Figure 1. A circular phylogenetic tree of the human race including two Caucasians (Dr. James Watson and Dr. Craig Ventor), a Chinese (YH), and a Korean (KOREF). At terminal nodes, ‘CEU’, ‘CHB’, ‘JPT’, and ‘YRI’ represent Caucasian, Han Chinese, Japanese, and African, respectively. It was drawn with allele sharing distance (Bowcock et al. 1994; Mountain and Cavalli-Sforza 1997) and neighbor joining methods (Saitou and Nei 1987). Phylogenic analyses were conducted in MEGA4 (Tamura et al. 2007). Commonly called autosomal SNPs (31,460 markers) were used.
SNP is one of genetic variations that are found in different individuals and is commonly used to measure their genetic distance. KoreanGenome.org’s research produced a phylogenetic neighbor-joining-method (NJ method) chart in which mtDNA, chromosome Y, and autosome based linage trees were represented based on single nucleotide polymorphism (SNP) markers:
1) 32,204 autosome markers called in 93 samples (Fig. 1) (Random Korean: 8, KOREF, KOREF’s mother, HapMap Phase III: 80, Dr. Craig Venter (HuRef), Dr. James Watson, YH (Han Chinese),
2) Chromosomal Y markers (Fig. 2),
3) mtDNA markers (Fig. 3).
In earlier archaeology studies, Koreans were known to be the descendants of Altaic or proto-Altaic tribes (Lee et al. 2008; Nelson 1993). In other DNA based studies, originated from both southern and northern parts of East Asia (Jin et al. 2003; Jin et al. 2009; Karafet et al. 2001; Kim et al. 2000).
Koreans are thereby known as an admixed population, and the most prevalent Y-chromosome and mtDNA haplogroups were O2b and D4a each (Hammer et al. 2006; Jin et al. 2009).
The SRY465 mutation that defines the O2b Y-chromosomal haplogroup (proto-Koreans) is known that it had aroused from an ancestral O2* haplogroup belonging to a man who at least already had belonged to a specific “proto-Tungus-Korean” tribe (or who already had resided within Greater Manchuria) (Hammer et al. 2006; Tymchuk 2009). After the O2b divergence, another subclade, O2b1, likely had diverged after the proto-Koreans formation about 1,640 ~ 7,960 years ago.
KOREF’s Y-chromosome had two proto-Korean markers (SRY465 and IMS-JST022454) that define the O2b haplogroup. Annotated fifteen maternal mutations are known as mtDNA sub-haplogroup D4a markers. The haplogroup, D4, was reported as the most prevalent haplogroup in Korea (Lee et al. 2006; Umetsu et al. 2005). Thus KOREF can be considered as the direct descendant of proto-Koreans of the Y-chromosome and mtDNA founders.
While the ancestral Korean 02b lineage is deemed to have emerged in a proto-Tungus-Korean tribe residing somewhere in Greater Manchuria, at the same time, the O2b Korean samples cluster closely with Japanese in Tokyo and Han Chinese in Beijing.
The autosomal linage drawn with NJ method indicated that the Korean donor can be regarded as the one who has the most common genetic traits within Koreans because he was clustered with other Korean samples between Japanese in Tokyo (JPT) and Han Chinese in Beijing (CHB) (Fig. 1). We think that our sequencing project will contribute to the overall human genetics including the understanding of human diversity especially in northern Asia.
Note: Markers of the O3 haplogroup prevalent in China and the 47z mutation of the O2b1 prevalent in Japan were not detected and therefore likely represents a mutation or lineage that arose in Japan.