2015 paper concludes that migrants from Northeast China via Korea bearing the CY JC virus genotype brought the ALDH2 mutation to Central Japan forming the Yayoi populations

https://static-content.springer.com/image/art%3A10.1186%2Fs13323-015-0031-1/MediaObjects/13323_2015_31_Fig2_HTML.gif

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.

 

Miyamori, Daisuke et al., Tracing Jomon and Yayoi ancestries in Japan using ALDH2 and JC virus genotype distributions Investigative Genetics 2015 6:14 DOI: 10.1186/s13323-015-0031-1 ©  Miyamori et al. 2015

Overall findings of this study were that the ALDH2 variant is significantly higher in the population with the CY genotype JCV (51.5 %) than in the population with the MY genotype (24.2 %) (p < 0.05) in Japan

Abstract

Background

According to the dual structure model, 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 around the year 300 BC. Some reports show that the Yayoi are linked to a mutation of the aldehyde dehydrogenase 2 gene (ALDH2).

Recent viral studies indicate two major groups found in the Japanese population: a group with the CY genotype JC virus (JCV) and a group with the MY genotype JCV. It is unclear whether either genotype of the JC virus is related to the Jomon or Yayoi.

In this study, we attempted to detect JCV genotypes and ALDH2 mutations from the DNA of 247 Japanese urine samples to clarify the relationship between the dual structure model and the JCV genotype through ALDH2 mutation analysis and JCV genotyping.

Findings

The ALDH2 polymorphism among 66 JC virus-positive samples was analyzed, and it was found that the ALDH2 variant is significantly higher in the population with CY genotype JCV (51.5 %) than in the population with the MY genotype (24.2 %) (p < 0.05).

Conclusion

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.

JC virus ALDH2 mutation Japanese

Introduction

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, 8, 9, 10, 19, 20, 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.

https://static-content.springer.com/image/art%3A10.1186%2Fs13323-015-0031-1/MediaObjects/13323_2015_31_Fig1_HTML.gif

Fig. 1

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].

https://static-content.springer.com/image/art%3A10.1186%2Fs13323-015-0031-1/MediaObjects/13323_2015_31_Fig2_HTML.gif

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]

This JCV distribution may support the dual structure model of the Japanese population. However, there have been no studies verifying the correlation between the distribution of the CY genotype JCV and the dual structure model.

Therefore, through the detection of the ALDH2 mutation among JCV-positive Japanese samples, we investigated its correlation with the CY genotype JCV, and we discuss whether the dual structure model is also supported by JCV genotype in this study. …

Results

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].

Conclusion

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.

Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

…………………………………………………………………………………………………….

See also another 2015 paper:

Timothy A. Jinam, Hideaki Kanzawa-Kiriyama and Naruya Saitou, Human genetic diversity in the Japanese Archipelago: dual structure and beyond Genes Genet. Syst. (2015) 90, p. 147–152

The paper concludes that “genetic data strongly support the dual-structure model proposed by Hanihara (1991) whereby the Hondo Japanese are the result of admixture between the Jomon and Yayoi ancestral populations (Fig. 2). The indigenous Ainu and Ryukyuan populations retain a genetic identity that most likely traces back to Jomon ancestors, while at the same time show indications of recent admixture with the Hondo Japanese”…whilst noting that “The genetic substructure in the Hondo Japanese also hints at a more complex model of human migrations and interactions than the dual structure model implies”.

*******************

On the origins of the ALDH2*487gene associated with the marked facial flushing and alcohol intoxication trait of East Asians, an earlier 2009 paper traced the source of this mutation and phenotype to Yunnan, South coastal, East coastal regions of China, on a cline decreasing gradually towards inland China, West, Northwest and North China:

“Five major haplotypes based on five SNPs across the ALDH2gene 40 kb were found in all East Asian populations. The frequencies of the ancestral haplotype GCCTG and the East Asian special haplotype GCCTA containing the atypical ALDH2*487Lys allele were 44.8% and 14.9%, respectively. The frequency of the atypical ALDH2*487Lys allele or the East Asian specific haplotype GCCTA is high in Yunnan, South coastal, east coastal of China, and decreased gradually toward inland China, West, Northwest and North China. Combined with demographic history in East Asian, our results showed that the presence of ALDH2*487Lys allele in peripheral regions of China might be the results of historical migration events from China to these regions. The origin of ALDH2*487Lys could be possibly traced back to ancient Pai-Yuei tribe in South China.” – Source: .Luo HR, Wu GS, Pakstis AJ, Tong L, Oota H, Kidd KK, and Zhang YP. 2009. Origin and dispersal of atypical aldehyde dehydrogenase ALDH2*487Lys. Gene. 435:96–103. PDF fulltext link

This proposed origin in the Pai-Yuei population group was expanded upon in Jennifer Gueldner, et al.,’s “Emerging Associations of the ALDH2*2 Polymorphism with Disease Susceptibility“, Gueldner et al., J Drug Metab Toxicol 2016, 7:2 http://dx.doi.org/10.4172/2157-7609.1000202

Characterization of ALDH2*2 ALDH2 was first identified in 1987, with the X-Ray crystallographic structure of the gene product elucidated in 1999 [25]. Although the ALDH2*1 allele is most common in populations worldwide, the allele frequency of the ALDH2*2 variation as either homozygous or heterozygous is 35-45% in East Asians [8,26]. All individuals with ALDH2 enzymatic deficiency examined to date remarkably carry the same amino acid substitution, which can be traced back approximately 2000-3000 years to the Han Chinese [27]. Luo et al. noted that the specific halpotype carrying the ALDH2*2 allele was highest in frequency in the Yunnan, South coastal, and East coastal areas of China and decreases in frequency further inland. According to archeological and historical evidence from this time period, evidence points to the Pai-Yuei tribe as an origin of the mutation, as they occupied the Southeastern coast of China into the Yunnan area as early as 16 B.C. Нe Pai-Yuei people established an independent country in this area, which lasted for around 160 years until it was conquered by other tribes. Нe Yuei people then scattered to other areas of South and Southwest China, Vietnam, and Нailand where they integrated with other tribes, especially the Han tribe [27]. Нis scattering correlates with the distribution of the ALDH2*2 mutation amongst people of East Asian descent”

[See also William Meacham’s Defining the Hundred Yue Bulletin of the Indo-Pacific Prehistory Association]

In another 2010 study however, it was further found that the

“geographic distribution of ALDH2*504Lys, … The allele is essentially absent in all parts of the world except East Asia. The ALDH2*504Lys allele has its highest frequency in Southeast China, and occurs in most areas of China, Japan, Korea, Mongolia, and Indochina with frequencies gradually declining radially from Southeast China. As the indigenous populations in South China have much lower frequencies than the southern Han migrants from Central China, we conclude that ALDH2*504Lyswas carried by Han Chinese as they spread throughout East Asia. Esophageal cancer, with its highest incidence in East Asia, may be associated with ALDH2*504Lys because of a toxic effect of increased acetaldehyde in the tissue where ingested ethanol has its highest concentration. While the distributions of esophageal cancer and ALDH2*504Lys do not precisely correlate, that does not disprove the hypothesis. In general the study of fine scale geographic distributions of ALDH2*504Lys and diseases may help in understanding the multiple relationships among genes, diseases, environments, and cultures.” – Source: Hui Li, et al., Refined Geographic Distribution of the Oriental ALDH2*504Lys (nee 487Lys) VariantAnn Hum Genet. 2009 May; 73(Pt 3): 335–345. doi:  10.1111/j.1469-1809.2009.00517.x

Advertisements

How did 3rd ~ 4th c. Roman coins end up in the 12th~15th c. Katsuren Castle on Okinawa?

Above: A coin issued by the Roman Empire and recently excavated from castle ruins in Okinawa is shown Monday at the Uruma Municipal Govt office in Okinawa Below: Other relics unearthed from the site include a coin from the 17th century Ottoman Empire Photo: KYODO

Above: A coin issued by the Roman Empire and recently excavated from castle ruins in Okinawa is shown Monday at the Uruma Municipal Govt office in Okinawa Below: Other relics unearthed from the site include a coin from the 17th century Ottoman Empire Photo: KYODO

 

Ancient Roman coins unearthed from castle ruins in Okinawa  KYODO SEP 26, 2016, via Japan Times

Coins issued in ancient Rome have been excavated from the ruins of a castle in Okinawa Prefecture, the local board of education said, the first time such artifacts have been discovered in Japan.

The board of education in the city of Uruma said the four copper coins, believed to date back to the Roman Empire in the third to fourth centuries, were discovered in the ruins of Katsuren Castle, which existed from the 12th to 15th centuries.

Okinawa’s trade with China and Southeast Asia was thriving at the time and the finding is “precious historical material suggesting a link between Okinawa and the Western world,” the board of education said.

Each coin measures 1.6 to 2 cm in diameter. The designs and patterns on both sides are unclear due to abrasion.

Based on X-ray analysis, however, the board said the coins appear to bear an image of Constantine I and a soldier holding a spear. Other relics unearthed from the site include a coin from the 17th century Ottoman Empire, as well as five other round metallic items that also appear to be coins.

The ruins of Katsuren Castle were registered in 2000 on the World Heritage list as part of the Gusuku Sites and Related Properties of the Kingdom of Ryukyu, a group of ancient monuments and castle ruins in the island prefecture.

The coins will be displayed at Uruma City Yonagusuku Historical Museum in central Okinawa until Nov. 25.


Corrected: On Sept. 28 we corrected the caption and added a new photo of the Roman coin

Archaeologists find world’s oldest fishhooks on Okinawa Island

 

Sakita Cave

FIshhooks carved from shells from Sakitari Cave

World’s oldest fishhook found on Okinawa by Michael Price, Science Magazine Sep 16, 2016

There’s no telling what kinds of fishermen’s tales they told, but the early modern humans who lived on tiny Okinawa Island between mainland Japan and Taiwan nearly 30,000 years ago are the world’s oldest known anglers. Now, archaeologists have discovered the oldest known fishhooks in a limestone cave in the island’s interior, dating back nearly 23,000 years. The fishhooks, all carved from shells, were found in Sakitari Cave, which was occupied seasonally by fishermen taking advantage of the downstream migrations of crabs and freshwater snails. Unlike their mainland counterparts, who fashioned tools and beads out of shells and stones, the ancient people of Okinawa Island used shells almost exclusively. Japanese archaeologists excavating the cave discovered both a finished and an unfinished fishhook that had been carved and ground from sea snail shells. By radiocarbon dating pieces of charcoal found in the same layer as the fishhooks, the researchers determined the hooks were between 22,380 and 22,770 years old. Accounting for margin of error, that gives them an edge over similar fishhooks found in East Timor (between 23,000 and 16,000 years old) and New Ireland in Papua New Guinea (20,000 to 18,000 years old). The findings lend support to the idea that these early modern humans were more advanced with maritime technology than previously thought, and that they were capable of thriving on small, geographically isolated islands.

 

 

Further source references:

This finding possibly reverses the finding that fishing technology emerged from the south Island South East Asia, diffusing northwards along the Pacific Rim. The direction of diffusion may thus have been in the opposite direction. While archaeologists may have found the oldest fishhook artefacts and this is evidence of early fishing technology in the Pacific Rim region, the oldest known maritime fishers were previously believed to have been the nearby prehistoric Timor islanders. See Fishing techniques of the Jomon people may have diffused from fishermen of the Wallacea-Spice Islander / Sundaland-Sahul region

This finding would also be more concordant with Matsumoto’s GM study The origin of the Japanese race based on genetic markers of immunoglobin G  which found that none of the Japanese populations surveyed, including the Ainu or those from the Okinawa and southern islands shared the same GM marker pattern as southern Melanesian or Micronesian groups southern group, who showed a remarkably high frequency of the afb1b3 marker (excepting a very small component of the mainland Japanese in Osaka and Sendai that attributable to later admixing influxes from the continent). Other Japanese early fishing technology have shown similarities to prehistoric Northeast Pacific Rim fishing lithics.

日本人の起源に迫る「サキタリ洞人」の登場