Hirofumi Matsumura

Mitochondrial DNA analysis of Jomon skeletons from the Funadomari site, Hokkaido, and its implication for the origins of Native American.

Ancient DNA recovered from 16 Jomon skeletons excavated from Funadomari site, Hokkaido, Japan was analyzed to elucidate the genealogy of the early settlers of the Japanese archipelago. Both the control and coding regions of their mitochondrial DNA were analyzed in detail, and we could securely assign 14 mtDNAs to relevant haplogroups. Haplogroups D1a, M7a, and N9b were observed in these individuals, and N9b was by far the most predominant. The fact that haplogroups N9b and M7a were observed in Hokkaido Jomons bore out the hypothesis that these haplogroups are the (pre-) Jomon contribution to the modern Japanese mtDNA pool. Moreover, the fact that Hokkaido Jomons shared haplogroup D1 with Native Americans validates the hypothesized genetic affinity of the Jomon people to Native Americans, providing direct evidence for the genetic relationships between these populations. However, probably due to the small sample size or close consanguinity among the members of the site, the frequencies of the haplogroups in Funadomari skeletons were quite different from any modern populations, including Hokkaido Ainu, who have been regarded as the direct descendant of the Hokkaido Jomon people. It appears that the genetic study of ancient populations in northern part of Japan brings important information to the understanding of human migration in northeast Asia and America.

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

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.

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

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.

Origins and genetic features of the Okhotsk people, revealed by ancient mitochondrial DNA analysis

AbstractIn order to investigate the phylogenetic status of the Okhotsk people that were distributed in northern and eastern Hokkaido as well as southern Sakhalin during the fifth to the thirteenth centuries, DNA was carefully extracted from human bone and tooth remains excavated from archaeological sites. The hypervariable region 1 sequences of the mitochondrial DNA (mtDNA) control region were successfully amplified and 16 mtDNA haplotypes were identified from 37 individuals of the Okhotsk people. Of the 16 haplotypes found, 6 were unique to the Okhotsk people, whereas the other 10 were shared by northeastern Asian people that are currently distributed around Sakhalin and downstream of the Amur River. The phylogenetic relationships inferred from mtDNA sequences showed that the Okhotsk people were more closely related to the Nivkhi and Ulchi people among populations of northeastern Asia. In addition, the Okhotsk people had a relatively closer genetic affinity with the Ainu people of Hokkaido, and were likely intermediates of gene flow from the northeastern Asian people to the Ainu people. These findings support the hypothesis that the Okhotsk culture joined the Satsumon culture (direct descendants of the Jomon people) resulting in the Ainu culture, as suggested by previous archaeological and anthropological studies.

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

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.

An Son and the Neolithic of Southern Vietnam

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.

Temporal variation and interaction between nutritional and developmental instability in prehistoric Japanese populations

We examined nutritional and developmental instability in prehistoric Japan, using data from 49 individuals across 13 archaeological sites. Hypoplasia incidence was used as a measure of nutritional stress, and fluctuating asymmetry (of upper facial breath, orbital breadth, and orbital height) as an indirect assessment of developmental instability. Abundant resources due to a stable climate during the Middle Jomon (5,000-3,000 BP) encouraged population growth, which led to regional cultural homogeneity and complexity. A population crash on Honshu in the Late/Final Jomon (roughly 4,000-2,000 BP) led to regionally divergent subsistence economies and settlement patterns. We find that the nutritional stress was consistent between periods, but developmental instability (DI) decreased in the Late/Final Jomon. While the DI values were not statistically significant, the higher values for Middle Jomon may result from sedentism, social stratification, and differential access to resources. On Hokkaido, Jomon culture persisted until the Okhotsk period (1,000-600 BP), marked by the arrival of immigrants from Sakhalin. Nutritional stress was consistent between Middle and Late/Final Jomon, but DI increased in the Late/Final. Nutritional and developmental instability decreased from Late/Final to Okhotsk, suggesting a positive immigrant effect. We expected to find an association between stress markers due to the synergistic relationship between nutrition and pathology. The data support this hypothesis, but only one finding was statistically significant. While high critical values from small sample sizes place limits on the significance of our results, we find that the impact of environmental and cultural change to prehistoric Japanese populations was minimal.

Health and the experience of childhood in late Neolithic Viet Nam

The article aims to examine aspects of mortuary behavior in late Neolithic/early Bronze Age (Phung Nguyen phase) populations represented at the site of Man Bac in Viet Nam, specifically how mortuary behavior illuminates the role of children, and adult attitudes toward children. In addition, the authors discuss biological characteristics of the human sample, focusing particularly on the child burials, in order to explore aspects of childhood palaeohealth. The methodology includes combining various measures of health—including palaeodemography (childhood mortality), analysis of oral health (Early Childhood Caries or ECC), and analysis of physiological health (Cribra Orbitalia and LEH)—with studies of culturally defined mortuary practices to suggest that, while children clearly had significant health deficiencies and many suffered early deaths, their treatment in mortuary rites shows significant economic value and social esteem placed on children.

An Archaic Homo Molar from Northern Vietnam1

fabrice demeter, anne-marie bacon, nguyen kim thuy, vu the long, hirofumi matsumura, ha huu nga, mathieu schuster, nguyen mai huong, and yves coppens Laboratoire de Paleoanthropologie et Prehistoire, College de France, 11 Place Marcelin Berthelot, 75005 Paris, France (fabrice.demeter@college-de-france.fr) (Demeter and Coppens)/Unite Ecoanthropologie et Ethnobiologie UMR 5145 du CNRS, Departement Homme, Nature, Societes du MNHN (Demeter)/UPR 2147 du CNRS, 44, rue du l’Amiral Mouchez, 75014 Paris, France (Bacon)/National Center for Social Sciences and Humanities of Vietnam, Institute of Archaeology, 61, Phan Chu Trinh, Hanoi, Vietnam (Thuy, Long, Nga, Huong)/Sapporo Medical University, Department of Anatomy, Minami 1, Mishi 17, ChuoKu, Sapporo 060-8556, Japan (Matsumura)/ULP, Universite Louis Pasteur, Institut de Geologie (EOSTCGS CNRS-UMR 7517), 1, rue Blessig, 67084 Strasbourg cedex, France (Schuster). 28 i 04

Metric analyses of an Early Holocene human skeleton from Gua Gunung Runtuh, Malaysia

A nearly complete human skeleton dating to the Early Holocene (epi-Paleolithic culture) excavated from Gua Gunung Runtuh, Malaysia, is described. Cranial, dental, and limb bone measurements are recorded on the skeleton, and compared with early and modern skeletal samples from Southeast Asia and Australia. The comparisons demonstrate that the Gua Gunung specimen is most similar to Australian Aborigines in dental and limb measurements, while the cranial measurements indicate a close affinity to Mesolithic samples from Malaysia and Flores. These findings further suggest that the Gua Gunung skeleton, as well as other fossils from Tabon and Niah, are representative of an early group of people who occupied Sundaland during the late Pleistocene, and may be the ancestors of Australian Aborigines. Some of the dental and limb bone measurements exhibited by the ancestors persist in Southeast Asian populations until the early Holocene. Differences in cranial traits have, however, accumulated since the late Pleistocene in Australian Aborigines and early Southeast Asian peoples.