Details of a Researcher - MATSUMURA Hirofumi

Papers - MATSUMURA Hirofumi

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Out of Africa:ホモ・サピエンスのユーラシアへの拡散とアジア人の起源

Matsumura Hirofumi

生物の科学遺伝 ( エヌ・ティー・エス ) 70 ( 6 ) 451 - 459 2016

Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone.

Ron Pinhasi, Daniel Fernandes, Kendra Sirak, Mario Novak, Sarah Connell, Songül Alpaslan-Roodenberg, Fokke Gerritsen, Vyacheslav Moiseyev, Andrey Gromov, Pál Raczky, Alexandra Anders, Michael Pietrusewsky, Gary Rollefson, Marija Jovanovic, Hiep Trinhhoang, Guy Bar-Oz, Marc Oxenham, Hirofumi Matsumura, Michael Hofreiter

PloS one ( PUBLIC LIBRARY SCIENCE ) 10 ( 6 ) e0129102 2015 [Refereed] [International journal]

The invention and development of next or second generation sequencing methods has resulted in a dramatic transformation of ancient DNA research and allowed shotgun sequencing of entire genomes from fossil specimens. However, although there are exceptions, most fossil specimens contain only low (~ 1% or less) percentages of endogenous DNA. The only skeletal element for which a systematically higher endogenous DNA content compared to other skeletal elements has been shown is the petrous part of the temporal bone. In this study we investigate whether (a) different parts of the petrous bone of archaeological human specimens give different percentages of endogenous DNA yields, (b) there are significant differences in average DNA read lengths, damage patterns and total DNA concentration, and (c) it is possible to obtain endogenous ancient DNA from petrous bones from hot environments. We carried out intra-petrous comparisons for ten petrous bones from specimens from Holocene archaeological contexts across Eurasia dated between 10,000-1,800 calibrated years before present (cal. BP). We obtained shotgun DNA sequences from three distinct areas within the petrous: a spongy part of trabecular bone (part A), the dense part of cortical bone encircling the osseous inner ear, or otic capsule (part B), and the dense part within the otic capsule (part C). Our results confirm that dense bone parts of the petrous bone can provide high endogenous aDNA yields and indicate that endogenous DNA fractions for part C can exceed those obtained for part B by up to 65-fold and those from part A by up to 177-fold, while total endogenous DNA concentrations are up to 126-fold and 109-fold higher for these comparisons. Our results also show that while endogenous yields from part C were lower than 1% for samples from hot (both arid and humid) parts, the DNA damage patterns indicate that at least some of the reads originate from ancient DNA molecules, potentially enabling ancient DNA analyses of samples from hot regions that are otherwise not amenable to ancient DNA analyses.

DOI PubMed

Demographic transitions and migration in prehistoric East/Southeast Asia through the lens of nonmetric dental traits.

Hirofumi Matsumura, Marc F Oxenham

American journal of physical anthropology ( WILEY-BLACKWELL ) 155 ( 1 ) 45 - 65 2014.09 [Refereed] [International journal]

The aim of this study is to examine and assess the nonmetric dental trait evidence for the population history of East and Southeast Asia and, more specifically, to test the two-layer hypothesis for the peopling of Southeast Asia. Using a battery of 21 nonmetric dental traits we examine 7,247 individuals representing 58 samples drawn from East and Southeast Asian populations inhabiting the region from the late Pleistocene, through the Neolithic, Bronze Age, Iron Age, and into the historic and modern periods. The chief data reduction technique is a neighbor-joining tree generated from the triangular matrix of mean measure of divergence values. Principal findings indicated a major dichotomization of the dataset into (1) an early Southeast Asian sample with close affinities to modern Australian and Melanesian populations and (2) a very distinct grouping of ancient and modern Northeast Asians. Distinct patterns of clinal variation among Neolithic and post-Neolithic Mainland Southeast Asian samples suggest a center to periphery spread of genes into the region from Northeast Asia. This pattern is consistent with archaeological and linguistic evidence for demic diffusion that accompanied agriculturally driven population expansion in the Neolithic. Later Metal Age affinities between Island and Mainland coastal populations with Northeast Asian series is likely a consequence of a South China Sea interaction sphere operating from at least 500 BCE, if not from the Neolithic. Such results provide extensive support for the two-layer hypothesis to account for the population history of the region.

DOI PubMed

Hoabinhians: A key population with which to debate the peopling of Southeast Asia

Hirofumi Matsumura, Marc F. Oxenham, Nguyen Lan Cuong

Emergence and Diversity of Modern Human Behavior in Paleolithic Asia ( Texas A&M University Press ) 117 - 132 2014.01

人類進化と疾患

松村博文

札幌医保健科学雑誌 ( 札幌医科大学保健医療学部 ) 4 ( 4 ) 1 - 7 2014 [Refereed] [Invited]

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保健医療総論1における学生へのアンケー卜を用いた学習効果に関する検討

吉戰淳一, 後藤葉子, 佐藤公美子, 根木亨, 中村充雄, 中井夏子, 長多好萬, 横山まどか, 大塚知子, 古名丈人, 池田望, 齋藤重幸, 古畑智久, 松村博文

札幌医保健科学雑誌 4 73 - 78 2014 [Refereed]

A comparative study of stress episode prevalence and duration among Jomon period foragers from Hokkaido.

Daniel H Temple, Jennifer N McGroarty, Debbie Guatelli-Steinberg, Masato Nakatsukasa, Hirofumi Matsumura

American journal of physical anthropology 152 ( 2 ) 230 - 8 2013.10 [Refereed] [International journal]

This study reconstructs linear enamel hypoplasia (LEH) prevalence and stress episode duration among Jomon period foragers from Hokkaido, Japan (HKJ). Results are compared to Jomon period samples from coastal Honshu, Japan (HSJ) and Tigara Inupiat from Point Hope, Alaska (PHT) to provide a more comprehensive perspective on the manifestation of stress among circum-Pacific foragers. LEH were identified macro- and microscopically by enamel surface depressions and increased perikymata spacing within defects. Individuals with more than one anterior tooth affected by LEH were labeled as LEH positive. Stress episode durations were estimated by counting the number of perikymata within the occlusal wall of each LEH and multiplying that number by constants reflecting modal periodicities for modern human teeth. LEH prevalence and stress episode duration did not differ significantly between the two Jomon samples. Significantly greater frequencies of LEH were found in HKJ as compared to PHT foragers. However, HKJ foragers had significantly shorter stress episode durations as compared to PHT. This suggests that a greater proportion of HKJ individuals experienced stress episodes than did PHT individuals, but these stress events ended sooner. Similarity in stress experiences between the two Jomon samples and differences between the HKJ and PHT are found. These findings are important for two reasons. First, stress experiences of foraging populations differ markedly and cannot be generalized by subsistence strategy alone. Second, due to significant differences in episode duration, stress experiences cannot be understood using prevalence comparisons alone.

DOI PubMed

Metric characteristics of human limb bones in Asian and Japanese populations

Masatomi Kudaka, Hitoshi Fukase, Ryosuke Kimura, Tsunehiko Hanihara, Hirofumi Matsumura, Aiko Saso, Tadahiko Fukumine, Hajime Ishida

Anthropological Science 121 ( 1 ) 49 - 62 2013 [Refereed]

Twelve metric variables of the humerus, radius, femur, and tibia were investigated in 11 male samples from northeastern and eastern Asian populations. Variations among regions and correlations between latitude and respective measurements and indices were calculated and a principal component analysis was conducted to elucidate human limb bone characteristics. Significant correlation and marginally significant correlation were found for the maximum subtrochanteric diameter (r = 0.662, P = 0.027) and the platymeric index (r = -0.583, P = 0.060) with latitude, respectively, suggesting that the femur of northern Asians had a wide and flat subtrochanteric shape. The second principal component of the principal component analysis shows that the northeastern samples with comparatively long shaft length and thin and flat shaft diameters were discriminated from the southern samples the second principal component was significantly correlated with latitude (r = -0.743, P = 0.009). The estimated Fst value of 0.432-0.336 shows that the variation in limb bone measurements across regions is rather large, at approximately two or three times the low levels of interregional variation (0.078-0.180) in analyses of cranial and dental data. Limb bone morphology has been repeatedly proposed to be more strongly influenced by environmental and nutritional factors than cranial and dental traits, but this study is the first to confirm it on the basis of statistical analysis. © 2013 The Anthropological Society of Nippon.

DOI

Population dispersal from East Asia into Southeast Asia: Evidence from cranial and dental Morphology

Hirofumi Matsumura, Marc Oxenham

Bioarchaeology of East Asia: Movement, Contact, Health ( University Press of Florida ) 179 - 209 2013

Population history of northern Vietnamese inferred from nonmetric cranial trait variation

Tsunehiko Hanihara, Hirofumi Matsumura, Yoshinori Kawakubo, Nguyen Lan Coung, Nguyen Kim Thuy, Marc F. Oxenham, Yukio Dodo

ANTHROPOLOGICAL SCIENCE ( ANTHROPOLOGICAL SOC NIPPON ) 120 ( 2 ) 157 - 165 2012.08 [Refereed]

In this study, nine nonmetric cranial traits were recorded for ancient human remains excavated at early prehistoric (the late Pleistocene, early Holocene, and Pre-Pottery Neolithic) and late prehistoric (the Neolithic and early Iron age) archeological sites in northern Vietnam. The comparative samples consist of prehistoric and early historic crania from the lower Yangtze River basin, together with recent cranial series from Vietnam, Thailand, South China, and Australia. The results, based mainly on the measure of divergence, are as follows: (1) the early prehistoric northern Vietnam group is distinct from the subsequent inhabitants of northern Vietnam and neighboring populations; (2) the cranial series of northern Vietnam and the surrounding region from the late prehistoric to recent times through early historic period exhibit relative homogeneity, suggesting population continuity; (3) the recent Han Chinese from southern China, one of the possible representatives of East Asians, are relatively distant from all groups from the prehistoric age onwards; and (4) a clear separation of Aboriginal Australians from all the comparative samples, including the early prehistoric northern Vietnamese, is evident. These findings suggest partial support for the two opposing hypotheses, i.e. the two-layer model and the regional-continuity model, for the population history of Southeast Asians, at least, in the northern Vietnamese region. This may be further compatible with the recent hypothesis for modern human dispersals: an earlier out-of-Africa expansion of Australians than other contemporary Eurasians including Southeast Asians.

DOI

歯の特徴による日本人の形成とアジア太平洋の人々 (特集古人類学・最新研究の動向) -- (日本列島人の形成史)

松村博文

季刊考古学 ( 雄山閣 ) 118 ( 118 ) 74 - 78 2012.02

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Microstructural analysis of linear enamel hypoplasia and estimation of stress episode duration in Jomon period dental remains from Hokkaido with comparisons to other cold-adapted foragers

Mcgroarty Jennifer, Temple Daniel H, Guatelli-Steinberg Debbie, Nakatsukasa Masato, Matsumura Hirofumi

AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 147 210 2012 [Refereed]

Mitochondrial DNA analysis of Hokkaido Jomon skeletons: remnants of archaic maternal lineages at the southwestern edge of former Beringia.

Noboru Adachi, Ken-ichi Shinoda, Kazuo Umetsu, Takashi Kitano, Hirofumi Matsumura, Ryuzo Fujiyama, Junmei Sawada, Masashi Tanaka

American journal of physical anthropology ( WILEY-BLACKWELL ) 146 ( 3 ) 346 - 60 2011.11 [Refereed] [International journal]

To clarify the colonizing process of East/Northeast Asia as well as the peopling of the Americas, identifying the genetic characteristics of Paleolithic Siberians is indispensable. However, no genetic information on the Paleolithic Siberians has hitherto been reported. In the present study, we analyzed ancient DNA recovered from Jomon skeletons excavated from the northernmost island of Japan, Hokkaido, which was connected with southern Siberia in the Paleolithic period. Both the control and coding regions of their mitochondrial DNA (mtDNA) were analyzed in detail, and we confidently assigned 54 mtDNAs to relevant haplogroups. Haplogroups N9b, D4h2, G1b, and M7a were observed in these individuals, with N9b being the predominant one. The fact that all these haplogroups, except M7a, were observed with relatively high frequencies in the southeastern Siberians, but were absent in southeastern Asian populations, implies that most of the Hokkaido Jomon people were direct descendants of Paleolithic Siberians. The coalescence time of N9b (ca. 22,000 years) was before or during the last glacial maximum, implying that the initial trigger for the Jomon migration in Hokkaido was increased glaciations during this period. Interestingly, Hokkaido Jomons lack specific haplogroups that are prevailing in present-day native Siberians, implying that diffusion of these haplogroups in Siberia might have been after the beginning of the Jomon era, about 15,000 years before present.

DOI PubMed

Do Body Proportions Among Jomon Foragers from Hokkaido Conform to Ecogeographic Expectations? Evolutionary Implications of Body Size and Shape Among Northerly Hunter-Gatherers

Daniel H. Temple, Hirofumi Matsumura

INTERNATIONAL JOURNAL OF OSTEOARCHAEOLOGY ( WILEY-BLACKWELL ) 21 ( 3 ) 268 - 282 2011.05 [Refereed]

This study documents and interprets adaptive postcranial morphology among prehistoric Jomon period foragers from Hokkaido, Japan (HKJ). The Hokkaido climate is differentiated from other Japanese islands by freezing winters with sea-ice accumulation in the northern regions. Increased brachial and crural indices are, however, observed among HKJ foragers, while body mass (BM) has not yet been estimated for these groups. Based on previous observations and paleoclimatic reconstructions, it was predicted that increased BM and increased distal relative to proximal limb lengths would typify HKJ foragers. Similar BM was observed between HKJ foragers and groups from colder environments. Intralimb indices do, however, suggest similarity between HKJ foragers and groups from high-latitude, warm environments. It is likely that HKJ foragers retained cold-derived BM in association with Pleistocene migrations to Hokkaido via Northeast Asia. That is, enlarged BM among HKJ foragers is associated with long-term evolution in a colder environment. Relatively elongated distal limbs may represent morphological response to a slightly warmer environment. Following migration to Japan from a colder environment, elongation of distal limb segments resulted in elevated brachial and crural indices. Relatively elongated distal appendages may also reflect positive nutritional status as HKJ people experienced lesser rates of systemic stress than other Jomon groups. It is also possible that elongated distal relative to proximal limbs are associated with neutral mutation and genetic drift. This interpretation suggests a neutral mutation associated with relative limb length in some HKJ ancestor with subsequent spread of this allele through isolation and drift. Ontogenetic and temporal studies of intralimb indices among Jomon people are necessary to further evaluate these interpretations. Copyright (C) 2009 John Wiley & Sons, Ltd.

DOI

Genotype frequencies of the ABCC11 gene in 2000-3000-year-old human bones from the Epi-Jomon and Jomon sites in Hokkaido, Japan

Hisako Kazuta, Takehiro Sato, Yukio Dodo, Hirofumi Matsumura, Tetsuya Amano, Hajime Ishida, Ryuichi Masuda

ANTHROPOLOGICAL SCIENCE ( ANTHROPOLOGICAL SOC NIPPON ) 119 ( 1 ) 81 - 86 2011.04 [Refereed]

In order to investigate further the allele frequencies of the adenosine triphosphate-binding cassette sub-family C11 (ABCC11) gene, which determines earwax phenotypes, among ancient populations in Hokkaido, Japan, the single-nucleotide polymorphism and the 27 bp deletion in the ABCC11 gene were analyzed in ancient DNA extracted from 38 Epi-Jomon, 24 Jomon, and one Satsumon specimens excavated from various archaeological sites in Hokkaido. Of the specimens analyzed, 10 Epi-Jomon and three Jomon specimens were successfully genotyped. One homozygote for the 27 bp deletion was found first in one Epi-Jomon specimen. Including previously reported data on the Okhotsk people and modern Ainu, exact tests of population differentiation showed that allele frequencies of the ABCC11 gene between the Jomon people and Ainu were statistically significantly different, whereas those between the Jomon and Epi-Jomon people and those between the Epi-Jomon people and Ainu were not significantly different. This result indicates that the Ainu, direct descendants of the Jomon people, were genetically affected by populations who possessed high frequencies of allele A (recessive dry allele) of the ABCC11 locus after the Jomon period.

DOI

On the origin of pre-Angkorian peoples: perspectives from cranial and dental affinity of the human remains from Iron Age Phum Snay, Cambodia

Hirofumi Matsumura, Kate M. Domett, Dougald J. W. O'Reilly

ANTHROPOLOGICAL SCIENCE ( ANTHROPOLOGICAL SOC NIPPON ) 119 ( 1 ) 67 - 79 2011.04 [Refereed]

This article presents the results of an assessment of the morphological affinities of the skeletal remains from a large mortuary assemblage, dated to Iron Age, in Phum Snay, a village in Banteay Meanchey Province, northwest Cambodia. The purpose of the research is to address the origin of these pre-Angkorian people. Multivariate comparisons using cranial and dental metrics, as well as dental nonmetric traits, demonstrate that the characteristic affinities intermediate between the early Holocene Hoabinhian groups akin to Australo-Melanesians and the present-day people in the mainland Southeast Asia. This finding suggests that the ancient people of Phum Snay preserved genetic traits of early indigenous populations, whereas modern mainland Southeast Asians, including Cambodians, were more affected by gene flow from later migrants from East Asia into this region.

DOI

An son and the neolithic of Southern Vietnam

Peter Bellwood, Marc Oxenham, Bui Chi Hoang, Nguyen Kim Dzung, Anna Willis, Carmen Sarjeant, Philip Piper, Hirofumi Matsumura, Katsunori Tanaka, Nancy Beavan-Athfield, Thomas Higham, Nguyen Quoc Manh, Dang Ngoc Kinh, Nguyen Khanh Trung Kien, Vo Thanh Huong, Van Ngoc Bich, Tran Thi Kim Quy, Nguyen Phuong Thao, Fredeliza Campos, Yo-Ichiro Sato, Nguyen Lan Cuong, Noel Amano

Asian Perspectives ( University of Hawaii Press ) 50 ( 1-2 ) 144 - 175 2011 [Refereed]

Between 4500 and 3500 years ago, partially intrusive Neolithic populations in the riverine basins of mainland Southeast Asia began to form mounded settlements and to develop economies based on rice cultivation, fishing, hunting, and the domestication of animals, especially pigs and dogs. A number of these sites have been excavated in recent years and they are often large mounds that can attain several meters in depth, comprising successive layers of alluvial soil brought in periodically to serve as living floors. The site of An Son is of this type and lies in a small valley immediately north of the Mekong Delta in southern Vietnam. Excavated on five occasions since 1978, and most recently in 2009, it was occupied from the late third into the late second millennium b.c. An Son has produced evidence that attests the domestication of pigs and dogs in all layers apart (perhaps) from the most basal one, which was not investigated in 2009, together with the growing of rice of the subspecies Oryza sativa japonica, of Chinese Neolithic origin. The oldest pottery has simple incised and punctate zoned decoration with parallels in central Thailand, especially in the basal phases at Nong Nor and Khok Phanom Di. From its middle and later occupation phases (1800-1200 b.c.), An Son has produced a number of supine extended burials with finely decorated pottery grave goods that carry some unique forms, especially vessels with wavy or serrated rims. The An Son burials represent a Neolithic population that expressed a mixture of both indigenous Hoabinhian and more northerly (probably Neolithic southern Chinese) cranial and dental phenotypes, perhaps representing a likely ancestral population for some of the modern Austroasiatic-speaking populations of mainland Southeast Asia. © 2013 by the University of Hawai'i Press.

DOI

Polymorphisms and allele frequencies of the ABO blood group gene among the Jomon, Epi-Jomon and Okhotsk people in Hokkaido, northern Japan, revealed by ancient DNA analysis.

Takehiro Sato, Hisako Kazuta, Tetsuya Amano, Hiroko Ono, Hajime Ishida, Haruto Kodera, Hirofumi Matsumura, Minoru Yoneda, Yukio Dodo, Ryuichi Masuda

Journal of human genetics ( NATURE PUBLISHING GROUP ) 55 ( 10 ) 691 - 6 2010.10 [Refereed] [International journal]

To investigate the genetic characteristics of the ancient populations of Hokkaido, northern Japan, polymorphisms of the ABO blood group gene were analyzed for 17 Jomon/Epi-Jomon specimens and 15 Okhotsk specimens using amplified product-length polymorphism and restriction fragment length polymorphism analyses. Five ABO alleles were identified from the Jomon/ Epi-Jomon and Okhotsk people. Allele frequencies of the Jomon/Epi-Jomon and Okhotsk people were compared with those of the modern Asian, European and Oceanic populations. The genetic relationships inferred from principal component analyses indicated that both Jomon/Epi-Jomon and Okhotsk people are included in the same group as modern Asian populations. However, the genetic characteristics of these ancient populations in Hokkaido were significantly different from each other, which is in agreement with the conclusions from mitochondrial DNA and ABCC11 gene analyses that were previously reported.

DOI PubMed

Morphometric Features of Femurs in the Okhotsk People

MATSUMURA HIROFUMI, HADOSON MAKU J, KAWAMURA KENTARO, KASHIWA TAKASHI

Anthropol Science Jpn Ser ( The Anthropological Society of Nippon ) 118 ( 2 ) 69 - 82 2010 [Refereed]

Skeletal femoral measurements were recorded for Okhotsk Cultural people (5–12 century) uncovered from northern and eastern Hokkaido, Japan, in order to clarify the regional differences among the two Okhotsk groups, and to find those specific features in comparison with the other ethnic groups in Hokkaido represented by Neolithic Jomon, Epi-Jomon and modern Ainu. The results demonstrated that the femurs of the eastern Okhotsk sample, mainly from the Moyoro Shell Mound site, are significantly larger in length of the shaft, thickness of the proximal shafts, diameters of the head and neck than those of the northern Okhotsk sample from the Ohmisaki and Hamanaka sites, and also than the Jomon/Epi-Jomon and Ainu femurs. Meanwhile, the northern Okhotsk people less differed in morphometric femoral features from the Jomon/Epi-Jomon and Ainu than the eastern Okhotsk sample did. Discriminant function analyses using these femoral measurements divided the two Okhotsk samples and Jomon/Ainu at high level of accuracies (>90%), with finding the difference in both the femoral size and proportion among the shaft length and/or thickness at various portions.

DOI CiNii

Mitochondrial DNA haplogrouping of the Okhotsk people based on analysis of ancient DNA: an intermediate of gene flow from the continental Sakhalin people to the Ainu

Takehiro Sato, Tetsuya Amano, Hiroko Ono, Hajime Ishida, Haruto Kodera, Hirofumi Matsumura, Minoru Yoneda, Ryuichi Masuda

ANTHROPOLOGICAL SCIENCE ( ANTHROPOLOGICAL SOC NIPPON ) 117 ( 3 ) 171 - 180 2009.12 [Refereed]

In order to further understand the genetic status of the Okhotsk people, who were distributed in southern coastal regions of the Okhotsk Sea during the 5th-13th centuries, nucleotide variations in the hypervariable region (HVR) and the coding regions of mitochondrial DNA (mtDNA) were analyzed. Targeting the coding regions provides reliable genetic information even from ancient DNAs that may have suffered post-mortem damage. MtDNA haplogroups of 38 individuals were classified according to mtDNA lineages known in northeastern Asian people. Comparisons of mtDNA haplogroup frequencies between the Okhotsk people and other Asian populations revealed that the genetic structures of the Okhotsk people are very similar to those of populations currently living around lower regions of the Amur River and the Ainu of Hokkaido. The results support our previous Study on molecular phylogeny of mtDNA HVR I sequences, and strongly suggest that the Okhotsk people originated around the lower regions of the Amur River and became an intermediate of gene flow from the continental Sakhalin people to the Ainu.

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