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Monday, May 7, 2012

Eurogenes' GEDmatch ADMIXTURE ancestry test guide


Update 27/11/2013: I've made the new K13 the default Eurogenes admix test at GEDmatch. It seems to hit the spot for most people. See here.

Update 07/10/2013: An upgraded version of the popular EUtest is now available at GEDmatch. See here.

Update 11/10/2012: The Jtest and EUtest are now available at GEDmatch, and these have superseded most of my tests offered there, except those that include Amerindian references samples. Also, the Jtest and EUtest come with a variety of "Oracle" ethnic matching tools. For more info see here.

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First of all, below is a list of the geographic locations or ethnic groups in which the clusters from the Eurogenes' Gedmatch tests peak. I can't post any population averages or maps at present, but will do so as soon as possible. I really need more people to fill in their ancestry details at Gedmatch when they run these tests, otherwise producing more detailed guides won't be possible.


K9
South Asian - South India
Caucasus - Georgia
Southwest Asian - Bedouin
North Amerindian + Arctic - Northwest America
Siberian - Central Siberia
Mediterranean - Sardinia
East Asian - Eastern China
West African - Nigeria
North European - Lithuania


K10
South Asian - South India
Caucasus - Georgia
Southwest Asian - Bedouin
North Amerindian + Arctic - Northwest America
Siberian - Central Siberia
Mediterranean - Sardinia
East Asian - Eastern China
West African - Nigeria
East European - Belarus
North Atlantic - Ireland


K11
South Asian - South India
Caucasus - Georgia
Southwest Asian - Bedouin
North Amerindian + Arctic - Northwest America
Siberian - Central Siberia
Mediterranean - Sardinia
East Asian - Eastern China
West African - Nigeria
Volga-Ural - Western Volga
South Baltic - Lithuania
North Atlantic - Ireland


K12
South Asian - South India
Caucasus - Georgia
Southwest Asian - Bedouin
North Amerindian + Arctic - Northwest America
Siberian - Central Siberia
Mediterranean - Sardinia
East Asian - Eastern China
West African - Nigeria
Volga-Ural - Western Volga
South Baltic - Lithuania
Western European - Western Ireland
North Sea - Southern Norway


K12b

Western European - Cornwall
Siberian - Central Siberia
East African - Masaai
West Central Asian - Balochistan
South Asian - South India
West African - Nigeria
Caucasus - Georgia
Finnish - Eastern Finland
Mediterranean - Sardinia
Southwest Asian - Bedouin
North European - Lithuania
East Asian - Eastern China


K13

North European - Lithuania
West African - Nigeria
Mediterranean - Sardinia
Northeast African - Ethiopia Oromo
North Eurasian - Central Siberia
South Asian - South India
Southwest Asian - Bedouin
Pygmy - Mbuti Pygmy
Caucasus - Georgia
East Siberian - Koryaks
East Asian - Eastern China
Amerindian - South America
West Central Asian - Balochistan


Hunter-Gatherer vs. Farmer (Gedmatch edition)

Anatolian Farmer - Western Caucasus
Baltic Hunter Gatherer - Lithuania
Middle Eastern Herder - Bedouin
East Asian Farmer - Eastern China
South American Hunter Gatherer - South America
South Asian Hunter Gatherer - South India
North Eurasian Hunter Gatherer - Central Siberia
East African Pastoralist - Masaai
Oceanian Hunter Gatherer - Papua New Guinea
Mediterranean Farmer - Sardinia
Pygmy Hunter Gatherer - Mbuti Pygmy
Bantu Farmer - West Africa

Now, the K12 test is the most useful analysis in the context of my project, which focuses on the genetic substructures of groups from north of the Alps and Carpathians. Therefore, most of this post will be dedicated to that test, and especially to the European and West Eurasian clusters it features. Indeed, below is an MDS plot showing synthetic samples made from the allele frequencies of the seven West Eurasian clusters from the K12.




It's pretty easy to see what's going on there. The four North European clusters are positioned close together on the left of the plot. However, the Western European and North Sea clusters both show significant affinity to the Mediterranean cluster, by pulling towards its direction.

Note also that the Mediterranean and Caucasus clusters are placed about half way between the South Baltic and Southwest Asian clusters across dimension one. This is in line with geography, because the Mediterranean Basin and Caucasus Mountains are located between Northern Europe and the Middle East.

However, the Mediterranean and Caucasus clusters are sharply differentiated across dimension two. This also fits geography, because there's obviously a huge distance between the populations of the Western Mediterranean (in which the Mediterranean cluster peaks) and the Caucasus.

Below are a few spatial maps, showing the distribution of selected clusters from the K12 analysis (courtesy of Eurogenes project member FR7). The data is still fairly limited, so those of you who want your countries/ethnic groups represented, please encourage more people to take the Eurogenes K12 test at Gedmatch, and state their ancestry when they do.