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Sunday, August 24, 2014

Genetic structure in the Western Balkans

PLoS ONE has a new paper by Kovacevic et al. on the genetic structure of Western Balkan populations. Here's the abstract:

Contemporary inhabitants of the Balkan Peninsula belong to several ethnic groups of diverse cultural background. In this study, three ethnic groups from Bosnia and Herzegovina - Bosniacs, Bosnian Croats and Bosnian Serbs - as well as the populations of Serbians, Croatians, Macedonians from the former Yugoslav Republic of Macedonia, Montenegrins and Kosovars have been characterized for the genetic variation of 660 000 genome-wide autosomal single nucleotide polymorphisms and for haploid markers. New autosomal data of the 70 individuals together with previously published data of 20 individuals from the populations of the Western Balkan region in a context of 695 samples of global range have been analysed. Comparison of the variation data of autosomal and haploid lineages of the studied Western Balkan populations reveals a concordance of the data in both sets and the genetic uniformity of the studied populations, especially of Western South-Slavic speakers. The genetic variation of Western Balkan populations reveals the continuity between the Middle East and Europe via the Balkan region and supports the scenario that one of the major routes of ancient gene flows and admixture went through the Balkan Peninsula.

Among the most eye catching figures from the study is this TreeMix graph with ten migration edges or admixture events. Note the 44% migration edge running from the base of the Eastern European branch to the French. Is this perhaps a legacy of the Proto-Celts and early Germanics? In any case, something similar can be seen on this TreeMix graph from the supplementary PDF to Skoglund et al. 2014, where a French genome is modeled as a clade closely related to Upper Paleolithic Siberian forager MA-1, but with considerable Sardinian admixture.

Also, the position of the Poles at the tip of the tree, and thus near the North Russians, is somewhat curious. However, I know that several of these individuals are ethnic Poles from Estonia, so that might be the problem.

Update 25/08/2014: Here's a typical Eurogenes Principal Component Analysis (PCA) of West Eurasia with the new samples from this paper (Bosnians, Kosovars, Macedonians, Montenegrins and Serbs).


Kovacevic L, Tambets K, Ilumäe A-M, Kushniarevich A, Yunusbayev B, et al. (2014) Standing at the Gateway to Europe - The Genetic Structure of Western Balkan Populations Based on Autosomal and Haploid Markers. PLoS ONE 9(8): e105090. doi:10.1371/journal.pone.0105090

Wednesday, August 6, 2014

Haplotype-based PCA of West Eurasia and Europe

The Principal Component Analyses (PCA) below are based on pairwise Identity-by-Descent (IBD) sharing inferred with fastIBD. My aim was to create PCA that took into account haplotype information to see how they might differ from similar plots based on unlinked loci (such as here).

Clearly, they're less reflective of geography and isolation-by-distance, and instead more profoundly influenced by relatively recent isolation, founder effects and/or rapid expansions, especially in Northern and Eastern Europe, and in particular among the Finns, Balts and East Slavs. Unfortunately, I don't have time to say much more about these results. But feel free to post any questions or observations in the comments below. I have done something very similar in the past, but with far fewer samples (see here).

Please note, to ensure that the PCA were as informative as possible I was forced to drop several populations that produced unusual results, probably because of extreme founder effects. This is why, for instance, there are no Ashkenazi Jews on any of the plots, and the only Finns you'll find come from western Finland.

I'll try this again on a much larger dataset when more samples come in, and also include populations from Central and South Asia.

Update 7/8/2014: Apparently some people are wondering what the plots with Finns and Jews look like. Here you go...