Characterization of Danube Swabian population samples on a high-resolution genome-wide basis

Abstract

Background: German-derived ethnicities are one of the largest ethnic groups in Hungary, dating back to the formation of the Kingdom of Hungary, which took place at the beginning of the 11th century. Germans arrived in Hungary in many waves. The most significant immigration wave took place following the collapse of the Ottoman Empire in East-Central Europe which closed the 150 year long Ottoman occupation. To date, there are no comprehensive genome-wide studies investigating the genetic makeup of the Danube Swabians. Here we analyzed 47 Danube Swabian samples collected from elderly Swabian individuals living in the Dunaszekcső-Bár area, in Danube side villages of Southwest Hungary. These Swabians, according to self-declaration, did not admix with other ethnic groups for 3-6 succeeding generations. Using Illumina Infinium 720 K Beadchip genotype data, we applied allele frequency-based and haplotype-based genome-wide marker data analyses to investigate the ancestry and genetic composition of the collected Danube Swabian samples.

Results: Haplotype-based analyses like identity by descent segment analysis show that the investigated Danube Swabians possess significant German and other West European ancestry, but their Hungarian ancestry is also prominent. Our results suggest that their main source of ancestry can be traced back to Western Europe, presumably to the region of Germany.

Conclusion: This is the first analysis of Danube Swabian population samples based on genome-wide autosomal data. Our results establish the basis for conducting further comprehensive research on Danube Swabians and on other German ethnicities of the Carpathian basin, which can help reconstruct their origin, and identify their major archaic genomic patterns.

Keywords: Admixture; Ethnic group; Genome-wide data; Haplotype; Population genetics; Swabians.

Fig. 1

Principal Component Analysis results of Swabians and 1000 Genomes Project populations plotted to the first four principal components. Eigenvalues of eigenvectors 1, 2, 3 and 4 were 2.647, 1.590, 1.419 and 1.388, respectively. 353 of the calculated eigenvectors had eigenvalues higher than 1.000. Each symbol represents one individual. GBR – British from England and Scotland; FIN – Finnish in Finland; IBS – Iberian populations in Spain, TSI – Toscani in Italy; CEU – Utah residents with Northern and Western European ancestry from the CEPH collection

Fig. 2

Principal Component Analysis results of Swabians and various European populations plotted to the first four principal components. Eigenvalues of eigenvectors 1, 2, 3 and 4 were 3.986, 2.420, 2.040 and 1.688, respectively. 531 of the calculated eigenvectors had eigenvalues higher than 1.000. Each symbol represents one individual

Fig. 3

ADMIXTURE analysis results of Swabians and investigated European populations with K = 2–3. Cross-validation error was the lowest applying 2 clusters. Cross-validation error values at K = 2, K = 3 was 0.86212 and 0.86379, respectively. The cross-validation error data can be found on Supplemental Fig. 2. Each column represents one individual, each column group represents a population

Fig. 4

TreeMix analysis results. The calculated maximum likelihood tree. Residual fit of this analysis showing the standard error of the calculations can be found on Supplemental Fig. 4

Fig. 5

F_st (Fixation index) matrix calculated by the SMARTPCA software, showing the average pairwise allele frequency differentiations between the investigated Danube Swabians and various European populations. Standard error of the F_st calculations can be observed at the Supplemental Fig. 5

Fig. 6

Results of haplotype-based investigations. a Average pairwise IBD sharing results, b Average length and number of shared IBD segments between Danube Swabians and other investigated groups, c Average genome-wide autozygozity calculations of investigated populations