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fredag 2. august 2013

Ste7 and modern European variation

I have this time followed the same procedure as for the La Braña analysis and extracted in total 13k SNP's that matched the 1000 genome reference SNP's. I further imputed these markers to a panel of project participants and reference populations, and then linkage pruned these down in Plink to 7k SNP's. I then run the data through the unlinked Chromopainter-Finestructure pipeline editing out the European populations from the output file resulting in 6k of European panel SNPs.

Again because of the very small number of SNP's the inferred structure can be both noisy and inaccurate especially for the defined groups that consists of only one individual. I also again used the "superindividuals" functionality in Finestructure for all individuals except Ste7 based on earlier 289k SNP haplotype linked clustering.

The Ste7 individual was found in Funnelbeaker culture context in Gökheim, South Sweden and appears to represent the first farmers in Fennoscandia.

The result shows not unexpected that Ste7 shows strongest affiliations to Europe's more southern populations like especially Sardinians and Iberians, then Bulgarians, Albanians. Also some other close by populations shows stronger affiliations like Romanians, Hungarians, French, Austrian, Polish and Croat. Strangely neither the single Greek individual, Basque, Italians and Spanish shows any larger affiliation but this could be an artefact of the low resolution and large variation at individual level for the Greek individual but not for the Basque, Italians and Spanish overall.

CC Europe Unlinked 6k

Also Ste7 shows a surprising strong sharing to the two mixed Norwegian individuals with party Saami ancestry "NOR-SAM" and two of the North-Saami individuals "SA1-2" as the more Central-European populations. This link is not seen between the Saamis and the Central-European populations so it could reflect part ancestry with a more Saami or La Braña like populations. This finding could also be the result of large individual variation (error margin) due to the low resolution (only 6k SNPs).

Other populations that show less affiliation than the above of the more southern populations are Basque, Spanish and Italians. Further north the British, Germans, Danish, Finns and Scandinavians. Further east also Ukraine, Russians, Lithuanians, Mordovians and Vologda Russians shows less affiliation.

CC Europe Ste7 detailed

CC Europe Ste7 PCA D1-D2

Conclusion: It appears like Ste7 are mainly of southern European ancestry but may also have "local" or ancient ancestry (se La Braña posts) as there appears to be affiliation with part of the Saami samples as well.

EDIT 20/9-13

Download individual results

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