Abstract
SNP markers provide the primary data for population structure analysis. In this study, we employed whole-genome autosomal SNPs as a marker set (54,836 SNP markers) and tested their possible effects on genetic ancestry using 320 subjects covering 24 regional groups including Northern ( = 16) and Southern ( = 3) Asians, Amerindians ( = 1), and four HapMap populations (YRI, CEU, JPT, and CHB). Additionally, we evaluated the effectiveness and robustness of 50K autosomal SNPs with various clustering methods, along with their dependencies on recombination hotspots (RH), linkage disequilibrium (LD), missing calls and regional specific markers. The RH- and LD-free multi-dimensional scaling (MDS) method showed a broad picture of human migration from Africa to North-East Asia on our genome map, supporting results from previous haploid DNA studies. Of the Asian groups, the East Asian group showed greater differentiation than the Northern and Southern Asian groups with respect to Fst statistics. By extension, the analysis of monomorphic markers implied that nine out of ten historical regions in South Korea, and Tokyo in Japan, showed signs of genetic drift caused by the later settlement of East Asia (South Korea, Japan and China), while Gyeongju in South East Korea showed signs of the earliest settlement in East Asia. In the genome map, the gene flow to the Korean Peninsula from its neighboring countries indicated that some genetic signals from Northern populations such as the Siberians and Mongolians still remain in the South East and West regions, while few signals remain from the early Southern lineages.
Highlights
The X and Y chromosomes and mitochondrial DNA recombine to a much lesser extent than do autosomes [1]
Gene flow between the Korean Peninsula and neighboring countries Genome map and an NJ tree [18,19] for Korea-China-Japan are shown in Fig. 4, where the genome map is a further extension of the World and Asian map (Fig. 2)
Dots representing the Chinese are located at the bottom and those for Japanese are at the top, while some outliers in South East (SE) Korea and Kobe in Japan are shown on the right hand side
Summary
The X and Y chromosomes and mitochondrial DNA (mtDNA) recombine to a much lesser extent than do autosomes [1] This limited, or non-existent, recombination in haploid SNPs (single nucleotide polymorphisms) has been used to trace the evolutionary lineages of individuals and populations showing either maternal or paternal transmission. An advanced technology, termed whole genome sampling analysis, has enabled the genotyping of nearly one megabyte of diploid autosomal SNPs at a time [2] These autosomal SNPs are a reservoir for human evolutionary history, nearly 100 times larger than that of lesser (non-) recombining SNPs, and include the entire range from highly conserved to highly polymorphic SNPs. when individuals and populations of different races and regions are compared using the whole genome approach, a large proportion of the redundant and recombining regions exacerbate the difficulties encountered in exploring evolutionary relationships, common traits and disease susceptibilities between populations
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