Genetic Structure of Europeans: A View from the North–East

Abstract

Using principal component (PC) analysis, we studied the genetic constitution of 3,112 individuals from Europe as portrayed by more than 270,000 single nucleotide polymorphisms (SNPs) genotyped with the Illumina Infinium platform. In cohorts where the sample size was >100, one hundred randomly chosen samples were used for analysis to minimize the sample size effect, resulting in a total of 1,564 samples. This analysis revealed that the genetic structure of the European population correlates closely with geography. The first two PCs highlight the genetic diversity corresponding to the northwest to southeast gradient and position the populations according to their approximate geographic origin. The resulting genetic map forms a triangular structure with a) Finland, b) the Baltic region, Poland and Western Russia, and c) Italy as its vertexes, and with d) Central- and Western Europe in its centre. Inter- and intra- population genetic differences were quantified by the inflation factor lambda (λ) (ranging from 1.00 to 4.21), fixation index (Fst) (ranging from 0.000 to 0.023), and by the number of markers exhibiting significant allele frequency differences in pair-wise population comparisons. The estimated lambda was used to assess the real diminishing impact to association statistics when two distinct populations are merged directly in an analysis. When the PC analysis was confined to the 1,019 Estonian individuals (0.1% of the Estonian population), a fine structure emerged that correlated with the geography of individual counties. With at least two cohorts available from several countries, genetic substructures were investigated in Czech, Finnish, German, Estonian and Italian populations. Together with previously published data, our results allow the creation of a comprehensive European genetic map that will greatly facilitate inter-population genetic studies including genome wide association studies (GWAS).

Across language families: Genome diversity mirrors linguistic variation within Europe

“…The exception to the results of the present study is thus nicely justified in this scenario, suggesting that when a Finno‐Ugric language was introduced in Hungary, the genetic buildup of the population changed only in part, thus retaining similarities with its geographic neighbors, an example of the process called élite dominance by Renfrew (1992). On the contrary, the same case cannot be easily made for Basques (Alonso et al, 2005; Rodríguez‐Ezpeleta et al, 2010; Young et al, 2011; Martinez‐Cruz et al, 2012) or Finns, for whom, to the best of our knowledge, no available evidence suggests a similar model of partial demographic replacement associated with language replacement (Nelis et al, 2009). Thus, the comparative linguistic/genomic analysis, attempted in the present study, seems able to single out and precisely assess these differences in the population histories of the three non‐IE members of our sample.…”

Small effective population size and genetic homogeneity in the Val Borbera isolate

“…Despite clustering analysis of the villages showing no significant stratification (P-value 40.05 for both first and second principal components, Supplementary Figure 8), F ST values indicate some extent of structuring, which has already been observed in isolates, 43,44 even for populations with recent shared genealogy. 45 We speculate that the slight observed stratification can be related to the high proportion of marriages occurring between inhabitants of the same village, as demonstrated by analysis of marriage acts and surnames (data not shown).…”

Genome-wide patterns of population structure and admixture in West Africans and African Americans

“…Nonetheless, recent studies of microsatellite and DNA sequence variation suggest a significant population structure exists within sub-Saharan Africa, with geography, language, and mode of subsistence (e.g., hunter-gatherer, pastoralist, agriculturalist) as potential key factors (2,12,13,19). Given that high-density genotype data have revealed discernible population structure within other continental populations (e.g., Europe, East Asia) and even among geographical regions within countries (e.g., Switzerland, Finland, United Kingdom) (20)(21)(22)(23)(24), there is strong reason to believe that high-density genotype data from African and African-American populations can elucidate patterns of genetic structure among these populations further.…”