Autosomal African admixture in Yemeni populations

[beyoku]

Approximately 30% of mtDNA lineages in South Arabian samples are African L haplotypes, whose origin has usually been attributed to migration and assimilation of African females into the Arabian population over approximately the last 2,500 years. Few In contrast, few Y chromosome lineages of clear recent sub-Saharan African origin have been found in Southern Arabian populations.

This bias in maternal and paternal lineages is in accord with historical accounts of the female bias in the Middle Eastern slave trade. In order to evaluate autosomal African ancestry, we collected high-resolution SNP genotype data from a geographically representative set of 62 Yemenis selected from a collection of 552 samples acquired in the Spring of 2007. The ancestry of chromosomal segments in the Yemeni population was estimated using a haplotype-based local ancestry estimation method, HAPMIX. The HAPMIX method is based on a two way admixture model that requires two phased reference populations; we used the HapMap Yoruba in Ibadan, Nigeria (YRI), Luhya in Webuye, Kenya (LWK), Maasai in Kinyawa, Kenya (MKK), and CEPH US residents with ancestry from northern and western Europe (CEU) samples. The three African reference populations include two Bantu-speaking groups (YRI and LWK) and one Nilotic-speaking group (MKK).

We estimated local ancestry in the Yemeni sample with all three European-African reference population combinations (CEU-YRI, CEU-LWK, CEU-MKK). The correlations among African ancestry calculated using all three reference population combinations are high (r > 0.98 in all pairwise correlations). Furthermore, there is no significant difference between the average proportion of African ancestry in Yemenis calculated using either of the two Bantu-speaking reference populations: CEU-YRI (mean 0.062, sd 0.044) and CEU-LWK (mean 0.076, sd 0.049) (p=0.13, two-tailed Welch two sample t-test). However, the average African ancestry calculated using the Maasai reference population (CEU-MKK, mean 0.148, sd 0.060) is significantly greater from that calculated using either the Yoruba or Luhya reference populations (p < 0.0001 in both comparison, two-tailed Welch two sample t-test). These data suggest that the source population for the African ancestry of the Yemeni population is more similar to the contemporary Maasai population than either the Luhya or Yoruba.

Abstract

Geniuses..

I would like to see every study that samples non Africans to included a homogeneous Horner reference sample.

[Bandar Qasim]

So they are about 15% African when Maasai are used as references? Imagine if they used proper Cushites..

It's strange that Yemenis got 6% Africa with the Yoruba samples. That's even higher than what most Habesha got on 23andMe with the Yoruba samples or am I reading this wrong?

[Lemba]

So they are about 15% African when Maasai are used as references? Imagine if they used proper Cushites..

It's strange that Yemenis got 6% Africa with the Yoruba samples. That's even higher than what most Habesha got on 23andMe with the Yoruba samples or am I reading this wrong?

Perhaps some of these Yemenis are 50/50 between "Cushites" and "Bantu Kenyans" hence why they can get as high as 6% when compared to Yoruba's and other west Africans. The cushite component is probably older and pre-dates slavery, more to do with Ethiopians coming into the Arabian peninsula, the component that links them with west africans could also be from an old migraiton or perhaps from slavery, because Kenya was a hotspot (and there are kenyans bantus there)

[beyoku]

So they are about 15% African when Maasai are used as references? Imagine if they used proper Cushites..

It's strange that Yemenis got 6% Africa with the Yoruba samples. That's even higher than what most Habesha got on 23andMe with the Yoruba samples or am I reading this wrong?

Exactly, Ethioboy please pay attention to the findings. How do you think your ancestry will be affected if they tested your ancestry with a reference of "proper Cushites"....dont give us no BS about 'overlapping Proto-Eurasian clusters' either LOL.

Any Idea who would best represent "proper Cushites"?

I am pretty sure while Yemenis are pretty homogeneous (as Arabs) there are even more Homogeneous groups that exist in the Horn of Africa or below it. E-M2 is found in greater frequency in the Middle East and North Africa than it is in Ethiopia.

This study is from the ASHG 2010 Abstracts......boy o boy I wish i could get a hold of that E-M2 Cruciani 2008 Abstract that gives an East Africa origin of E-M2....sigh...who knows what populations were sampled.

Maybe we can create Hypothesis in a different thread? Any takers?

[Lol_Race]

So they are about 15% African when Maasai are used as references? Imagine if they used proper Cushites..

It's strange that Yemenis got 6% Africa with the Yoruba samples. That's even higher than what most Habesha got on 23andMe with the Yoruba samples or am I reading this wrong?

I don't think you can equate the "African" calculated in a proper study with the "African" in the Ancestry Painting. The Ancestry Painting is probably the least accurate measure of African ancestry there is.

The African mtDNA of Yemenis is split; some of it is related to Northeast African mtDNA, while some of it is related to Southeast African mtDNA. The latter is believed to have entered Yemen during the slave trade. To compare, Bedouins were 3.2% "Niger-Kordofanian", while the Beta Israel were 3.0% "Niger-Kordofanian" in the unsupervised global runs from last year's study by Tishkoff et al. No Yemenis were included in those STRUCTURE runs, except for the Yemenite Jews, who are not representative of the rest of the Yemeni population.

I'm glad they decided to include the Maasai.

[Bandar Qasim]

Any Idea who would best represent "proper Cushites"?

That's a tough one, I would say certain Oromos and Somalis. Iraqw had the highest amount of Cushitic in the Tishkoff study but formed their own sub-clusters at K=7 and beyond while the Oromos didn't (Eastern Africa run).

I don't think you can equate the "African" calculated in a proper study with the "African" in the Ancestry Painting. The Ancestry Painting is probably the least accurate measure of African ancestry there is.

The methodology seems fairly similar, the 6.2% Yoruba mean for Yemenis in this study could be explained by their contacts with the Swahili empire whereas Ethiopians didn't.

[Lol_Race]

The methodology seems fairly similar, the 6.2% Yoruba mean for Yemenis in this study could be explained by their contacts with the Swahili empire whereas Ethiopians didn't.

I don't know about that. I agree that Yemenis probably have more Bantu ancestry than Ethiopians, but I don't believe that the African percentage from this study (using the Niger-Kordofanians as a reference), is equivalent to the "African" in the Ancestry Painting. Different studies using the Luhya Bantu Kenyans, who are relatively similar to the Yoruba, have shown that Ethiopians do have some affinities with the clusters created by the Bantus. This poor reference obviously leads to the "African" ancestry of Ethiopians being underestimated, but I don't know about the results of any study approaching the absurdity of the Ancestry Painting.

Any Idea who would best represent "proper Cushites"?

I don't think there's any way to select one proper "Horner" reference. If we want to clean up this mess (for Horners as well as neighbouring groups), a study sampling several East African, and other neighbouring groups, will be essential.

[ethioboy]

Abstract

Geniuses..

I would like to see every study that samples non Africans to included a homogeneous Horner reference sample.

In the behar study both horners and a variety of different middle easterners and europeans were used as well as yoruba, biaka pygmies, san, and mandenkas, they had as much sub saharan african admix as the egyptians. And yemeni jews had almost no admix

---------- Post added 2010-09-09 at 01:52 ----------

Exactly, Ethioboy please pay attention to the findings. How do you think your ancestry will be affected if they tested your ancestry with a reference of "proper Cushites"....dont give us no BS about 'overlapping Proto-Eurasian clusters' either LOL.

Any Idea who would best represent "proper Cushites"?

I am pretty sure while Yemenis are pretty homogeneous (as Arabs) there are even more Homogeneous groups that exist in the Horn of Africa or below it. E-M2 is found in greater frequency in the Middle East and North Africa than it is in Ethiopia.

This study is from the ASHG 2010 Abstracts......boy o boy I wish i could get a hold of that E-M2 Cruciani 2008 Abstract that gives an East Africa origin of E-M2....sigh...who knows what populations were sampled.

Maybe we can create Hypothesis in a different thread? Any takers?

Dude an ample amount of horners were used in the behar study and they still came out majority eurasian. No different than saudis or egyptians. Just because they are darker doesnt mean they have more african admix. I hope you arent forgetting that mutations happen as a result of environmental factors as well.

Same reason why we can get mistaken for each other because we come from the around the red sea area.




BTW: Even the tishkoff study which everyone seems to take as the gospel when it comes to african genetics shows the Yemeni population sampled to be just like their bedouin cousins. No different and not any more admix than 12%

[Ezana]

Very interesting study; thanks for sharing.

[Doctoris Scientia]

In the behar study both horners and a variety of different middle easterners and europeans were used as well as yoruba, biaka pygmies, san, and mandenkas, they had as much sub saharan african admix as the egyptians. And yemeni jews had almost no admix

---------- Post added 2010-09-09 at 01:52 ----------


Dude an ample amount of horners were used in the behar study and they still came out majority eurasian. No different than saudis or egyptians. Just because they are darker doesnt mean they have more african admix. I hope you arent forgetting that mutations happen as a result of environmental factors as well.

Same reason why we can get mistaken for each other because we come from the around the red sea area.




BTW: Even the tishkoff study which everyone seems to take as the gospel when it comes to african genetics shows the Yemeni population sampled to be just like their bedouin cousins. No different and not any more admix than 12%

Horners weren't used as reference groups in the Behar study... African reference groups were taken from Yoruban, Biaka, and Khoisan populations. Middle Eastern populations were only sampled for the unsupervized Global Structure, in regard to Tishkoff 2009.