Genetic structure in Northern Europe with 250K SNPs

A new study on genetic structure in Northern Europeans has appeared in PLoS ONE. Below is the STRUCTURE results for the Northern European populations. At K=2, the two clusters are centered on Eastern Finns and Germans-Brits, with Western Finns being intermediate and Swedes closer to the German-Brit (green) cluster). At K=3 Nordic populations are split into two clusters centering on Swedes and Eastern Finns. The pattern for K=4 is less distinct, except that the German-Brit cluster is split into blue and green components that don't appear to have any population specificity.


Interestingly, the researchers also carried out an analysis of the populations which included the HapMap populations:

When data from HapMap Han Chinese+Japanese and Yoruba individuals was included in the analysis, the MDS plot of IBS formed a triangle of the three continents in the first two dimensions, with the third dimension separating the European populations clinally from each other (Fig. S3). In the histograms of IBS between the five European populations and each HapMap population (Fig. 4a), the studied populations were most similar with the CEU and least similar with YRI. Interestingly, the similarity with the Asians varied between populations, being higher for Eastern Finns, Western Finns and Swedes than for the Germans and British (p less than 10⁻¹⁴ for all comparisons except for GER and BRI whose distributions did not differ). The same pattern was also observed when comparing the allele frequencies in the study populations and in CEU and CHB+JPT: the Eastern Finns had the largest proportion of SNPs deviating towards the Asian frequencies (Table S2; p less than 10⁻⁵), also when markers with smallest differences were excluded (data not shown).

They were able to differentiate between the effects of genetic drift and eastern influence by looking at the direction of the divergence:

To study the extent of eastern influence, we counted in each of the five European populations the number of markers where the population's allele frequency and the CHB+JPT allele frequency deviated from the CEU allele frequency to the same direction, and the number of markers where the allele frequencies deviated in opposite directions. We then compared the numbers to the null hypothesis that all the five populations stem from the same proto-European population (approximated by the CEU frequencies) from which they have subsequently diverged via genetic drift in the absence of admixture. In such a case, one would expect the number of markers drifting into a given direction (e.g. towards the Asian frequencies) to be similar across the populations, whereas a varying degree of eastern admixture in each population would result in disparate marker proportions. Using the number of deviating markers instead of the absolute size of the deviations should even out some of the effects of differing extent of drift in the populations.

This parallels my comment of an earlier study:

Under the theory of "drift due to isolation", the Finns might be distant from other Europeans, but not specifically at an East Eurasian direction.

The paper also discusses genetic structure within Finland:

The information about the grandparental birthplaces of the Finnish samples enabled a more detailed analysis of population structure within Finland. In the multidimensional scaling plot of IBS within Finland (Fig. 2c,d, Fig. S1b), the first dimension showed the division to Eastern and Western Finland; the Häme samples settled between the clusters. The second dimension showed a north-south gradient within Eastern and the third dimension within Western Finland. Here the Swedish-speaking Ostrobothnians showed no separation from their Finnish-speaking neighbours, whereas in the MDS plot of the European populations, the Finnish samples closest to the Swedes were almost exclusively Swedish-speakers (data not shown), and in the Structure analysis the Swedish-speaking Finns showed twice as large an admixture with the Sweden-dominated cluster as the other Western Finnish samples did (48.9% versus 24.6%, data not shown).

PLoS ONE doi: 10.1371/journal.pone.0003519

Genome-Wide Analysis of Single Nucleotide Polymorphisms Uncovers Population Structure in Northern Europe

Elina Salmela et al.

Abstract

Background
Genome-wide data provide a powerful tool for inferring patterns of genetic variation and structure of human populations.

Principal Findings
In this study, we analysed almost 250,000 SNPs from a total of 945 samples from Eastern and Western Finland, Sweden, Northern Germany and Great Britain complemented with HapMap data. Small but statistically significant differences were observed between the European populations (FST = 0.0040, p less than 10⁻⁴), also between Eastern and Western Finland (FST = 0.0032, p less than 10⁻³). The latter indicated the existence of a relatively strong autosomal substructure within the country, similar to that observed earlier with smaller numbers of markers. The Germans and British were less differentiated than the Swedes, Western Finns and especially the Eastern Finns who also showed other signs of genetic drift. This is likely caused by the later founding of the northern populations, together with subsequent founder and bottleneck effects, and a smaller population size. Furthermore, our data suggest a small eastern contribution among the Finns, consistent with the historical and linguistic background of the population.

Significance
Our results warn against a priori assumptions of homogeneity among Finns and other seemingly isolated populations. Thus, in association studies in such populations, additional caution for population structure may be necessary. Our results illustrate that population history is often important for patterns of genetic variation, and that the analysis of hundreds of thousands of SNPs provides high resolution also for population genetics.

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