September 18, 2013

Genetic structure of Kuwaiti population

PLoS ONE 8(9): e74913. doi:10.1371/journal.pone.0074913

Genetic Substructure of Kuwaiti Population Reveals Migration History

Osama Alsmadi et al.

The State of Kuwait is characterized by settlers from Saudi Arabia, Iran, and other regions of the Arabian Peninsula. The settlements and subsequent admixtures have shaped the genetics of Kuwait. High prevalence of recessive disorders and metabolic syndromes (that increase risk of diabetes) is seen in the peninsula. Understanding the genetic structure of its population will aid studies designed to decipher the underlying causes of these disorders. In this study, we analyzed 572,366 SNP markers from 273 Kuwaiti natives genotyped using the illumina HumanOmniExpress BeadChip. Model-based clustering identified three genetic subgroups with different levels of admixture. A high level of concordance (Mantel test, p=0.0001 for 9999 repeats) was observed between the derived genetic clusters and the surname-based ancestries. Use of Human Genome Diversity Project (HGDP) data to understand admixtures in each group reveals the following: the first group (Kuwait P) is largely of West Asian ancestry, representing Persians with European admixture; the second group (Kuwait S) is predominantly of city-dwelling Saudi Arabian tribe ancestry, and the third group (Kuwait B) includes most of the tent-dwelling Bedouin surnames and is characterized by the presence of 17% African ancestry. Identity by Descent and Homozygosity analyses find Kuwait’s population to be heterogeneous (placed between populations that have large amount of ROH and the ones with low ROH) with Kuwait S as highly endogamous, and Kuwait B as diverse. Population differentiation FST estimates place Kuwait P near Asian populations, Kuwait S near Negev Bedouin tribes, and Kuwait B near the Mozabite population. FST distances between the groups are in the range of 0.005 to 0.008; distances of this magnitude are known to cause false positives in disease association studies. Results of analysis for genetic features such as linkage disequilibrium decay patterns conform to Kuwait’s geographical location at the nexus of Africa, Europe, and Asia.

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9 comments:

Umi said...

The variety in African admixture in the 3rd group suggests recent admixture.. Probably from Swahili slaves during the Zanj revolt. Their African admixture is unlikely caused by prehistoric events.

The 2nd group of Kuwaitis seem to be mostly pure Arabians.

The distinct structures in such a small country is rather remarkable.

Annie Mouse said...

I must say I dont know a lot obout Kuwaiti history. But usually the major cities contain the most recent arrivals, with the original population are concentrated in remote villages and traditional folk (including nomads). Nomads of course travel so they tend to be a bit more diverse.

Kuwait is coastal, and lies on Africas very threshold, hard to imagine it would be devoid of African. I would expect immigrants from deeper into arabia to contain less African.

Umi said...

@Annie,

The Yemenite Jews, who historically lived much much closer to Africa and are essentially local pre-Islamic Arabian converts, seem to have almost half the amount of African ancestry as that 3rd group of Kuwaitis. Yemenites Jews can be used as a benchmark of the genetic profile of pre-Islamic Arabians. So, the elevated African ancestry in certain Kuwaits is almost certainly caused by the recent Swahili slave trade and not from prehistoric dispersals of Africans into the Middle East.

Kristiina said...

Why should African haplogroups and in particular MtDNA L clades always come from the slaves? L has been found in Iberia and Near East in ancient specimens, so these Afro-Eurasian contacts are not a recent development, and I am not so sure that it was slaves who had so many offspring to leave a strong genetic mark. If so, they were surely very beautiful and intelligent women.

Umi said...

@Kristiina,

If you do a detailed genetic analysis on Gulf Arabians you will find out that a big portion, if not most of their African ancestry does not come from the nearest African region (the Horn of Africa/Ethiopia) but from way further inland as in Central Africa/Bantu related admixture.

This can only be explained by the Swahili slave trade.

Also, many haplogroup studies have already detected non-trivial levels of E1b1a-M2 in the Gulf Arab region, while this is completely absent in native Horn Africans/Ethiopians and relic Jewish populations of Arabia.. Again, clearly pointing to Swahili/Bantu slave trade related admixture.

Kurti said...

Though Arabs and Persians make up the majority, Kuwaitis are made up of more populations. You got in Kuwait allot of Balochi, Iraqis, Kurds, Palestinians, and some Indians too.


Kristiina said...

In the paper I have printed out, I have the following frequencies (not exhaustive and I added UAE and Qatar frequencies in it):

L3b Palestinians 0.01; Jordanians 0.03; Yemenites 0.01; Qatar 1.9; UAE 2.2; Egyptians 0.01; Sudanians 0.02; Kenians 0.06
L3d Palestinians 0.03; Jordanians 0.01; Arabians 0.01; Yemenites 0.04; Qatar 4.8; UAE 3.3; Sudanians 0.01;
L3e1 Palestinians 0.01; Egyptians 0.01; Kenians 0.05; L3e all Qatar 1.9; UAE 3.3;
L3e2 Syrians 0.01, Palestinians 0.01; Kenians 0.02
L3e3 Palestinians 0.02, Yemenites 0.02; Kenians 0.03
L3e5 Yemenites 0.01 (not found in other populations)
L3f Iraquies 0.02;Syrians 0.01; Jordanians 0.01; Arabians 0.01; Yemenites 0.02; Sudanians 0.07; Ethiopians 0.05; Kenians 0.08
L3h Palestinians 0.01, Arabians 0.02; Sudanians 0.03; Ethiopians 0.01; Kenians 0.04
L3i Arabians 0.01; Yemenites 0.01; Ethiopians 0.01
L3x Jordanians 0.01; Egyptians 0.02; Ethiopians 0.04; Kenians 0.01
L4g Syrians 0.01, Palestinians 0.01; Egyptians 0.01; Sudanians 0.03; Ethiopians 0.03; Kenians 0.14
L2a/L2c Jordanians 0.01; Yemenites 0.01; Egyptians 0.02; Sudanians 0.08; Ethiopians 0.01; Kenians 0.03
L2a1 Iraquies 0.04;Syrians 0.02; Palestinians 0.03 Jordanians 0.01; Yemenites 0.01; UAE 3.3; Egyptians 0.02; Sudanians 0.07; Ethiopians 0.05; Kenians 0.03
L2a1a Palestinians 0.01, Arabians 0.01; Yemenites 0.03
L2a1b3 Palestinians 0.01, Bedouins 0.03; Egyptians 0.01; Sudanians 0.01; Ethiopians 0.03; Kenians 0.02
L2a2 Arabians 0.01; Egyptians 0.01; Sudanians 0.03; Ethiopians 0.02
L2c2 Jordanians 0.01; Arabians 0.01 (not found in other populations)
L6 Yemenites 0.07; Ethiopians 0.01
L5a1 Egyptians 0.02; Sudanians 0.01; Ethiopians 0.01; Kenians 0.01
L5a1 Egyptians 0.02; Sudanians 0.03; Ethiopians 0.01; Kenians 0.01
L1b Syrians 0.01; Jordanians 0.01; Egyptians 0.01; Sudanians 0.04; Ethiopians 0.03; Kenians 0.02
L1c Iraquies 0.02; Yemenites 0.01; UAE 1.1; Sudanians 0.01; Kenians 0.02
L0a1 Syrians 0.01; Palestinians 0.01; Jordanians 0.01; Bedouins 0.03; Yemenites 0.02; Egyptians 0.05; Sudanians 0.09; Ethiopians 0.04; Kenians 0.05; L0 all Qatar 4.8
L0a2 Iraquies 0.01; Yemenites 0.04; Sudanians 0.01; Ethiopians 0.01; Kenians 0.05
L0k Yemenites 0.01 (not found in other populations)

http://www.biomedcentral.com/1471-2148/8/45

Many haplogroups seem to have the highest frequencies in Ethiopia or Sudan. In my eyes, it seems that higher frequencies in Qatar and UAE of L3b and L1c, perhaps also L3e, may be a result of this slave trade, but I would not say the same for Qatar and UAE haplogroups L3d, L2a1, L1b and L0. I would say that L clades have come to Near East along different routes and at different times.

andrew said...

It is worth noting that Kuwait has been a key node of Indian Ocean maritime routes since at least 3000 BCE.

Yemen has been an important source of mariners in much of that time period on those maritime routes, but rarely been a destination for those trade routes in an of itself. So, using Yemen as a benchmark of ancient admixture isn't necessarily appropriate. Linkage disequalibrium studies of the autosomes of people who have those mtDNA haplogroups might be more useful in discriminating between various hypothetical sources of the current population genetic mix.

Umi said...

@Kristiina,

Many L sub-clades have quite confusing origins. So, it is best not to assume based on a single letter sub-clades that it comes from region X or Y in Africa. Especially with clades like L3f and L2a, which are relatively frequent all over Africa. Deeper sub-clade analyses show their origins with far less ambiguity.

In order to ascertain whether an L clade in the Middle East is of 'Ancient'/'Prehistoric' or 'Medieval' (Swahili slave trade) origin, it's best to look up the deep sub-clade in this L database spreadsheet:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2427203/bin/mmc1.xls

Generally, if the L clade is common in Central Africa or the Swahili countries (Tanzania, Kenya, Mozambique etc.), it obviously doesn't have a deep history in the Middle East. However, if it is more restricted to the Horn African countries or Sudan or Egypt it is more likely that it has been around in the Arabia/Near East for a long time.

Examples of 'ancient' L clades in the Middle East: L0f2, L0a1d, L0a1c, L1b1a2, L5a1, L2a1d, most L4, L6, L3i, L3k, L3h, L3x types.

Examples of recently introduced L clades to the Middle East: various L0's and L1's (except the above mentioned), certain L2's - especially L2a1a & L2a1b, of the L3's mainly L3e especially and some L3b/d's and of L3f L3f1b looks like a slave trade marker in the Middle East.

The second half of haplogroups are typically completely absent in Christian Ethiopian groups and Jewish populations of Arabia. Hence, you can conclude from their prevalence in Muslim Arabs in the Middle East that it was facilitated by the slave trade along the Swahili coast.