Heritage of Japan

Image of a maize weevil impression from the surface of a pottery fragment.
CREDIT: Prof. Hiroki Obata

Researchers from Kumamoto University have studied nationwide maize weevil impressions from 10,000 year-old pottery,  from the southern Japanese island of Tanegashima,  to pottery fragments from the Sannai-Maruyama site in northern Aomori., to Tatesaki archaeological site in Hokkaido.

The study comparing the differential in the size of  nationwide samples of weevil impressions in the west from the 20 per cent larger ones in the northeast revealed that pots in the west stored acorns while pots in northeastern climes stored chestnuts.

As chestnuts are not native to Hokkaido,  the presence of the maize weevils is evidence that the Jomon people of Tohoku  from south of Hokkkaido, carried supplies including chestnuts infested by weevils, over the Tsugaru Strait by ship.

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See excerpts from the study below:

Hiroki Obata et al, Discovery of the Jomon era maize weevils in Hokkaido, Japan and its mean, Journal of Archaeological Science: Reports (2018). DOI: 10.1016/j.jasrep.2018.10.037 Dec 19, 2018

Ancient Japanese pottery includes an estimated 500 maize weevils
by Kumamoto University.

Researchers have discovered an ancient Japanese pottery vessel from the late Jomon period (4500-3300 BP) with an estimated 500 maize weevils incorporated into its design. The vessel was discovered in February 2016 from ruins in Hokkaido, Japan. This extremely rare discovery provides clues on the cultivation and distribution of chestnuts, food in the Jomon era, and the spirituality of ancient Japanese people.

Maize weevils are beetles of the Dryophthorinae subfamily, and are destructive pests of stored rice and grains. By 2003, Jomon-period pottery and pottery fragments containing foreign-body impressions had been collected by various researchers from multiple archeological sites around Japan. Surveys of these impressions exposed hundreds of seed and insect traces on and in the pottery. Over the years, researchers found that maize weevils constituted over 90 percent of all recorded insect impressions.

In 2010, Professor Obata’s research group from Kumamoto University (KU) in Japan found maize weevil impressions in 10,000 year-old pottery that had been recovered from the southern Japanese island of Tanegashima. They showed that maize weevils, which were thought to have come from the Korean Peninsula, had damaged stored food, such as acorns and chestnuts, long before rice cultivation began in the area.

In 2012, the KU research group found maize weevils impressions in pottery fragments from the Sannai-Maruyama site in the northern Japanese prefecture of Aomori. The fact that weevils inhabited an area with a cold winter is an indicator for the distribution food by humans and a warm indoor environment that persisted throughout winter. It is presumed that weevil infestation of stored food was well underway in the Jomon period.

Interestingly, when comparing the body size of 337 maize weevil impressions found nationwide, the team discovered that the body length of maize weevils from eastern Japan was about 20 percent longer than that of western Japan. It is presumed that this body-length discrepancy is due to the different nutritional values between the types of foods they infested—the sweet chestnuts of eastern Japan vs the acorns of western Japan.

Chestnuts are not native to Hokkaido and previous studies surmised that people carried them to the northern Japanese island. The discovery of weevils at the Tatesaki archaeological site in Hokkaido is evidence that the Jomon people of Tohoku (south of Hokkaido) carried supplies, including chestnuts infested by weevils, over the Tsugaru Strait by ship.

See more photos and read more about the research here.

References and further readings:

Hiroki Obata et al, Discovery of the Jomon era maize weevils in Hokkaido, Japan and its mean, Journal of Archaeological Science: Reports (2018). DOI: 10.1016/j.jasrep.2018.10.037 Dec 19, 2018

Ancient Japanese pottery includes an estimated 500 maize weevils -The rare discovery of a vessel with a high number of weevils provides clues to life in ancient Japan (Kumamoto University website) The images above are used in compliance with the image use restrictions from this webpage. See more photos and read more about the research here.

Fig. 1: High-resolution spectra of mtDNA haplogroups in the Japanese population.

From: Genetic and phenotypic landscape of the mitochondrial genome in the Japanese population  (Open Access pub. under Creative Commons license)

c Stacked bar plots of the frequencies of the macrohaplogroups within the geographical regions in Japan and subpopulations from 1KG. The geographical regions in Japan are defined as Hokkaido, Tohoku, Kanto-Koshinetsu, Chubu-Hokuriku, Kinki, Kyushu, and Okinawa from northeast to southwest areas of Japan, as described elsewhere42.

Below is an excerpt of the open access 2020 paper:

Yamamoto, K., Sakaue, S., Matsuda, K. et al. Genetic and phenotypic landscape of the mitochondrial genome in the Japanese population. Commun Biol 3, 104 (2020). https://doi.org/10.1038/s42003-020-0812-9 PDF

Abtstract

The genetic landscape of mitochondrial DNA (mtDNA) has been elusive. By analyzing mtDNA using the whole genome sequence (WGS) of Japanese individuals (n = 1928), we identified 2023 mtDNA variants and high-resolution haplogroups. Frequency spectra of the haplogroups were population-specific and were heterogeneous among geographic regions within Japan. Application of machine learning methods could finely classify the subjects corresponding to the high-digit mtDNA sub-haplogroups. mtDNA had distinct genetic structures from that of nuclear DNA (nDNA), characterized by no distance-dependent linkage disequilibrium decay, sparse tagging of common variants, and the existence of common haplotypes spanning the entire mtDNA. We did not detect any evidence of mtDNA–nDNA (or mtDNA copy number–nDNA) genotype associations. Together with WGS-based mtDNA variant imputation, we conducted a phenome-wide association study of 147,437 Japanese individuals with 99 clinical phenotypes. We observed pleiotropy of mtDNA genetic risk on the five late-onset human complex traits including creatine kinase (P = 1.7 × 10−12).

… Here we provide a comprehensive analysis that characterizes the genetic and phenotypic landscape of mitochondria in the Japanese population. (i) We constructed a high-resolution mtDNA variant list and haplotype classifications in the Japanese population based on deep WGS of ~2000 individuals. (ii) We conducted unsupervised clustering of the mtDNA variant patterns and assessed their correspondence with defined haplogroups by using a set of machine learning (ML) methods. (iii) We quantitatively assessed positional distributions and LD structure of the mtDNA variants by parallelly comparing with those of nDNA. (iv) We performed genome-wide scans to investigate the mtDNA–nDNA and mtCN–nDNA genotype associations. (v) Finally, we conducted mitochondrial genomewide genotype imputation of genome-wide association study (GWAS) data of more than 140,000 Japanese individuals, by using the population-specific WGS reference data. We then conducted a PheWAS [Phenome-wide association study] of 99 complex human disease and quantitative traits.

RESULTS

High-resolution mtDNA variant and haplogroup lists in the Japanese population

We re-analyzed the previously reported WGS data of the Japanese population (n = 1928)18. We realigned the WGS reads on the human reference genome GRCh37, which includes the revised Cambridge Reference Sequence (rCRS, NC_012920.1) as the human reference mitochondrial genome. The rCRS has been widely used in mitochondrial genome analyses including Japanese individuals. We only used the reads uniquely mapped on the mitochondrial region to avoid the contamination of nuclear copies of the mitochondrial genome (nuMTs)19. In this study, we focused on the analyses of homoplasmy. Then, we identified 2023 variant sites, of which 63 sites were multiallelic (the mean depth = 1488; Supplementary Data 1). Of these, 516 variants (25.5%) were newly identified in our WGS data. Minor allele frequency (MAF) spectra indicated that the majority of the identified variants were rare in Japanese; rare variants (MAF < 0.5%), low-frequency variants (0.5% ≤ MAF < 5%), and common variants (MAF ≥ 5%) accounted for 79.3%, 16.4%, and 4.3%, respectively (Supplementary Fig. 1). We observed clear concordances of the alternative allele frequencies with those in the previously reported two Japanese databases (1507 and 1025 variants with 3.5 KJPN [n = 3552] and Giib-JST mtSNP [n = 672], respectively; Supplementary Fig. 2)7,20,21. As previously reported22,23, mutational spectrum indicated a high transition to transversion (Ti/Tv) ratio of 16.44 (Supplementary Fig. 3).

Next, each individual was classified into the mtDNA haplogroup based on a variant list detected by the WGS using HaploGrep (v2.1.14)24. Haplogroups are classifications of the mtDNA haplotypes defined according to a set of the specific mtDNA variants. As mtDNA is a haploid genome, the detected variants could be directly used for haplogroup classification without phasing. Nomenclature of each haplogroup is hierarchically defined based on the number of the letters (from one to nine), which was divided into sub-haplogroups (e.g, “D4b” as three letters). The number of the haplogroups monotonically increased from the macrohaplogroup (n = 11 at one letter) to the sub-haplogroups with larger number of letters (n = 310 at nine letters; Supplementary Data 2). Increments in the number of the haplogroups became limited from seven to nine letters (Fig. 1a, b).

The frequency distribution of each haplogroup was obtained according to geographical regions in Japan (as defined by BioBank Japan Project: Hokkaido, Tohoku, Kanto-Koshinetsu, Chubu-Hokuriku, Kinki, Kyushu, and Okinawa from northeast to southwest areas of Japan; Supplementary Fig. 4)18 and all the populations from the 1000 Genomes Project Phase 3 (1KG, n = 2504; Fig. 1c)25. In the Japanese population, macrohaplogroups A, B, D, M, and N had more than 1% of frequencies across all the regions. In the regions from Hokkaido to Kyushu, macrohaplogroup D was most prevalent (>28%), followed by M and B. In contrast, the different spectrum was observed in Okinawa (the islandic region at the most southwest area in Japan), where M and B were more prevalent (37.5% and 25%, respectively) than D (18.8%). Furthermore, although the D4a and D4b haplogroups were prevalent from Hokkaido to Kyushu, the D4c haplogroup was prevalent in Okinawa (Supplementary Fig. 5). Although the haplogroup spectra in 1KG East Asians (EAS) were relatively similar to those in Japanese, R was more enriched in 1KG EAS, and D, G, and M were more frequent in Japanese. 1KG populations other than EAS showed distinct haplogroup patterns from the Japanese population. M, A, H, and L were most prevalent in 1KG South Asians, Americans, Europeans, and Africans (AFR), respectively. Especially, 1KG AFR showed the least diversity within macrohaplogroups, of which African-specific macrohaplogroup of L accounted for >90% of frequencies.

Fig. 1: High-resolution spectra of mtDNA haplogroups in the Japanese population

c Stacked bar plots of the frequencies of the macrohaplogroups within the geographical regions in Japan and subpopulations from 1KG. The geographical regions in Japan are defined as Hokkaido, Tohoku, Kanto-Koshinetsu, Chubu-Hokuriku, Kinki, Kyushu, and Okinawa from northeast to southwest areas of Japan, as described elsewhere42.

Fig. 1: High-resolution spectra of mtDNA haplogroups in the Japanese population.

From: Genetic and phenotypic landscape of the mitochondrial genome in the Japanese population

Unsupervised ML approaches deconvoluted mtDNA classification patterns. To evaluate how the defined haplogroups reflect the mtDNA diversity within a population, we conducted unsupervised clustering of the subjects based on the mtDNA variants and evaluated the concordances with haplogroup assignments. We adopted three unsupervised ML classification approaches of phylogenetic approach, principal component analysis (PCA), and uniform manifold approximation and projection for dimensionality reduction (UMAP). We first constructed the phylogenetic tree of the WGS individuals, which was illustrated as an unrooted tree type (Fig. 2a). The tree branch was mainly divided into the major two lineages at the root base, which were known as the “M” and “N” clusters. Each major lineage was further divided into sub-lineages corresponding to the sub-haplogroups. Next, we applied the linear dimensionality reduction technique of PCA and examined up to the 20 PCs. The explained variances were 12.6% for the top 20 PCs. As the two-dimensional plot of the PC1 and PC2 was difficult to fully capture the cluster classifications (Supplementary Fig. 6), we adopted the three-dimensional plot consisting of the top three PCs (Fig.2b). The major M and N clusters were also illustrated as distinct groups in the PCA plot. In contrast to the M cluster, the N cluster was further divided into sub-haplogroups, such as A5a, B4a, B4b, B4c, B5*, F1a, F1b, N9a, and N9b.

Fig. 2 Unsupervised ML-based sample classification of the Japanese mtDNA variant data. All the three unsupervised ML method classifications were performed on the WGS variant data of the Japanese population (n = 1928). a The unrooted phylogenetic tree using maximum-parsimony method. b The 3D plot of the top three components of PCA. c The plot of the two components of UMAP. Each color and marker represents haplogroups. Distinction between the M and N haplogroup clusters is displayed with dotted lines in each panel.

Fig 2

Fig 2 UMAP

UMAP is a recently developed nonlinear dimensionality reduction algorithm, which has a merit in preserving the topology of the local and global structure26. Although UMAP has been previously applied to high-dimensional biological data such as single-cell RNA sequencing27, here we applied it to the genomic data of the mtDNA variants. An application of UMAP could classify the subjects into >20 clusters, which was concordant with the pre-defined sub-haplogroups with three letters (Fig.2c). UMAP could differentiate the sub-haplogroups belonging to the same macrohaplogroup in more detail (e.g., D4a, D4b1, D4b2,D4c, D4e, and D4g belonging to D). On the other hand, we did not find the clear delineation between the M and N clusters, which was observed in the phylogenetic approach and PCA. Several sub-haplogroups with small sample sizes were clustered closely with other macrohaplogroups (e.g., M7c clustered with D macrohaplogroup). These observations could be the potential limitations of UMAP. As each ML classification method hadunique advantages to classify mtDNA variations, we would propose a value of applying multiple ML methods to comprehensively visualize haplogroup diversity within a population.Distinct characteristics of mtDNA variant structure from nDNA. Due to lack of recombination and higher mutation rate, LD structure and tag variant distribution in mtDNA are considered to be distinct from those in nDNA, whereas the details have been unclear especially in non-Europeans. Thus, we conducted a comprehensive assessment of these features in Japanese by using the WGS data. In addition to calculate the haplotype correlations (r2) between common mtDNA variant pairs (MAF≥5%,n=80), we estimated those obtained from the randomly selected autosomal phased haplotypes with adjustment on variant positional differences (±8.3 kbp). Fractions of the variant pairs with high correlations were relatively smaller in mtDNA than in nDNA (2.4% and 20.2% of the variant pairs with r2≥0.9 in mtDNA and nDNA, respectively; Fig.3a).When we checked distance-dependent decay of LD, we observed clear LD decay in the nDNA variant pairs according to physical distances between the variant pairs, which would reflect LD blocks (R=−0.092,P=1.0 × 10−7, as highlighted with red; Fig.3b). However, mtDNA variant showed no distance-dependent LD decay (R=0.022,P=0.21). Although there existed controversial discussions16,28, our results did not support the hypothesis of potential recombination events in mtDNA. Lack of recombination and relatively weak LD in mtDNA should propose that the common mtDNA variants are sparsely tagged bythe surrounding single-nucleotide polymorphisms (SNPs) when compared with nDNA. The numbers of the tag variants per common variant were smaller in mtDNA than in nDNA, even when the variant distances were adjusted (Fig.3c). As many as 13.8% of the common mtDNA variants did not have any tag variants with r2≥0.5, whereas only 5.0% in nDNA. Systematic visualization of pairwise LD patterns revealed that mtDNA variants did not constitute LD blocks among neighboring variants (Fig.3d). On the other hand, we observed multiple common haplotypes spanning the entire mtDNA (n=8), which might have been the consequence of lack of recombination and no distance-dependent LD decay. Interestingly, mtDNA variants without any tag variants were mostly identified in the D-loop region, one of the non-coding but functional regions in mtDNA. By using WGS data, we highlighted the characteristics of the mtDNA variants28, which were (i) no distance-dependent LD decay (i.e., absence of LD blocks) and (ii) sparse tagging of the common variants, in non-European population. In addition, we could newly detect existence of the common haplotypes spanning the entire mtDNA. No evidence of mtDNA–nDNA genotype association. Mitochondrial function is regulated not only by the genes encoded in mtDNA but also by those in nDNA. As these two typesof genes confer synergistic biological functions6, co-evolutionof the genetic variants embedded within them5, namely “mtDNA–nDNA genotype association”, has been suggested17. Thus, we tested the hypothesis that there might exist preferential transmission between nDNA and mtDNA at a genotype level. To explore footprints of the mtDNA–nDNA genotype association,we conducted a genome-wide scan to assess genotype distribution dependence between mtDNA and nDNA variants using the WGS data. We investigated 86 common mtDNA (MAF≥5%) and the genome-wide 7,124,343 nDNA variants (MAF≥1%), but there was no significant mtDNA–nDNA genotype association when multiple comparisons were considered (P=5.0 × 10−8/86=5.8 × 10−10; Fig.4a). Even when we focused on the variants located within ±10 kbp of the previously defined nDNA mito-chondrial genes (n=1105)29, we still did not detect a significant association. In addition, we investigated the associations by using the imputed GWAS data (n=141,552; see details in the next section). We analyzed the association between the 8 mtDNA(MAF≥5%) and the 7,402,102 nDNA variants (Rsq≥0.7 and MAF≥1%), but no significant signals were detected (P=5.0 ×10−8/8=6.3 × 10−9). We neither observed the enrichment of the association signals in the mitochondrial-related gene variants in nDNA (Fig.4b).

DISCUSSION

UMAP is a recently developed nonlinear dimensionality reduction algorithm, which has a merit in preserving the topology of the local and global structure26. Although UMAP has been previously applied to high-dimensional biological data such as single-cell RNA sequencing27, here we applied it to the genomic data of the mtDNA variants. An application of UMAP could classify the subjects into >20 clusters, which was concordant with the pre-defined sub-haplogroups with three letters (Fig. 2c). UMAP could differentiate the sub-haplogroups belonging to the same macrohaplogroup in more detail (e.g., D4a, D4b1, D4b2, D4c, D4e, and D4g belonging to D). On the other hand, we did not find the clear delineation between the M and N clusters, which was observed in the phylogenetic approach and PCA. Several sub-haplogroups with small sample sizes were clustered closely with other macrohaplogroups (e.g., M7c clustered with D macrohaplogroup). These observations could be the potential limitations of UMAP. As each ML classification method had unique advantages to classify mtDNA variations, we would propose a value of applying multiple ML methods to comprehensively visualize haplogroup diversity within a population.

Distinct characteristics of mtDNA variant structure from nDNA
Due to lack of recombination and higher mutation rate, LD structure and tag variant distribution in mtDNA are considered to be distinct from those in nDNA, whereas the details have been unclear especially in non-Europeans. Thus, we conducted a comprehensive assessment of these features in Japanese by using the WGS data. In addition to calculate the haplotype correlations (r2) between common mtDNA variant pairs (MAF ≥ 5%, n = 80), we estimated those obtained from the randomly selected autosomal phased haplotypes with adjustment on variant positional differences (±8.3 kbp). Fractions of the variant pairs with high correlations were relatively smaller in mtDNA than in nDNA (2.4% and 20.2% of the variant pairs with r2 ≥ 0.9 in mtDNA and nDNA, respectively; Fig. 3a). …

Our study demonstrated a successful imputation of the mtDNA variants by using the large-scale WGS as a reference panel. …

In conclusion, through the large-scale WGS and PheWAS of mtDNA, our study could comprehensively elucidate the genetic and phenotypic landscapes of mtDNA in the Japanese population.

A new study could throw light on the origins of the migrants who brought rice culture to Japan and Korea…

New study suggests early rice farmers in three separate geographic locations independently domesticated rice.

Damien Dempsey/ Flickr/ Creative Commons

By Dennis Normile 2 November 2015 Science AAAS

Rice—one of the world’s most important crops—was domesticated more than once, according to a new study. The work could lead to a better understanding of how civilizations arose throughout Asia and whether they developed independently, or whether agricultural and cultural advances in one region were copied in others. It could also guide programs to improve the grain crop that more than half of the world’s population depends on.

There are four main varieties of rice: japonica, a short-grained rice grown in Japan, Korea, and eastern China; indica, a long-grained variety common in India, Pakistan, and most of Southeast Asia; aus, grown primarily in Bangladesh; and aromatic rice, which includes more exotic varieties such as India’s basmati and Thailand’s jasmine.

Scientists have primarily focused on indica and japonica because archaeological findings suggest both have a long history of cultivation. Researchers generally agree that humans living in what is now southern China domesticated japonica between 8200 and 13,500 years ago. The precise locale within southern China is still debated. But the spread of agriculture resulted in a more stable food supply that allowed hunter-gatherers to settle in villages with increasing populations and the more complex societies and cultures that led to the rise of Eastern civilizations.

Those claiming one domestication event believe indica emerged from crosses between japonica and wild species as rice cultivation spread through Asia. This hypothesis is strongly supported by Bin Han, a geneticist at the Chinese Academy of Sciences’ Institute of Plant Physiology and Ecology in Shanghai, and colleagues in an October 2012 paper in Nature. In this scenario, aus and aromatic varieties emerged from later crosses.

Those arguing for two separate domestication events generally agree that japonica emerged in southern China, but they contend that indica was independently domesticated in a region straddling India and western Indochina.

The new analysis, from a group led by Terence Brown of the University of Manchester in the United Kingdom, adds a third and separate domestication locale, for aus, in a region stretching from central India to Bangladesh.

Interestingly, both the Han and Brown teams rely on the same genetic data: sequences from 446 samples of wild rice and over 1000 cultivated varieties. But just as two detectives examining a crime scene might think the clues point to different culprits, the two teams reach differing conclusions. Both analyses center on what are called domestication sweeps, regions of the genomes of cultivated rice varieties that differ from wild populations and that researchers believe were selected for by early farmers seeking to enhance desirable plant traits. These include regions that allow plants to grow vertically and thus more densely, as opposed to spreading over the ground, and to keep ripe grain on the stalk, instead of shedding it as most wild varieties do, a characteristic called shattering.

Han and his colleagues contend that that the domestication sweeps found in all cultivated Asian rice varieties are very similar and can be traced back to a single group of wild ancestors in southern China. But the Brown team says the genetic evidence indicates that the genes that proved advantageous for farming were present in many wild rice varieties widely distributed across the southern Asian continent. Early farmers in three separate geographic locations were all striving to select rice plants showing the same desirable traits. And that resulted in similar domestication sweeps appearing in three different varieties of cultivated rice. “Rice domestication was a multiregional process separately producing the indica, japonica, and aus types of rice,” the group writes online today in Nature Plants.

The methods are “rigorous and well substantiated,” says Susan McCouch, a rice geneticist at Cornell University. Brown and his colleagues “clearly demonstrate that the most parsimonious and coherent interpretation for the data is that there were at least three independent domestications of [rice] from well differentiated ancestral populations in Asia,” she says.

Han is sticking to his conclusions. The new paper is “definitely wrong with the data analysis,” he wrote in an email. He says his team will publish a detailed rebuttal shortly.

There are some sticky questions. Briana Gross, a plant geneticist at the University of Minnesota, Duluth, says there is convincing evidence that at least one of the major domestication sweeps—causing white grains—arose in japonica, and spread to other variety groups. If the three varieties were domesticated separately, she asks how did this trait get into all three?

Even McCouch acknowledges this latest finding is unlikely to be the last word. “I look forward to the many discussions this paper is likely to provide.

Source: PNAS study  Fig. 1 Cishan site in North China, proposed centre of millet domestication in East Asia

Broomcorn millet, barnyard millet, and foxtail millet were all species of millet cultivated by the Jomon people of Japan (see 1995, D’Andrea). Millet finds are from late Middle Jomon sites in Hokkaido, late Jomon Kazaharai site in Aomori, Northeastern Japan (see 1995, D’Andrea); and Yayoi Nabatake site in Kyushu (Cowan, The Origins of Agriculture p. 24). Broomcorn millet was present in southwestern Japan by the 2,000 B.C. (Crawford, Gary, Transitions to Agriculture, p 121). Foxtail millet cultigens are found in a widespread sphere from Southwestern Asia, Europe to Transcaucasian Russia and the Far East (C.W. Cowan et al., The Origins of Agriculture, p. 24; Rao et al., 1987). It is thought that from China foxtail millet spread westward towards Europe (Oelke, E.A., 1990).

It was earlier established that China is at the primary center of the diversity of broomcorn millet cultivation (see C.W. Cowan et al., The Origins of Agriculture, p. 23; Zeven and Zhukovsky, 1975:32). A new study on the origins of millet domestication, could establish the routes of dispersal of millet cultivation/gathering, storage pit usage and associated tools to Japan, and thereby also shed some light on the possible origins of the incoming migrations of people during the Jomon or on early exchanges with the continent. Historical documents show that foxtail millet was an important crop during Zhou dynasty China, while the earliest foxtail millet sites are from Hunamni and Hohnamni Bronze Age sites in South Korea ( C.W. Cowan et al., The Origins of Agriculture, p. 25). All evidence points to millet plant domestication and cultivation in Japan earlier than the Late Jomon period, and certainly, by the end of the Late Jomon period in northeastern Japan (Gremillion, KJ, People, Plants, and Landscapes: Studies in Paleoethnobotany, pp 102-103)

Research analysis in “Earliest domestication of common millet (Panicum miliaceum) in East Asia extended to 10,000 years ago” concluded that

“the earliest significant common millet cultivation system was established in the semiarid regions of China by 10,000 cal yr BP, and that the relatively dry condition in the early Holocene may have been favorable for the domestication of common millet over foxtail millet. Our study shows that common millet appeared as a staple crop in northern China ≈10,000 years ago, suggesting that common millet might have been domesticated independently in this area and later spread to Russia, India, the Middle East, and Europe. Nevertheless, like Mesopotamia, where the spread of wheat and barley to the fertile floodplains of the Lower Tigris and Euphrates was a key factor in the emergence of civilization, the spread of common millet to the more productive regions of the Yellow River and its tributaries provided the essential food surplus that later permitted the development of social complexity in the Chinese civilization.”

The above study reported “the discovery of husk phytoliths and biomolecular components identifiable solely as common millet from newly excavated storage pits at the Neolithic Cishan site, China, dated to between ca. 10,300 and ca. 8,700 calibrated years before present (cal yr BP). After ca. 8,700 cal yr BP, the grain crops began to contain a small quantity of foxtail millet. Our research reveals that the common millet was the earliest dry farming crop in East Asia, which is probably attributed to its excellent resistance to drought.”

Foxtail millet (Setaria italica) and common millet (or broomcorn millet; Panicum miliaceum) were among the world’s most important and ancient domesticated crops. They were staple foods in the semiarid regions of East Asia (China, Japan, Russia, India, and Korea) and even in the entire Eurasian continent before the popularity of rice and wheat, and are still important foods in these regions today….

Thirty years ago, the world’s oldest millet remains, dating to ca. 8,200 calibrated years before present (cal yr BP), were discovered at the Early Neolithic site of Cishan, northern China. The site contained >50,000 kg of grain crops stored in the storage pits (7–9). Until now, the importance of these findings has been constrained by limited taxonomic identification with regard to whether they are from foxtail millet (S. italica) or common millet (P. miliaceum), because the early reported S. italica identifications are not all accepted (4,9–12). This article presents the phytoliths, biomolecular records, and new radiocarbon dating from newly excavated grain crop storage pits at the Cishan site. Large modern reference collections are used to compare and contrast microfossil morphology and biomolecular components in different millets and related grass species (13). The renewed investigations show that common millet agriculture arose independently in the semiarid regions of China by 10,000 cal yr BP. Our findings contribute to our knowledge of agricultural origins across the globe and have broader implications for understanding the development of human societies.

The Cishan site (36°34.511′ N, 114°06.720′ E) is located near the junction between the Loess Plateau and the North China Plain at an elevation of 260–270 m above sea level (Fig. 1). The archaeological site, containing a total of 88 storage pits with significant quantities (≈109 m³) of grain crop remains, was excavated from 1976 to 1978 (7, 8). Each storage pit included 0.3- to 2-m-thick grain crops, which were well preserved and found in situ in the 3- to 5-m-deep loess layer (9). All grain remains have been oxidized to ashes soon after they were exposed to air. Archaeological excavations also revealed the remains of houses and numerous millstones (Fig. S1), stone shovels, grind rollers, potteries, rich faunal remains, and plant assemblages including charred fruits of walnut (Juglans regia), hazel (Corylus heterophylla), and hackberry (Celtis bungeana) (7–9). Only 2 ¹⁴C dates of charcoal from previously excavated H145 and H48 storage pits yielded uncalibrated ages of 7355 ± 100 yr BP and 7235 ± 105 yr BP, respectively (8). These remains represent the earliest evidence for the significant use of dry-farming crop plants in the human diet in East Asia. They also suggest that by this time agriculture had already been relatively well developed here.

According to archeobotanical research, the early charred grains of common millet occurred during the initial stages of various Early Neolithic sites (Fig. 1), including Dadiwan (ca. 7.8–7.35 cal kyr BP) (21), Xinglonggou (ca. 8.0–7.5 cal kyr BP) (22), and Yuezhuang (ca. 7.87 cal kyr BP) (23) in North China, but foxtail millet was barely present during these stages. Lee et al. (24) have speculated that the Early Neolithic predominance of broomcorn over foxtail millet at Xinglonggou and Yuezhuang ca. 6000 cal B.C. might be a regional phenomenon, implying that broomcorn millet might have been domesticated earlier than foxtail millet. Our analytical results of both phytoliths and biomolecular components have established that the earliest cereal remains stored in the Cishan Neolithic sites, during ca. 10,300–8,700 cal yr BP, are not foxtail millet, but only common millet. After 8,700 cal yr BP, the grain crops gradually contained 0.4–2.8% foxtail millet. Our study also suggests that common millet was used as a staple food significantly earlier than foxtail millet in northern China. It provides direct evidence to show that, by 10,000 cal yr BP, the early people in northern China had developed various methods of maintenance and multiplication of millet seeds for the next generation, and had known how to store crops of staple food in secure, dry places of storage pits during the Early Neolithic epoch.

Common millet has the lowest water requirement among all grain crops; it is also a relatively short-season crop, and could grow well in poor soils (5, 6, 25). The geographical distribution of both foxtail millet and common millet in China (Fig. S4) shows that foxtail millet is more common in the semiwet eastern areas, and its optimal growth occurs at mean annual temperature (MAT) from 8 to 10 °C and mean annual precipitation (MAP) from 450 to 550 mm. However, common millet is more adapted to the drier interior areas, and its optimal growing conditions occur at MAT from 6 to 8 °C and MAP from 350 to 450 mm (5, 6). The origin and dispersal of millet agriculture is a key problem closely related to the history of human impact on the environment and transformation of natural vegetation.

Paleoenvironmental data from the Weinan section (26–29) (Fig. 1) in the southern part of the Loess Plateau between the Cishan and Dadiwan sites are crucial for understanding the early stage of the forager–cultivator transition. The early Holocene was a period of significant environmental change marked by dry climate conditions as inferred from sediment texture (26, 28), magnetic susceptibility (26, 28), pollen (27), phytoliths (28), and mollusk assemblages (29). These proxy records show an environmental transition from cold–dry (ca. 11,000–8,700 cal yr BP) to warm–wet (ca. 8,700–5,500 cal yr BP) conditions. Many lacustrine and loess records from the Chinese Loess Plateau to Central Asia also support the scenario of a dry climate during the early Holocene (30–34). Under the drier climate conditions, soil development was slowed, and the soil developed on the underlying older and coarser loess of the glacial period was poor in nutrients (28). This raises the possibility that common millet was more significant than foxtail millet in the early stages of food production in North China because it was more adaptable than foxtail millet to the dry condition prevailing during the early Holocene. The common millet cultivation may involve complex selection by natural forces and human activities, although no clear evidence has been documented in this region for the transitions from gathering to cultivation and/or from a wild ancestor to domesticated common millet.

…

References and source readings:

COWAN, C.Wesley., WATSON, Patty Jo; BENO, Nancy L., The Origins of Agriculture: An International Perspective p. 23-24).

D’Andrea, A. C. 1995. Later Jomon Subsistence in Northeastern Japan: New Evidence from Palaeoethnobotanical Studies. Asian Perspectives 34 (2): 195-227

This paper discusses prehistoric subsistence and the development of plant husbandry in northeastern Tohoku (northern Honshu). Archaeobotanical sampling was carried out at two sites in eastern Aomori Prefecture. Tominosawa is a Middle Jomon village site which produced a spectrum of nut and weedy plant species similar to that recovered from contemporary sites in southwestern Hokkaido. At the Kazahari site, pithouses from two phases of occupation were sampled for archaeobotanical remains: Tokoshinai IV (c. 1000 B.C.) and Fukurashima (c. 150 B.C.). The pithouse deposits produced evidence for Late Jomon rice, foxtail millet, and broomcorn millet dating to the first millennium B.C. Sampling of later Fukurashima contexts produced evidence of rice, foxtail and broomcorn millet, Japanese barnyard millet, and hemp. These data demonstrate that rice and millets have been present in northeastern Tohoku since c. 1000 B.C.

NASU, Hiroo The Initial Form of Rice and Millet Cultivation during the Final Jomon-Yayoi Transition Era from the View of Archaeobotanical Weed Assemblages Bulletin of the National Museum of Japanese History Vol. 187 July 2014

Gremillion, Kristen J., People, Plants, and Landscapes: Studies in Paleoethnobotany, pp. 102-3

Crawford, Gary, Transitions to Agriculture in Prehistory, pp 117-132, Monographs in Archaeology, No. 4 Prehistory Press p. 121

Oelke, E.A., Oplinger, E.S., Putnam, D.H., Durgan, B.R., Doll, J.D. and Undersander, D.J. (1990) Millets, in Alternative Field Crops Manual)

Setaria introduction

Dotaku bells found on Awajishima Island (The Yomiuri Shimbun, May 20, 2015)

Source: The Yomiuri Shimbun

Seven dotaku bronze bells from the mid-Yayoi period, or around the second century B.C., were found in Minami-Awaji, Hyogo Prefecture, on Awajishima island, the prefectural and municipal boards of education said Tuesday.

The bells were found in a pile of sand taken from the city’s coastal district Matsuho, and they were named “Matsuho dotaku.”

This is the fourth-largest number of dotaku bells to be excavated from a single site. The biggest trove, 39 bells, was found at the Kamo Iwakura Ruins in Unnan, Shimane Prefecture. The latest discovery is the oldest trove of dotaku bells to be unearthed at one time. Experts say “These dotaku bells are worthy to be designated as national treasures as they could help understand the use of dotaku bells in ancient rituals.”

The dotaku bells are from 22 to 32 centimeters in height and from 13 to 19 centimeters in base width, and do not have any drawings on them. One of the seven bells has a handle — called a chu — with a lozenge-shaped cross section. This is believed to be the oldest type of dotaku bell, and only 11 other bells of this type have been confirmed in the nation so far.

Meanwhile, three of the seven bells have 8- to 13-centimeter tongues made of bronze. This is the largest number of tongues found at once.

Picture illustrates what a tongue is Photo: The Yomiuri Shimbun

There are no other known cases of a number of dotaku bells with tongues found buried at one time. So there is a possibility that the recently discovered bells were used in the oldest form of rituals in which many dotaku bells were buried together.

Clue for use of dotaku bells in rituals

The seven dotaku bronze bells discovered on Awajishima island can provide clues for the study of their use in rituals in early times.

The practice of burying a number of dotaku bells together is believed to have been concentrated in two periods — the mid-Yayoi period — from the first century B.C. through to the first century — and the late-Yayoi period at the end of the second century. However, the latest discovery has pushed back the beginning of the practice by more than a century, and some theorize that the practice resumed after a certain period.

Salt, and iron, aside from rice, were the most precious economic and trading commodities and resources of ancient East Asian states. When the rulers of the polities controlled or monopolized trade in those resources, they gained the keys to the kingdom (See Chinese Discourses on Salt and Iron and Yellow River Emperor Huang Ti is said to have presided over a war fought over salt).

Photo: Ryo Murakami

Japan developed its own unique method of salt production because the islands lacked salt lakes and rock salt mines. Moshio salt-making techniques involving seawater and seaweed gathered from the Seto-uchi Inland Sea began 2,500 years ago, and the region remained the most important of salt centres in Japan throughout (see “Salt” by Mark Kurlansky, p. 373). The Shio no Michi or salt road to the inland regions such as Shinshu-Nagano was one of the most important trade routes, with salt being the most important commodity of all.

Below is an article on the ancient heritage of salt production …the article focuses on methods that have been known in Japan since at least the 5th c. that are still seen today, although even earlier salt production centres, and salt production involving evaporation pots from 100 sites have been found, and have been known since the prehistoric and neolithic Jomon period.

Preserving Japan’s Sea Salt Making Tradition (Preserving Japan’s Sea Salt Making Tradition by Laura Cocora and Kaori Brand United Nations University

Japan’s culture is one of sea salt. For centuries, salt production has been an important activity throughout Japan and coastal communities have developed sophisticated techniques for producing this vital mineral from seawater.

One of the oldest records of salt making appears in the eighth-century chronicles of Kojiki and Nihon shoki, Japan’s oldest mythological and historical writings. There it is said that when the ship that brought water for the imperial table became too old to be used, it was turned into firewood used to boil thick brine down to salt that was then given away to the provinces. Snapshots of salt making scenes also appear in court poetry and in noh theatre. Typically, they depict the lonesomeness and isolation of salt shores.

Outside the world of literature, the importance of salt is reflected in the presence of salt routes, place names associated with salt and shrines where salt gods are worshipped. Salt is used as a cleansing and purifying agent in a variety of ritual contexts.

Salt making in Noto Peninsula

The small artisanal salt farms still found today on the shores of Noto Peninsula in Ishikawa Prefecture stand as a symbol of the co-evolution of human societies and their environment in the context of the extraction and use of salt as a fundamental marine resource.

Salt production in Noto dates back at least as far as the fifth century, when small ceramic pots were used to boil the seawater. Later, these techniques fell into oblivion, as a new salt manufacturing method, known as the agehama style, started to develop sometime around the eighth century. The new method consisted of two separate stages — water was first drawn from the sea and spread on banked sand terraces to evaporate and the resulting brine was then boiled down over a specially constructed kiln.

Even after technological advances led to the introduction of a more efficient, labour-saving production method elsewhere in Japan, older agehama techniques live on in the Noto Peninsula. Their survival was the result of a locally-specific combination of natural environmental characteristics and socio-economic factors.

The peninsula’s rocky shoreline, with minimal tidal flows, and its climate (characterized by high humidity and limited sunshine) were not suitable for the new method that relied on the flooding of terraces by natural tidal variations.

Despite the not so favourable natural conditions, the tax policies of the Edo period’s (1603-1868) ruling local authorities, the Kaga Clan, played a crucial role in shaping the peninsula’s identity as a salt producing area. During the Edo period, rice was the basis of the taxation system, but cultivable land was scarce in Noto. Under the Kaga Clan’s ‘rice for salt’ system, farmers who did not own enough land to allow them to pay their rice taxes and secure the food necessary for their subsistence borrowed rice from the government, paying for it in salt at a fixed rate.

The clan held a monopoly on the salt trade, with profits from sales being used to pay up to a quarter of the daimyo’s (territorial lord) travels to the capital Edo (now Tokyo) as part of the system of alternate attendance established by the Edo shogunate (feudal military dictatorship).

The rice for salt system was instrumental in making salt production one of the most important occupations of people along the coasts of Noto, while restricting the salt workers’ freedom for social or geographical mobility.

Thus, the salt terraces that once lined the peninsula’s shores — which can still be seen in photographs from the 1940s — emerged as veritable ‘cultural landscapes’. These reflected not only the specific constraints and opportunities of the natural environment, but also a unique socio-economic context that fused the local people’s dependence on natural resources with their control by the elites.

The knowledge heritage of agehama salt making

In 1868, the Meiji Restoration marked the end of feudalism and launched an era of modernization influenced by western models. Overall social and economic restructuring, the abolition of the clan monopoly on salt, and the introduction of new policies and technologies led to a sharp decline in traditional salt production in Noto Peninsula. With new employment opportunities offering different life choices, former salt makers moved to other industries and salt terraces disappeared from the landscape.

When a new wave of salt industry modernization measures — introduced by the central government in 1958 — threatened to wipe out traditional production, the local administration of Suzu City in Ishikawa Prefecture provided funding to the families still practising this cultural tradition. Eventually, only one family remained. In recognition of its value, both culturally and as a tourism resource, agehama-style salt making was designated an intangible folk cultural asset of Ishikawa Prefecture in 1992 and a national intangible folk cultural asset by the Culture Agency in 2008, stimulating new initiatives to revive traditional techniques in recent years.

Agehama-style salt making, as practiced today in Noto, evokes the shadows of the salt farms as places of intense labour and the working and social conditions of the people employed in salt making. However, it is not only in the reconstruction of the past that its value resides, but also in the transmission of the traditional knowledge and practices that are vital to its survival.

On a first level, such traditional knowledge encompasses the architectural aspects, equipment and ways of production associated with salt making. While many of the tools and materials used have undergone little change for centuries, others have been replaced with new ones in the quest for comfort and efficiency. The artisanal knowledge needed to craft these tools and build ovens using traditional techniques is increasingly in danger of being lost.

Agehama-style salt makers are also custodians of a wealth of experiential and traditional knowledge of their natural environment, which includes elements of integrated management of land and marine ecosystems. Such knowledge embraces various dimensions, from the salt makers’ renowned ability to predict the weather by reading cloud patterns and sea currents, to their empirical knowledge of the state and change of marine ecosystems and resources.

Although salt makers now tend to use cheap wood waste from construction sites as fuel, in the past, salt production practices were closely connected with inland regions through the supply of fuel wood, with salt makers owning and managing forest areas to ensure a sustainable wood supply. The two-stage process of agehama salt making reflects this interconnectedness in its effort to reduce fuel consumption by relying on human and natural forces to produce a highly saturated brine solution prior to boiling.

Such elements of sustainable land and resource use at the landscape level make salt farms more than just salt yielding sites. They have the potential of contributing to new approaches to resource conservation and use, such as ‘satoumi’, a recently introduced concept designating socio-ecological production landscapes in coastal areas, which are managed for the ecosystem services they provide.

The question that remains unanswered is how the knowledge associated with these unique cultural landscapes — which have developed as part of salt’s complex itinerary in the culture and history of Japan — can be integrated with scientific knowledge to develop models of resource use and management that maintain or enhance natural values in the landscape.

• ♦ •

This video was produced by Kaori Brand of United Nations University in collaboration with Ishikawa Prefecture as part of an initiative on traditional knowledge and the wisdom of satoyama/satoumi charcoal and salt making traditions in Ishikawa.

Creative Commons License
Preserving Japan’s Sea Salt Making Tradition (2010•06•09, Our World) by Laura Cocora is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.

The moat in Asuka, Nara Prefecture, that is believed to be part of the first burial site of Emperor Jomei (593-641) (Asahi Shimbun file photo)

Possible ruins of ancient emperor’s grave unearthed in Asuka
January 16, 2015, Asahi AWJ

By KAZUTO TSUKAMOTO/ Staff Writer
ASUKA, Nara Prefecture–Local archaeologists said Jan. 15 that they have unearthed the remnants of a possible mid-seventh century burial mound for an ancient emperor at the Koyamada ruins on the site of a school.

“The mound is highly likely the first burial site of Emperor Jomei (593-641), described in the ‘Nihon Shoki’ (The Chronicles of Japan) as the place where his body rested until it was later transferred to another location,” said Fuminori Sugaya, the director of the Archaeological Institute of Kashihara, Nara Prefecture.

The researchers made the estimate based on the ruin’s location, size and unique construction method.

The ancient emperor was the father of two more well-known emperors, Emperor Tenji (626-671) and Emperor Tenmu (?-686).

The ruins were excavated during archaeological digging associated with school replacement work on the site.

An aerial view of newly discovered remains at the burial mound Photo: Kazunori Takahashi

The excavation site contains what is believed to be part of a moat lined with boulders along one of its slopes, according to the researchers. The remnants of the moat measures 48 meters in length and 3.9 to 7 meters in width.

An artist rendering of how the burial mound originally looked (Provided by the Archaeological Institute of Kashihara)

While 40-centimeter quartz diorite boulders line the northern slope of the moat, the bottom is covered with stones measuring 15 cm to 30 cm.

The southern slope is covered with flagstones made of two-step chlorite schist that are topped with special flagstones known as “Haibara,” a type of rhyolite stone, stacked in a staircase pattern. The total number of steps in some areas is 10.

Based on speculation that the ruins are a moat belonging to a burial site, the researchers estimate the mound was square-shaped with each side measuring 50 to 80 meters, far larger in size than the ancient and renowned Ishibutai grave in Asuka, which measures 50 meters by 50 meters.

It is rare for chlorite schist and Haibara stones to be laid out around a burial mound.

The Dannozuka burial mound in Sakurai, Nara Prefecture, which has been designated as Jomei’s grave by the Imperial Household Agency, was built according to the same design and with the same materials.

The Raifuku (outer robe) of the ceremonial court costume of the Emperor Komei(r. 1846-1866). This ceremonial court costume originates in the Nara-period (710-784) Imperial Collections of Japan  Source: Japanese Symbols of Government

From a previous post “Ainu cloud motif and their creation myth of deity’s descent on five-colored cloud“, we traced the use of the cloud motif and symbolism in conjunction with deities or divinities, ancestors, sages and heroes to their early use both in art and in concepts in genealogies and myths of the peoples of the Northeast Eurasia or Far East.

From Eccentric Spaces, Hidden Histories: Narrative, Ritual, and Royal Authority” by David T. Bialock, comes an understanding of the origin of the “chinkon” and tama “cloudsoul” concept and the rites, and the purpose behind it and the cosmological framework that surrounded it:

Although Nihon shoki’s entry on Temmu’s rite is regarded as the earliest extant mention of the chinkon (spirit pacification), the graphs glossed as “mitama-furi” in the text are actually shokon, also read tama-yobai (“soul-summoning”). The conventional chinkon reading of the passage together with its vernacular gloss “mitama-furi” probably dates from a commentarial tradition transmitted by the Urabe lineage. Thus, according to a secret kun-reading given in the twenty-first scroll of the Shaku nihongi, the graphs were intended to be read “mitama-furi,” a ritual elsewhere represented in Shaku nihongi by the graphs chinkonsai. This eading of the graphs, now well established, was also argued for by Ban Nobutomo in his classic study Chinkon den, where he noted that the phrase “should be recorded as , but one can surmise that it was written in conformance with the usual Chinese practice.”51
… turn to some descriptions of the chinkon rite in the law codes and their commentaries, which have been the basis for most attempts to construct its ancient ritual function. These include the Taiho Code o 701 (extant only fragmentarily in the later Yoro Code), the Ryo no shuge (selected in 833), and the Ryo no guge (selected prior to 868). According to the Taiho Code , the chinkonsai was held in midwinter in the Eleventh Month on a tora no hi (days of the tiger), and followed by the daijosai on a u no hi (day of the rabbit), a period that coincided with the winter solstice. In Chinese yin-yang five agents thought, both of these days were identified with the agent wood (the beginning of the cycle), which corresponded to the direction east and the season spring. Both the month and days were a time when the positive yang pneumas were believed to mount upward and all things were held to be in a state of movement. It was thus an ideal time for initiating activities such as royal accessions. 52
turning to some actual definitions of the chinkon rite, we find the following explanation in the Ryo no gige under the heading chinkon: “The graph means to pacify. A person’s yang spirit (yoki) is called soul (tama). The tama moves about, meaning one summons back the tama that wanders about in a state of separation and pacifies it inside the body (literally “bowels”.] Therefore it is named “chinkon” (to pacify the soul), another definition from the Ryo no shuge contains some additional details: A person’s yang spirit is called ‘kon’ it moves about. A person’s yin spirit is called ‘haku’ it is white. Therefore one calls back the white soul wandering about in a state of separation and causes it to be pacified inside the bowels. Therefore it is called chinkon.
The exact source for the ideas contained in these descriptions remains uncertain, but the language recalls ancient Chinese ideas about the fate of the soul after death. According to the Li ji: the yang qi of the “cloudsoul” (hun) rises up to the sky (tian) after death, whereas the yin or dark elements associated with the body or “whitesoul” (po) return to the earth. 55 Another passage in the Li Ji , on the rites of mourning , speaks of summoning back the cloudsoul and returning it to the body (po)56. It was under the influence of such commentaries, according to Watanabe Katsuyoshi, that modern scholars developed the idea of a “soul that wanders about in separation from its body” and interpreted chinkon as a rite primarily aimed at preventing such separation by placating the “tama” and thereby obviating the illness and death that were held to result from such separation57.
The yin-yang five agents principles and the related concept of “qi” which informed the ritual setting (temporal and geomantic) of the chinkonsai and the descriptive language of the law doctors, were fundamental, of course to Chinese philosophical thought. In Daoism, the induction of qi into the body and its proper regulation became one of the basic practices for achieving longevity, a central concern of later Daoist literature, as in Xiang’er’s commentary on the Daodejing, which also functioned as a guide to the enlightened ruler.58 thus in Bokenkamp’s paraphrase of one Xiang’er passage “the pneumas of morning and evening should be caused to descend into the human body , where they should be mixed with the body’s own pneumas so that they are evenly distributed throughout.” On the other hand, this time citing directly from the Xiang’er “When the heart produced ill-omened and evil conduct, the Dao departs, leaving the sack (belly) empty. Once it is empty, deviance enters, killing the person.”60 As these citations make clear, the principle of balancing and harmonizing qu was of paramount importance; deviance” (xie) on the other hand, arose from a  failure to achieve a proper balance or mixing o pneumas resulting in illness and death. … The emphasis in the Xiang’er passage on the belly, for example, recalls what Watanabe characterizes as the peculiar language of the law commentaries where the aim of the rite was to draw the erring “tama” back into the “bowel“.  A related notion found in the Chuxue ji, a Tang period encyclopedia compiled at the order of Emperor Xuangzong (r. 712-756), states that on the winter solstice the yang qi is restored to the belly and hot things placed in qi are easily digested.61 If this Daoist medical advice offers a parallel to the ideas of the law doctors in their attempts to describe the chinkon rite, recipes for the production of immortality elixirs provide a suggestive context for understanding the relationship between the medicinal herb and Temmu’s spirit-summoning rite. An entry from scroll seventy-seven on “elixirs” in Yunqi qiqian (Seven Lots from the Satchel of the Clouds), an encyclopedia of older Daoist texts and extracts compiled under the Northern Song, describes a life-extending elixir called lingwan that allows one to “pacify the cloud souls, coagulate the white souls, and fly off into the seventy-four directions,” and in another passage “to sport about on the Five Mountain Peaks.” Not least interesting here is the combination of graphs chinkon, “pacify the cloud souls”) the same two graphs that are used for the Japanese chinkon or “mitama-furi” rite.  Another entry from the Inner Transmission of the Purple Sun Master (Ziyang zhenren neichuan, 399), collected in scroll 106 of the Yunji qiqian, relates that the consumption of zhu over a period of five years–the same medicinal herb ingested by Temmu–produces a glow in the body, gives one a vision that can see right through to the five viscera, and enables one to become an immortal.

By now it should be evident that Temmu’s ingestion of the herb hakuchi cannot be fully accounted for by a straitforward medical reading. The calendrical and yin-yang principles that informed its consumption and the accompanying shokon rite belonged to the same sphere of symbolic activity that would soon be housed in the Yin-Yang bureau and Medical bureau and as the following notice from Jito’s chronicle makes clear: “The Yin-yang Doctors, the priest (shoshi) Hozo and Doki, received twenty of ryo of silver.”64 The date of this third reference to Hozo, just prior to the establishment of the official Yin-Yang Bureau, indicates that he was one of than important group of technical experts who mediated the cultural assemblage transmitted from  the continent. Although the ingestion of the herb zhu (hakuchi) and its efficacy as both a medicinal and immortality elixir are well documented in Daoist lore and herbals the practice seems to have especially flourished in the period of the Southern dynasties (420-589) when Tao Hongjing composed his herbal and Daoist works.65  It can be assumed that Hozo, a Paekche immigrant would have been knowledgeable about this tradition–its influence having reached the Korean kingdom–as well as conversant with practices from Tao honjing’s region that were outside the written transmission.66  In the early Tang work Qianjinyaogang (Essential Prescriptions Worth a hundred Weight in Gold), composed by the Daoist master and physician Sun Simiao (d. 682) sometimes between 650 and 658. Predating the Tang medical reforms , this text transmitted a tradition very close to the earlier Southern dynasties ‘ tradition and contained detailed discussions on the preparation of zhu and its capacity to harmonize in accord with yin-yang five agents principles.67

The cosmological theory of resonance, much of which is recorded in the Gogyo taigi that reached Japan no later than the end of the seventh century invests Temmu’s ingestion of the elixir and the shokon rite with its reliopolitical significance. Held in the Eleventh Month on a a tora no hi (day of the tiger), the rite’s timing corresponded to the agent wood and the direction east. In Daoist medical lore pertaining to the five viscera, the cloudsoul (kon) resided in the liver (kan), which was identified with the element wood and controlled the eyes, hair, nail, and muscles. The liver was also known as the Office of the General, the faculty responsible for wise counsel; and its element wood was identified with “virtue” (jin) that actifies the myriad things making its analogous to the ruler.68 According to another text cited in Gogyo taigi, The lineage of Thearchs (DIXI pu), “Heaven and earth first arose, then generated the Heavenly Thearch (tenno) who rules through the virtue wood,” a formulation that derives from the symbolism of the hexagram zhen, identified variously with lightning, the dragon and the dark springs. The Yijing states that the thearch and myriad things arise from zhen, with zhen identified with the direction east.69 Although these correspondences add weight to the medical aim of this  hybrid rite, they do so by locating Temmu at the center of a radiating cosmological order, which gains additional significance because the rite took place at a critical juncture when the tenno was being newly adopted as a title of authority.70

The belief of musubi – binding the soul to keep it from wandering off (see also The symbolism of knots, and Frazer on the separable external soul)

During the Chinkonsai,

“The chief officiant counts eight times from one to ten, knotting the yufu each time. By tying knots in this symbol of the emperor’s life span, the officiant keeps his tama from slipping away. the eight times and eight knots refer to the eight musubi (binding) tama of deities.
As one can see by these examples, the mitamashizume or chinkon-sai was a ritual means to fix the emperor’s tama so that it would not leave his body. the ancient Japanese greatly feared wandering tama and made the utmost efforts to affix them. A similar ceremony is still being carried out secretly each year at the Isonokami shrine (Renri City, Nara prefecture). This ritual may have to do partly with the Kyujiki, a text which gives much more importance to the Mononobe clan whose ancestral deity is enshrined at Isonokami, than the Kojiki and Nihon Shoki.
Such tamafuri and tamashizume rituals were often popularly called iki-bon, the Bon of living spirits. the Buddhist Urabon festival of late summer, however, a festival primarily concerned with the souls of the dead, has now superseded in importance this ceremony for the souls of the living.”

Source: Rethinking Japan Vol 1.: Literature, Visual Arts & Linguistics (by Adriana Boscaro, Franco Gatti, Massimo Raveri)

The Taoist concept of soul summoning may have been transmitted via Korean immigrants, or directly by Chinese immigrants, or both.

A celestial being on a cloud motif seen on an ancient bronze bell of the Korean kingdom Silla. c. 833 Photo source: Imperial Japanese Commission to the Panama-Pacific International Exposition: Japanese Temples and their Treasures (The Shimbi Shoin 1915) Wikimedia Commons

Chinkon rituals of “shaking the soul”

From Ze’ev Erlich’s Torifune and tama furi:

TAMA FURI/ Furitama-no-Gyo
Tama(soul) Furi (shake) basic meaning is the self Chin-kon and relates directly to the furube-no-kamu-waza of Chinkon Saho.
Furitama ( Soul Shaking)
1. Stand with your legs apart about shoulder width .
2. Place your hands together with the right hand over the left. Leave space between them big enough for an imaginary ping pong ball.
3. Place your hands in that position in front of your stomach and 0shake them vigorously up and down.
4. While shaking them concentrate and repeat the words: Harae-do-no-Okami – an invocation to the kami of the place of harai.

The Object Furitama-no-gyo

The purpose of shaking the soul is to generate awareness of it within yourself. Kon, (the soul), in Shinto, is one of the four important elements along with Mei (life), Rei (spirit) and Ki (which means Spirit in its causal aspect – Ki is a kind of energy source). Kon is the most important of the four since human beings can also be described as Waketama (separated individual souls), which is another way of saying “children of the kami”.

…

In Chinese art, an ancient cloud “meander” motif is related to the Hun and Po concepts of the afterlife. The cloud is a commonly seen design and when repeated in a pattern symbolizes never-ending fortune.

Clouds, sometimes referred to as “auspicious clouds” (xiangyun 祥云), represent the heavens and also “good luck” because the Chinese word for cloud (yun 云) is pronounced the same as yun (运) meaning “luck” or “fortune”. Auspicious clouds may be seen on coins and charms or amulets.

The cloud motif or form often resembles the auspicious shape of the lingzhi “fungus of immortality”. These are concepts that are related to thunder and the ability to call down rain, and also closely related to dragon and star symbolism.  (Source: The Hidden or Implied Meaning of Chinese Charm Symbols)

Theories on the Taoist concepts of Hun and Po souls

Chinese Taoist or daoist texts

Hun controls yang spirits in the body,
Po controls yin spirits in the body,
all are made of qi.
Hun is responsible for all formless consciousness,
including the three treasures: jing, qi and shen.
Po is responsible for all tangible consciousness,
including the seven apertures: two eyes, two ears, two nose holes, mouth.
Therefore, we call them 3-Hun and 7-Po.

Master Hu continues with an elaboration of these dynamics; and ends by pointing out that, like all of cyclic existence, the relationship between Hun and Po is a seemingly “endless cycle,” which is transcended “only by the achieved,” i.e. by the Immortals (in their transcendence of all duality):

He Yin-Yang’s Framework For Understanding Hun & Po

Another way of understanding Hun and Po is as an expression of Yin and Yang. As Twicken points out, the Yin-Yang framework is the foundational model of Chinese metaphysics. In other words: it is in understanding how Yin and Yang relate to one another (as mutually-arising and inter-dependent) that we can understand how — from a Taoist perspective — all pairs of opposites “dance” together, as not-two and not-one: appearing without actually “existing” as permanent, fixed “entities.”

In this way of viewing things, Po is associated with Yin. It is the more dense or physical of the two “spirits,” and is known also as the “corporeal soul,” since it returns to earth — dissolving into gross elements — at time of the time of the death of the body.

Hun, on the other hand, is associated with Yang, since it is the more light or subtle of the two “spirits.” It’s known also as the “ethereal soul,” and at the time of death leaves body to merge into more subtle realms of existence.

In the process of Taoist cultivation, the practitioner seeks to harmonize the Hun and Po, in a way which gradually allows the Po (the more dense) aspects to more and more fully support the Hun (the more subtle) aspects. The outcome of this kind of refinement process is the manifestation of a way-of-being and way-of-perceiving known by Taoist practitioners as “Heaven on Earth.”

Staying & Moving In The Mahamudra Tradition

In the Tibetan Mahamudra tradition (associated primarily with the Kagyu lineage), a distinction is drawn between the “staying” and the “moving” aspects of mind.

The “staying” aspect of mind refers more-or-less to what is sometimes also called the “witnessing” capacity. It is the perspective from which the arising and dissolving of various phenomena (thoughts, sensations, perceptions) is observed. It is the aspect of mind which has the capacity to remain (and is quite naturally) “continuously present,” and unaffected by the “objects” or “events” that arise within it.

The “moving” aspect of mind refers to the various appearances which — like waves on an ocean — arise and dissolve. These are the “objects” and “events” that seem (at least initially) to have a space/time duration: an arising, an abiding, and a dissolution. As such, they seem to undergo change or transformation — in opposition to the “staying” aspect of mind, which is unchanging.

A Mahamudra practitioner trains, first, in the capacity to toggle back and forth between these two (“staying” and “moving”) perspectives (known also as the “mind-perspective” and the “event-perspective”). And then, eventually, to experience them as simultaneously-arising and indistinguishable (i.e. nondual) — in the way that waves and ocean, as water, actually are mutually-arising and indistinguishable.

Taoism Meets Mahamudra, For A Cup Of Tea

The resolution of the moving/staying polarity, I would suggest, is basically equivalent (or at least opens the way for) the transcending of what Master Hu refers to as the tangible-consciousness/formless-consciousness polarity; and the absorption of the more densely-vibrating Po into the more subtle Hun.

Or, to put it another way: the corporeal Po “serves” the ethereal Hun — in Taoist cultivation — to the extent that mind’s appearances become self-aware, i.e. conscious of their source & destination in/as the Hun — like waves becoming conscious of their essential nature as water.

Source: Hun and Po

Hun (Chinese: 魂; pinyin: hún; Wade–Giles: hun; literally: “cloud-soul”) and po (Chinese: 魄; pinyin: pò; Wade–Giles: p’o; literally: “white-soul”) are types of souls in Chinese philosophy and traditional religion. Within this ancient soul dualism tradition, every living human has both a hunspiritual, ethereal, yang soul which leaves the body after death, and also a po corporeal, substantive, yin soul which remains with the corpse of the deceased. Some controversy exists over the number of souls in a person; for instance, one of the traditions within Daoism proposes a soul structure of sanhunqipo 三魂七魄; that is, “three hun and seven po“. The historian Yü Ying-shih describes hun and po as “two pivotal concepts that have been, and remain today, the key to understanding Chinese views of the human soul and the afterlife.”^[1]

The Chinese characters 魂 and 魄 for hun and po typify the most common character classification of “radical-phonetic” or “phono-semantic” graphs, which combine a “radical” or “signific” (recurring graphic elements that roughly provide semanticinformation) with a “phonetic” (suggesting ancient pronunciation). Hun 魂 (or 䰟) and po 魄 have the “ghost radical” gui 鬼 “ghost; devil” and phonetics of yun 云 “cloud; cloudy” and bai 白 “white; clear; pure”.

Besides the common meaning of “a soul”, po 魄 was a variant Chinese character for po 霸 “a lunar phase” and po 粕 “dregs”. The Shujing “Book of History” used po 魄 as a graphic variant for po 霸 “dark aspect of the moon” – this character usually means ba 霸 “overlord; hegemon”. For example, “On the third month, when (the growth phase, 生魄) of the moon began to wane, the duke of Chow [i.e., Duke of Zhou] commenced the foundations, and proceeded to build the new great city of Lǒ” (tr. Legge 1865:434). The Zhuangzi “[Writings of] Master Zhuang” wrote zaopo 糟粕 (lit. “rotten dregs”) “worthless; unwanted; waste matter” with a po 魄 variant. A wheelwright sees Duke Huan of Qi with books by dead sages and says, “what you are reading there is nothing but the [糟魄] chaff and dregs of the men of old!” (tr. Watson 1968:152).

In the history of Chinese writing, characters for po 魄/霸 “lunar brightness” appeared before those for hun 魂 “soul; spirit”. The spiritual hun 魂 and po 魄 “dual souls” are first recorded in Warring States period (475–221 BCE) Seal Script characters. The lunar po 魄 or 霸 “moon’s brightness” appears in both Zhou Dynasty (1045–256 BCE) Bronzeware script and Oracle bone script, but not in Shang Dynasty (ca. 1600–1046 BCE) oracle inscriptions. The earliest form of this “lunar brightness” character was found on a (ca. 11th century BCE) Zhou oracle bone inscription (Yü 1987:370).

Etymologies

The po soul’s etymology is better understood than the hun soul’s. Schuessler (2007:290, 417) reconstructs hun 魂 “‘spiritual soul’ which makes a human personality” and po 魄 “vegetative or animal soul … which accounts for growth and physiological functions” as Middle Chinese γuən and pʰak from Old Chinese *wûn and *phrâk.

The (ca. 80 CE) Baihu Tang 白虎堂 gave pseudo-etymologies for hun and po through Chinese character puns. It explains hun 魂 with zhuan 傳 “deliver; pass on; impart; spread” and yun 芸 “rue (used to keep insects out of books); to weed”, and po 魄 withpo 迫 ” compel; force; coerce; urgent” and bai 白 “white; bright”.

What do the words hun and [po] mean? Hun expresses the idea of continuous propagation ([zhuan] 傳), unresting flight; it is the qi of the Lesser Yang, working in man in an external direction, and it governs the nature (or the instincts, [xing] 性). [Po] expresses the idea of a continuous pressing urge ([po] 迫) on man; it is the [qi] of the Lesser Yin, and works in him, governing the emotions ([qing] 情). Hun is connected with the idea of weeding ([yun] 芸), for with the instincts the evil weeds (in man’s nature) are removed. [Po] is connected with the idea of brightening ([bai] 白), for with the emotions the interior (of the personality) is governed. (tr. Needham and Lu 1974:87)

Etymologically, Schuessler says pò 魄 “animal soul” “is the same word as” pò 霸 “a lunar phase“. He cites the Zuozhuan (534 BCE, see below) using the lunar jishengpo 既生魄 to mean “With the first development of a fetus grows the vegetative soul”.

Pò, the soul responsible for growth, is the same as pò the waxing and waning of the moon”. The meaning ‘soul’ has probably been transferred from the moon since men must have been aware of lunar phases long before they had developed theories on the soul. This is supported by the etymology ‘bright’, and by the inverted word order which can only have originated with meteorological expressions … The association with the moon explains perhaps why the pò soul is classified as Yin … in spite of the etymology ‘bright’ (which should be Yang), hun’s Yang classificiation may be due to the association with clouds and by extension sky, even though the word invokes ‘dark’. ‘Soul’ and ‘moon’ are related in other cultures, by cognation or convergence, as in Tibeto-Burman and Proto-Lolo–Burmese *s/ʼ-la “moon; soul; spirit”, Written Tibetan cognates bla “soul” and zla “moon”, and Proto-Miao–Yao *bla “spirit; soul; moon”. (2007:417)

Lunar associations of po are evident in the Classical Chinese terms chanpo 蟾魄 “the moon” (with “toad; toad in the moon; moon”) and haopo 皓魄 “moon; moonlight” (with “white; bright; luminous”).

The semantics of po 魄 “white soul” probably originated with 霸 “lunar whiteness”. Zhou bronze inscriptions commonly recorded lunar phases with the terms jishengpo 既生魄 “after the brightness has grown” and jisipo 既死魄 “after the brightness has died”, which Schuessler explains as “second quarter of the lunar month” and “last quarter of the lunar month”. Chinese scholars have variously interpreted these two terms as lunar quarters or fixed days, and (Shaughnessy 1992:136–145) Wang Guowei‘s lunar-quarter analysis the most likely. Thus, jishengpo is from the 7th/8th to the 14th/15th days of the lunar month and jisipo is from the 23rd/24th to the end of the month. Yü (1987:370) translates them as “after the birth of the crescent” and “after the death of the crescent”. Etymologically, lunar and spiritual po <pʰak < *phrâk 魄 are cognate with bai < bɐk < *brâk 白 “white” (Matisoff 1980, Yü 1981, Carr 1985). According to Hu Shih (1946:30), po etymologically means “white, whiteness, and bright light”; “The primitive Chinese seem to have regarded the changing phases of the moon as periodic birth and death of its [po], its ‘white light’ or soul.” Yü (1981:83) says this ancient association between the po soul and the “growing light of the new moon is of tremendous importance to our understanding of certain myths related to the seventh day of the months.” Two celebrated examples in Chinese mythology are Xi Wangmu and Emperor Wu meeting on the seventh day of the first lunar month and The Princess and the Cowherd or Qixi Festival held on the seventh day of the seventh lunar month.

The etymology of hun < γuən < *wûn 魂 is comparatively less certain. Hu (1946:31) said, “The word hun is etymologically the same as the word yun, meaning “clouds.” The clouds float about and seem more free and more active than the cold, white-lighted portion of the growing and waning moon.” Schuessler cites two possibilities.

Since pò is the ‘bright’ soul, hún is the ‘dark’ soul and therefore cognate to yún 雲 ‘cloud’ [Carr 1985:62], perhaps in the sense of ‘shadowy’ because some believe that the hún soul will live after death in a world of shadows [Eberhard 1967:17]. (2007:290)

Both Chinese hun and po are translatable as English “soul” or “spirit“, and both are basic components in “soul” compounds. In the following examples, all Chinese-English translation equivalents are from DeFrancis (2003).

• hunpo 魂魄 “soul; psyche”
• linghun 靈魂 “soul; spirit”
• hunling 魂靈 “(colloquial) soul; ghost”
• yinhun 陰魂 “soul; spirit; apparition”
• sanhunqipo 三魂七魄 “soul; three finer spirits and several baser instincts that motivate a human being”
• xinpo 心魄 “soul”

Hunpo and linghun are the most frequently used among these “soul” words.

Joseph Needham and Lu Gwei-djen, eminent historians of science and technology in China, (1974:88) define hun and po in modern terms. “Peering as far as one can into these ancient psycho-physiological ideas, one gains the impression that the distinction was something like that between what we would call motor and sensory activity on the one hand, and also voluntary as against vegetative processes on the other.”

Farzeen Baldrian-Hussein (2008:521) cautions about hun and po translations: “Although the term “souls” is often used to refer to them, they are better seen as two types of vital entities, the source of life in every individual. The hun is Yang, luminous, and volatile, while the po is Yin, somber, and heavy.”

History

Based on Zuozhuan usages of hun and po in four historical contexts, Yü (1987:370) extrapolates that po was the original name for a human soul, and the dualistic conception of hun and po “began to gain currency in the middle of the sixth century” BCE.

Two earlier 6th century contexts used the po soul alone. Both describe Tian 天 “heaven; god” duo 奪 “seizing; taking away” a person’s po, which resulted in a loss of mental faculties. In 593 BCE (Duke Xuan 15th year, tr. Legge 1872:329), after Zhao Tong 趙同 behaved inappropriately at the Zhou court, an observer predicted: “In less than ten years [Zhao Tong] will be sure to meet with great calamity. Heaven has taken his [魄] wits away from him.” In 543 BCE (Duke Xiang 29th year, tr. Legge 1872:551), Boyou 伯有 from Zheng (state) acted irrationally, which an official interpreted as: “Heaven is destroying [Boyou], and has taken away his [魄] reason.” Boyou’s political enemies subsequently arranged to take away his hereditary position and assassinate him.

Two later 6th century Zuozhuan contexts used po together with the hun soul. In 534 BCE (Duke Zhao 7th year, tr. Legge 1872:618), the ghost of Boyou 伯有 (above) was seeking revenge on his murderers, and terrifying the people of Zheng. The philosopher and statesman Zi Chan, realizing that Boyou’s loss of hereditary office had caused his spirit to be deprived of sacrifices, reinstated his son to the family position, and the ghost disappeared. When a friend asked Zi Chan to explain ghosts, he gave what Yu (1972:372) calls “the locus classicus on the subject of the human soul in the Chinese tradition.”

When a man is born, (we see) in his first movements what is called the [魄] animal soul. [既生魄] After this has been produced, it is developed into what is called the [魂] spirit. By the use of things the subtle elements are multiplied, and the [魂魄] soul and spirit become strong. They go on in this way, growing in etherealness and brightness, till they become (thoroughly) spiritual and intelligent. When an ordinary man or woman dies a violent death, the [魂魄] soul and spirit are still able to keep hanging about men in the shape of an evil apparition; how much more might this be expected in the case of [Boyou]. … Belonging to a family which had held for three generations the handle of government, his use of things had been extensive, the subtle essences which he had imbibed had been many. His clan also was a great one, and his connexions [sic] were distinguished. Is it not entirely reasonable that, having died a violent death, he should be a [鬼] ghost?

Compare the translation of Needham and Lu (1974:86), who interpret this as an early Chinese discourse on embryology.

When a foetus begins to develop, it is (due to) the [po]. (When this soul has given it a form) then comes the Yang part, called hun. The essences ([qing] 情) of many things (wu 物) then give strength to these (two souls), and so they acquire the vitality, animation and good cheer (shuang 爽) of these essences. Thus eventually there arises spirituality and intelligence (shen ming 神明).”

In 516 BCE (Duke Zhao 20th year, tr. Legge 1872:708), the Duke of Song (state) and a guest named Shusun 叔孫 were both seen weeping during a supposedly joyful gathering. Yue Qi 樂祁, a Song court official, said:

“This year both our ruler and [Shusun] are likely to die. I have heard that joy in the midst of grief and grief in the midst of joy are signs of a loss of [xin 心] mind. The essential vigor and brightness of the mind is what we call the [hun] and the [po]. When these leave it, how can the man continue long?” Hun and po souls, explains Yu (1987:371), “are regarded as the very essence of the mind, the source of knowledge and intelligence. Death is thought to follow inevitably when the hun and the p’o leave the body. We have reason to believe that around this time the idea of hun was still relatively new.”

Soon after death, it was believed that a person’s hun and po could be temporarily reunited through a ritual called the fu 復 “recall; return”, zhaohun 招魂 “summon the hun soul”, or zhaohun fupo 招魂復魄 “to summon the hun-soul to reunite with the po-soul”. The earliest known account of this ritual is found in the (3rd century BCE) Chu Ci poems Zhaohun 招魂 “Summons of the Soul” and Dazhao 大招 “The Great Summons” (Csikszentmihalyi 2006:140–141). For example, Wu/Shaman Yang 巫陽 summons a man’s soul in Zhaohun.

O soul, come back! Why have you left your old abode and sped to the earth’s far corners, deserting the place of your delight to meet all those things of evil omen?

O soul, come back! In the east you cannot abide. There are giants there a thousand fathoms tall, who seek only for souls to catch, and ten suns that come out together, melting metal, dissolving stone …
O soul, come back! In the south you cannot stay. There the people have tattooed faces and blackened teeth, they sacrifice flesh of men, and pound their bones to paste …
O soul, come back! For the west holds many perils: The Moving Sands stretch on for a hundred leagues. You will be swept into the Thunder’s Chasm and dashed in pieces, unable to help yourself …
O soul, come back! In the north you may not stay. There the layered ice rises high, and the snowflakes fly for a hundred leagues and more…
O soul, come back! Climb not to heaven above. For tigers and leopards guard the gates, with jaws ever ready to rend up mortal men …

O soul, come back! Go not down to the Land of Darkness, where the Earth God lies, nine-coiled, with dreadful horns on his forehead, and a great humped back and bloody thumbs, pursuing men, swift-footed … (tr. Hawkes 1985:244–5)

Hu (1946:31–32) proposed, “The idea of a hun may have been a contribution from the southern peoples” (who originated zhaohun rituals) and then spread to the north sometime during the sixth century BCE. Calling this southern hypothesis “quite possible”, Yu (1987:373) cites the Chuci (associated with the southern state of Chu) demonstrating “there can be little doubt that in the southern tradition the hun was regarded as a more active and vital soul than the p’o. The Chuci uses hun 65 times and po 5 times (4 in hunpo, which the Chuci uses interchangeably with hun, Brashier 1996:131).  [On the other hand, it has been shown that that cloud symbolism and the cloudsoul hun has been a distinctive belief and genealogical tradition of all the northeast Asians and Central Asians since prehistoric times which suggests a much earlier northern provenance originating with the tumuli-building peoples.]

The identification of the yin-yang principle with the hun and po souls evidently occurred in the late fourth and early third centuries BCE (Yü 1987:374), and by “the second century at the latest, the Chinese dualistic conception of soul had reached its definitive formulation.” The Liji (11, tr. Legge 1885:444) compounds hun and po with qi “breath; life force” and xing “form; shape; body” in hunqi 魂氣 and xingpo 形魄. “The [魂氣] intelligent spirit returns to heaven the [形魄] body and the animal soul return to the earth; and hence arose the idea of seeking (for the deceased) in sacrifice in the unseen darkness and in the bright region above.” Compare this modern translation (Yü 1987:374), “The breath-soul (hun-ch’I 魂氣) returns to heaven; the bodily soul (hsing-p’o 形魄) returns to earth. Therefore, in sacrificial-offering one should seek the meaning in the yin-yang 陰陽 principle.” Yü summarizes hun/po dualism.

Ancient Chinese generally believed that the individual human life consists of a bodily part as well as a spiritual part. The physical body relies for its existence on food and drink produced by the earth. The spirit depends for its existence on the invisible life force called ch’i, which comes into the body from heaven. In other words, breathing and eating are the two basic activities by which a man continually maintains his life. But the body and the spirit are each governed by a soul, namely, the p’o and the hun. It is for this reason that they are referred to in the passage just quoted above as the bodily-soul (hsing-p’o) and the breath-soul (hun-ch’i) respectively. (Yü 1987:376)

Loewe (1979:9) explains with a candle metaphor; the physical xing is the “wick and substance of a candle”, the spiritual po and hun are the “force that keeps the candle alight” and “light that emanates from the candle”.

The Yin po and Yang hun were correlated with Chinese spiritual and medical beliefs. Hun 魂 is associated with shen 神 “spirit; god” and po 魄with gui 鬼 “ghost; demon; devil” (Carr 1985:62). The (ca. 1st century BCE) Lingshu Jing medical text spiritually applies Wu Xing “Five Phase” theory to the Zang-fu “organs”, associating the hun soul with liver (Chinese medicine) and blood, and the po soul with lung (Chinese medicine) and breath.

The liver stores the blood, and the blood houses the hun. When the vital energies of the liver are depleted, this results in fear; when repleted, this results in anger. … The lungs store the breath, and the breath houses the po. When the vital energies of the lungs are depleted, then the nose becomes blocked and useless, and so there is diminished breath; when they are repleted, there is panting, a full chest, and one must elevate the head to breathe. (tr. Brashier 1996:141)

The Lingshu (Brashier 1996:142) also records that the hun and po souls taking flight can cause restless dreaming, and eye disorders can scatter the souls causing mental confusion. Han medical texts reveal that hun and po departing from the body does not necessarily cause death but rather distress and sickness. Brashier (1996:145–6) parallels the translation of hun and po, “If one were to put an English word to them, they are our “wits”, our ability to demarcate clearly, and like the English concept of “wits,” they can be scared out of us or can dissipate in old age.”

During the Han Dynasty, the belief in hun and po remained prominent, although there was a great diversity of different, sometimes contradictory, beliefs about the afterlife (Hansen 2000:119; Csikszentmihalyi 2006:116–117, 140–142). (Many of Japanese tumuli period funerary beliefs were influenced by Han Dynasty period beliefs.) Han burial customs provided nourishment and comfort for the po with the placement of grave goods, including food, commodities, and even money within the tomb of the deceased (Hansen 2000:119). Chinese jade was believed to delay the decomposition of a body. Pieces of jade were commonly placed in bodily orifices, or rarely crafted into jade burial suits.

Generations of sinologists have repeatedly asserted that Han-era people commonly believed the heavenly hun and earthly po souls separated at death, but recent scholarship and archaeology suggest that hunpo dualism was more an academic theory than a popular faith. Anna Seidel analyzed funerary texts discovered in Han tombs, which mention not only po souls but also hun remaining with entombed corpses, and wrote (1982:107), “Indeed, a clear separation of a p’o, appeased with the wealth included in the tomb, from a hun departed to heavenly realms is not possible.” Seidel later (1987:227) called for reappraising Han abstract notions of hun and po, which “do not seem to have had as wide a currency as we assumed up to now.” Pu Muzhou surveyed usages of the words hun and po on Han Dynasty bei 碑 “stele” erected at graves and shrines, and concluded (1993:216, tr. Brashier 1996126), “The thinking of ordinary people seems to have been quite hazy on the matter of what distinguished the hun from the po.” These stele texts contrasted souls between a corporeal hun or hunpo at the cemetery and a spiritual shen at the family shrine. Kenneth Brashier (1996:158) reexamined the evidence for hunpo dualism and relegated it “to the realm of scholasticism rather than general beliefs on death.” Brashier (1996:136–137) cited several Han sources (grave deeds, Houhanshu, and Jiaoshi Yilin) attesting beliefs that “the hun remains in the grave instead of flying up to heaven”, and suggested it “was sealed into the grave to prevent its escape.” Another Han text, the Fengsu Tongyi says, “The vital energy of the hun of a dead person floats away; therefore a mask is made in order to retain it.”

Divisible hun and po soul concepts in Daoism 

Hun 魂 and po 魄 spiritual concepts were important in several Daoist traditions. For instance (Baldrian-Hussein 2008:522), “Since the volatile hun is fond of wandering and leaving the body during sleep, techniques were devised to restrain it, one of which entailed a method of staying constantly awake.”

The sanhunqipo 三魂七魄 “three hun and seven po” were anthropomorphized and visualized. Ge Hong‘s (ca. 320 CE) Baopuzi frequently mentions the hun and po “ethereal and gross souls”. The “Genii” Chapter argues that these dual souls cause illness and death.

All men, wise or foolish, know that their bodies contain ethereal as well as gross breaths, and that when some of them quit the body, illness ensues; when they all leave him, a man dies. In the former case, the magicians have amulets for restraining them; in the latter case,The Rites [i.e., Yili] provide ceremonials for summoning them back. These breaths are most intimately bound up with us, for they are born when we are, but over a whole lifetime probably nobody actually hears or sees them. Would one conclude that they do not exist because they are neither seen nor heard? (2, tr. Ware 1966:49–50)

This “magicians” translates fangshi 方士 “doctor; diviner’ magician”. Both fangshi and daoshi 道士 “Daoist priests” developed methods and rituals to summon hun and po back into a person’s body. The “Gold and Cinnabar” chapter records a Daoist alchemical reanimation pill that can return the hun and po souls to a recent corpse: Taiyi zhaohunpo dan fa 太乙招魂魄丹法 “The Great One’s Elixir Method for Summoning Souls”.

In T’ai-i’s elixir for Summoning Gross and Ethereal Breaths the five minerals [i.e., cinnabar, realgar, arsenolite, malachite, and magnetite] are used and sealed with Six-One lute as in the Nine-crucible cinnabars. It is particularly effective for raising those who have died of a stroke. In cases where the corpse has been dead less than four days, force open the corpse’s mouth and insert a pill of this elixir and one of sulphur, washing them down its gullet with water. The corpse will immediately come to life. In every case the resurrected remark that they have seen a messenger with a baton of authority summoning them. (4, tr. Ware 1966:87)

For visualizing the ten souls, the Baopuzi “Truth on Earth” chapter recommends taking dayao 大藥 “great medicines” and practicing a fenxing 分形 “divide/multiply the body” multilocation technique.

My teacher used to say that to preserve Unity was to practice jointly Bright Mirror, and that on becoming successful in the mirror procedure a man would be able to multiply his body to several dozen all with the same dress and facial expression. My teacher also used to say that you should take the great medicines diligently if you wished to enjoy Fullness of Life, and that you should use metal solutions and a multiplication of your person if you wished to communicate with the gods. By multiplying the body, the three Hun and the seven Po are automatically seen within the body, and in addition it becomes possible to meet and visit the powers of heaven and the deities of earth and to have all the gods of the mountains and rivers in one’s service. (18, tr. Ware 1966:306)

The Daoist Shangqing School has several meditation techniques for visualizing the hun and po. In Shangqing Neidan “Internal Alchemy”, Baldrian-Hussein says,

the po plays a particularly somber role as it represents the passions that dominate the hun. This causes the vital force to decay, especially during sexual activity, and eventually leads to death. The inner alchemical practice seeks to concentrate the vital forces within the body by reversing the respective roles of hun and po, so that the hun (Yang) controls the po (Yin). (2008:533)

Number of souls

The number of human “souls” has been a long-standing source of controversy among Chinese religious traditions. Stevan Harrell (1979:521) concludes, “Almost every number from one to a dozen has at one time or another been proposed as the correct one.” The most commonly believed numbers of “souls” in a person are one, two, three, and ten.

One “soul” or linghun 靈魂 is the simplest idea. Harrell gives a fieldwork example.

When rural Taiwanese perform ancestral sacrifices at home, they naturally think of the ling-hun in the tablet; when they take offerings to the cemetery, they think of it in the grave; and when they go on shamanistic trips, they think of it in the yin world. Because the contexts are separate, there is little conflict and little need for abstract reasoning about a nonexistent problem. (1979:523)

Two “souls” is a common folk belief, and reinforced by yin-yang theory. These paired souls can be called hun and Three “souls” comes from widespread beliefs that the soul of a dead person can exist in the multiple locations. The missionary Justus Doolittle recorded that Chinese people in Fuzhou

believe each person has three distinct souls while living. These souls separate at the death of the adult to whom they belong. One resides in the ancestral tablet erected to his memory, if the head of a family; another lurks in the coffin or the grave, and the third departs to the infernal regions to undergo its merited punishment. (1865 II:401–2)

Ten “souls” of sanhunqipo 三魂七魄 “three hun and seven po” is not only Daoist; “Some authorities would maintain that the three-seven “soul” is basic to all Chinese religion” (Harrell 1979:522). During the Later Han period, Daoists fixed the number of hun souls at three and the number of po souls at seven. A newly deceased person may return (回魂) to his home at some nights, sometimes one week (頭七) after his death and the seven po would disappear one by one every 7 days after death. According to Needham and Lu (1974:88), “It is a little difficult to ascertain the reason for this, since fives and sixes (if they corresponded to the viscera) would have rather been expected.” Three hun may stand for the sangang 三綱 “three principles of social order: relationships between ruler-subject, father-child, and husband-wife” (Needham 1974:89). Seven po may stand for the qiqiao 七竅 “seven apertures (in the head, eyes, ears, nostrils, and mouth)” or the qiqing 七情 “seven emotions (joy, anger, sorrow, fear, worry, grief, fright)” in traditional Chinese medicine (Baldrian-Hussein 2008:522). Sanhunqipo also stand for other names.

Source: Hun and Po

Chinkon is a revived Shinto practice today in Japan, as a soul-binding or soul-summoning procedure or rite for healing (an ancient shamanic calling back the wandering soul spirit) Chinkon  kishin and as a ‘Chinkon’  (‘Pacifying and Deepening the soul’ exercise, which is “a quiet journey into  the interior. This involves meditation, and focusing on specific  mental images. These three elements, purification, spiritual movements, and meditation, are the bases of Shinto training” see Green Shinto’s “Spiritual exercises: misogi, furitama and chinkon” article. The chinkon ritual practice was revived by Shinto scholar Honda Chikaatsu who based the practice on the Chinkonsai court ritual and the Kojiki account of Okinaga Tarashi Hime’s medium spirit possession, see Birgit Staemmler’s “Chinkon Kishin: Mediated Spirit Possession in Japanese New Religions” at p 117.

The cloudsoul hun, we theorize, was likely a far older motif of Northeast Asia from prehistoric times, as the cloud spirals are a common motif in ceramics of the prehistoric Jomon people of Japan as well as the Amur populations(see Ainu cloud motif), although interpretations lend themselves variously to both solar as well as cloud symbols. As a pre-Hun and proto-Tartar-Mongol belief, cloud-symbol-associated sky, storm and thunder god beliefs likely spread westwards influencing early Indo-European and Anatolian populations as well as all of East Asian civilization, see Jacqueline Taylor Basker’s, “The Cloud as a Symbol“.  Cloud symbolism is given detailed treatment in Camman Schuyler’s article “The Symbolism of the Cloud Collar“, The Art Bulletin, Vol. 33, No. 1 (Mar., 1951), pp. 1-9 URL: http://www.jstor.org/stable/3047324, as well as Hubert Damisch’s “A Theory of Cloud: Toward a History of Painting“. In The Language of Kilim of Anatolia, Uzeyir Ozeyurt showed that Mongolian princes of Hitay and Anatolian Hittite village weaving used the same fertility motifs, and that many basic motifs are shared between East and West, including cloud spirals and storm/thunder meander patterns. We may therefore surmise that while the cloud-soul meaning was lost during the cloud motif’s diffusion westwards, cloud symbolism associations with a divinity’s descent, and particularly that of sky-storm gods, remained.

Aug 17, 2014 Latin American Herald Tribune reports…

LIMA — A study has revealed genetic links between people who inhabited northern Peru more than 1,000 years ago and Japanese, El Comercio newspaper reported Thursday.

Japanese physical anthropologist Ken-ichi Shinoda performed DNA tests on the remains of human bodies found in the East Tomb and West Tomb in the Bosque de Pomas Historical Sanctuary, which are part of the Sican Culture Archaeological Project, funded by Japan’s government.

The director of the Sican National Museum, Carlos Elera, told the daily that Shinoda found that people who lived more than 1,000 years ago in what today is the Lambayeque region, about 800 kilometers (500 miles) north of Lima, had genetic links to the contemporaneous populations of Ecuador, Colombia, Siberia, Taiwan and to the Ainu people of northern Japan.

The studies will be continued on descendents of the Mochica culture, from the same region, who are currently working on the Sican Project and with people who live in the vicinity of the Bosque de Pomac Historical Sanctuary.

Peruvian archaeologist Luis Chero told El Comercio that “currently, the DNA results have great value because they can be understood to show that there were people who arrived in these zones from Asia and who then converted these zones into the great culture of the New World.”

The results of the studies will be presented at an exhibit on the Sican culture that will be set up for a year at the Tokyo Museum of Science and Nature.

Also to be displayed at that exhibit will be gold, silver and copper jewelry found in the tombs of the ancient Sican rulers and priests.

The traditional view that humans fall into three major populations, Africans, East Asians, and Europeans, with the latter two diverging from the African ancestors ∼55,000 years ago, has been re-examined by a group of researchers, who have come to a bold and different conclusion — and who have put forward a new view that East Asians diverged from Africans first, and that only later did the Europeans diverge from the East Asian grouping.

The study also proposes a new theory of origins of the Ainu. The long-debated and mystifying European appearance of the Ainu people is explained, as congruent with the idea that the Ainu people emerged at the point of time when Europeans were beginning to diverge from East Asians.

The results of the research has just been published in the Genome Biology and Evolution Journal, entitled “Divergence of East Asians and Europeans Estimated Using Male- and Female-Specific Genetic Markers” by Yoshio TATENO et al. Genome Biol Evol (2014) 6 (3): 466-473. doi: 10.1093/gbe/evu027

Excerpted from the paper:

“We sequenced Y-STR makers in Y chromosome and collected complete mtDNAs for many East Asian and European individuals to reexamine that view” … “focused on the divergence of three major populations — Africans, Europeans, and East Asians—and East Asians and Europeans in particular, because they lived together for a while after coming out of Africa and likely interbred, perhaps similar to the hybridizations reported between Neanderthals and modern humans (Noonan 2006). After the divergence between Mongoloid (East Asian) and Caucasoid (European) people ~55,000 years ago (Nei and Roychoudhury 1993), they might have still interbred while en route to settlement in their present localities…”

“For the male lineages, we used the Y-STR markers for 453 individuals covering Japanese, Korean, Mongolian (Khalkh), American, and European people. We determined the evolutionary distances (RST) among them, and constructed a phylogenetic tree using the NJ method (Saitou and Nei 1987), as shown in figure 1. The Y-STR tree revealed that the male ancestral lineage contained two clades (Yap-A and Yap-B). While Yap-A clade includes the East Asian individuals only, Yap-B clade contains the East Asian and European individuals together. Surprisingly, the European males never formed an independent clade. Instead, they formed separate clades within Yap-B.”

Fig. 1

” We then constructed a phylogenetic tree (Mt tree) for the 72 complete mtDNAs including the four ethnic groups, as shown in figure 2. We used Kimura’s two parameter method (Kimura 1980) for computing evolutionary distances among them and the NJ method for the tree construction. The Mt tree revealed two female descendant clades (Mt A and Mt B). Mt B consisted of the East Asian females only, while Mt A contained the East Asian and European females together. As in the case of males, the European females did not form an independent clade, but comprised several groups within the Mt A tree. As the Mt A cluster includes roughly as many European individuals as East Asian individuals, it is not clear which of them is ancestral to the other. The node marked with the blue circle in figure 2 suggests that the East Asians are ancestral to the Europeans. The bootstrap value of the node is 99%. Therefore, both male and female lineages suggest that Europeans diverged from within East Asian ancestors or that they interbred with East Asian individuals up to a certain divergence time.

Fig. 2

Our next question was thus to estimate the divergence time of the European clade within the East Asian lineage, for males and females separately. To address that question, we computed the evolutionary distance (RST) between every pair of the male individuals to construct the Y-STR tree in figure 1. The researchers’ conclusion was that “the divergence time of the European males is ∼40,100 years ago” while they “estimated the divergence time of the European females, as ∼41,500 years ago.”

“Our results suggest that the European people settled down in their territories ∼41,000 year ago, and have developed their own cultures and languages since then.

On the other hand, the East Asians were classified into two clusters; one is Type 1 East Asians denoted as Yap-A [this is the grouping that carries C,D hgs and YAP+ genes, i.e. the Jomon and Ainu ancestral line] and Mt B clusters in the male and female trees, respectively, and the other is Type 2 East Asians denoted as Yap-B and Mt A clusters in the male and female trees, respectively.

While Type 1 includes East Asian individuals only, Type 2 contains East Asians and European individuals together.

FIG. 4.— The general view of the East Asian and European divergences is summarized in figure 4.

Fig. 4

Fig. 4 Phlyogenetic tree of the major human populations Africans, Type 1 East Asians, Europeans and Type 2 East Asians

“Both the Y-STR and mtDNA trees consistently show that Europeans diverged from East Asian ancestors ∼41,000 years ago.”

Dealing with the question of differences in facial morphology and phenotypes, the paper proposed:

“Population genetic theory indicates that 41,000 years, or about 2,000 generations, are long enough to accumulate SNPs in the same loci in each lineage (Kimura 1983; Nei 1987) to account for the present genetic and phenotypic differences between the East Asians and Europeans, but too short to acquire independent loci between them. Recently, Liu (2012) reported on five genes responsible for the facial morphology of European people. The East Asian people must have the counterparts that differ at the SNP level from those in the European people. As our phylogenetic trees demonstrate, the European alleles at the five loci have diverged from the ancestral East Asian alleles.

Our result contrasts with the traditional view that Europeans and East Asians simultaneously diverged from African ancestors 55,000 years ago. It is noteworthy, however, that Shinoda (2007) investigated into the haplogroups of mtDNA, and revealed a number of evolutionary haplotype lineages. The lineages include L3 (African), N (East Asian), W (European), and L3 to N to R (East Asian) and then HV (European) among others. Though they did not explain their results, their haplotype lineages can now be understood by our finding that the Europeans diverged from the East Asians. Therefore, the discrepancy between the traditional view and ours lies mainly in that the traditional view was based on autosomal genes that evolved much slower than Y-STR or mtDNA, and could not distinguish the evolutionary lineages at the individual level. Note that, as estimated earlier, the evolutionary rate of mtDNA is 2.4 × 10−8 per site per year, while that of nuclear neutral sequences is 2.0 × 10−9 per site per year (Fukami Kobayashi 2005). The discrepancy also is due to the fact that while we dealt with many male and female individuals in our study, the other studies did not.

Our result contrasts with the traditional view that Europeans and East Asians simultaneously diverged from African ancestors 55,000 years ago. It is noteworthy, however, that Shinoda (2007) investigated into the haplogroups of mtDNA, and revealed a number of evolutionary haplotype lineages. The lineages include L3 (African), N (East Asian), W (European), and L3 to N to R (East Asian) and then HV (European) among others. Though they did not explain their results, their haplotype lineages can now be understood by our finding that the Europeans diverged from the East Asians. Therefore, the discrepancy between the traditional view and ours lies mainly in that the traditional view was based on autosomal genes that evolved much slower than Y-STR or mtDNA, and could not distinguish the evolutionary lineages at the individual level.

… according to the classification agreed at the Y Chromosome Consortium (2002) and elsewhere (Karafet et al. 2008), we found that all individuals in the Yap-B1 in figure 1 belonged to either haplogroup C or D, while the majority in the Yap- B2 belonged to haplogroup O. Since Yap-B1 includes mainly Japanese and Korean males, in which 91% individuals share haplotype O2b, the Korean and Japanese males are definitely closest to one another within East Asian humans. We also found a high frequency of the O2b haplotype in Manchu (Northern China) and Korean-Chinese samples (Katoh et al. 2005b; Kim et al. 2011).
The origin of the Ainu people is still an unresolved issue (Tajima et al. 2004). On the basis of our results, we propose a possible scenario for the origin of the Ainu people, who now live in the north-most island of the Japanese archipelago, Hokkaido. The Ainu people have European phenotypic characters, but they are genetically closer to East Asians than to Europeans (Watanabe 1975). These contradictory features of the Ainu people are puzzling. As shown in figure 4, Europeans may have diverged from East Asians ∼41,000 years ago, it is possible that hybrid individuals were born before the divergence, and some of them looked more like the Europeans while possessing a generally East Asian genotype. We suggest that the ancestor of the Ainu people was such a group of the hybrid individuals. We note that the present Ainu people share the mtDNA haplotype not with the Japanese but with the European living in Siberia, Russia (Adachi et al. 2009). Thus, we furthermore suggest that the ancestor of the Ainu originated in northern Eurasia and took a route through Siberia and north China before settling in northern regions of Japan and nearby places. There is a report that other people than the Ainu also lived in the northern regions but disappeared (Adachi et al. 2009). As the people in Okinawa islands are closest to the Ainu people in the East Asians (Jinam et al. 2012), they might also be descendants from of mixing of East Asian and European lineages.

Conclusion:
Phylogenetic trees of Y-STR makers and Mt genes suggest that the Europeans interbred with East Asians until ∼41,000 years ago. On the other hand, East Asians diverged from their African ancestors ∼55,000 years ago. Therefore, we suggest that the European and East Asian lineages diverged ∼41,000 years ago.

***

What are the implications for Japanese settlement and migrational history theory:

To recap, this is what we can glean from this study with respect to the populating of Japan.

– East Asians diverged from their African ancestors ∼55,000 years ago –>

Earliest East Asian grouping

YAP-A   which is made up of C, D and YAP+ hgs. This group comprises mainly of Khalkh Mongolians and predominantly Japanese (all arching Japanese grouping, note: ancestral lineages Jomon, Ainu showed highest frequencies of YAP+, but a significant component of the lineages of the modern Japanese population today still carry a strong signal of the ancient YAP+ gene. YAP+ is an ancient Out-of-Africa marker – borne only by group), Koreans and Europeans in somewhat more miniscule numbers. (This is presumably is the oldest Out-of-Africa grouping, because it includes YAP+ genes.)

The study proposes that Ainu arose out of hybrid individuals were born before the divergence of Europeans from East Asians ∼41,000 years ago, and some of whom looked more like the Europeans while possessing a generally East Asian genotype may have diverged. The ancestor of the Ainu originated in northern Eurasia and took a route through Siberia and north China before settling in northern regions of Japan and nearby places.

The study also proposes that the people in Okinawa islands being closest to the Ainu people in the East Asians (Jinam et al. 2012),were likely descendants from of mixing of East Asian and European lineages.

According to the study, the Y-STR tree (focusing on male lineages comprising Japanese, Korean, Mongolian (Khalkh), American, and European people only), revealed that the male ancestral lineage contained two clades (Yap-A and Yap-B). While Yap-A clade includes the East Asian individuals only, Yap-B clade contains the East Asian and European individuals together.

– East Asian and European groups diverge at around 41,000 ya

in the East Asian-only group – Yap-B1 in figure 1 belonged to either haplogroup C or D [Other studies have proposed that C and D lineages are the earliest or among the earliest groups to settle East Asia.  Hg C is thought to have come from a southerly possibly coastal origin, while D from a either a southerly or southwesterly direction]  However, since Yap-B1 includes mainly Japanese and Korean males, in which 91% individuals share haplotype O2b, the Korean and Japanese males are definitely closest to one another within East Asian humans (a high frequency of the O2b haplotype also found in Manchu (Northern China) and Korean-Chinese samples).

– The branching of NO – and the branching of Y-DNA O into subclades on the continent is a highly complex picture and the roots of the tree only beginning to be understood.  According to the study the majority of Yap- B2 belonged to haplogroup O.  The European males never formed an independent clade. Instead, they formed separate clades within Yap-B.

A few points I wish to make here:

Given that the study’s groupings of Yap A and YAP B1 and B2 groups involve the haplogroups C, D and O, it is surprising that the paper does not cite or try to reconcile the results of important studies that have proposed the origins and migrational paths for these groups.  For example,

• The study not cite a important paper that throws light of the timing and place where the divergence of the NO haplogroup could have occurred in East Asia – the 2006 paper “A counter-clockwise northern route of the Y-chromosome haplogroup N from Southeast Asia towards Europe”  Rootsi et al. European Journal of Human Genetics (2007) 15, 204–211. doi:10.1038/sj.ejhg.5201748:

Abstract: “…our detailed analysis of hg N suggests that its high frequency in east Europe is due to its more recent expansion westward on a counter-clock northern route from inner Asia/southern Siberia, approximately 12–14 ky ago. The widespread presence of hg N in Siberia, together with its absence in Native Americans, implies its spread happened after the founder event for the Americas. The most frequent subclade N3, arose probably in the region of present day China, and subsequently experienced serial bottlenecks in Siberia and secondary expansions in eastern Europe. Another branch, N2, forms two distinctive subclusters of STR haplotypes, Asian (N2-A) and European (N2-E), the latter now mostly distributed in Finno-Ugric and related populations. These phylogeographic patterns provide evidence consistent with male-mediated counter-clockwise late Pleistocene–Holocene migratory trajectories toward Northwestern Europe from an ancestral East Asian source of Paleolithic heritage.”

Excerpts from the body of the paper:

” … the spatial distributions for ancestral paragroup NO-M214^*, paragroup N-M231^* and the prevalent hg O-M175 (Figure 2a, c, d) are generally congruent and highlight Southeast Asia as the most parsimonious source region of these clades. The spread pattern of paragroup NO^*approximates the same regions of Southeast Asia as paragroup N^*, although being present at an even lower frequency compared with N^{*18, 19} (data from Kayser et al¹⁹ updated in present study). More notable, however, is the fact that the spatial dynamics of the whole N and O haplogroups greatly differ from each other. The split between N^* and O is dated to 34.64.7 thousand years (ky). The age of STR variation of hg O in Southeast Asia probably exceeds 26 ky,¹⁰ and its numerous subclades currently predominate in southern and southeastern Asia extending into northern China, Manchuria and some Siberian populations,^{7, 9, 11,20, 21} as well as westward to the eastern sector of the Indian subcontinent¹⁰ and eastward to Oceania.

The phylogeography of the NO^* and N^* lineages (Figure 2a, d) and the presence of N^* chromosomes in southern East Asia (South China and Cambodia, see Supplementary Table 1) suggests that this region could be the source of the initial spread of hg N. In this scenario, the Altay/Sayan/southern Siberia region might have been a place of transition of hg N westward as all major subclades of hg N are still to be found there. …

In summary, Y chromosome haplogroup N presents a case of gene flow to eastern Europe that has its likely ultimate source in east Asia.”

See also the other paper by SHi H, et al, “Genetic Evidence of an East Asian Origin and Paleolithic Northward Migration of Y-chromosome Haplogroup N” and also  Austro-Asiatic Tribes of Northeast India Provide Hitherto Missing Genetic Link between South and Southeast Asia Mohan Reddy et al., PLoS ONE. 2007; 2(11): e1141. 2007 (alternative theory for the origin of O-M95 in the Austro-Asiatic tribes of N-E India.

***

• Important research involving Y-DNA C, or that of D and YAP+ such as that by Hua Zhong et al., Global distribution of Y-chromosome haplogroup C reveals the prehistoric migration routes of African exodus and early settlement in East Asia. J Hum Genet. 2010 Jul;55(7):428-35. doi: 10.1038/jhg.2010.40. Epub 2010 May 7; Inferring human history in East Asia from Y chromosomes Chuan-Chao Wangand Hui Li^* Investigative Genetics 2013, 4:11  doi:10.1186/2041-2223-4-11 The above 2014 study was based on 242 Japanese, 85 Korean, 77 Khalkh Mongolian, and 49 European bins. The Korean samples were collected in Seoul, while the Khalkh Mongolian samples were obtained in Ulaanbaatar, Mongolia. The Khalkh were chosen because “The Khalkh are the major population in Mongolia, representing ∼ 80% of the total population, the language spoken in Mongolia has its origins in the Khalkh language.” but other groups at the root of the haplogroup D and YAP+ allele such as Tibetans, Qiang, Yunnanese, Buryats etc., in addition to the Japanese, are ancestral lineages of the haplogroup D. ; Extended Y chromosome investigation suggests postglacial migrations of modern humans into East Asia via the northern route. Mol Biol Evol. 2011 Jan;28(1):717-27. doi: 10.1093/molbev/msq247. Epub 2010 Sep 13.; 

The 2014 paper in ignoring the aforementioned research papers leaves hanging other fundamental questions: Before East Asia, what was the route taken out of Africa of all these founding haplogroups – a southern one or northern one, single migration route or multiple (See Single, Rapid Coastal Settlement of Asia Revealed by Analysis of Complete Mitochondrial Genomes, Vincent Macaulay et al.,  Science 13 May 2005: Vol. 308 no. 5724 pp. 1034–1036DOI:10.1126/science.1109792; ; Extended Y chromosome investigation suggests postglacial migrations of modern humans into East Asia via the northern route. Zhong H, et al. Mol Biol Evol. 2011 Jan;28(1):717-27.

Finally, the Japanese samples are classified broadly as Japanese samples (but Ainu and Okinawan and ancient Jomon DNA, are usually differentiated from modern Honshu Japanese samples, here it is all lumped here into one great grouping). Would the study’s results have showed a vastly different picture had they tested against specific samples of Ainu, ancient Jomon (different locations in Japan), as well as against against different continental populations of Altai-Buryat Mongols, Tibetans, Tungusic-Amur or Nikhs peoples, Yakuts, Evenkhs, Kazakhs???

See also:

DNA analyses and inferred genetic origins of the Ainu

Making sense of DNA data and the origins of the Japanese

YAP-positive element in the Y-chromosomes of the Ainu people

Resources on Ainu DNA

Reconstructed scene of what the Miyako-zuka pyramid looked like

A pyramid has been uncovered by archaeologists at Asuka, Nara, NHK World news announced his evening.

Pyramids, though not unknown in Japan, are very rare. The Zuto and Doto pagoda pyramids also in Nara are from the 8th century, but this newly discovered pyramid, is believed to be from the latter part of the 6th century (and contemporaneous with the reign of Prince Shotoku).

Miyakozuka pyramid site

Located in Asuka village, a village already well known for its many unusual megalithic discoveries, this pyramid is located at Miyako-zuka only 400 metres away from the Ishibutai tomb.

Ishibutai tomb’s occupant is thought to be related that of the Miyako-zuka tomb

The Ishibutai tomb thought to be the tomb of the Soga no Umako, a powerful minister of the imperial court and leader of the ruling clan of the Yamato state. Miyako-zuka is believed to pre-date the Ishibutai tomb.

Experts believe the pyramid likely belonged to the father of Soga no Umako. Soga no Iname (蘇我 稲目, 506 – March 22, 570). Soga no Iname was a leader of the Soga clan and a statesman during the reign of Emperor Kimmei in the Asuka period. He was the first person to hold the position of Ōomi that can be verified with reasonable accuracy, in 536 AD.

Pyramids, the closest ones in proximity to Japan’s, are found in Jilin (modern-day China) which belonged to the Korean Kingdom of Koguryo (in yellow above)

According to the experts, based on a reading of the text of the ancient Nihon Shoki (see photos above) Soga no Iname is the most likely candidate for the occupant of the pyramid tomb, and because his two wives are known to have been from the Koguryo Kingdom,  this provides a strong reason why the pyramidal tomb design of Koguryo would have been introduced at this time.

…

Update from Jiji Press via The Yomiuri Shimbun, 15th Aug, 2014

6th century tomb likely step pyramid in shape

NARA (Jiji Press)—A large ancient rectangular tomb in the village of Asuka in Nara Prefecture may have had a rare pyramid shape, according to a group of archeologists.

The Miyakozuka tomb is believed to have been built in the latter half of the sixth century.

It was likely a step pyramid made of multiple stone layers, experts at the municipal education board and Kansai University’s Archaeological Research Institute said Wednesday.

The tomb may have been influenced by ancient tumuli built near the border between China and North Korea given its similar structure, according to the experts.

It is thought that Soga no Iname, a Yamato Dynasty leader who died in 570, was buried in the tomb. He is known to have had close links with people from China and the Korean Peninsula who immigrated to Japan.

After excavating the mound and surrounding areas of the Miyakozuka tomb, the group of archeologists found stair-like architectural remains at three locations.

Four layers of stones were found at one location, and one layer was discovered at each of the two other locations.

Based on the findings, the group said it believes the tomb had a pyramid-like structure with seven or eight stone layers.

The mound is estimated to have been at least 4.5 meters high on the east side and 7 meters high on the west, with each side being more than 40 meters long.

Soga no Iname is known to have had strong ties to Koguryo as he is believed to have had two wives from the ancient Korean kingdom.

The village of Asuka is known for many megalithic discoveries. They include the Ishibutai tomb believed to have been built in the seventh century for Soga no Umako, son of Iname, who died in 626.

Clay pots and ironware were unearthed from the Miyakozuka tomb in a survey started in 1967 by the Kansai University research institute and others. But the size of the mound, its structure and other details remained unknown.

For further reading, see Sakai’s list of 12 pyramids

The pyramids of Suzuki Akira

Japan archaeological find shows 1,400-year-old roots of silk weaving.

City of Shimotsuke education board A terracotta image of a person weaving silk with a loom. The figurine was found in a sixth-century burial mound in Shimotsuke, 50 miles north of Tokyo.

by Mitsuru Obe, AWSJ Mar 6, 2014

Japan’s prewar economic development depended in significant part on exports of one item–silk. Young girls recruited from poor farm families worked day and night to make Japan the world’s biggest silk exporter, allowing it to purchase raw materials, warships and other Western industrial technology.

Now an archaeological find is showing the industry’s ancient roots. In the first such discovery in Japan, researchers unearthed a terracotta figure depicting a woman weaving silk on a loom. The find came from a sixth-century burial mound, or kofun, in Shimotsuke, some 50 miles north of Tokyo.

The unglazed pottery figure, known as haniwa, provides evidence that techniques of silk weaving already existed in the sixth century and that women played a central role in the manufacturing of silk at that early date.

Shimotsuke used to be a major silk manufacturing region, with the local silk industry designated by the United Nations Educational, Scientific and Cultural Organization as an example of intangible cultural heritage.

Immigrants from China are believed to have brought sericulture and silk weaving to Japan around the fifth century. Rice farmers grew mulberry trees and wove silk during the off-season.

The figure of a weaving woman, 69 centimeters high, was found near the burial chamber of an 80-meter-long tomb mound, where a local chieftain or a prominent weaver was apparently buried, said Tomonori Kimura, a official in charge of cultural affairs for the city of Shimotsuke. The city unveiled the find this week.

Silk was apparently used to make kimonos and may have been offered as a gift to the court, according to the researchers.

They also discovered a clay figure depicting a more primitive loom, 22 other clay figures and some 360 unglazed pots.

Such grave mounds were built between the third and the seventh century by the ruling clan that went on to establish Japan’s present-day imperial household. The practice was also widely adopted by local chieftains.

Various kinds of terracotta figures were buried with the dead, including horses, birds, swords, shields and soldiers. The exact reason for such clay offerings is not known, but Mr. Kimura speculated that they may have been meant to honor the achievements of the deceased during his or her lifetime.

City of Shimotsuke education board This reconstruction shows what a sixth-century figurine of a woman weaving silk might have originally looked like.

A 2009 study found that the Japanese in Central Japan and Chiba share a genetic trait with the Han Chinese Hakka and Minnam populations (with origins in Central China) – high frequencies of their ALDH2*504Lys allele marker and concluded that migrants likely carried the gene marker from ancient populations in East China to Japan During the Yayoi period. The marker is associated with high incidence rates of oesophageal cancer. See excerpts from the study below:

 Figure 1. The geographic distribution of ALDH2*504Lys allele frequency. The grey scale refers to the interpolated allele frequency and correspondences are on the right, e.g. 0.12 means an allele frequency of 12% in the region. The open red triangles represent the locations of the population samples. The encircling black lines are the 0.12 and 0.24 frequency borders.

“In total, the map shows a pattern of a single center of expansion within East Asia. The highest frequencies appear in a restricted area in Southeast China, among the Han Chinese in south Fujian province and east Guangdong province (the Hakka and Minnam populations), decreasing gradually to the north and west. Hakka from Changting County in Fujian have the highest frequency, 40.9%. The Hakka population samples from Taiwan and Sichuan also exhibit high frequencies, indicating that Hakka have maintained a high frequency during their migrations. The allele frequencies in other Han Chinese populations range from 9% to 40%, exhibiting a cline clearly decreasing from southeast to northwest, except for two small peaks in Shanghai in East China and Shandong in Central China.

Another high frequency area for the ALDH2*504Lys allele is Central Japan with 34.1% in Chiba. However, this high frequency area seems to be an extension from East China. The frequency decreases from around 30% in Honshu to around 10% in Ryukyu and Hokkaido, corresponding well to the migration history of modern Japanese (the descendants of Yayoi People, Hammer et al., 2006). Therefore, it is most probable that the ALDH2*504Lys allele in Japan was brought by the early Yayoi migrants from mainland East Asia.”

The researchers also “hypothesize that the oriental ALDH2*504Lys variant might have originated in the ancient Han Chinese population in Central China and spread to most areas of East Asia with the expansion of Han Chinese and their genetic influences on neighboring populations over the past few thousand years.”

Source of study: Hui Li, et al., Refined Geographic Distribution of the Oriental ALDH2*504Lys (nee 487Lys) Variant, Annals of Human Genetics, Volume 73, Issue 3, pages 335–345, May 2009 doi: 10.1111/j.1469-1809.2009.00517.x