian of long standing by heritage, though he is by birth

AWood said...

I kind of got excited for a moment as I realized I was related to Daniel MacArthur on Chromosome 10 on my mother's side. Then I realized there were other cousin with overlap on that segment from UK, Ireland, Sweden, and Scotland leaving a S.Asian origin unlikely.

sf said...

Razib,

MOCKBA = Moscow capital city of Russia.

Annie Mouse said...

If you look at my text I am talking about the source of the South Asian. South Asian from the colonial period when Europeans had a lot of contact with India, or South Asian in his aboriginal lines (admixture or misallocation).

There was talk in the comments on the previous article on Dan that he has two potential lines of aboriginal heritage.

I suggest YOU read the comments.

rec1man said...

North Kannadi is a Dalit-Untouchable caste.

Very likely one his male ancestors was a british soldier in South India, who had an untouchable mistress

Amanda S said...

My understanding is that British soldiers serving in India in the eighteenth century were encouraged to take Indian wives and raise Christian families with them, hence the creation of the Anglo Indian community.

There is a strong history of people who are fair skinned enough to get away with it to hide their origins from their children and the community in general when they emigrated from India. There was a Who Do You Think You Are tv program on the British comedian Alastair McGowan which covered this history.

Another example is the singer Cliff Richard who spent much of his career denying his Indian roots and talking vaguely about his Portuguese ancestry. The Portuguese proceeded the British in South India so in many cases there is a mixture of Indian, Portuguese and British ancestry for Anglo Indians from South India.

apostateimpressions said...

"My understanding is that British soldiers serving in India in the eighteenth century were encouraged to take Indian wives and raise Christian families with them, hence the creation of the Anglo Indian community."

Amanda, can you point to any historical documentation for that? I have never heard of such a thing in the British Empire on any continent. I can believe it of Roman Catholic Latins in South America but I would be very surprised if the COE ever had such a policy or any such influence.

Amanda S said...

A brief summary on the history of the Anglo Indian community is given on the webpage http://www.movinghere.org.uk/galleries/roots/asian/angloindians/angloindians.htm. AI, you can do your own searches for further information. The policy was not COE inspired but was implemented by the East India Company.

apostateimpressions said...

Amanda, I have ever met only one indigenous Brit with any Indian ancestry, his great-grandmother. It is extremely unusual. I wouldnt pay too much notice to the BBC, they have their own political agenda to genocide the indigenous British nation ASAP through mass immigration. It is their great PC crusade. They cherry pick celebrities in their series "Who Do You Think You Are" who always turn out to have some supposedly unexpected Jewish, gypsie or other exotic ancestry to try and convince us that we are a mixed nation. It is state propaganda and not to be confused with reality. Britain and Ireland are islands in the far NW of Europe and all of the genetic analalysis confirms what we would expect, that we are among the least admixed of European nations, along with the Sardinians it seems in the SW. The British Empire was highly race conscious. The public schools were raised on Plato and Cicero. We were considered a high breed with a mission to civilize other countries, with law, democracy, capitalism etc. Certainly there was a small amount of mixing but it was strongly frowned upon (touch of the "tar brush") and exceptional -- nothing like what the British state propaganda is now trying to make out. People stigmatise the Indo-Aryan theory because it is blithely deemed old British propaganda; well we need to open our eyes to state propganda today.

hamarfox said...

AI, you're of course correct that, at least in the English-speaking world, the British bear the brunt of ancestral misrepresentation by the media and such articles as linked, and that this, naturally, is for political reasons (though I'm sure Germans, Dutch, and French get their fair share of misrepresentation in their own language's articles). But, yes, BBC reports and trash documentaries such as Channel 4's 'Are you English?', which capitalised on the guaranteed noisiness of DNAprint's AncestryByDNA calculator to essentially lie to people, and the viewer, about their likely ancestries, should be shunned in favour of published science and personal research.

As for Anglo-Indians, by the 19th century they were an unwanted class, shunned by Britons and Indians alike, so any 17th/18th century 'encouragement' of such mixtures would still be irrelevant to Cliff Richard's and McGowan's (and MacArthur's) more recent and, in McGowan's case, patently obvious admixture.

MacArthur probably does have Anglo-Indian heritage, however. Families with colonial ties are probably overrepresented in Australia compared with Britain, even if they returned home from India for a few generations. This would be best explained simply by the 'man-of-the-world' traditions of certain upper-middle class families whose attitudes took them around the empire a few times, over generations, before they finally settled down (often in Australia).

giorgoa said...

I m dod852 and i noticed that i have south asian values at about 9% at chromosomes 10 and 11.I m greek.Is there a way to determine if this romani admixture or not

Grendal said...

Drifting away from the South Asian connection,Orkney was historically settled by Norwegian vikings and so were parts of Argyll, though those who came round to Argyll may even have been born in Orkney rather than Norway. My wife is a McArthur from the Hebridean Island of Islay in Argyll and, when she was pregnant with our children, developed a large dark patch around each eye. "Oh," said the doctor, "that is a pregnancy mask. You have Scandanavian ancestry." Could the "Orkney" and "Argyll" readings on the chart overlap and confuse?
Also, many Scots claim "Romany" genes but I suspect most are descended from itinerant worker from Ireland and the Highland Clearances in Scotland who traveled similar routes to Romanies looking for work. Argyll is historically rural with poor agriculture and most of the "tinkers" (travellers) there now are gaelic speakers suggesting Irish or Scottish roots.
Are there any studies mapping Romany genes in Scotland. Given the use of "cant" words in their local dialects I suspect any Romaney travellers would be more likely to settle in Eastern Scotland, eg Edinburgh, Perthshire, Aberdeenshire and the Eastern Borders.