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. 2012 Mar;76(2):128-41.
doi: 10.1111/j.1469-1809.2011.00701.x.

Turkish population structure and genetic ancestry reveal relatedness among Eurasian populations

Uğur Hodoğlugil  1 , Robert W Mahley
Affiliations

Turkish population structure and genetic ancestry reveal relatedness among Eurasian populations

Uğur Hodoğlugil et al. Ann Hum Genet. 2012 Mar.

Abstract

Turkey has experienced major population movements. Population structure and genetic relatedness of samples from three regions of Turkey, using over 500,000 SNP genotypes, were compared together with Human Genome Diversity Panel (HGDP) data. To obtain a more representative sampling from Central Asia, Kyrgyz samples (Bishkek, Kyrgyzstan) were genotyped and analysed. Principal component (PC) analysis reveals a significant overlap between Turks and Middle Easterners and a relationship with Europeans and South and Central Asians; however, the Turkish genetic structure is unique. FRAPPE, STRUCTURE, and phylogenetic analyses support the PC analysis depending upon the number of parental ancestry components chosen. For example, supervised STRUCTURE (K=3) illustrates a genetic ancestry for the Turks of 45% Middle Eastern (95% CI, 42-49), 40% European (95% CI, 36-44) and 15% Central Asian (95% CI, 13-16), whereas at K=4 the genetic ancestry of the Turks was 38% European (95% CI, 35-42), 35% Middle Eastern (95% CI, 33-38), 18% South Asian (95% CI, 16-19) and 9% Central Asian (95% CI, 7-11). PC analysis and FRAPPE/STRUCTURE results from three regions in Turkey (Aydin, Istanbul and Kayseri) were superimposed, without clear subpopulation structure, suggesting sample homogeneity. Thus, this study demonstrates admixture of Turkish people reflecting the population migration patterns.

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Conflict of interest statement

Conflict of Interest

The Authors have no conflict of interest to disclose.

Figures

Figure 1
Figure 1
Geographical locations of samples used in this study. Turkish (Istanbul, Aydin, and Kayseri) and Kyrgyz samples are shown in red; populations from the HGDP are shown in black.
Figure 2
Figure 2
PC analysis demonstrating genetic relatedness across major geographic regions, including HGDP, Turkish, and Kyrgyz samples. Each symbol represents one individual. (A) PC analysis of 52 populations from the HGDP (n = 938), Turkish (n = 63), and Kyrgyz (n = 16) samples. (B) PC analysis focusing on selected Eurasian populations (including Turkish and Kyrgyz populations) (n = 451).
Figure 3
Figure 3
PC analysis demonstrating genetic relatedness in selected HGDP, Turkish, and Kyrgyz samples. Each symbol represents one individual. (A) PC analysis of Turks vs. European and Middle Eastern populations. Turkish samples were from three regions of Turkey (Aydin, Istanbul, and Kayseri). (B) PC analysis of Turks vs. Central Asian (including Kyrgyz) and South Asian (Pakistani) populations.
Figure 4
Figure 4
Estimated individual ancestry and population structure in 339 individuals by FRAPPE analysis. Representative HGDP populations selected from all continental/geographical regions and combined with Turkish and Kyrgyz samples (n = 339). Populations are labeled above the figure, with their geographic affiliations below. Each individual is represented by a thin vertical line, which is partitioned into K colored segments (K = 7). Colors represent the inferred ancestry from parental populations. White lines separate individuals of different populations.
Figure 5
Figure 5
Supervised population structure analysis. Parental ancestry contributions were calculated for Turkish samples using supervised STRUCTURE analysis. Each individual is represented by a thin vertical line. White lines separate individuals of different populations. (A) Three clusters were forced to correspond to Middle Eastern (Druze and Palestinian), European (French, Italian, Tuscan, and Sardinian), and Central Asian (Uygur, Hazara, and Kyrgyz) populations at K = 3. (B) Four clusters were forced to correspond to Middle Eastern, European, South Asian (Balochi, Brahui, Burusho, Makrani, Pathan, and Sindhi), and Central Asian populations at K = 4.
Figure 6
Figure 6
Phylogenetic tree of Eurasian populations. Neighbor-joining tree of 33 Eurasian populations (selected from HGDP, Turkish, and Kyrgyz populations) based on pairwise Fst matrix calculated with smartpca. The phylogenetic tree was constructed with MEGA4 software.
Figure 7
Figure 7
Decay of LD over distance. SNP pairs were partitioned into bins at 5-kb intervals; for each bin number, SNP pairs with r2 > 0.8 (A) and D′ > 0.8 (B) were plotted. Each group has 48 individuals to eliminate possible effects of sample size. The populations shown are European (French, Italian, Tuscan, and Sardinian), Middle Eastern (Druze and Palestinian), Central Asian (Hazara, Uygur, and Kyrgyz), South Asian (Balochi, Brahui, Burusho, Makrani, Pathan, and Sindhi), Northeast Asian (Mongola, Tu, Oroqen, Xibo, Daur, and Hezhen), native American (Colombian, Surui, Karitiana, Maya, and Pima), and African (Bantu, Biaka Pygmy, Mbuti Pygmy, Mandenka, Yoruba, and San).
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