The Contribution of Genetic Diversity to Subdivide Populations Living in the Silk Road of China

<div><p>There are several indigenous ethnic populations along the silk road in the Northwest of China that display clear differences in culture and social customs, perhaps as a result of geographic isolation and different linguistic traditions. However, extensive trade and other interactions probably facilitated the admixture of different gene pools between these populations over the last two millennia. To further explore the evolutionary relationships of the 13 ethnic populations residing in Northwest China and to reveal the features of population admixture, the 9 most-commonly employed CODIS loci (D3S1358, TH01, D5S818, D13S317, D7S820, CSF1PO, vWA, TPOX, FGA) were selected for genotyping and further analysis. Phylogenetic tree and principal component analysis revealed clear pattern of population differentiation between 4 populations living in Sinkiang Uighur Autonomous Region and other 9 populations dwelled in the upper regions of Silk Road. R matrix regression showed high-level gene flow and population admixture dose exist among these ethic populations in the Northwest region of China. Furthermore, the Mantel test suggests that larger percent of genetic variance (21.58% versus 2.3%) can be explained by geographic isolation than linguistic barriers, which matched with the contribution of geographic factors to other world populations.</p></div

Mantel tests of three different types of distances.

<p>Note: Dgen stands for genetic distance, Dgeo as geographic distance, and Dlan language distance.</p

Name of the studied populations, number of chromosomes, geographic coordinates, linguistic background, religion and reference.

a<p>: Han_XA represents the Han population living in Xi'an, while Han_XJ represents the Han population in Sinkiang Uighur Autonomous Region.</p>b<p>: “Lamaism” is a branch of Buddhism that is popular in some regions of China, especially in West China.</p

Neighbor-joining phylogenetic tree based on D_A distance.

<p>Neighbor-joining phylogenetic tree based on D_A distance.</p

Regression plots of 13 populations.

<p>Regression plots of 13 populations.</p

Pairwise D_A distance among the 13 populations.

<p>Pairwise D_A distance among the 13 populations.</p

Geography of the studied region.

<p>Note: 1, Kashgar; 2, Han_XA; 3, Hui; 4, Mongol; 5, Uyghur; 6, Kazakh; 7, Uzbek; 8, Kirghiz; 9, Salar; 10, Tu; 11, Dongxiang; 12, Yugur; 13, Baoan; 14, Han_XJ. The dash line with arrow is the Silk Road within China; from Xi'an to Kashgar and beyond. The numbers from 2 to 14 are the locations of 13 populations in this study.</p

Plot of principal component analysis.

<p>Note:a. Scatter plot of the first two principal components (PC1, PC2). b. Scatter plot of the PC2 and PC3</p

Genetic polymorphism of 13 populations for the 9 STR system.

<p>Genetic polymorphism of 13 populations for the 9 STR system.</p

Additional file 1 of GBC: a parallel toolkit based on highly addressable byte-encoding blocks for extremely large-scale genotypes of species

Additional file 1: Table S1. The basic compression performance comparison between GBC and alternative tools. Table S2. The comparison of GBC’s compression and decompression speed under multiple threads in the 1000GP3 dataset. Table S3. The data query performance comparison between GBC and alternative tools. Table S4. The comparison of LD calculation speed between GBC and alternative tools in the 1000GP3 and SG10K datasets. Table S5. The file management performance comparison between GBC and alternative tools. Table S6. BEG and MBEG coding tables for genotypes of diploid species