Jomon: Paleolithic Contingent in Modern Japanese

new

Admin
Administrator

Posts: 81,210

Jomon: Paleolithic Contingent in Modern Japanese Aug 25, 2018 19:44:33 GMT

Quote

Post by Admin on Aug 25, 2018 19:44:33 GMT

Discussion
This is the first study on the ancient nuclear genome of the Neolithic hunter-gatherers who lived on the Japanese Archipelago. We observed more post-mortem changes in the Sanganji Jomon sample than in two other archaic human examples (~0.8% in Sanganji Jomon, Supplementary Table S7). Environmental conditions (for example, temperature, humidity, pH value, geochemical properties of soil) or use of different sample treatments may affect the condition of the ancient DNA. We did not treat the ancient DNA with uracil DNA glycosylase and endonuclease VIII, which remove C to T misincorporation from the sequence reads. This is to reduce the number of experimental steps so as to minimize the risk of contamination in library preparations. We also chose to see the post-mortem damage specific to ancient DNA to more clearly evaluate the ancient origin of the extracted DNA. This may be the reason that the DNA damage was high in Sanganji Jomon sequences.

PCA and phylogenetic analyses revealed the genetic relationships between the Sanganji Jomon and the modern human populations that we compared. We found that Sanganji Jomon was genetically quite distinct from the other modern East Eurasians. Our Jomon genotypes are still mostly based on a single read per SNP site, whereas the 1000 Genomes Project data24 had at least 4–6 × coverage. We need to be careful about the effect of genotype error rate even if we use only transversion sites (error rate=0.0129%). However, PCA plots using all sites (Figure 1 and Supplementary Figures S7 and S9) and those using transversion only (Supplementary Figures S8) are more or less the same, and TreeMix trees using all sites (Figure 4 and Supplementary Figures S16 and S18) and those using transversion only (Supplementary Figure S17) also showed similar positions for the Sanganji Jomon. Therefore, we believe that the phylogenetic relationship of the Sanganji Jomon can still be reliably estimated with our data.

Some cranial metric and dental analyses suggested that the ancestral population of the Jomon people originated from Southeast Asia,3, 39, 40, 41, 42, 43 whereas other morphological analyses44, 45 and mtDNA sequence data9 suggested that their ancestors were of Northeast Asian origin. However, neither hypothesis was supported from our analysis using direct Jomon nuclear genome sequences. Our results suggest that the Jomon people were descendants of an ancestral East Eurasian population prior to population diversifications recognizable today.
The possibility that the Sanganji Jomon ancestors diverged before the Native Americans was also inferred through the maximum-likelihood tree, neighbor-joining tree, and the D-statistic tests, but this is still inconclusive because of the small number of SNPs in the analyses. However, all the results suggest a deep Jomon divergence within East Asia, close to the Native American split. The effect of genotype errors also need to be taken into account in interpreting the apparent deep divergence of the Jomon people. A relatively large amount of genotype errors in the Jomon data set would induce their long tree branch and/or genetic similarity between the Jomon and outgroups (for example, non-East Eurasians and archaic humans) as artifacts, placing the Jomon closer to the root of outgroup-East Eurasian splits and/or showing gene flow between Jomon and those outgroups. However, since we did not observe any of those artifacts, and the inferred genotype error rate in the transversion-only sites (0.0129%) is quite small, it is unlikely that the Jomon was erroneously located at the basal position of East Eurasians. The ages of the most recent common ancestors of mitochondrial DNA haplogroups N9b and M7a (considered indigenous to Jomon and modern Japanese, and called the Jomon haplotype), were estimated to be 22 000 YBP and 23 000 YBP, respectively.10 These estimates also support a deep divergence of the Jomon people.

We also examined whether the uniqueness of the Sanganji Jomon in East Eurasia was the result of gene flow from non-East Eurasians, but the evidence for this was not suggested (Supplementary Figures S22, S24 and S25). This indicates that the ancestor of the Sanganji Jomon had been genetically isolated from continental populations after their divergence. However, our results do not deny a possibility of small fraction of gene flow between the Jomon people and the non-East Eurasians, which might not be detected in the current study because of the small amount of the determined Jomon genome sequences. The TreeMix tree and the D-statistic tests also confirm the lack of non-East Eurasian contaminations in the Jomon data via reagents because if there were such contamination during experiments, the effect would be artificially detected as gene flow in those analyses. Genetic affinity between modern East Eurasians and Melanesian compared with Sanganji Jomon was inferred, but these results were also ambiguous because of the data limitation. Further genomic sequencing of Jomon genomes in future studies will clarify such questions.

Our results show that the populations genetically closest to Sanganji Jomon are those that live on the Japanese Archipelago. The current Japanese population is widely accepted to be a result of admixture of indigenous Jomon and later migrant people, whereby the latter were agricultural people that came from continental Asia into the Japanese Archipelago probably via the Korean Peninsula during and after the Yayoi era. Until now, this hybridization scenario has not been verified directly at the genomic level. Our result based on PCA, TreeMix and neighbor-joining trees, Neighbor-Net networks, and D-statistic tests clarified that the Jomon people genetically contributed to the modern Japanese Archipelago populations. The genetic similarity would not be explained by contamination from Japanese archipelago populations during experiments, because the direction of gene flow estimated in TreeMix tree was from Jomon to JPT, not from JPT to Jomon (Figure 4), and the D((KHV or CHS, CHB) Jomon) value in D-statistic tests (Figure 6a) was not negative with significant Z-score (JPT was genetically closer to CHB than to CHS or KHV). Furthermore, if there was contamination from modern Japanese, the Jomon would be genetically closer to CHB than to CHS and KHV, leading to negative D-values and probably significant Z-scores. Therefore, we can conclude that the modern Japanese Archipelago populations are the admixture of the Jomon people and other populations with genetic affinities with modern Northeast Asians. This result is consistent with the conclusion based on the genetic analyses of modern human populations.1 However, it is difficult to pin-point the geographic origins of the candidate populations because of lack of genetic data of relevant ancient populations.

The amount of genetic contribution from the Jomon people varied among the Japanese Archipelago populations (Figures 2b and 3a and Supplementary Figure S15). The Ainu and the Ryukyuan share more alleles with the Jomon than the mainland Japanese, suggesting smaller genetic contributions from continental populations in those two populations than for the mainland Japanese, in agreement with previous findings.1, 2, 4, 13, 46, 47, 48, 49, 50 This supports the dual-structure model of Hanihara,3, 50 which is a widely accepted theory that explains the history of the three current populations that inhabit the Japanese Archipelago, and which predicts that the mainland Japanese are more admixed with agricultural continental people than the Ainu and the Ryukyuan, with major admixture occurring in and after the Yayoi period.

PC1 values of some Ainu individuals were similar to that of Sanganji Jomon, whereas PC2 separated the Ainu people from Sanganji Jomon (Figure 2b). It is probable that the ancestors of the Ainu people experienced admixture with other population(s) (for example, continental population(s) not used in the current study) after the Jomon period, and they are thus genetically differentiated from the Jomon people.51 The candidate population is the Okhotsk people, who inhabited the Northeastern costal area of the Hokkaido region, Japan, from the 5th to 13th century. They were morphologically close to modern southern Siberians such as the Nivkhi and Ulchi people,52, 53, 54, 55 who were not included in the current study. Recent studies suggest that the descendants of the Hokkaido Jomon people had admixed with the Okhotsk people and became ancestors of the modern Ainu.56, 57, 58, 59

Jinam et al.2 recently estimated the proportion of the Jomon ancestry in the mainland Japanese using the f4-ratio test35under a specified phylogenetic scenario. The estimated proportion of Jomon ancestry differs depending on the compared populations and were within the range of 13–21%. Jinam et al.2 also used ADMIXTURE60 and found that the mainland Japanese was best explained by two ancestry components. One of them has very high proportions in many Ainu individuals, and is considered to be Jomon ancestry if we assume that the Ainu people are largely descendants of the Jomon. The average proportion of this Jomon component in the mainland Japanese was 17%, which is within the range of f4-ratio test results.2 The same genome-wide SNP data were also used for ABC analysis, and the highest likelihood model estimated the admixture proportion from the Jomon ancestry to the mainland Japanese to be 36% (22–53%, 95% confidence interval).50 We used TreeMix for estimating Jomon ancestry proportions in this study, and the frequency was 12% as shown in Figure 4. We note that it is possible that the frequency was underestimated if the Jomon people had some population substructure and the northern Jomon including the Sanganji Jomon only indirectly contributed to the modern Japanese, and/or if there are contamination during experiments from the Japanese Archipelago populations. Previously, the proportion of the Jomon component in the modern mainland Japanese was estimated to be 35% based on partial mtDNA sequences of modern human populations46and 23–40% based on application of a demographic model of population admixture.61 Although the Jomon admixture proportion is still debatable, we would like to conclude that the Jomon component in the mainland Japanese is probably lower than 20%.

Journal of Human Genetics volume62, pages213–221 (2017)

Last Edit: Aug 25, 2018 19:44:55 GMT by Admin

Admin
Administrator

Posts: 81,210

Jomon: Paleolithic Contingent in Modern Japanese Feb 4, 2019 17:57:30 GMT

Quote

Post by Admin on Feb 4, 2019 17:57:30 GMT

It is believed that the modern Japanese ethnic population consists of a mixture of the Jomon people, who have existed in Japan since at least the New Stone Age, and the Yayoi people, who migrated to western Japan from China via Korea approximately 2000 to 3000 years ago and were responsible for spreading rice cultivation [25] (Fig. 1). There are many studies that describe this dual structure model of the Japanese people based on analysis of elements such as the human Y chromosome, mitochondria, single nucleotide polymorphism (SNP), archeological data and historical records [3, 7–10, 19–21, 26, 28]. Sokal and Thompson [26] interpreted the cause of the genetic distribution to have resulted from the selection, admixture and resolving power of a locus that reflects a particular population event. The aldehyde dehydrogenase 2 gene (ALDH2) is one of the examples among studies.

This map shows the migration of the Yayoi people and the Jomon people. The Jomon people moved to the north and south of Japan after the Yayoi people migrated to central Japan

Previous studies have shown that approximately 2000 to 3000 years ago, a variant of ALDH2 was present within the Chinese population. Citing historical evidence [18], researchers speculated that people with this ALDH2 variant migrated to western Japan 2000 to 3000 years ago. Oota et al. [22] claimed that based on actual DNA evidence, this ALDH2 variant was a young haplotype associated with low levels of genetic diversity. Therefore, it may be possible that this mutation of the ALDH2 gene and the Yayoi migration from China to Japan happened in roughly the same period.

The JC virus (JCV), one of the polyomaviruses, is a useful marker in tracing the dispersal of human populations [30]. This is because once an individual is infected asymptomatically with JCV during childhood [23, 24], the initially infected JCV strain persists in renal tissue for life, and other strains of JCV are unable to infect the already infected individual [2, 13, 29]. There are more than 20 main JCV genotypes that are distributed in geographically distinct domains throughout the world [30]. Two major types of JCV genotypes, CY and MY, are found in the Japanese archipelago [14] (Fig. 2a). The genotype CY is commonly distributed in western Japan, northeast China, and Korea [5, 6] and is not found in other places [27, 32]. Earlier studies suggested that the Chinese might have brought the CY genotype JCV to Japan when they migrated from China [14]. The genotype MY is commonly distributed in eastern Japan and among Native Americans [27, 32].

Fig. 2
a Map showing the distribution of the two major JCV genotypes (CY and MY) in Japan. The areas in which CY and MY were found more frequently (i.e., at rates >75 %) are indicated as CY-rich or MY-rich areas, respectively. The area designated as the intermediate area is where the genotypes CY and MY were found at almost identical frequencies. This map was created utilizing data reported by Kitamura et al. [14]. b The geographic distribution of the ALDH2 variant. The orange area indicates where the frequency of the ALDH2 variant is over 24 % of the population. The ALDH2 mutation-rich area is central Japan. This map was created utilizing data reported by Li et al. [17]

JCV was detected in 66 samples. Among them, the genotype CY was detected in 33 samples and the genotype MY was detected in 33 samples. Among the 33 CY detected samples, the ALDH2 variant was detected in 17 samples (51.5 %). Among the 33 MY detected samples, the ALDH2 variant was detected in only 8 samples (24.2 %). All of the ALDH2 variants were Glu/Lys heterozygotes. Lys/Lys homozygotes were not detected in the samples. The ALDH2 variant was found more commonly in people who carry the CY genotype JCV than in people who carry the MY genotype JCV (Table 1) (p value 0.04, odds ratio 0.30).

Table 1
Association between the JCV genotype and the ALDH2 variant

MY genotype CY genotype
ALDH2 variant 8 17
(Glu/Lys heterozygote)
ALDH2 wild type 25 16
(Glu/Glu homozygote)
Total 33 33
Lys/Lys homozygote was not detected in this study.

Discussion
The results of the present study suggest that the ALDH2 variants are more prevalent in people with CY genotype JCV than in people with MY genotype JCV (Table 1).

In an earlier study, the CY genotype JCV was found to be more common in western Japan, and the MY genotype JCV was found to be more common in Eastern Japan [14] (Fig. 2a). The CY genotype JCV was also found in China [5, 6], but the MY genotype JCV was found mainly in the Japanese archipelago and in North and South America [32]. Estimated from the substitution rate of the JCV genome, the MY clade occurred more than approximately 10,000 to 30,000 years ago [31], and the CY clade occurred approximately 10,000 years ago. Therefore, the MY genotype JCV initially occurred in the Japanese archipelago and spread to the Americas, and later, the CY genotype JCV migrated from China to Japan. It is possible that the ALDH2 mutation only occurred within people who carry the CY genotype JCV, explaining why it is uncommon for people who carry the MY genotype JCV to have the ALDH2 mutation. Another study indicates that Native Americans do not have the ALDH2 mutation [4]. Combining this information with the results of Zheng et al. [32], we can speculate that people who carry the MY genotype JCV may not have originally had the ALDH2 mutation. Those findings also support the relation of the CY genotype JCV with the ALDH2 mutation. Therefore, it is inferred that the ALDH2 gene mutation spread into East Asia in the past few thousand years. This may be a good example of a locus subjected to selection, displaying wide distribution, and high frequency with low associated variation, confined to a continental region.

However, there are some people with the ALDH2 mutation and the MY genotype JCV, and some people are without the ALDH2 mutation and with the CY genotype JCV.

It is believed that there are several reasons for this. First, extensive genetic mixing between Yayoi and Jomon is expected to have occurred after the major migration 2000 to 3000 years ago and before the present day, when our samples were collected. Second, the ALDH2 genes from both parents are passed down and combined forming their child’s ALDH2 gene type. As a result, there is a 50 % possibility of inheriting the ALDH2 mutation from a father or mother carrying the gene. However, in the case of the JCV genotype, the possibility of infection with JCV from one’s father or mother is affected by the number of exposures to their urine. As a result, if the infection rate of one JCV genotype is high within a given area, subsequent generations are less likely to be infected by JCV of other genotypes, which in turn becomes less common through natural selection. Minority groups of viral genotypes are excluded by the dominant genotype within a given area during a given period. These differences in the acquisition of infection from a local majority or minority strain of a virus or the inheritance of a mutant or non-mutant version of a gene on the other might be the cause of the differences in distribution of the JCV genotypes and the ALDH2 mutation in Japan (Fig. 2a, b).

After a study reported evidence of greater genetic affinity between Ainu and Ryukyuan people (i.e., people indigenous to Okinawa and a surrounding chain of islands between Japan and Taiwan) than between either group from the Japanese mainland populations [11], it was suggested that the Jomon migrated to the north and south of the Japanese archipelago in response to the Yayoi migration from China to western Japan (Fig. 1). Because the ALDH2 mutation is thought to be common among Yayoi, the distribution of the CY genotype JCV is believed to be the same as the distribution of those people who have the ALDH2 mutation (Fig. 2a, b). However, Kitamura et al. [14] reported that the most common genotype found in Okinawa is CY. This is contradictory to the idea of the Jomon migration to Okinawa and Tohoku (the northeast region of the main island of Japan) with their MY genotype JCV, following the migration of the Yayoi people to the main islands of the Japanese archipelago. According to our model, all specimens from before the Yayoi arrival would lack both the ALDH2 mutation and the CY viral genotype while bearing the MY genotype. Further studies are necessary to examine other aspects of the Yayoi arrival. The potential value of studying ancient DNA in pre-Yayoi era specimens of the Ryukyuans and other populations in Japan using viral genome capture techniques and ALDH2 mutation analysis could help solve the mystery of the apparent rarity of the MY variant JCV in modern Ryukyuan populations [15].

From these findings, it may be inferred that the ALDH2 mutation, which is related to the Yayoi, is related to CY genotype JCV. When the Yayoi migrated to the Japanese archipelago, they brought the ALDH2 mutation as well as the CY genotype JCV.

Investig Genet. 2015; 6: 14.

Admin
Administrator

Posts: 81,210

Jomon: Paleolithic Contingent in Modern Japanese Feb 18, 2019 18:23:57 GMT

Quote

Post by Admin on Feb 18, 2019 18:23:57 GMT


Table 1. Descriptive statistics for IQs and related variables for prefectures in Japan.

Prefecture	Latitude	Height (cm)	IQ (test score)	Skin color	Income (1000 yen)	Labor prop. (%)	Homicide (/100,000)	Divorce (/100,000)	Fertility (/100,000)	Infant mortality (/100,000)	Suicide (/100,000)

Aichi	35.2	170.38	328.2	48.3	2970	66.88	8.94	19.89	14.1	26.9	21.1
Akita	39.7	171.7	345.7	70.3	2438	60.42	5.61	16.83	13.3	25.2	38.1
Aomori	40.8	171.44	325.8	58.2	2365	63.14	7.49	21.70	14.1	28.4	35.8
Chiba	35.6	171.08	317	40	3048	67.61	10.9	20.93	12.7	26.2	22.7
Ehime	33.8	170.08	325.4	45.6	2534	61.84	11.27	20.69	14	21.3	27.1
Fukui	36.1	171.21	349.2	65.6	2839	62.02	6.72	16.69	15.37	27.4	26.3
Fukuoka	33.6	170.24	313.2	50.3	2721	65.40	10.9	23.04	13.4	26.1	26.2
Fukushima	37.7	170.53	318.4	56.5	2803	62.23	6.48	20.16	15.2	27.5	29.2
Gifu	35.4	170.67	333.4	55	2779	63.72	7.72	17.41	13.7	28.0	25.7
Gunma	36.3	170.81	329.8	53.1	2877	64.29	9.66	19.87	14	27.2	27.7
Hiroshima	34.4	169.9	322.2	45.2	3013	64.01	10.03	19.83	14.3	24.8	23.6
Hokkaido	43.1	170.98	311.5	50.4	2608	64.91	8.4	24.20	11.9	25.7	28.2
Hyogo	34.7	170.79	323.4	56	2868	64.96	11.44	20.42	13.2	24.1	23.9
Ibaraki	36.3	170.9	319	41.8	2945	65.71	9.84	19.97	13.7	26.7	25.1
Ishikawa	36.6	171.56	335.3	59.9	2929	64.03	7.4	16.77	14	28.6	24.2
Iwate	39.7	170.88	311.9	62.2	2427	61.29	7.41	17.82	14.1	31.6	35.2
Kagawa	34.3	170.26	330	44.5	2746	62.19	12.97	20.28	14.8	25.5	22.2
Kagoshima	31.6	170.23	313.1	34.8	2297	60.47	7.89	20.29	15.5	28.4	28.9
Kanagawa	35.4	171.21	316.9	45.8	3341	68.34	9.02	21.20	12.6	28.6	19.8
Kochi	33.6	170.1	294.4	23.3	2248	60.48	12.38	21.77	13.4	30.9	31.3
Kumamoto	32.8	170.32	322.9	48.1	2319	61.47	8.75	20.24	15.5	26.9	26.6
Kyoto	35	171.32	318.2	70.8	2904	65.38	8.97	19.95	12.1	24.9	22.5
Mie	34.7	170.66	317.8	50.7	2968	63.62	7.58	19.53	13.9	27.4	23.2
Miyagi	38.3	170.76	319.2	50.5	2645	65.63	8.1	20.15	12.8	27.6	25.6
Miyazaki	31.9	170	325.3	37.9	2236	61.44	8.42	23.14	15.8	26.2	31.6
Nagano	36.6	170.54	320.3	47.3	2894	61.28	6.86	18.12	14.8	20.0	25.6
Nagasaki	33.2	170.53	323.5	32.2	2209	61.61	6.65	19.44	15	29.9	27.7
Nara	34.7	170.77	327.3	57.2	2749	64.96	8.51	18.91	12.3	26.9	21
Niigata	37.9	171.49	318.8	52.8	2771	62.09	7.91	15.10	13.9	24.5	32.1
Okayama	34.7	170.06	316.1	49.3	2770	62.52	9.74	19.53	14.2	24.7	26.1
Okinawa	26.2	169.09	271.8	40.1	2056	65.13	14.66	26.77	17.8	25.6	22
Ooita	33.2	170.19	315.4	49.8	2631	61.40	7.52	20.35	14.9	28.0	25.8
Osaka	34.7	170.91	303.9	57.3	3126	66.33	14.64	24.63	12.6	26.3	23
Saga	33.2	170.44	315.1	45.5	2484	61.88	8.79	19.00	15.4	23.0	27.7
Saitama	35.9	170.98	315.5	43.8	3027	68.33	9.77	20.73	12.7	25.9	22.7
Shiga	35	171.37	319.2	61.3	3217	65.74	7.98	18.25	14.5	30.1	24.4
Shimane	35.5	170.54	322.1	66.6	2444	59.01	6.62	15.87	15.6	25.8	31.8
Shizuoka	35	170.44	327.1	45.6	3271	64.51	9.06	19.93	14.3	25.2	24.1
Tochigi	36.6	170.45	319.9	40.2	3050	65.70	9.15	20.46	14.2	30.3	27.8
Tokushima	34.1	170.29	324.4	40.3	2754	61.83	8.06	19.31	13.4	32.4	22.1
Tokyo	35.7	171.14	320.9	60.2	4409	68.99	10.51	21.64	10.7	25.6	22.4
Tottori	35.5	171.21	325.8	39	2459	61.51	6.3	19.95	14.9	25.6	28.9
Toyama	36.7	171.46	342.2	51.3	3144	62.47	6.86	15.60	13.8	28.5	28.7
Wakayama	34.2	170.93	314.9	38.5	2543	61.52	11.39	21.95	13.8	27.7	29.8
Yamagata	38.2	171.28	330.6	66	2461	60.71	5.7	16.86	14.5	28.0	29.9
Yamaguchi	34.2	170.22	324.2	53.5	2875	60.98	9.46	19.08	14.3	24.7	26.3
Yamanashi	35.7	170.65	320.2	47.8	2765	63.08	9.9	19.85	13.7	22.9	38.5

Latitude is correlated with IQ (r = 0.44) and height (r = 0.70). From many collected IQ measurements, the Japanese average IQ has been estimated to be 104, which is slightly lower than the Chinese and Korean averages (Lynn & Vanhanen, 2006; Lynn, 2008, Lynn and Meisenberg, 2010, Lynn and Vanhanen, 2012). Assuming that the Japanese population has a standard deviation of 15 as in England, north–south IQ difference is estimated to be 11 points, with the prefecture with the highest IQ prefecture (Akita) having 107 while the one with the lowest (Okinawa) having 96. This is surprising in that it challenges the much-touted homogeneity of Japanese people.

Latitude and height are correlated at 0.70, more than between latitude and IQ. The difference is at most 2.6 cm, or about one inch. To see if these results depend on some possible outliers, Spearman's rho and Kendall's tau were calculated. Latitudes correlate with height at 0.72 and 0.71, and height and IQ at 0.24 and 0.43. Other variables also showed the same directional coefficients as Table 1, while some of the values were slightly lower than Pearson's. Together, these analyses suggest that the correlations above have validity.

The regions facing the Korean peninsula or the Asian continent have greater snowfall and are several degrees colder than those facing the Pacific Ocean. This might be the reason that people in the former prefectures have lighter skin than those in the latter. Skin whiteness is positively correlated with latitude (r = 0.47) and also with IQ (r = 0.42), as studies based on both theoretical and empirical grounds (Meisenberg, 2004, Rushton and Templer, 2012, Templer and Arikawa, 2006, Templer and Rushton, 2011). It would be also due to genetic admixture with south east Asians from the sea route, although there exists no such description in the written history that dates back to 1500 years ago.

In keeping with the previous research findings, IQ correlates negatively with homicide rate (Wilson and Herrnstein, 1985, Herrnstein and Murray, 1994, Templer et al., 2007; Lynn, 2008; Rushton & Templer, 2009), and fertility (Meisenberg, 2009, Meisenberg, 2010, Vining, 1982).

IQ has a positive correlation with IQ (Voracek, 2004, Voracek, 2009). However, after partialing out the influence from latitude, the partial correlation of IQ/homicide became − 0.079. Hence, it seems more appropriate to conclude that weaker sunlights in the northern prefectures tend to make people feel depressed, which results in higher suicide rates. Also infant mortality does not correlate with other variables, presumably because Japan has well-developed medical institutions. Medical treatments are readily accessible for relatively poor people thanks to a long-established, nationally inclusive medical insurance system.

Note the similarity of the gradients of these variables from north to south as shown in Fig. 1.

Many people worldwide seem to have an image of Japan as a highly homogeneous nation. However, the Japanese islands were initially populated by the hunter–gatherer Jomon people (Y haplogroup C1, C3 & D1) and experienced a great deal of immigration from the Korean peninsula and mainland China from 2900 to 1500 years ago. These incoming Yayoi people (Y haplogroup O2b from Korea and O3 from China) brought wet-rice agriculture and bronze and iron tools to the islands. Because of these cultural advancements, they had shown much more fecundity and have in number dominated the native Jomon people. There still exists a genetic cline from the Western Yayoi population in the Eastern Jomon population in Japan (Hammer et al., 2006). Haplogroups, C1, C3 and D2 are most common among the Ainu people in the northmost Japan (almost 100%) and in the Okinawans in southmost Japan (about 60%),while the western regions closer to the Korean peninsula are more densely populated by Yayoi descendant haplogroup of O2b and O3 (60–70%).

Jomon

Since the continental Northeast Asians (Han Chinese and Korean) have a higher intelligence compared to the rest of the Eurasian population, it would be natural to assume that these Yayoi people were more intelligent. This conjecture is based on the facts: 1. The fossil evidence shows that the Yayoi people were 5–8 cm (2–3 in.) taller than the Jomon; 2. Modern-day Koreans are about 3 cm (1.2 in.) taller than the Japanese; 3. The IQs of Chinese and Korean people have continuously outscored that of Japanese people (estimated to be 106 and 105, respectively). Hence, it is reasonable to expect that the prefectures closer to the continent exhibit higher intelligence than those in the Northeast.

Okinawa

However, this tendency was not observed and instead there exists a simple intelligence gradient from south to north. This may be due to an almost perfect admixture within the last 1500 year (about more than 60 generations) as far as genes for taller stature and higher intelligence are concerned, as well as the selective pressures of the last 1500 years of civilization, which have been strong enough to reshape the original east–west IQ gradient into the current north–south cline. This conclusion would be in line with the Hawks, Wang, Cochran, Harpending, and Moyzis (2007)idea of ever-accelerating human evolution. They insist that more and more beneficial mutations swept populations, after the advent of agricultural civilizations with metallurgy, letters and complex hierarchical organizations. The Japanese north–south gradient in height and intelligence can be evidence that modern humans have evolved to higher intelligence within the last two millennia.

Intelligence
Volume 41, Issue 5, September–October 2013, Pages 512-516

Last Edit: Feb 18, 2019 18:25:45 GMT by Admin

Admin
Administrator

Posts: 81,210

Jomon: Paleolithic Contingent in Modern Japanese Feb 19, 2019 18:50:31 GMT

Quote

Post by Admin on Feb 19, 2019 18:50:31 GMT

The Jomon period of the Japanese Archipelago, characterized by cord-marked ‘jomon’ potteries, has yielded abundant human skeletal remains. However, the genetic origins of the Jomon people and their relationships with modern populations have not been clarified. We determined a total of 115 million base pair nuclear genome sequences from two Jomon individuals (male and female each) from the Sanganji Shell Mound (dated 3000 years before present) with the Jomon-characteristic mitochondrial DNA haplogroup N9b, and compared these nuclear genome sequences with those of worldwide populations.

We found that the Jomon population lineage is best considered to have diverged before diversification of present-day East Eurasian populations, with no evidence of gene flow events between the Jomon and other continental populations. This suggests that the Sanganji Jomon people descended from an early phase of population dispersals in East Asia. We also estimated that the modern mainland Japanese inherited <20% of Jomon peoples’ genomes. Our findings, based on the first analysis of Jomon nuclear genome sequence data, firmly demonstrate that the modern mainland Japanese resulted from genetic admixture of the indigenous Jomon people and later migrants.

Introduction
Genome-wide single-nucleotide polymorphism (SNP) data analyses1, 2 support the dual-structure model3, 4 for the formation of modern Japanese populations, in which indigenous Jomon people admixed with later migrants who brought rice agriculture. The Jomon culture geographically ranged from Hokkaido to the Okinawa islands, and the Jomon people inhabited the Japanese Archipelago from ~16000 to 2500 years before present (YBP).5, 6 The origins and phylogenetic relationships of the Jomon people, however, are still elusive.

Ancient DNA sequences of the Jomon people provide direct evidence of their genetic characteristics. Mitochondrial DNA (mtDNA) sequences of the Jomon people and their haplotypes have been determined for many individuals.7, 8, 9, 10, 11, 12 Haplogroup N9b, whose frequency is generally low in modern East Eurasians,13, 14 was found to be quite frequent in the mtDNA of the Jomons.9, 10, 11 This suggests a long-term isolation of the Jomons from continental populations. However, inferring human population history only from mtDNA data are insufficient because of their limited genetic information. Thanks to new technologies, it is now possible to analyze nuclear genome sequences of ancient human remains15, 16, 17, 18, 19, 20, 21, 22, 23 and those of modern human individuals.24 We therefore determined the nuclear genome sequences of two Jomon individuals and compared them with available data so as to infer the origin of modern Japanese.

Admin
Administrator

Posts: 81,210

Jomon: Paleolithic Contingent in Modern Japanese Feb 20, 2019 18:23:16 GMT

Quote

Post by Admin on Feb 20, 2019 18:23:16 GMT

We estimated error rates in 16 modern/archaic human genomes16, 19, 22 as well as in Sanganji Jomon. Although the error rate of the Sanganji Jomon sequence was 0.828–0.848% over all sites, the error rate was only 0.011–0.015% in the transversion sites, which is comparable with the rate in modern humans (Supplementary Table S7). PickingBases (PB) removed more errors compared with MarkDuplicates (Supplementary Table S7). We found more transition substitutions (A/G or C/T) in Sanganji Jomon than in other modern humans, which appears to be caused by post-mortem changes characteristic of ancient DNA (Supplementary Tables S8-S9). We also would like to note that Jomon-specific transversion substitutions (0.0129%) and unreported transversions in dbSNP 141(0.0113%) were comparable (Supplementary Table S7). Similar values were also observed in modern human data, and this comparison strengthens the low error rate of the Sanganji Jomon nucleotide sequences. Interestingly, the number of SNPs reported in dbSNP was small in Sanganji Jomon compared with other non-Africans; for example, 4169 and 5270 in Sanganji Jomon and Han, respectively (Supplementary Table S7). This observation is consistent with our expectation that many Jomon SNPs are unreported in dbSNP. We confirmed the reliability of PB in PCA, and the result using PB are concordant with that of MarkDuplicates, and are not biased (Figure 1a and Supplementary Figure S7). Because of smaller sequence error rates of PB than that of MarkDuplicates, we used data sets treated with PB for further analyses. In total, 28 288 sites were masked as N with PB.

Figure 1

Genetic relationship between Sanganji Jomon and other modern and archaic humans
We investigated the genetic relationships between Sanganji Jomon and modern humans from different parts of the world, including Africans, West Eurasians, East Eurasians, Native Americans and Sahulians37 (descendants of people who migrated to Sahul land); see the map shown in Supplementary Figure S1.

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.

Figure 2

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).