~33% of a Malagasy genotype, first pass

By Razib Khan | August 1, 2011 4:01 am

Last week I begged for a Malagasy genotype. I didn’t quite get that, but I got the second best thing: a part Malagasy-genotype. I decided to take it for a spin.

But first some preliminaries. Here’s what we know about this individual (or what this individual knows):

- 25% French (paternal grandfather)
– 18.75% West African? 6.25% French? (paternal grandmother French Antilles)
– 19% Indian Muslim Bohras from Bombay + 6.25% Malagas, Sakalava tribe, royal family of Mahajanga (maternal grand -father)
– 25% Malagasy (Sakalava, maternal grandmother mtDNA haplogroup M23)

This is a very mixed individual in terms of ancestry. As for the Malagasy people, we know both a lot and a little about them. They’re a hybrid population, more or less, of Austronesians with a very close connection to the to the Dayaks of southern Borneo. I have hypothesized that these Austronesians were part of a circum-Indian ocean trading network which was marginalized by the rise of Islam in the second half of the first millennium. Such an early date would explain why the Malagasy seem to have been only lightly touched by Indic cultural influences, let alone Islamic ones. There is also the African component to their ancestry, which is more prominent in the lowland populations to the west of the island of Madagascar. The Sakalava are a somewhat more African group (as opposed to the Merina of the eastern highlands, who are more Austronesian).

Below are some results from ADMIXTURE and PCA generated with EIGENSOFT. Most of the PCA plots were not too useful, because I didn’t fine-tune the populations ahead of time too much (this is a first pass), so I didn’t post them. The ADMIXTURE runs are those which seem highly informative to me. There were three data sets into which I merged the part-Malagasy individual:

– #1, A Southeast Asian focused one, using mostly the Pan-Asian Consortium populations

– #2, An Asian focused data set which used the HGDP

– #3, An African focused data set which used the Henn et al. populations as well as some HGDP ones


#1 is plagued by a thin marker set. The Southeast Asian groups had ~56,000 markers, but the part-Malagasy individual only shared ~22,000 with them. Still, I made a go of it. I probably overcompensated in #2, as I used ~590,000 markers (the HGDP has a pretty good overlap with the 23andMe raw data). Finally, #3 had ~180,000 markers, which I feel to be very sufficient for this sort of exploratory endeavor.

Population K1 K2 K3 K4 K5 K6 K7 K8 K9 K10 K11 K12 K13
Taiwan Aborigine 0% 0% 0% 2% 0% 0% 5% 23% 69% 0% 0% 0% 0%
Hmong 0% 0% 3% 78% 0% 0% 7% 4% 3% 2% 0% 0% 2%
Jinuo 0% 0% 73% 2% 0% 0% 9% 1% 1% 3% 1% 0% 9%
Wa 0% 0% 5% 4% 0% 0% 17% 2% 1% 7% 0% 0% 63%
Malagasy 31% 0% 2% 0% 6% 26% 0% 0% 0% 2% 31% 0% 3%
Alorese 0% 83% 0% 0% 1% 2% 0% 3% 2% 0% 0% 8% 0%
Javanese 0% 4% 1% 1% 0% 0% 1% 25% 8% 22% 1% 5% 32%
Lamaholot 0% 61% 0% 1% 1% 3% 1% 13% 7% 2% 0% 8% 2%
Mentawai 0% 0% 0% 0% 0% 0% 0% 98% 0% 1% 0% 0% 0%
West Javanese 0% 4% 1% 1% 0% 2% 0% 26% 9% 22% 1% 4% 31%
Toraja 0% 13% 0% 1% 1% 1% 3% 44% 21% 7% 0% 2% 5%
Indian 1% 1% 0% 0% 2% 59% 0% 0% 0% 1% 25% 1% 11%
Japanese 1% 1% 2% 3% 0% 1% 87% 1% 1% 1% 0% 0% 1%
Kensiu Negrito 0% 0% 0% 0% 0% 0% 1% 1% 1% 2% 0% 90% 4%
Utah, white 1% 0% 0% 0% 2% 20% 0% 0% 0% 0% 74% 0% 3%
Luhya 78% 0% 1% 0% 2% 18% 0% 0% 0% 0% 1% 0% 0%
Mamanwa 0% 1% 0% 0% 83% 0% 0% 9% 3% 0% 0% 2% 0%
West Mindanao 0% 6% 1% 4% 3% 3% 11% 36% 24% 5% 2% 1% 4%
West Luzon 0% 4% 1% 5% 2% 2% 16% 36% 24% 4% 1% 1% 4%
Karen 9% 1% 6% 6% 0% 0% 18% 2% 1% 8% 0% 1% 50%
Plang 1% 1% 8% 5% 0% 0% 12% 6% 2% 18% 1% 2% 43%
HTin 1% 0% 1% 1% 0% 0% 0% 2% 0% 84% 1% 0% 10%
Han Taiwan 0% 0% 6% 16% 0% 0% 45% 10% 13% 3% 0% 0% 7%

Population K1 K2 K3 K4 K5 K6 K7 K8 K9 K10
Mbuti Pygmies 0% 100% 0% 0% 0% 0% 0% 0% 0% 0%
Biaka Pygmies 0% 9% 6% 0% 0% 0% 0% 59% 0% 25%
French 0% 0% 100% 0% 0% 0% 0% 0% 0% 0%
Papuan 1% 0% 0% 99% 0% 0% 0% 0% 0% 0%
Cambodians 75% 0% 0% 2% 10% 5% 8% 0% 1% 0%
Japanese 0% 0% 0% 0% 0% 0% 98% 0% 1% 0%
Han 28% 0% 0% 0% 0% 1% 70% 0% 1% 0%
Mandenka 0% 0% 0% 0% 0% 0% 0% 0% 0% 100%
Yakut 0% 0% 3% 0% 0% 0% 1% 0% 95% 0%
San 0% 0% 0% 0% 0% 0% 0% 100% 0% 0%
Bant S Africa 0% 4% 0% 0% 0% 0% 0% 23% 0% 73%
Tujia 34% 0% 0% 0% 0% 3% 63% 0% 0% 0%
Yizu 12% 1% 0% 1% 0% 9% 78% 0% 0% 0%
Miaozu 48% 0% 0% 0% 0% 1% 51% 0% 0% 0%
Hezhen 1% 0% 0% 0% 0% 1% 69% 0% 29% 0%
Xibo 4% 0% 2% 0% 1% 2% 73% 0% 18% 0%
Dai 88% 0% 0% 0% 0% 2% 10% 0% 0% 0%
Lahu 11% 0% 0% 0% 0% 82% 7% 0% 0% 0%
She 49% 0% 0% 0% 0% 0% 51% 0% 0% 0%
Naxi 4% 0% 0% 1% 0% 9% 85% 0% 1% 0%
Tu 8% 0% 4% 0% 3% 3% 74% 0% 7% 0%
Bantu Kenya 0% 5% 2% 0% 1% 0% 0% 7% 0% 84%
Malagasy 5% 1% 37% 0% 11% 3% 0% 4% 4% 36%
Indian 0% 0% 0% 0% 99% 0% 0% 0% 0% 0%

Population K1 K2 K3 K4 K5 K6 K7 K8 K9 K10
Hadza 16% 0% 76% 1% 5% 1% 1% 1% 0% 0%
Yemen Jews 0% 0% 0% 84% 0% 0% 0% 0% 0% 15%
Ethiopian 19% 0% 4% 52% 25% 0% 1% 0% 0% 0%
Sandawe 6% 0% 1% 2% 90% 1% 0% 1% 0% 0%
Biaka Pygmies 0% 0% 0% 0% 0% 100% 0% 0% 0% 0%
Mbuti Pygmies 0% 0% 0% 0% 0% 0% 100% 0% 0% 0%
French 0% 0% 0% 20% 0% 0% 0% 0% 1% 80%
Cambodians 0% 100% 0% 0% 0% 0% 0% 0% 0% 0%
Mandenka 98% 0% 0% 0% 0% 1% 0% 0% 0% 0%
Yoruba 96% 0% 0% 0% 0% 4% 0% 0% 0% 0%
Bant S Africa 72% 0% 0% 0% 0% 9% 1% 17% 0% 0%
Bantu Kenya 77% 0% 1% 2% 12% 5% 2% 0% 0% 0%
Malagasy 32% 13% 0% 3% 5% 4% 1% 0% 7% 36%
Luhya 77% 0% 2% 1% 12% 5% 3% 0% 0% 0%
Indian 0% 1% 0% 0% 0% 0% 0% 0% 99% 0%
San 8% 2% 0% 1% 0% 1% 0% 79% 3% 6%

I don’t really trust the proportions for the Pan-Asian focused data set. But I figured I should report them. No idea why the Malagasy shows so much Yakut. Could be an artifact from the hybridization? As for the rest, it seems that the African ancestry of this individual isn’t too atypical for an East African Bantu.

  • Charles Nydorf

    The idea that a Yakut signal might come from hybridization is interesting to me. I’m Ashkenazic and consistently show about 1% North Asian at Dodecad. The particular kind of North Asian is Yakut.

  • Daniel

    I somehow missed your first request, I’ve got two Malagasy friends who I’m sure would love to help out. I’ve emailed them, I’ll let you know.

  • http://washparkprophet.blogspot.com ohwilleke

    Talk about just in time results. Half the time it seems like you can’t even get simple blood test for a flu infection turned around that fast.

  • Paul Ó Duḃṫaiġ

    Razib,

    I can provide you with a Filipina 23andme sample (from my “Other Half”, 1/8 Spanish), might help with regards having a wider austronesian speaker sample — especially if Daniel delivers on his two Malagasy friends.

    -Paul

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    paul, that would be nice!

  • pconroy

    Razib,

    My father has a 3/4 French 1/4 Malagasy relative, I could reach out to if you are interested??

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    paul, yeah, i would be interested! this individual is a touch mixed, making me more cautious about taking anything away (especially in all the PCAs).

  • Garvan

    The Pan-Asian database includes 12 Dayk. I don’t see them in the first table, so I wondered if you combined them with other populations, or had some reason to omit them?

  • Lank

    Interesting stuff!

  • not too smart

    I am adopted and have been asked all my life”what are You” Human is not enough Just went to take tests to find dna results and can only take maternal want to know paternal too is there any test that would do that for a female who knows nothing about father? know this is alittle out of field for this blog but I trust your opinions and would value your suggestions

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Gene Expression

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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