Jomon: Paleolithic Contingent in Modern Japanese Feb 6, 2017 20:23:34 GMT
Post by Admin on Feb 6, 2017 20:23:34 GMT
Figure 1. Principal component analysis with genome sequence data. (a) Sanganji Jomon and 1000 Genomes Project worldwide humans based on 68 542 SNPs with PB. (b) Sanganji Jomon and 1000 Genomes Project East Eurasians based on 46 158 SNPs with PB.
PCA When worldwide populations are compared, PCA illustrates the genetic similarity of Sanganji Jomon and East Eurasians compared with African, European, Sahulian and Native American peoples (Figure 1a, Supplementary Figures S7-S11). However, Sanganji Jomon is located slightly closer to the center of the three major population groups in Figure 1a. This indicates the genetic uniqueness of Sanganji Jomon among East Eurasians, and/or the effect of post-mortem changes in ancient DNA, although the latter is unlikely because the result using only transversion sites showed very similar results (Supplementary Figures S8 and S10). Next, we investigated the genetic relationship between the Sanganji Jomon and East Eurasians. Comparison with 1000 Genomes Project24 East Asians (JPT (Japanese Tokyo), CHB (Han Chinese in Beijing), CHS (Southern Han Chinese), CDX (Chinese Dai in Xishuangbanna, China) and KHV (Kinh in Ho Chi Minh City, Vietnam)) based on 46 158 SNP sites show that the Sanganji Jomon is located quite apart from the other modern East Eurasians, and modern Japanese are situated between the Sanganji Jomon and continental East Eurasians (Figure 1b). Although the Sanganji Jomon data were merged for sequence data of A1 and B, the PCA plot location of the Sanganji Jomon was similar to Figure 1b when A1 and B were independently analyzed (Supplementary Figure S13). We therefore surmise that the merged data are reliable for further analyses. The uniqueness of the Sanganji Jomon was also observed when only transversion sites were used (Supplementary Figure S12), again indicating that the uniqueness was not the result of post-mortem changes.
The comparison with the genome-wide SNP data of HGDP populations27 also showed the unique status of the Sanganji Jomon, who was positioned far apart from all modern East Eurasians in PC2 and PC3, although only 6864 SNPs were used. (Figure 2a,Supplementary Figure S14). The uniqueness of the Sanganji Jomon within East Eurasians is consistent with the results including Europeans and Africans. When the Ainu, the mainland Japanese and the Ryukyuan from the Japanese Archipelago1 and CHB28 were compared with Sanganji Jomon, PC1 separated the Ainu and Sanganji Jomon from the other populations (Figure 2b). The population closest to the Sanganji Jomon was the Ainu, followed by the Ryukyuan and then the mainland Japanese. It appears that PC1 corresponds to the degree of genetic contribution from the Jomon people to the other Japanese Archipelago populations, whereas PC2 separated the Ainu from Sanganji Jomon. When the genomic data of 1000 Genomes Project East Asians24 were included in the PCA analysis (Figure 2b), PC3 separated the Ainu from the Sanganji Jomon (Supplementary Figure S15).
Figure 2. Principal component analysis with genome-wide SNP data. (a) Sanganji Jomon and HGDP East Eurasians based on 6864 SNPs with PB. (b) Sanganji Jomon, individuals of three populations inhabiting the Japanese Archipelago (Ainu, mainland Japanese and Ryukyuan), and Chinese Beijing (CHB) based on 5392 SNP sites with PB.
Allele sharing analysis Allele sharing analysis using 5392 SNP sites (Figure 3a) showed that the Ainu had the highest percentage of allele sharing with the Sanganji Jomon, followed by the Ryukyuan, the mainland Japanese and CHB, similar to the projection of PC1 in Figure 2b. Using the HGDP East Eurasian data set with 7081 SNP sites (Figure 3b), the mainland Japanese had the highest allele sharing with the Sanganji Jomon. Interestingly, southern East Eurasians (green bars) had slightly higher allele-sharing percentages than northern East Eurasians (blue bars), although we have to be careful with the effect of post-mortem changes.
Figure 3. Allele sharing between Sanganji Jomon and modern humans. Vertical line indicates the frequency of having the same allele with the Sanganji Jomon. (a) Comparison with Japanese Archipelago populations and Chinese Beijing (CHB) based on 5392 SNP sites with PB, (b) comparison with HGDP East Eurasians, Sahulians and Native Americans based on 7081 SNP sites with PB. Colors blue, green, brown and violet indicate northern East Eurasians, southern East Eurasians, Sahulians and Native Americans, respectively.