==> Symposium Home Page
Modern Human Diversity on Genes and Culture
- with special reference to Asia and Oceania -
==> Symposium Home Page written in Japanese
(as of January 24, 2013)
### Day 1: Monday, February 3rd, 2014
Genome-wide scan data on divergence and polymorphism are an irreplaceable source for reconstructing the vanished past of living forms. Based on such data about humans and non-human primates, this paper summarizes our published as well as ongoing studies on species divergence times, ancient population sizes and relative roles of natural selection along the primate lineage leading to modern humans. The maximum likelihood and Markov chain Monte Carlo methods were used to estimate the species divergence time and the ancestral population size simultaneously and the results indicated that the primate population size was typically about 105 but the hominid lineage experienced a rather severe bottleneck throughout the Middle Pleistocene. Divergence and polymorphism data have also suggested that 85% of the total mutations are deleterious, 0.2% are advantageous and 15% are selectively neutral. Performing computer simulation for models of linked and unlinked multiple loci (amino acid sites) per genome, we have evaluated relative roles of selected and neutral mutations in their substitution processes and extents of genetic variance maintained in a population. Comparison between simulation and theoretical results shows the presence of significant interference of selection acting upon multiply segregating loci, suggesting the possibility that the rates of selected mutations are underestimated.
13:10 - 13:50 Special Lecture
Naoyuki Takahata, President, SOKENDAI, Hayama, Japan
Title: Demography and natural selection in the human lineage
2008 President, SOKENDAI (Graduate University for Advanced Studies), Japan
2001 Vice-President, SOKENDAI, Japan
1997 Professor and Dean, Department of Biosystems Science, SOKENDAI, Japan
1992 Professor and Director, Coordination Center for Research and Education, SOKENDAI, Japan
1986 Associate Professor, Department of Population Genetics, National Institute of Genetics, Mishima, Japan
1977 Researcher, Department of Population Genetics, National Institute of Genetics, Mishima, Japan
1977 Ph. D., Department of Biology, Kyushu University, Fukuoka, Japan
13:50 - 14:30 Talk 1
Peter Bellwood, Professor, Australian National University, Canberra, Australia
Title: Neolithic foundation migrations from Formosa to Lapita, 2200 to 1000 BC: archaeological, linguistic and genetic perspectives
Neolithic foundation population movements from southern China and Taiwan (Formosa in Austronesian terms), via Island SE Asia and into Oceania, can be studied from three separate disciplinary perspectives. The archaeological perspective identifies a movement of material culture with a food producing economy in three directions southwards and eastwards from southern China, Taiwan and the Philippines, with the relevant data also decreasing in age towards the south and east. The linguistic perspective offers a pattern of subgroup formation and geographical differentiation within the Austronesian language family as it is spoken now, but I ask if those subgroups that can be identified now reflect precisely the migration directions of closely related groups of foundation speakers more than 3500 years ago. The third perspective comes from human biology, with three components: skeletal (especially cranial) morphology, ancient DNA, and the DNA of the living. Only the first two can give direct answers about how, where, and out of what biological origins people migrated during the Neolithic. We should be cautious about inferring sources, directions and dates of migration only from the haploid or autosomal DNA of the living, which for all populations must also reflect tens of millennia of admixture brought about by migration.
Peter Bellwood is an Emeritus Professor in the School of Archaeology and Anthropology at the Australian National University (ANU) in Canberra. His areas of specialization include the prehistory of Southeast Asia and the Pacific from archaeological, linguistic and biological perspectives; the worldwide origins of agriculture and resulting cultural, linguistic and biological developments; interdisciplinary connections between archaeology, linguistics and human biology; and the worldwide history of human migration. He is currently involved in archaeological fieldwork projects in the Philippines and Vietnam, and is the author of First Farmers (Blackwell 2005), First Migrants (Wiley-Blackwell 2013), and Prehistory of the Indo-Malaysian Archipelago (ANU Press 2007, third edition under revision in 2014).
14:30 - 15:10 Talk 2
Elizabeth Matisoo-Smith, Professor, University of Otago, Dunedin, New Zealand
Title: Is it time to reconsider our models for Pacific prehistory? Evidence from ancient and modern human and commensal studies
Since the 1980s a general scenario regarding the human settlement of the Pacific has been constructed based on linguistic, archaeological and some basic genetic data. This picture focuses on two major colonization events -- an early Pleistocene settlement of Near Oceania followed by the later Lapita colonization of Remote Oceania. These Lapita colonists are generally seen the immediate ancestors of the Polynesians and most Micronesians. Mitochondrial DNA data obtained initially from commensal animals (those transported by humans during colonisation) and more recently from human populations suggest that things may be slightly more complicated than this traditional two wave theory often presented. I argue that it may be time to reconsider our ideas about population origins and history particularly of Remote Oceania.
2009 Professor of Biological Anthropology, Department of Anatomy and Allan Wilson Centre for Molecular Ecology and Evolution, University of Otago, Dunedin, New Zealand.
2008 Professor, Department of Anthropology, Faculty of Arts, and Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, New Zealand.
2007 Associate Professor, Department of Anthropology, Faculty of Arts, and Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, New Zealand.
2000 Senior Lecturer, Department of Anthropology, Faculty of Arts, and Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, New Zealand.
1998 Lecturer, Department of Anthropology, Faculty of Arts, University of Auckland, New Zealand.
1997 Ph.D., Department of Anthropology, University of Auckland, New Zealand.
1990 M.A., Department of Anthropology, University of Auckland, New Zealand.
1985 B.A., Anthropology, University of California, Berkeley, U.S.A.
15:30 - 16:00 Talk 3
Michiko Intoh*, Professor, National Ethnological Museum & SOUKENDAI, Suita, Japan
Title: Human migrations and/or cultural contacts in Oceania
Archaeology, linguistic and genetic studies had demonstrated that the history of human dispersals into Oceania, particularly into Micronesia, was complex. Linguistic model of Austronesian speaking population movements has been widely used by archaeologists. A series of excavations conducted on Fais Island in the Central Caroline Islands had demonstrated somewhat different origin of Fais people from that indicated in the linguistic model.
This paper demonstrates 1800 years' history of Fais Island classified into four cultural phases based on the excavated materials, such as potsherds, natural stones, fishhooks, faunal remains including dog, pig, chicken and rat, etc. Detailed analyses of these artefacts well indicate that prehistoric Fais Islanders had kept active interactions with a number of islands within Micronesia as well as somewhere Island South-East Asia, throughout the cultural phases, possibly as a living strategy on resource limited environment. It will be pointed out that various materials, ideas, animals, etc. could well be transferred through such active interactions, and should not be misinterpreted as the results of colonization alone. Finally, this paper questions the nature of the prehistoric cultural contacts recently suggested for the islands between western Micronesia and Melanesia.
2000 Professor, Department of Social Research, National Museum of Ethnology, Japan
1995 Professor, Department of International Cultural Studies, Hokkaido Tokai University, Japan
1988 Associate Professor, Department of International Cultural Studies, Hokkaido Tokai University, Japan
1976 Assistant Professor, School of Arts and Science, Tokyo Woman's Christian University, Japan
1989 Ph.D., Department of Anthropology, University of Otato, New Zealand
1982 M.A. (with Distinction), Department of Anthropology, University of Otato, New Zealand
1976 B.A., School of Arts and Science, Tokyo Woman's Christian University, Japan
16:00 - 16:40 Talk 4
Mark Stoneking, Professor, Max Planck Institute for Evolutionary Anthropology, Leibzig, Germany
Title: Into and Out of Taiwan: Genetic Evidence Concerning the Austronesian Expansion
A Taiwan origin for the expansion of the Austronesian languages and their speakers is well supported by linguistic and archaeological evidence. However, human genetic evidence is more controversial, and genetic studies have largely ignored the role of genetic diversity within Taiwan as well as the origins of Formosans. We address these issues via analysis of a complete mitochondrial DNA genome sequence of ~8000 year old skeleton from Liang Island (located between China and Taiwan) and 550 complete mtDNA genome sequences from 8 aboriginal (highland) Formosan and 4 other Taiwanese groups. We show that the mtDNA sequence from the skeleton is closest to Formosans, provides a link to southern China, and has the most ancestral haplogroup E sequence found among extant Austronesian speakers. Bayesian phylogenetic analysis allows us to reconstruct a history of early Austronesians arriving in Taiwan in the north ~6000 years ago, spreading rapidly to the south, and leaving Taiwan ~4000 years ago to spread throughout Island Southeast Asia and Oceania.
1999 Group Leader, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, and Honorary Professor of Biological Anthropology, University of Leipzig
1998 Professor of Anthropology, Pennsylvania State University
1994 Associate Professor of Anthropology, Pennsylvania State University
1990 Assistant Professor of Anthropology, Pennsylvania State University
1989 Associate Research Scientist, Cetus Corporation, Emeryville, California
1987 Postdoctoral Fellow, Department of Biochemistry, University of California, Berkeley
1986 Ph.D. in Genetics, University of California, Berkeley
16:40 - 17:10 Talk 5
Yoshio Yamaoka*, Professor, Oita University, Oita, Japan
Title: Human migrations inferred by Helicobacter pylori genes
Helicobacter pylori is not only a well known gastroduodenal pathogen but also a useful marker for tracing prehistoric footprints of human populations. Because H. pylori transmits mainly through vertical infection and has been carried in our stomach from generation to generation, its geneology well reflects that of human. We investigated genes of H. pylori from a wide variety of ethnicity and predicted the journey of ancient people after the departure from the African Continent in 100,000 - 50,000 B.C. Analysis of genotypes of single genes, multi locus sequence typing, and also with the aid of next generation sequencer, we identified a group of H. pylori strains that diverged remarkably old era in Okinawa, Japan.
2010-Present Professor, Department of Medicine-Gastroenterology, Baylor College of Medicine, U.S.A.
2009-Present Professor, Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, JAPAN
2004 Associate Professor, Department of Medicine-Gastroenterology, Baylor College of Medicine, U.S.A.
2002 Assistant Professor, Department of Medicine-Gastroenterology, Baylor College of Medicine, U.S.A.
2001 Instructor, Department of Medicine-Gastroenterology, Baylor College of Medicine, U.S.A.
1997 Research Associate, Department of Medicine-Gastroenterology, Baylor College of Medicine, U.S.A.
1997 Ph.D. Department of Gastroenterology, Kyoto Prefectural University of Medicine, JAPAN
1990 M.D. Kyoto Prefectural University of Medicine, JAPAN
1983 B.S. Research Technology, Kyoto University, JAPAN
17:10 - 17:40 Talk 6
John Whitman, Professor, National Institute of Japanese Language, Tachikawa, Japan
Title: Pre-Zhou languages on the Chinese litoral: Reassessing old ideas about Tai-Kadai, Austronesian, and Japanese
Since the earliest days of theorizing about the origins of the Japanese language (e.g. Matusmoto 1928), one popular view has attempted to connect the Japonic family in part (Murayama 1976) or in whole (Benedict 1990) with Austronesian or the broader Austro-Tai family proposed by Benedict (1942). Benedict's (1990) treatment suffers from construal of Formosan languages as a "single witness" (1990: 7) as well as some misinterpretations of the Japonic data (Vovin 1994). However 3 factors suggest that the time is ripe for a reassessment of Benedict's basic idea: the availability of a new reconstruction of proto-Austronesian (Blust and Trussel 2010); new research supporting a pAN/Kra-Dai affinity (Ostapirat 2005), and archaeological (Miyamoto 2009) and linguistic (Whitman 2011) evidence suggesting a locus for proto-Japonic on the Yellow Sea littoral.
2011 Professor, Department of Crosslinguistic Studies, Institute for Japanese Language and Linguistics, Japan
2003 Professor, Department of Linguistics, Cornell University, U.S.A.
1995 Associate Professor, Department of Linguistics, Cornell University, U.S.A.
1987 Assistant Professor, Department of Linguistics, Cornell University, U.S.A.
1985 Assistant Professor, Department of Linguistics, Harvard University, U.S.A.
1985 Ph.D. in Linguistics, Faculty of Arts & Sciences, Harvard University, U.S.A.
1980 M.A., Department of Literature and Linguistics, University of Tsukuba, Japan
1976 B.A., Harvard University, USA
17:40 - 18:10 Talk 7
Minoru Sakamoto*, Professor, REKIHAKU & SOUKENDAI, Sakura, Japan
Title: Application of radiocarbon dating for archeology
It is needless to say that radiocarbon dating is applied for various archeological materials. However, it is somewhat difficult to make use of the archaeological chronology. The "radiocarbon age" should be interpreted to "calendar age", and the uncertainty of the age also gives unpleasant impression to construct chronology. The calibration curve for radiocarbon dating based on tree-rings determined by dendrochronology has been developed, and wiggle-matching method achieves high precision radiocarbon dating of wood remains. As for Japanese archeology, detailed chronology based on pottery chronology is established, and radiocarbon dating of charred material adhering to potsherd shows a good coincidence in order. This leads to a detailed chronology with actual age of Jomon Period, and a new aspect of the beginning of the Yayoi period. IntCal calibration curve for the northern hemisphere is mainly based on trees grown in the high latitude region, however certain offsets from IntCal of Japanese tree ring turned out to be clear in relation to the transition from Yayoi to the Kofun period. To obtain the detailed chronology, radiocarbon dating of regional tree ring is required as well as the research collaboration between archaeology.
2013 Professor, Research Department of National Museum of Japanese History, Japan
2004 Associate Professor, Research Department of National Museum of Japanese History, Japan
1994 Assistant Professor, Museum Science Department of National Museum of Japanese History, Japan
1994 Ph.D. Graduate School of Science, the University of Tokyo, Japan
1992 M.A., Graduate School of Science, the University of Tokyo, Japan
1989 B.A., Faculty of Science, The University of Tokyo, Japan
### Day 2: Tuesday, February 4th, 2014
9:00 - 9:30 Talk 8
Jun Gojobori*, Assistant Professor, SOKENDAI, Hayama, Japan
Title: mtDNA variation in Mesoamerica and human migrations to New World
The New World was the last continent colonized by Anatomically Modern Humans, Homo sapiens. The first migrants entered New World from Asia through Beringia during the ice age; however, the date, the route and the number of founding populations are still under debate. We determined complete mitogenome sequences of 113 unrelated individuals from two indigenous populations of Mesoamerica, Mazahua and Zapotec. Phylogenetic tree and principal component analysis showed that these two populations are distantly related to each other. We reconstructed the demographic history of Zapotec using Bayesian Skyline Plot. Our results show that the date of entering the New World as around 15,000 years ago, predating the opening of an ice-free corridor. This suggests that the migration route was the Pacific coast. Our estimation shows that the female effective population size of founding population was a few thousand.
2011- Assistant Professor, School of Advanced Sciences, Graduate University for Advanced Studies (SOKENDAI), Japan
2008-2011 Postdoctoral fellow, School of Advanced Sciences, SOKENDAI, Japan
2007-2008 Postdoctoral fellow, Department of Biological Sciences, Faculty of Science, University of Tokyo, Japan
2007 Ph.D., Department of Biological Sciences, Faculty of Science, University of Tokyo, Japan
2003-2006 Visiting student, Department of Ecology and Evolution, University of Chicago, U.S.A.
2003 M.A., Department of Biological Sciences, Faculty of Science, University of Tokyo, Japan
2001 B.A., Department of Biological Sciences, Faculty of Science, University of Tokyo, Japan
9:30 - 10:00 Talk 9
Ritsuko Kikusawa*, Associate Professor, National Ethnological Museum & SOKENDAI, Suita, Japan
Title: Culture contact and language diversity in Oceania
Change is one of the integral characteristics of human language and is a contributing factor resulting in the diversification of languages. Every language undergoes continuous change (though usually without the knowledge of its speakers), yielding variants or "dialects", which, under certain conditions, may eventually become recognized as separate languages. Language change which takes place without any external or intentional contributing factor is referred to as "natural change", as opposed to "contact induced change", which is the result of some influence from another language(s).
Linguistic changes in specific languages are identified by applying the Comparative Method, an established method in historical linguistics for comparing languages typically used to trace back linguistic changes in order to identify their genetic affiliation and to determine how related languages developed. In this presentation, I will first describe how the Comparative Method has been applied to languages with little written documentation, and what the results tell us about the development (=diversification) of the languages in Oceania. Then, I will refer to some cases with languages in Oceania where the application of the Method becomes problematic. I will describe issues behind the methodology, and suggest ways whereby they might be reconciled.
2006 Associate Professor, Department of Comparative Studies, The Graduate University for Advanced Studies (SOKENDAI), Japan (current position)
2005 Associate Professor, Department of Advanced Studies in Anthropology, National Museum of Ethnology, Japan (current position)
2000 Associate Professor, Research Institute for Languages and Cultures of Asia and Africa, Tokyo University of Foreign Studies, Japan
2000 Ph.D. (Linguistics), Department of Linguistics, University of Hawai'i at Manoa, U.S.A.
1995 Assistant Professor, Research Institute for Languages and Cultures of Asia and Africa, Tokyo University of Foreign Studies, Japan
1993 M.A. (Linguistics), Graduate School of Humanities, University of Tokyo, Japan
1990 B.A. (Linguistics), Faculty of Arts, University of Tokyo, Japan
10:00 - 10:40 Talk 10
Koji Lum, Professor, Binghamton University, Binghamton, U.S.A.
Title: Human settlement, malaria, and chronic diseases of the Pacific: a mtDNA Perspective
Humans first began to settle the large intervisible islands of Near Oceania during the Pleistocene and extended into the smaller, more widely dispersed islands of Remote Oceania during the Holocene. The final phases of the latter expansion also included the settlement and resettlement of marginal, resource poor islands of Micronesia and Melanesia by Polynesians. These population expansions influenced the malaria-selected alleles currently found across the Pacific and may be mediating the chronic disease rates associated with cultural change and modernization in the Pacific today. These processes will be explored from the perspective of mtDNA, both as a neutral marker for population origins and as a potentially selected locus of more recent metabolic adaptations.
2010-present Professor, Departments of Anthropology and Biological Sciences, Faculty of Biomedical Anthropology Program, Binghamton University, New York, U.S.A.
2003-2010 Associate Professor, Departments of Anthropology and Biological Sciences, Faculty of Biomedical Anthropology Program, Binghamton University, New York, U.S.A.
2000-2003 Lecturer, Department of International Affairs and Tropical Medicine, Tokyo Women's Medical University, Japan
1998-2000 JSPS Postdoctoral Fellow, Molecular Evolution Group, Institute of Statistical Mathematics, Tokyo, Japan
1995-1998 NSF/Sloan Molecular Evolution Postdoctoral Fellow, University of Utah, Salt Lake City, U.S.A.
1995 Ph.D., Department of Genetics and Molecular Biology, John A. Burns School of Medicine, University of Hawai'i, Manoa, U.S.A.
1988 B.A., Department of Genetics, University of California, Berkeley, U.S.A.
10:40 - 11:20 Talk 11
Maude Phipps, Professor, Monash University, Bandar Sunway, Malaysia
Title: Population structure and Adaptation in Indigenous tribes of Malaysia
The indigenous communities of Peninsular Malaysia the "Orang Asli" (OA) comprise 0.6 percent of the Malaysian population. They have been broadly classified into three groups, the Negrito, Senoi, and Proto-Malay based on linguistic, physical and cultural differences. Each group can be further subdivided into 6 sub-groups, making a total of 18. The OA are indigenous to Malaysia, and over the years, we and others have found strong genetic evidence to indicate that the Negritos in particular, may be the descendants of the earliest Homo sapiens who migrated out of Africa during the first major wave some 70,000 years or so ago. Even in the current day, their lifestyles and cultural practices are markedly different from the majority of the national population who comprise Malays, Chinese, Indians and other ethnic groups. Since 2006, we have been working with OA communities, studying their health and genetics through a benefits sharing and community engagement approach. Numerous field investigations throughout Peninsula Malaysia have been conducted by our multi institutional research group, and we have had interesting findings. We have leveraged on both conventional and more recent genotyping technologies such as microarrays and deep sequencing to map SNP genetic diversity and structure in OA groups using both mitochondrial and nuclear genomics. Comparative SNP analysis with other South East Asian and global populations reveal that they form distinct unique clusters. The results are consistent with population bottlenecks, elements of drift, reduced 'known' diversity and relative isolation for millennia. We also report unique / novel variants and are currently scrutinizing high density microarray and sequencing data for signatures of positive and negative selection.
Academic Background (University posts and Visiting positions)
2011-2014 Professor of Human Molecular Genetics, Jeffrey Cheah School of Medicine and Health Sciences, Malaysia, Faculty of Medicine, Nursing and Health Sciences, Monash University, Australia
2013 Visiting Scholar, Institute of Human Genetics, University of California (San Francisco), USA
2010 Visiting Scholar, Centre for GeoGenetics, University of Copenhagen, Denmark.
2008 Associate Professor, Jeffrey Cheah School of Medicine and Health Sciences, Malaysia, Faculty of Medicine, Nursing and Health Sciences, Monash University, Australia.
2000 Associate Professor, Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Malaysia,
1998 Visiting Scholar UNESCO Human Genome Fellowship, Department of Pathology, University of Western Australia, Australia.
1996 Visiting Researcher, CICHE programme, Histocompompatibility and Tissue Typing Laboratory, Churchill Hospital and University of Oxford, UK,
1996 Lecturer, Department of Allied Health Sciences, Faculty of Medicine, University of Malaya, Malaysia
1994 Ph.D., Department of Pathology and Darwin College, University of Cambridge, UK
1989 B. Sc. Hons (Class 1) ., Department of Genetics, University of Malaya, Malaysia
11:20 - 11:50 Talk 12
Timothy Jinam*, Post-doctoral fellow, National Institute of Genetics, Mishima, Japan
Title: Genome-wide SNP studies of Malaysian and Philippine Negritos
The Southeast Asian region is widely viewed as a corridor for early human migrations. Scattered within the islands of Andaman, Philippines and the Malay Peninsula, there exist populations that are phenotypically unique from their neighbors. These groups are collectively termed 'Negrito' and are traditionally associated with darker skin, frizzy hair, short stature and a hunter-gathering lifestyle. Previous studies of uniparental markers revealed that these Negrito groups are genetically heterogenous and that they retain traces of the ancient migrants to the Southeast Asian region. Here we determined close to one million genome-wide SNP in four Philippine (Aeta, Agta, Mamanwa, Batak) and one Malaysian (Jehai) Negrito populations using Affmetrix 6.0 genechip and compared them with neighboring populations, including Andamanese Negritos. Results show that these Negrito groups are genetically distinct from one another, while displaying signs of admixture with their neighboring non-Negrito populations.
2012 Post-Doctoral Researcher, Division of Human Genetics, National Institute of Genetics, Japan
2011 Ph.D., Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Japan
2007 M.MedSc., Department of Molecular Medicine, University of Malaya, Malaysia
2003 B.BiomedSc., Faculty of Medicine, University of Malaya, Malaysia
13:00 - 13:30 Talk 13
Peter Joseph Matthews, Associate Professor, National Ethnological Museum & SOUKENDAI, Suita, Japan
Title: Natural habitats, human habitats, and the spread of edible aroids
In the Asia-Pacific region, the main aroids of economic and historical interest are Alocasia macrorrhizos, Amorphophallus paeonifolius, Colocasia esculenta, and Cyrtosperma merkusii. A South American relative, Xanthosoma saggitfolium, is also widespread, most likely as a result of introduction by Spanish ships. Each edible aroid has distinct ecological requirements in cultivation, in wild but modified or disturbed habitats, and in natural wild habitats (as far as the latter are known).
In studies of crop history, little attention has been given to the physical diversity of human, natural, and intermediate habitats. Plants are very sensitive to physical differences in environment. Over long periods of time, the spread of edible aroids in Asia and the Pacific is likely to have been driven by direct human action (propagation, cultivation, and transplantation), and by opportunistic invasion of human habitats (gardens and settlements) and modified wild habitats (mostly near human settlement).
In this paper, I introduce a recent study of genetic diversity in Colocasia esculenta (taro), discuss the physical diversity of habitats in which different morphotypes and genotypes of taro can be found, and suggest priorities for future research on the origins and spread of edible aroids.
1999-present Associate Professor, National Museum of Ethnology, Osaka
1996-1999 Research Fellow, National Museum of Ethnology, Osaka
1993-1994 JSPS Visitor, Department of Botany, Faculty of Science, Kyoto
1990-1991 Postdoctoral Fellow (Science and Technology Agency Fellowship),
National Institute for Vegetables, Ornamental Plants and Tea
(NIVOT), Ano, Japan
1991 PhD, Department of Prehistory, Research School of Pacific Studies,
& Population Genetics Laboratory, Research School of Biological
Sciences, ANU, Canberra, Australia
13:30 - 14:00 Talk 14
Hitomi Hongo*, Associate Professor, SOKENDAI, Hayama, Japan
Title: Resource exploitation in the early Neolithic and the transision to food production: zooarchaeological evidence from Southwest Asia
Northern part of so-called "Fertile Crescent", the upper Tigris and Euphrates Basin and the foothills of Taurus and Zagros Mountains, stretching from present Turkey to Iran, is one of the centers of animal and plant domestication. Recent research on animal bone remains from early Neolithic sites in this region helped our understanding of the timing and the process of domestication of ungulates (sheep, goats, cattle, and pigs). We also begin to understand that the shift from hunting and gathering to food production was not straightforward and there was a complex mosaic of sedentary hunter-gatherers and early farming communities during the Prepottery Neolithic (c.10000-7000BCE). There was a smooth transition from foraging to farming in the upper Euphrates Basin, but the communities in the upper Tigris Basin seem to have failed in the transition. The spread of domesticates to the surrounding region was not uniform, either, and there seems to have been a complex natural and social condition for accepting the new technology of food production.
I will discuss the results of analysis of animal bone remains from archaeological sites in the upper Tigris region, namely Hasankeyf Hoyuk dated to 10th millennium calibrated BC, before domestication of ungulates began, and Cayonu occupied 10th to 8th millennium BC where process of domestication can be traced.
2006 Associate Professor, Department of Evolutionary Study of Biosystems, Graduate University for Advanced Studies (SOKENDAI), Japan
1997 Assistant Professor, Department of Phylogeny and Systematics, Primate Research Institute, Kyoto University, Japan
1995 Lecturer, International Research Center for Japanese Studies, Japan
1996 Ph.D. Department of Anthropology, Harvard University, U.S.A.
1986 M.A., Department of History and Anthropology, University of Tsukuba, Japan
1984 B.A., Collage of Liberal Arts, International Christian University, Japan
14:00 - 14:30 Talk 15
Ryohei Takahashi*, Post-doctoral fellow, SOKENDAI, Hayama, Japan
Title: Zooarchaeological study of introduction of Sus scrofa into the prehistoric Ryukyu Islands based on ancient DNA analysis
From historical record, the oldest date for the introduction of wild boar or domestic pigs (Sus scrofa) to the Ryukyu Islands, southern Japan, was in the 14th century AD. It has been believed that only Ryukyu wild boar (S. s. riukiuanus) inhabited the Ryukyu Islands before this date. Some Sus samples from prehistoric sites in the Ryukyu Islands, however, had different genetic characteristics from modern Ryukyu wild boar by ancient DNA analysis. Based on this result, I propose two possible hypotheses: first, introduction of Sus to the Ryukyu Islands took place during prehistoric times; second, there were at least two genetic lineages of wild boar inhabited the prehistoric Ryukyu Islands. To investigate these two hypotheses, I increased size of samples of modern Ryukyu wild boar, and carried out mtDNA analysis.
2013 Research Fellow, Department of Evolutionary Studies of Biosystems, SOKENDAI, Japan
2012 Ph.D., Department of Evolutionary Studies of Biosystems, SOKENDAI, Japan
2007 B.A., Department of Animal Science, Tokyo University of Agriculture, Japan
14:30 - 15:00 Talk 16
Masahiko Kumagai, Post-doctoral fellow, Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Japan
Title: Domestication history of rice inferred by ancient DNA and modern genomics
Agricultural crops have been utilized and developed by humans all over the world since Neolithic age. Studying the evolutionary history of crop species provides new insights for the history of human migrations and cultural exchanges. In Asia, domestication of rice is thought to be started around 10,000 years ago, and rice remains are excavated from many archaeological sites in East Asia. To conduct ancient DNA analysis of these rice remains, we constructed the background information of genetic diversity of rice chloroplast DNA and developed DNA markers. Then we succeeded in analyzing 950 - 2800 years old rice single seed remains unearthed from Japan and Korea. The result showed unexpected large genetic diversity of rice varieties in ancient day East Asia compering with taht of produced in present day. We also analyzed recentry pubrished genome resequencing data of modern rice focusing on relationships of two major varietal groups japonica and indica. From genome wide phylogenetic and population genetic analyses, we found hybridizations and resulting gene introgressions between these two groups have played important role for generating diverse genetic diversity of rice landraces.
2011 PostDoc, Agrogenomics Research Center, National Institute of Agrobiological Sciences, Japan
2011 Ph.D., Department of Biological Sciences, Graduate School of Science, University of Tokyo, Japan
2007 M.A., Department of Biological Sciences, Graduate School of Science, University of Tokyo, Japan
2005 B.A., Department of Biology, Faculty of Science, Tokyo Metropolitan University, Japan
15:30 - 16:00 Talk 17
Shuhei Mano*, Associate Professor, Institute of Statistical Mathematics & SOUKENDAI, Tachikawa, Japan
Title: Approximate Baysian computation in population genomics
Approximate Bayesian computation (ABC) is a likelihood-free approach for Bayesian inferences based on a rejection algorithm that applies a tolerance of dissimilarity between summary statistics from observed and simulated data. In this talk, I will discuss (1) difficulties in the algorithm and how to overcome them, and (2) applications of ABC to population genomic inferences. For the first issue a possible way to circumvent lack of sufficiency and non-zero tolerance by employing the kernel method will be presented. For the second issue some examples of applications of the kernel-based ABC method to human and primate demography problems will be presented.
2010 Associate Professor, Department of Statistical Sciences, SOKENDAI & The Institute of Statistical Mathematics, Japan
2004 Lecturer (2005-Associate Professor), Graduate School of Natural Sciences, Nagoya City University, Japan
2003 Assistant Professor, School of Medicine, Tokai University, Japan
2001 Postdoctoral Researcher, National Institute of Genetics & National Institute of Advanced Industrial Science and Technology, Japan
1999 Ph.D. Graduate School of Science, Osaka University, Japan
16:00 - 16:30 Talk 18
Ituro Inoue*, Professor, National Institute of Genetics & SOKENDAI, Mishima, Japan
Title: Detection of ancestry informative HLA alleles confirms the admixed origins of Japanese population
The HLA (human MHC) region, spanning 3.8 Mb segment at 6p21, is the most gene-rich in human genome and has been associated with more than 100 different diseases, mostly autoimmune diseases such as type 1 diabetes, rheumatoid arthritis, psoriasis, multiple sclerosis, and others. Recently, it became a major topic that substantial numbers of drug adverse effects are strongly associated with the HLA alleles indication the medical importance of the region.
The other feature of HLA region is highly polymorphic nature, showing almost 10,000 alleles of HLA genes. The polymorphisms in HLA region are powerful tool for studying human evolutionary processes. We investigated genetic structure of Japanese by using five-locus HLA genotypes (HLA-A, -B, -C, -DRB1, and - DPB1) of 2,005 individuals from 10 regions of Japan. We found a significant level of population substructure in Japanese; particularly the differentiation between Okinawa Island and mainland Japanese. By using a plot of the principal component scores, we identified ancestry informative alleles associated with the underlying population substructure. We examined extent of linkage disequilibrium (LD) between pairs of HLA alleles on the haplotypes that were differentiated among regions. The LDs were strong and weak for pairs of HLA alleles characterized by low and high frequencies in Okinawa Island, respectively. The five-locus haplotypes whose alleles exhibit strong LD were unique to Japanese and South Korean, suggesting that these haplotypes had been recently derived from the Korean Peninsula. The alleles characterized by high frequency in Japanese compared to South Korean formed segmented three-locus haplotype that was commonly found in Aleuts, Eskimos, and North- and Meso-Americans but not observed in Korean and Chinese. The serologically equivalent haplotype was found in Orchid Island in Taiwan, Mongol, Siberia, and Arctic regions. It suggests that early Japanese who existed prior to the migration wave from the Korean Peninsula shared ancestry with northern Asian who moved to the New World via the Bering Strait land bridge. These results may support the admixture model for peopling of Japanese Archipelago.
1978-1984 ; Faculty of Medicine, Kagoshima University
1984-1988 ; Graduate course, Department of Biochemistry,
Faculty of Medicine, Kagoshima University,
Awarded the degree of PhD in Biochemistry.
Research and professional experience
1987-1989 ; Special Researcher of Japan Society for the Promotion of Science, Tokushima University
1989-1991 ; Post-doctoral fellow, Department of Biochemistry,
University of Utah
1991-1993 ; Research Associate, Howard Hughes Medical Institute,
University of Utah
1993-1997 ; Research Associate, Department of Human Genetics,
University of Utah
1997-2000 ; Associate Professor, Institute for Molecular and Cellular Regulation, Gunma University
2000-2006 ; Associate Professor, Institute of Medical Science, University of Tokyo
2006-2010; Professor, School of Medicine, University of Tokai
2008-2010; Director, Institute of Medical Sciences, University of Tokai
2010-present; Professor, National Institute of Genetics
16:30 - 17:00 Talk 19
Hideaki Kanzawa-Kiriyama*, Ph.D. student, Department of Genetics, SOKENDAI, Mishima, Japan
Title: Jomon genomics
Clarifying the genetic relationship between Neolithic Japanese Hunter-Gatherers, so called Jomon people, and modern human populations is one of the keystones to understand the complex history of modern Japanese and continental East Eurasian populations. The Jomon period ranged from 16000 to 3000 years before present, and while their origin and relationship with modern humans have been long debated, details remain unclear. I investigated mitochondrial DNA and nuclear DNA of Jomon individuals excavated from four different regions. Mitochondrial DNA shows the genetic uniqueness of Jomon people. Furthermore, I obtained draft sequence of Jomon genome, and the nuclear genome sequences clearly evidenced that Jomon people diverged from the common ancestors of both northern and southern East Eurasians but postdated the divergence of East Eurasian and Melanesians. Another controversial problem is the genetic relationship between archaic humans and modern humans. I observed the genetic relationship not only between Jomon and Vindija Neanderthal but also between Jomon and Denisovan. Especially, the existence of Denisovan DNA material in Jomon people will be one of the main debates connected to not only the history of Japanese but also the origin and population structure of East Eurasians.
2009 B.S., Department of Biology, Niigata University, Japan
2014 Ph.D., Department of Genetics, Graduate University for Advanced Studies (SUKENDAI), Japan
17:00 - 17:30 Talk 20
Naruya Saitou*, Professor, National Institute of Genetics & SOKENDAI, Mishima, Japan
Title: Origin and establishment of Japonesians
Japanese Archipelago ranges geographically from Hokkaido to Okinawa islands stretching over 4,000 km, and was populated more than 40,000 years ago by Paleolithic people. Jomon culture, defined by the presence of cord marked ("jomon" in Japanese) pottery, lasted from 16,000 to 3,000 years ago, followed by Yayoi culture and historical times from Kofun period at 3rd Century A.D. I would like to call Japanese Archipelago as "Japonesia" following Shimao Toshio. At present, Japonesians can be roughly divided into three populations; Ainus, Mainlanders, and Ryukyuans. We found small but clear common genetic feature between Ainus and Ryukyuans though genome-wide SNP data analyses (Japanese Archipelago Human Population Genetics Consortium, 2012; Journal of Human Genetics, vol. 57, 787-795). This pattern basically supports dual structure model of Japonesians proposed by Kazuro Hanihara and other physical anthropologists. We recently determined genome-wide SNP data of people from Izumo area, which is geographically close to Korean Peninsula. Principal Component Analysis revealed unique characteristics of Izumo people; they are genetically more different from Korean than Kanto area people. This new finding suggests existence of dual structure within Mainlanders; old migrants from south who brought rice agriculture and new migrants mainly from Korean Peninsula.
2006 Professor (concurrent), Department of Biological Sciences, Graduate School of Science, University of Tokyo, Japan
2002 Professor (concurrent), Department of Genetics, School of Life Science, SOKENDAI, Japan
2002 Professor, Division of Population Genetics, National Institute of Genetics, Japan
1992 Associate Professor (concurrent), Department of Genetics, School of Life Science, SOKENDAI, Japan
1991 Associate Professor, Division of Evolutionary Genetics, National Institute of Genetics, Japan
1989 Assistant Professor, Department of Anthropology, Faculty of Science, University of Tokyo, Japan
1987 JSPS post-doctoral fellow, Department of Anthropology, Faculty of Science, University of Tokyo, Japan
1986 Ph.D., Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, U.S.A.
1981 M.S., Department of Anthropology, Graduate School of Science, University of Tokyo, Japan
1979 B.S., Department of Biology, Faculty of Science, University of Tokyo, Japan
*Member of SOKENDAI Strategic Research Project
"Comprehensive study on creation of genetic and cultural diversity through modern human dispersal"
chaired by Naruya Saitou