An Okhotsk adult female human skeleton (11th/12th century AD) with possible SAPHO syndrome from Hamanaka 2 site, Rebun Island, northern Japan

Okamoto, Yuka; Ishida, Hajime; Kimura, Ryosuke; Sato, Takehiro; Tsuchiya, Nanae; Murayama, Sadayuki; Fukase, Hitoshi; Nagaoka, Tomohito; Adachi, Noboru; Yoneda, Minoru; Weber, Andrzej; Katô, Hirofumi

doi:10.1537/ase.160608

Cited by 8 publications

(10 citation statements)

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“…The ratio of reads mapped to Y and X chromosomes, the R Y value, was 0.0017, which was calculated using ry_compute.py ( Skoglund et al 2013 ), indicating that NAT002 was female. This finding was consistent with previous results regarding morphological- and Amelogenin gene-based sex identification ( Okamoto et al 2016 ). The total error rate of the NAT002 sequence estimated based on chimpanzee (PanTro2) and high-quality modern Japanese genomes was 0.11%, indicating a relatively low level of postmortem damage ( supplementary fig.…”

Section: Resultssupporting

confidence: 93%

“…Previous studies have reported that the HLA-B gene, especially the HLA-B*27 allele, is strongly associated with SAPHO syndrome ( Carneiro and Sampaio-Barros 2013 ). Therefore, to investigate the genetic susceptibility to hyperostosis of NAT002, which was inferred as SAPHO syndrome by a previous study ( Okamoto et al 2016 ), we determined the human leukocyte antigen (HLA) type of this individual using HLA-VBSeq ( Nariai et al 2015 ), TARGT ( Pierini et al 2020 ), and HLA EXPLORE (Omixon, Budapest, Hungary). The HLA-B alleles that showed the top two average depths in the typing with HLA-VBSeq were HLA-B*40:02:01 (average depth, 22.93×) and HLA-B*40:06:01:01 (average depth, 12.57×), implying that this individual is a heterozygote of B*40:02:01 and B*40:06:01:01.…”

Section: Resultsmentioning

confidence: 99%

“…1 b and c ). The radiocarbon ( 14 C) calibrated age of NAT002 was estimated to be 1,060–1,155 calAD (68.2%), and hyperostosis was diagnosed as synovitis, acne, pustulosis, hyperostosis, osteitis (SAPHO) syndrome without dermatological observations ( Okamoto et al 2016 ). In this study, we performed whole-genome sequencing of NAT002 to resolve the issues regarding the origins of the Okhotsk people and their genetic contribution to the Ainu population.…”

Section: Introductionmentioning

confidence: 99%

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Whole-Genome Sequencing of a 900-Year-Old Human Skeleton Supports Two Past Migration Events from the Russian Far East to Northern Japan

Sato

Adachi

Kimura

et al. 2021

Genome Biology and Evolution

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Recent studies on paleogenomics have reported some Paleolithic and Neolithic genomes that have provided new insights into the human population history in East and Northeast Asia. However, there remain some cases where more recent migration events need to be examined to elucidate the detailed formation process of local populations. Although the area around northern Japan is one of the regions archaeologically suggested to have been affected by migration waves after the Neolithic period, the genetic source of these migrations are still unclear. Thus, genomic data from such past migrant populations would be highly informative to clarify the detailed formation process of local populations in this region. Here, we report the genome sequence of a 900-year-old adult female (NAT002) belonging to the prehistoric Okhotsk people, who have been considered to be the past migrants to northern Japan after the Neolithic period. We found a close relationship between NAT002 and modern Lower Amur populations and past admixture events between the Amur, Jomon, and Kamchatka ancestries. The admixture dating suggested migration of Amur-related ancestry at approximately 1,600 BP, which is compatible with the archaeological evidence regarding the settlement of the Okhotsk people. Our results also imply migration of Kamchatka-related ancestry at approximately 2,000 BP. In addition, human leukocyte antigen (HLA) typing detected the HLA-B*40 allele, which is reported to increase the risk of arthritis, suggesting the genetic vulnerability of NAT002 to hyperostosis, which was observed around her chest clavicle.

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Section: Resultssupporting

confidence: 93%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Whole-Genome Sequencing of a 900-Year-Old Human Skeleton Supports Two Past Migration Events from the Russian Far East to Northern Japan

Sato

Adachi

Kimura

et al. 2021

Genome Biology and Evolution

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“…The cool temperature of Rebun Island (mean annual temperature in the period 1978–2002 was 6.6 °C 21 ) and the presence of shell promotes good preservation of organic materials at the Hamanaka 2 site. Since 2011, archaeological excavations have yielded human remains, rich faunal remains, lithics and pottery fragments 22–25 .…”

Section: Methodsmentioning

confidence: 99%

Palaeoproteomic identification of breast milk protein residues from the archaeological skeletal remains of a neonatal dog

Tsutaya

Mackie

Koenig

et al. 2019

Sci Rep

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Accurate postmortem estimation of breastfeeding status for archaeological or forensic neonatal remains is difficult. Confident identification of milk-specific proteins associated with these remains would provide direct evidence of breast milk consumption. We used liquid chromatography coupled to tandem mass spectrometry (MS) to confidently identify beta-lactoglobulin-1 (LGB1) and whey acidic protein (WAP), major whey proteins associated with a neonatal dog ( Canis lupus familiaris ) skeleton (430–960 cal AD), from an archaeological site in Hokkaido, Japan. The age at death of the individual was estimated to be approximately two weeks after birth. Protein residues extracted from rib and vertebra fragments were analyzed and identified by matching tandem MS spectra against the dog reference proteome. A total of 200 dog protein groups were detected and at least one peptide from canine LGB1 and two peptides from canine WAP were confidently identified. These milk proteins most probably originated from the mother’s breast milk, ingested by the neonate just before it died. We suggest the milk diffused outside the digestive apparatus during decomposition, and, by being absorbed into the bones, it partially preserved. The result of this study suggests that proteomic analysis can be used for postmortem reconstruction of the breastfeeding status at the time of death of neonatal mammalian, by analyzing their skeletal archaeological remains. This method is also applicable to forensic and wildlife studies.

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“…This shell-midden site is located on the coast of the Funadomari Bay on the northern part of Rebun Island, which lays 45 km east of the northern tip of Hokkaido Island (Fig 1C–1E). For nearly a century, archaeologists have recognised the abundance of archaeological remains dating to the Okhotsk cultural period in the Funadomari Bay area [40]. Archaeological excavations started in the region in 1949, focusing on the Hamanaka 2 site complex and unearthed pottery, hearths, shell-middens, marine mammal remains, human burials, and house pits, suggesting residential activities at the site during the Okhotsk period [41].…”

Section: Study Site and Environmental Settingmentioning

confidence: 99%

Barley (Hordeum vulgare) in the Okhotsk culture (5th–10th century AD) of northern Japan and the role of cultivated plants in hunter–gatherer economies

et al. 2017

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This paper discusses archaeobotanical remains of naked barley recovered from the Okhotsk cultural layers of the Hamanaka 2 archaeological site on Rebun Island, northern Japan. Calibrated ages (68% confidence interval) of the directly dated barley remains suggest that the crop was used at the site ca. 440–890 cal yr AD. Together with the finds from the Oumu site (north-eastern Hokkaido Island), the recovered seed assemblage marks the oldest well-documented evidence for the use of barley in the Hokkaido Region. The archaeobotanical data together with the results of a detailed pollen analysis of contemporaneous sediment layers from the bottom of nearby Lake Kushu point to low-level food production, including cultivation of barley and possible management of wild plants that complemented a wide range of foods derived from hunting, fishing, and gathering. This qualifies the people of the Okhotsk culture as one element of the long-term and spatially broader Holocene hunter–gatherer cultural complex (including also Jomon, Epi-Jomon, Satsumon, and Ainu cultures) of the Japanese archipelago, which may be placed somewhere between the traditionally accepted boundaries between foraging and agriculture. To our knowledge, the archaeobotanical assemblages from the Hokkaido Okhotsk culture sites highlight the north-eastern limit of prehistoric barley dispersal. Seed morphological characteristics identify two different barley phenotypes in the Hokkaido Region. One compact type (naked barley) associated with the Okhotsk culture and a less compact type (hulled barley) associated with Early–Middle Satsumon culture sites. This supports earlier suggestions that the “Satsumon type” barley was likely propagated by the expansion of the Yayoi culture via south-western Japan, while the “Okhotsk type” spread from the continental Russian Far East region, across the Sea of Japan. After the two phenotypes were independently introduced to Hokkaido, the boundary between both barley domains possibly existed ca. 600–1000 cal yr AD across the island region. Despite a large body of studies and numerous theoretical and conceptual debates, the question of how to differentiate between hunter–gatherer and farming economies persists reflecting the wide range of dynamic subsistence strategies used by humans through the Holocene. Our current study contributes to the ongoing discussion of this important issue.

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An Okhotsk adult female human skeleton (11th/12th century AD) with possible SAPHO syndrome from Hamanaka 2 site, Rebun Island, northern Japan

Cited by 8 publications

References 50 publications

Whole-Genome Sequencing of a 900-Year-Old Human Skeleton Supports Two Past Migration Events from the Russian Far East to Northern Japan

Whole-Genome Sequencing of a 900-Year-Old Human Skeleton Supports Two Past Migration Events from the Russian Far East to Northern Japan

Palaeoproteomic identification of breast milk protein residues from the archaeological skeletal remains of a neonatal dog

Barley (Hordeum vulgare) in the Okhotsk culture (5th–10th century AD) of northern Japan and the role of cultivated plants in hunter–gatherer economies

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