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Health

~33% of a Malagasy genotype, first pass

Gene ExpressionBy Razib KhanAugust 1, 2011 1:01 PM

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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.

PA_MA_K13.png

PopulationK1K2K3K4K5K6K7K8K9K10K11K12K13

Taiwan Aborigine0%0%0%2%0%0%5%23%69%0%0%0%0%

Hmong0%0%3%78%0%0%7%4%3%2%0%0%2%

Jinuo0%0%73%2%0%0%9%1%1%3%1%0%9%

Wa0%0%5%4%0%0%17%2%1%7%0%0%63%

Malagasy31%0%2%0%6%26%0%0%0%2%31%0%3%

Alorese0%83%0%0%1%2%0%3%2%0%0%8%0%

Javanese0%4%1%1%0%0%1%25%8%22%1%5%32%

Lamaholot0%61%0%1%1%3%1%13%7%2%0%8%2%

Mentawai0%0%0%0%0%0%0%98%0%1%0%0%0%

West Javanese0%4%1%1%0%2%0%26%9%22%1%4%31%

Toraja0%13%0%1%1%1%3%44%21%7%0%2%5%

Indian1%1%0%0%2%59%0%0%0%1%25%1%11%

Japanese1%1%2%3%0%1%87%1%1%1%0%0%1%

Kensiu Negrito0%0%0%0%0%0%1%1%1%2%0%90%4%

Utah, white1%0%0%0%2%20%0%0%0%0%74%0%3%

Luhya78%0%1%0%2%18%0%0%0%0%1%0%0%

Mamanwa0%1%0%0%83%0%0%9%3%0%0%2%0%

West Mindanao0%6%1%4%3%3%11%36%24%5%2%1%4%

West Luzon0%4%1%5%2%2%16%36%24%4%1%1%4%

Karen9%1%6%6%0%0%18%2%1%8%0%1%50%

Plang1%1%8%5%0%0%12%6%2%18%1%2%43%

HTin1%0%1%1%0%0%0%2%0%84%1%0%10%

Han Taiwan0%0%6%16%0%0%45%10%13%3%0%0%7%

PA_HGDP_GIH.png

PopulationK1K2K3K4K5K6K7K8K9K10

Mbuti Pygmies0%100%0%0%0%0%0%0%0%0%

Biaka Pygmies0%9%6%0%0%0%0%59%0%25%

French0%0%100%0%0%0%0%0%0%0%

Papuan1%0%0%99%0%0%0%0%0%0%

Cambodians75%0%0%2%10%5%8%0%1%0%

Japanese0%0%0%0%0%0%98%0%1%0%

Han28%0%0%0%0%1%70%0%1%0%

Mandenka0%0%0%0%0%0%0%0%0%100%

Yakut0%0%3%0%0%0%1%0%95%0%

San0%0%0%0%0%0%0%100%0%0%

Bant S Africa0%4%0%0%0%0%0%23%0%73%

Tujia34%0%0%0%0%3%63%0%0%0%

Yizu12%1%0%1%0%9%78%0%0%0%

Miaozu48%0%0%0%0%1%51%0%0%0%

Hezhen1%0%0%0%0%1%69%0%29%0%

Xibo4%0%2%0%1%2%73%0%18%0%

Dai88%0%0%0%0%2%10%0%0%0%

Lahu11%0%0%0%0%82%7%0%0%0%

She49%0%0%0%0%0%51%0%0%0%

Naxi4%0%0%1%0%9%85%0%1%0%

Tu8%0%4%0%3%3%74%0%7%0%

Bantu Kenya0%5%2%0%1%0%0%7%0%84%

Malagasy5%1%37%0%11%3%0%4%4%36%

Indian0%0%0%0%99%0%0%0%0%0%

PA_AFRO_K10.png

PCA3by1.png

PCA4by1.png

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.

PopulationK1K2K3K4K5K6K7K8K9K10

Hadza16%0%76%1%5%1%1%1%0%0%

Yemen Jews0%0%0%84%0%0%0%0%0%15%

Ethiopian19%0%4%52%25%0%1%0%0%0%

Sandawe6%0%1%2%90%1%0%1%0%0%

Biaka Pygmies0%0%0%0%0%100%0%0%0%0%

Mbuti Pygmies0%0%0%0%0%0%100%0%0%0%

French0%0%0%20%0%0%0%0%1%80%

Cambodians0%100%0%0%0%0%0%0%0%0%

Mandenka98%0%0%0%0%1%0%0%0%0%

Yoruba96%0%0%0%0%4%0%0%0%0%

Bant S Africa72%0%0%0%0%9%1%17%0%0%

Bantu Kenya77%0%1%2%12%5%2%0%0%0%

Malagasy32%13%0%3%5%4%1%0%7%36%

Luhya77%0%2%1%12%5%3%0%0%0%

Indian0%1%0%0%0%0%0%0%99%0%

San8%2%0%1%0%1%0%79%3%6%

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