Tsunehiko Hanihara's research while affiliated with Kitasato University and other places
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Publications (114)
This study assessed the regional diversity of the human cranial form by using geometric homologous models based on scanned data from 148 ethnic groups worldwide. This method adopted a template-fitting technique for a nonrigid transformation via the iterative closest point algorithm to generate the homologous meshes. Through the application of princ...
This study reports a cranio-morphometric analysis of female human remains from seven archaeological sites in China, Vietnam and Taiwan that date between 16,000 and 5300 BP. The aim of the analysis is to test the “two-layer” model of human dispersal in eastern Eurasia, using previously unanalysed female remains to balance the large sample of previou...
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...
Anatomically modern humans reached East Asia more than 40,000 years ago. However, key questions still remain unanswered with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of the region may elucidate a more detailed picture of the peopling of East Eurasia. Here, we analyze the whole-...
Anatomical modern humans reached East Asia by >40,000 years ago (kya). However, key questions still remain elusive with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of East Eurasia may shed light on the detail picture of peopling to East Eurasia. Here, we analyze the whole-genome s...
Ancient migrations in Southeast Asia
The past movements and peopling of Southeast Asia have been poorly represented in ancient DNA studies (see the Perspective by Bellwood). Lipson et al. generated sequences from people inhabiting Southeast Asia from about 1700 to 4100 years ago. Screening of more than a hundred individuals from five sites yielded...
The mode and timing of the dispersal of modern humans out of Africa and into Eurasia has important implications for the genetic and phenotypic structure of extant human populations. However, no consensus exists on the number, geographic route, and chronology of dispersal events. In this paper, we review competing dispersal models and evaluate their...
Dental phenotypic data are often used to reconstruct biological relatedness among past human groups. Teeth are an important data source because they are generally well preserved in the archaeological and fossil record, even when associated skeletal and DNA preservation is poor. Furthermore, tooth form is considered to be highly heritable and select...
Humans show various responses to the environmental stimulus in individual levels as “physiological variations.” However, it has been unclear if these are caused by genetic variations. In this study, we examined the association between the physiological variation of response to light-stimulus and genetic polymorphisms. We collected physiological dat...
Comparison of the distributions of (A) percentages of pupil constriction and (B) MEQ score for three major haplotypes of PER2. Thick middle lines in the boxes represent the medians, and the tops and bottoms of the boxes represent the third and the first quartiles, respectively. One dot represents one chromosome, and the numbers of chromosomes, n, a...
Relative maps for the SNPs examined in this study.
(A) Six SNPs on PER2 and (B) four SNPs on PER3 are numbered serially, and their rs numbers, alleles reported, and allele frequencies of JPT in the HapMap database are shown respectively.
(TIF)
Comparison of the distributions of percentages of melatonin suppression for PER2 alleles of (A) SNP1, (B) SNP5, and (C) SNP6. The thick middle lines in the boxes represent the medians, and the tops and bottoms of the boxes represent the third and the first quartiles, respectively. One dot represents one chromosome, and the numbers of chromosomes, n...
An NJ tree for the PER2 intron sequences and the divergence times of the haplotypes with 1000 bootstrap replicates.
The phased sequences that had homozygotes of three major haplotypes (Hap1, Hap2, and Hap3) in YRI, CEU, and JPT were obtained from the 1000 Genome Project (phase 3) database. The arrows represent divergence times.
(TIF)
Haplotype frequencies for (A) PER2 and (B) PER3. The numbers of local populations included in the geographical region are shown in parentheses. N represents the numbers of the individuals. The combined frequencies of the remaining haplotype (Residuals) are less than 1.0% in all the geographical regions.
(TIF)
Comparison of the distributions of percentages of melatonin suppression for major haplotypes of (A) PER2 and (B) PER3. The thick middle lines in the boxes represent the medians, and the tops and bottoms of the boxes represent the third and the first quartiles, respectively. One dot represents one chromosome, and the numbers of chromosomes, n, are s...
Difference of changes in percentages of melatonin suppression between the genotypes of PER2.
The percentages of melatonin suppression by light exposure in Hap1, Hap2, and Hap3 homozygotes. The data are shown as the mean + SD.
(TIF)
Comparison of the distributions of (A) percentages of pupil constriction and (B) MEQ score for four major haplotypes of PER3. The thick middle lines in the boxes represent the medians, and the tops and bottoms of the boxes represent the third and the first quartiles, respectively. One dot represents one chromosome, and the numbers of chromosomes, n...
Melatonin profiles of the subjects.
(A) The raw data of melatonin concentration in all the subjects. The bold line shows the average. The start time of light exposure (0 h) was individually set 3 and 3.5 hours before the midpoint of sleep of each subject. There was a large interindividual difference. The dots shows the melatonin concentration measu...
Ancestral allele frequencies of SNPs (A) in PER2 and (B) in PER3. Three groups, Subjects, Northern Kyushu and Ryukyu were genotyped in this study. N represents the number of individuals.
(TIF)
Crohn's disease (CD) involves chronic inflammation in the gastrointestinal tract due to dysregulation of the host immune response to the gut microbiome. Even though the host-microbiome interactions are likely contributors to the development of CD, a few studies have detected genetic variants that change bacterial compositions and increase CD risk....
Objectives:
A cline of frequencies of the derived allele of the ALDH2 gene, which causes a deficiency of an enzyme and "facial flushing" in humans who drink alcohol, has been known among the people of the Japanese archipelago. This cline is conventionally explained by admixture with immigrants from the Asian continent occurring during the Yayoi pe...
Various hypotheses for the peopling of the Japanese archipelago have been proposed, which can be classified into three models: transformation, replacement, and hybridization. In recent years, one of the hybridization models ("dual-structure model") has been widely accepted. According to this model, Neolithic hunter-gatherers known as Jomon, who are...
Sexual dimorphisms, which are phenotypic differences between males and females, are driven by sexual selection. Interestingly, sexually selected traits show geographical variations within species despite strong directional selective pressures. This paradox has eluded many evolutionary biologists for some time, and several models have been proposed...
The Ryukyu Islands are located to the southwest of the Japanese archipelago. Archaeological evidence has revealed the existence
of prehistoric cultural differentiation between the northern Ryukyu islands of Amami and Okinawa, and the southern Ryukyu
islands of Miyako and Yaeyama. To examine a genetic subdivision in the Ryukyu Islands, we conducted...
Different data types have previously been shown to have the same microevolutionary patterns in worldwide data sets. However, peopling of the New World studies have shown a difference in migration paths and timings using multiple types of data, spurring research to understand why this is the case. This study was designed to test the degree of simila...
As the hardest tissue in the body, teeth have the potential to offer a wealth of biological information to the forensic anthropologist, which can include the assessment of ancestry. Using a large data set of dental measurements, the efficacy of mesiodistal and buccolingual tooth dimensions to discriminate between broad, geographically based groups...
Sexual dimorphisms, which are phenotypic differences between males and females, are driven by sexual selection [1, 2]. Interestingly, sexually selected traits show geographic variations within species despite strong directional selective pressures [3, 4]. However, genetic factors that regulate varied sexual differences remain unknown. In this study...
Genetic and craniometric data have previously been shown to be in concordance with each other, suggesting that they both express the same microevolutionary forces (Relethford, 1994, Gonzalez-Jose et al., 2004). However, peopling of the New World studies often differ in opinion about using molecular data vs. osteological data, as they appear to demo...
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 charac...
Researchers have long had an interest in dental morphology as a genetic proxy to reconstruct population history. Much interest was fostered by the use of standard plaques and associated descriptions that comprise the Arizona State University Dental Anthropology System, developed by Christy G. Turner, II and students. This system has served as the f...
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 charac...
Gene flow and genetic drift are important factors affecting geographic variation of human phenotypic traits. In the present study, the effects of gene flow from an outside source on the pattern of within-and among-group variation of Hokkaido Ainu, one of the most generalized eastern Asian populations, are examined by applying R-matrix method to 24...
Whereas the Galβ1-4Gal epitope is rarely found in mammalian glycans, it has been found in glycans of various species of non-mammalian vertebrates, such as fish, amphibians, and birds. Although glycans containing Galβ1-4Gal in these vertebrates were detected by precise structural analysis of the glycans using mass spectrometry and/or NMR spectrometr...
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 crani...
Dental morphology is highly diverse among individuals and between human populations. Although it is thought that genetic factors mainly determine common dental variations, only a few such genetic factors have been identified. One study demonstrated that a nonsynonymous single-nucleotide polymorphism (370V/A, rs3827760) in the ectodysplasin A recept...
Degenerative changes of the spine in people of the Okhotsk culture were investigated in adult human skeletal remains from 38 males and 34 females. These findings were then compared with those in materials obtained from the medieval Kamakura period and early-modern peasants on Kumejima, Ryukyu Islands. The three samples clearly showed different patt...
We present an Aboriginal Australian genomic sequence obtained from a 100-year-old lock of hair donated by an Aboriginal man from southern Western Australia in the early 20th century. We detect no evidence of European admixture and estimate contamination levels to be below 0.5%. We show that Aboriginal Australians are descendants of an early human d...
The purpose of this study is to investigate the origin and expansion of the Jomon population, the Neolithic inhabitants of the Japanese archipelago, and peopling East/Northeast Asian region through a global comparison between the prehistoric samples from around the world.
R-matrix approach was applied to 20 nonmetric cranial traits for assessing th...
Abstract Using Mahalanobis' generalized distance for odontometric data and Smith's mean measure of divergence for nonmetric dental data, interpopulation similarities between four local Ainu groups from Sakhalin Island and Hokkaido, as well as their supposedly ancestral and neighboring populations, were analyzed. In this study, multidimensional scal...
The Japan Islands, a small island chain on the western rim of the circum-Pacific region, have experienced several Cultural contacts and human migrations from northern and eastern continental Asia. In this study, craniometric diversification of Asian peoples was assessed using the R-matrix method based on 21 metric traits in 25 representative male a...
The ability of cranial morphology to reflect population/phylogenetic history, and the degree to which it might be influenced by environmental factors and selection pressures have been widely discussed. Recent consensus views cranial morphology as largely indicative of population history in humans, with some anatomical cranial regions/measurements b...
Shovel shape of upper incisors is a common characteristic in Asian and Native American populations but is rare or absent in African and European populations. Like other common dental traits, genetic polymorphisms involved in the tooth shoveling have not yet been clarified. In ectodysplasin A receptor (EDAR), where dysfunctional mutations cause hypo...
The people associated with the Jomon culture, the Neolithic inhabitants of Japan, are one of the key groups in the population history of East Asia, because they retain many archaic characters that may be traced back to Eurasian Upper Palaeolithic hunter-gatherers. In this study, the regional diversity of the Jomon skeletal series was estimated by a...
To measure and compare the anterior loop length (ALL) for the mandibular canal and the mandibular incisive canal diameter (ICD) at its origin in cadavers using anatomy and cone beam computed tomography (CBCT) to safely install endosseous implants in the most distal area of the interforaminal region.
The ALL and ICD were measured using CBCT in 4 cad...
It is now generally held that the Neolithic Jomon people with generalized craniofacial features occupied the entire Japanese archipelago. Around 2300-1300 years BP, migrants from somewhere in eastern Asia to the southwestern part of Japan admixed with the indigenous Jomon descendants. Based on this population history, it is expected to find clinal...
The relative importance of ancient demography and climate in determining worldwide patterns of human within-population phenotypic diversity is still open to debate. Several morphometric traits have been argued to be under selection by climatic factors, but it is unclear whether climate affects the global decline in morphological diversity with incr...
Human populations across the world vary greatly in cranial morphology. It is highly debated to what extent this variability has accumulated through neutral processes (genetic drift) or through natural selection driven by climate. By taking advantage of recent work showing that geographic distance along landmasses is an excellent proxy for neutral g...
Gene flow and genetic drift are important factors affecting geographic variations in human phenotypic traits. In the present study, the effects of gene flow from an outside source on the pattern of within- and among-group variation of the Ainu from Sakhalin Island and three local groups of Hokkaido are examined by applying an R-matrix approach to m...
In and after the latest Neolithic period in Japan (approximately B.P. 2,300 years), there were two distinct waves of migration from eastern Asia. One is well known as successive episodes in which indigenous inhabitants of main-island Japan were intruded on by new arrivals with advanced technology, and of a different genetic stock. Another migration...
Human skeletal remains from the early-modern period (17th-19th centuries AD) of Kumejima Island, the Ryukyu Islands, were examined for dental disease, including dental caries, linear enamel hypoplasia (LEH), antemortem tooth loss (AMTL), and dental calculus. The materials used in this study consisted of 386 adult individuals, 105 male, 89 female, a...
The patterns of inter- and intra-regional variation among 12 major geographical groups from around the world were investigated based on 15 nonmetric dental traits. The R-matrix method was applied using a pooled within-group variance-covariance matrix estimated with the maximum likelihood method (tetrachoric correlation matrix) and the threshold val...
Population affinities and biological variation in human skeletal series associated with the Okhotsk culture from Hokkaido and Sakhalin Islands from the 5th to 12th centuries AD are investigated using 19 nonmetric cranial traits. The Okhotsk crania have a higher frequency of the supraorbital foramen than the Hokkaido Ainu and Jomon, while the freque...
To measure the anterior loop length (ALL) for the mandibular canal and diameter of the mandibular incisive canal at various points to ascertain the mesial distance from the mental foramen at which it is safe to install endosseous implants in the most distal area of the interforaminal region.
Using 38 cadavers (75 hemimandibles), the ALL and the dia...
Mesiodistal and buccolingual crown diameters were examined to describe and compare patterns of metric dental variation in five modem samples from the Ryukyu Island chain (Miyako, Ishigaki, Tokunoshima, and two samples from Okinawa Island). Principal component analysis applied to two separate datasets, raw measurement and standardized (C-score) data...
The origin and patterns of dispersal of anatomically modern humans are the focus of considerable debate. Global genetic analyses have argued for one single origin, placed somewhere in Africa. This scenario implies a rapid expansion, with a series of bottlenecks of small amplitude, which would have led to the observed smooth loss of genetic diversit...
Twenty-four non-metric tooth crown traits of Miyako, and Ishigaki Islanders, from the southernmost Ryukyu Islands, were investigated and compared with those of neighboring populations. The frequency of double-shoveling in Sakishima samples, and especially, Ishigaki Island, is lower than that found among Atayal people (Taiwan) and main-island Japane...
Twenty-four non-metric tooth crown traits of Miyako and Ishigaki Islanders, from the southernmost Ryukyu Islands, were investigated and compared with those of neighboring populations. The frequency of double-shoveling in Sakishima samples, and especially, Ishigaki Island, is lower than that found among Atayal people (Taiwan) and main-island Japanes...
Human skeletal remains from the early-modern period (17th–19th centuries AD) of Kumejima Island, the Ryukyu Islands, were examined for dental disease, including dental caries, linear enamel hypoplasia (LEH), antemortem tooth loss (AMTL), and dental calculus. The materials used in this study consisted of 386 adult individuals, 105 male, 89 female, a...
Nonmetric cranial variation of the Ryukyuans, including the Kumejima population, and their neighboring peoples was investigated. Among the populations compared, incidences of supernumerary ossicles in the Ryukyu series were high. The frequency of the supraorbital foramen of the Kumejima series was shown to be intermediate between those of the East...
When it was published in 1996 Bioarchaeology of Southeast Asia was the first book to examine the biology and lives of the prehistoric people of this region. Bringing together the most active researchers in late Pleistocene/Holocene Southeast Asian human osteology, the book deals with major approaches to studying human skeletal remains. Using analys...
Mesiodistal and buccolingual crown diameters of all teeth recorded in 72 major human population groups and seven geographic groups were analyzed. The results obtained are fivefold. First, the largest teeth are found among Australians, followed by Melanesians, Micronesians, sub-Saharan Africans, and Native Americans. Philippine Negritos, Jomon/Ainu,...
Vertebral assimilation was observed in an adult male Ainu skeleton from the Tokoro Chashi site of the early modem period in Tokoro, Hokkaido, Japan. The vertebral bodies and right zygapophyseal joint between the 12th thoracic and 1st lumbar vertebrae were completely united by osseous tissue, with anterior wedge shape and 42% loss of anterior verteb...
This study reevaluates the relationship between the prehistoric Jomon and modem Ainu based on 18 nonmetric cranial traits. Although the two Ainu series from the northeast coast and central/ southern regions of Hokkaido Island are always associated with Jomon, significant differences between the Ainu and Jomon were detected in the frequencies of sev...
In the present study, the frequency distributions of 20 discrete cranial traits in 70 major human populations from around the world were analyzed. The principal-coordinate and neighbor-joining analyses of Smith's mean measure of divergence (MMD), based on trait frequencies, indicate that 1). the clustering pattern is similar to those based on class...
The presence or absence of 24 nonmetric dental traits was examined to investigate the inter- and intraregional variation of Ryukyu Islanders. We compared the dentition of the Kadena sample from the central district of Okinawa Island in the Ryukyu Island chain to those of samples from Nakijin from the northern district of the same Okinawa Island, To...
This concludes a series of descriptive statistical reports on discrete cranial traits in 81 human populations from around the world. Four variants classified as vessel and nerve related characters were investigated: patent condylar canal, supraorbital foramen; accessory infraorbital foramen; and accessory mental foramen. A significant asymmetric oc...
Seven discrete cranial traits usually categorised as hyperostotic characters, the medial palatine canal, hypoglossal canal bridging, precondylar tubercle, condylus tertius, jugular foramen bridging, auditory exostosis, and mylohyoid bridging were investigated in 81 major human population samples from around the world. Significant asymmetric occurre...
This concludes a series of descriptive statistical reports on discrete cranial traits in 81 human populations from around the world. Four variants classified as vessel and nerve related characters were investigated: patent condylar canal; supraorbital foramen; accessory infraorbital foramen; and accessory mental foramen. A significant asymmetric oc...
Seven discrete cranial traits usually categorised as hyperostotic characters, the medial palatine canal, hypoglossal canal bridging, precondylar tubercle, condylus tertius, jugular foramen bridging, auditory exostosis, and mylohyoid bridging were investigated in 81 major human population samples from around the world. Significant asymmetric occurre...