The Koreans are geographically a Northeast Asian group, who are thought to be most closely related to Altaic language-speaking populations. Anthropological and archaeological evidence suggests that the early Korean population was related to Mongolian ethnic groups, who inhabited the general area of the Altai Mountains and the Lake Baikal regions of southeastern Siberia [1]. Based on archaeological data, the earliest modern human lithic cultures date from 25,000 to 45,000 years ago in the Altai Mountains and southeastern Siberia and the Korean Peninsula [2, 3]. According to Korea's founding myths, the Gojoseon (the first state-level society) was established around 2,333 BC in the region of southern Manchuria, but later stretched from the northeastern region of China to the northern part of the Korean Peninsula. Thus, the ancient Koreans (proto-Koreans) may have shared a common origin with the Northeast Asian groups who inhabited the general area of the southeastern Siberia and Manchuria during the Neolithic (8,000-1,000 BC) and Bronze (1,500-400 BC) Ages [1, 4].

However, like many debates on the genetic history of human populations, the origin of the Korean population remains controversial. Studies of classic genetic markers have shown that, among the East Asians, Koreans tend to have the closest genetic affinity with Mongolians [5, 6]. These findings support the first model, that a northeastern Asian origin is most likely, followed by a southeastward migration into the Korean Peninsula. The second model suggests a bi- and/or multidirectional route, with one migration through northeastern Asia and one through southeastern Asia. Recent surveys of genetic variation using two haploid markers (mitochondrial DNA and the Y chromosome) showed that the Korean population contains lineages typical of both Southeast and Northeast Asian populations [7–9]. These results led us to consider that the peopling of Korea might have involved multiple events, and that different aspects might be revealed by appropriate additional genetic markers and DNA samples.

Based on recent studies of Y-chromosome variation, the East Asian gene pool is almost completely contained within three major Y-chromosome lineages (haplogroups C, D and K) [7, 10]. East Asian populations have major expansions of haplogroup O-M175 lineages (a lineage within K), although there are significant genetic differences in other lineages between the populations [8, 11]. Most Y chromosomes found in the Korean population also belong to haplogroup O-M175 and its sublineages [8, 9]. The Korean population has a high frequency of the haplogroup O3-M122 lineage, which is shared mainly with Chinese and Southeast Asian populations. By contrast, the haplogroup O2b-SRY465 lineages (and its sublineage) are found with high frequency and diversity specifically among modern populations of Japan and Korea [8, 12, 13]. These chromosomes are absent in most populations in China, but they have been detected in some samples of Beijing-Han Chinese, Manchurians, Mongolians and Southeast Siberians [7, 8, 14].

Hammer and Horai [12] hypothesized that the haplogroup O2b-SRY465 and its sublineage, O2b1-47z, might be Yayoi male lineages, which contributed to the contemporary mainland Japanese population via a process of demic diffusion during the Yayoi period from the Korean Peninsula, around 2,300 years ago. Hammer et al.[13] also suggested that the haplogroup O2b1-47z mutation arose on an ancestral O2b-SRY465 chromosome during early phases of the Yayoi migration. This lineage is also distributed sporadically in the Mongol, Manchu and Southeast Siberian populations, and in Indonesia, the Philippines, Vietnam and Micronesia [8, 13, 14]. Lin et al.[15] suggested that the O2b1-47z Y chromosome associated with the Y2 allele might have originated from an ancestral population in Henan or the southern parts of Shanxi near the Yellow River in China.

Thus, to understand the male lineage history of Korea, more data from such informative genetic markers from Korea and its surrounding regions are necessary. In the present study, 25 Y-chromosome single-nucleotide polymorphism (Y-SNP) markers and 17 Y-chromosome short tandem repeat (Y-STR) loci (Yfiler) were genotyped in 1,108 men from East Asian, several populations, to not only identify haplogroup O2b lineages and trace their migration history, but also to distinguish populations with different genetic backgrounds.

This study was approved by the Ethics Committee and institutional review boards of Institute of Bio-Science and Technology in the Dankook University. Separate written informed consent was obtained for enrollment from all participants.

Y-SNP genotyping

Initially all the samples were analyzed for 12 Y-SNP markers (M9, M45, M89, M119, M122, M174, M175, M214, P31, SRY465, 47z and RPS4Y) using a previously described protocol [17]. The samples belonging to haplogroups C, D, K, NO, O3 and P were subjected to further typing with an additional 13 Y-SNP markers to designate the subclades: two three-plex, three two-plex and one single-plex SNaPshot assay were developed for these 13 Y-SNP markers (Figure 1). The nomenclature of the haplogroups followed that of the Y Chromosome Consortium [20]. Primers for PCR and single-base extension (SBE) reactions were designed (Primer 3.0 program; http://frodo.wi.mit.edu/primer3/, Cambridge, MA, USA) (see Additional file 1, Table S1; see Additional file 2, Table S2). Conditions of the SNaPshot assays were the same as those previously described [17], with the exception of PCR purification; in our assay, the PCR products were purified by adding 2 μl of an exonuclease I-shrimp alkaline phosphatase preparation (Exo-SAP; USB Corp., Cleveland, OH, USA) to 5 μl PCR product.

This survey of East Asian Y-SNPs identified 18 haplogroups, 15 of which were present in our Korean group (Table 2; see Additional file 3, Table S3). In general, we found the East Asian population groups to be characterized by male haplogroup homogeneity, showing mostly expansions of haplogroup O-M175 lineages (Figure 2). Haplogroups O3a3-P201, O2b*-SRY465, O3a*-M324, C3-M217 and O2b1-47z (a sublineage within O2b) were the most frequent found in Koreans, and accounted for 28.9, 22.5, 15.0, 12.3 and 8.9% of Korean Y chromosomes, respectively.

Population (n)	Samples of haplogroups in East Asian populations, n (%)
	C				D			F*	K*	L	T	NO*	N	O*	O1	O2			O3				P*	Q	R
	C*	C1	C2	C3	D*	D1	D2								O1a	O2*	O2b*	O2b1	O3*	O3a*	O3a3	O3a4
Northeast Asia
Korean (506)	1 (0.20)	1 (0.20)	0	62 (12.25)	0	0	8 (1.58)	0	0	3 (0.59)	0	0	23 (4.55)	0	11 (2.17)	5 (0.99)	114 (22.53)	45 (8.89)	2 (0.40)	76 (15.02)	146 (28.85)	0	0	7 (1.38)	2 (0.40)
Japanese (157)	0	8 (5.00)	0	11 (6.88)	0	0	46 (29.30)	0	0	0	0	0	4 (2.50)	0	3 (1.88)	1 (0.63)	8 (5.10)	38 (23.75)	0	11 (6.88)	27 (16.88)	0	0	0	0
Mongolian (81)
Buryat (36)	0	0	0	16 (44.44)	0	1 (2.78)	0	1 (2.78)	0	0	0	0	9 (25.00)	0	0	0	1 (2.78)	0	0	1 (2.78)	6 (16.67)	0	0	0	1 (2.78)
Khalkh (45)	0	0	0	21 (46.67)	0	1 (2.22)	0	0	0	0	0	0	6 (13.33)	0	0	0	0	0	0	3 (6.67)	11 (24.44)	0	0	1 (2.22)	2 (4.44)
N.China (115)
Beijing-Han (51)	0	0	0	3 (5.88)	0	1 (1.96)	1 (1.96)	0	0	0	0	0	1 (1.96)	0	8 (15.69)	1 (1.96)	1 (1.96)	0	3 (5.88)	11 (21.57)	21 (41.18)	0	0	0	0
Manchurian (30)	0	0	0	8 (26.67)	0	0	0	0	0	0	0	0	0	0	0	1 (3.33)	1 (3.33)	0	0	3 (10.00)	16 (53.33)	0	0	0	1 (3.33)
Xian (34)	0	0	0	8 (23.53)	0	3 (8.82)	0	0	0	0	0	0	2 (5.88)	0	3 (8.82)	2 (5.88)	1 (2.94)	0	0	0	13 (38.24)	0	0	1 (2.94)	1 (2.94)
Southeast Asia
South China (60)
Yunnan-Han (60)	1 (1.67)	0	0	5 (8.33)	0	1 (1.67)	0	7 (11.67)	0	0	0	0	4 (6.67)	0	5 (8.33)	7 (11.67)	0	0	1 (1.67)	3 (5.00)	22 (36.67)	0	0	3 (5.00)	1 (1.67)
Indonesian (37)	1 (2.70)	0	0	1 (2.70)	0	0	0	1 (2.70)	0	0	0	0	0	0	5 (13.51)	12 (32.43)	3 (8.11)	0	0	2 (5.41)	9 (24.32)	0	0	2 (5.41)	1 (2.70)
Filipino (64)	1 (1.56)	0	0	1 (1.56)	0	0	0	5 (7.81)	3 (4.69)	0	0	0	0	0	24 (37.50)	1 (1.56)	0	0	2 (3.13)	2 (3.13)	21 (32.81)	0	0	2 (3.13)	2 (3.13)
Thai (40)	0	0	0	1 (2.50)	0	1 (2.50)	0	1 (2.50)	0	0	0	0	0	0	1 (2.50)	28 (70.00)	0	1 (2.50)	0	0	4 (10.00)	0	0	1 (2.50)	2 (5.00)
Vietnamese (48)	0	0	0	6 (12.50)	0	1 (2.08)	0	0	1 (2.08)	0	0	0	1 (2.08)	0	2 (4.17)	5 (10.42)	2 (4.17)	2 (4.17)	1 (2.08)	14 (29.17)	13 (27.08)	0	0	0	0
Total (1,108)	4 (0.36)	9 (0.81)	0	143 (12.87)	0	9 (0.81)	55 (4.96)	15 (1.35)	4 (0.36)	3 (0.27)	0	0	50 (4.50)	0	62 (5.58)	63 (5.67)	131 (11.82)	86 (7.74)	9 (0.81)	126 (11.34)	309 (27.81)	0	0	17 (1.53)	13 (1.17)

O3-M122 was the commonest Chinese Y-chromosome haplogroup found, and its presence in Korea may originate from demic diffusion by way of south-to-north migration [9, 29, 30]. C-RPS4Y was the commonest Mongolian Y-chromosome haplogroup (C3 lineage), and this is shared primarily with populations in northern Asia (including Koreans) [9, 31, 32]. Our network and diversity analyses of C-RPS4Y and O3 may support a southern origin that migrated into East Asia via the southern route [10, 29] (Figure 3, Table 3). Interestingly, our Japanese group seemed to have both C1-M105 and C3-M217 chromosomes, whereas haplogroup C1-M105 was not present in most East Asian populations (except for Koreans), consistent with the previous report of Hammer et al. [13]. Haplogroup D2-M55 was found at high frequency only in Japanese subjects (29.3%), including 1.6% of Koreans, whereas it was absent elsewhere in these East Asian populations, except for the Beijing-Han group. Haplogroup D1-M15 was present at extremely low frequencies in the other East Asian populations. The occurrence of C1 and D2 chromosomes in Korea may be considered concordant with the historical views about the recent connection between the Korean and Japanese populations.

Haplogroup N-M231 was present in the Korean and Mongolian groups at moderate frequencies, suggesting that the early Korean population may have shared a common origin with Mongolian ethnic groups who inhabited the general area of the Altai Mountains and Lake Baikal regions of southeastern Siberia [1]. The K-M9 defined chromosomes (L, Q and R subtypes) were also found at low frequencies in the Korean group, and these mainly occur in central and south Asia [13, 33]. The presence of these haplogroups in the Korean population implies that the peopling of Korea probably involved multiple events [8, 9]. Based on the result of the MDS plot (Figure 4 and Additional file 4, Table S4), the Korean population contains lineages from both the southern and northern areas of East Asia.

Interestingly, the O2b1-47z sublineage seems to have diverged about 4,400 years ago (Table 6) rather than in the Yayoi period, consistent with a previous estimate of 4,000 years ago [13]. Therefore, the present data support the possibility of an ancient Korean origin of O2b1-47z, rather than a Japanese origin [13]. Although O2b1-47z is at its highest haplogroup frequency in the Japanese population, the Y-STR data reveal more diversity of O2b1-47z haplotypes in Koreans, as shown by the mean number of pairwise differences and allele size variation ratio (Table 5), supporting an origin of the O2b1-47z mutation in prehistoric Korea. The Japanese samples studied here were derived from Kyushu, Shikoku and southern Honshu (the region closest to Korea), implying that the high frequency of the O2b1 lineage in Japan may be explained by genetic drift [12, 16]. This finding is concordant with a previous report of Nonaka et al.[36], showing less diversity in Japan than in Korea (Table 5). TMRCA of O2b1-47z, and a star-cluster pattern in this study (Figure 3) and a previous study [13], all suggest the possible association of O2b1-47z with the peopling of Korea. However, because most of the Japanese O2b*-SRY465 and O2b1-47z samples were also in the core (or close to) of the cluster (Figure 3), it cannot exclude the possibility that the Japanese and the Koreans derive from the same proto-population outside of Korea (carrying these lineages) at roughly the same time. Thus, further studies of sufficient sampling in the vast East Asian region and genomewide genotyping should provide further insights.

Our results support the idea that both haplogroups O2b*-SRY465 and O2b1-47z had an in situ origin among Northeast Asians, particularly among the prehistoric Koreans, rather than in southeast Asia or Japan as previously envisaged. The combination of the O2b initial settlement (which became an indigenous proto-Korean component) in part with the relatively recent O3 and C3 lineages (which include a Chinese component) explains some of the main events formulating the current Y chromosome composition of the Korean population. Thus, our findings are consistent with linguistic, archaeological and historical evidence, which suggest that the direct ancestors of Koreans were proto-Koreans who inhabited the northeastern region of China and the Korean Peninsula during the Neolithic (8,000-1,000 BC) and Bronze (1,500-400 BC) Ages.