Identification of ancient viruses from metagenomic data of the Jomon people.

Ancient DNA studies provide genomic information about the origins, population structures, and physical characteristics of ancient humans that cannot be solely examined by archeological studies. The DNAs extracted from ancient human bones, teeth, or tissues are often contaminated with coexisting bacterial and viral genomes that contain DNA from ancient microbes infecting those of ancient humans. Information on ancient viral genomes is useful in making inferences about the viral evolution. Here, we have utilized metagenomic sequencing data from the dental pulp of five Jomon individuals, who lived on the Japanese archipelago more than 3000 years ago; this is to detect ancient viral genomes. We conducted de novo assembly of the non-human reads where we have obtained 277,387 contigs that were longer than 1000 bp. These contigs were subjected to homology searches against a collection of modern viral genome sequences. We were able to detect eleven putative ancient viral genomes. Among them, we reconstructed the complete sequence of the Siphovirus contig89 (CT89) viral genome. The Jomon CT89-like sequence was determined to contain 59 open reading frames, among which five genes known to encode phage proteins were under strong purifying selection. The host of CT89 was predicted to be Schaalia meyeri, a bacterium residing in the human oral cavity. Finally, the CT89 phylogenetic tree showed two clusters, from both of which the Jomon sequence was separated. Our results suggest that metagenomic information from the dental pulp of the Jomon people is essential in retrieving ancient viral genomes used to examine their evolution.

Post-last glacial maximum expansion of Y-chromosome haplogroup C2a-L1373 in northern Asia and its implications for the origin of Native Americans.

OBJECTIVES: Subbranches of Y-chromosome haplogroup C2a-L1373 are founding paternal lineages in northern Asia and Native American populations. Our objective was to investigate C2a-L1373 differentiation in northern Asia and its implications for Native American origins. MATERIALS AND METHODS: Sequences of rare subbranches (n = 43) and ancient individuals (n = 37) of C2a-L1373 (including P39 and MPB373), were used to construct phylogenetic trees with age estimation by BEAST software. RESULTS: C2a-L1373 expanded rapidly approximately 17.7,000-14.3,000 years ago (kya) after the last glacial maximum (LGM), generating numerous sublineages which became founding paternal lineages of modern northern Asian and Native American populations (C2a-P39 and C2a-MPB373). The divergence pattern supports possible initiation of differentiation in low latitude regions of northern Asia and northward diffusion after the LGM. There is a substantial gap between the divergence times of C2a-MPB373 (approximately 22.4 or 17.7 kya) and C2a-P39 (approximately 14.3 kya), indicating two possible migration waves. DISCUSSION: We discussed the decreasing time interval of "Beringian standstill" (2.5 ky or smaller) and its reduced significance. We also discussed the multiple possibilities for the peopling of the Americas: the "Long-term Beringian standstill model," the "Short-term Beringian standstill model," and the "Multiple waves of migration model." Our results support the argument from ancient DNA analyses that the direct ancestor group of Native Americans is an admixture of "Ancient Northern Siberians" and Paleolithic communities from the Amur region, which appeared during the post-LGM era, rather than ancient populations in greater Beringia, or an adjacent region, before the LGM.

Methodological issues in the Indo-European debate.

The Indo-European debate has been going on for a century and a half. Initially confined to linguistics, race-based anthropology and comparative mythology, it soon extended to archaeology, especially with the discovery of the Harappan civilization, and peripheral disciplines such as agriculture, archaeometallurgy or archaeoastronomy. The latest entrant in the field, archaeogenetics, is currently all but claiming that it has finally laid to rest the whole issue of a hypothetical migration of Indo-Aryan speakers to the Indian subcontinent in the second millennium BCE. This paper questions the finality of this claim by pointing to inherent limitations, methodological issues and occasional biases in current studies as well as in the interpretation of archaeological evidence.

Analysis of whole Y-chromosome sequences reveals the Japanese population history in the Jomon period.

The Jomon and the Yayoi are considered to be the two major ancestral populations of the modern mainland Japanese. The Jomon people, who inhabited mainland Japan, admixed with Yayoi immigrants from the Asian continent. To investigate the population history in the Jomon period (14,500-2,300 years before present [YBP]), we analyzed whole Y-chromosome sequences of 345 Japanese males living in mainland Japan. A phylogenetic analysis of East Asian Y chromosomes identified a major clade (35.4% of mainland Japanese) consisting of only Japanese Y chromosomes, which seem to have originated from indigenous Jomon people. A Monte Carlo simulation indicated that ~70% of Jomon males had Y chromosomes in this clade. The Bayesian skyline plots of 122 Japanese Y chromosomes in the clade detected a marked decrease followed by a subsequent increase in the male population size from around the end of the Jomon period to the beginning of the Yayoi period (2,300 YBP). The colder climate in the Late to Final Jomon period may have resulted in critical shortages of food for the Jomon people, who were hunter-gatherers, and the rice farming introduced by Yayoi immigrants may have helped the population size of the Jomon people to recover.

Intentional cranial modification from the Houtaomuga Site in Jilin, China: Earliest evidence and longest in situ practice during the Neolithic Age.

OBJECTIVES: Intentional cranial modification (ICM) was a long-established tradition used to reshape the head. Unfortunately, motivation of the act is unclear. It has been found in recent and contemporary human populations throughout the Old and New Worlds, yet the drawback of the quest into the origin, diffusion, and meanings of ICM is the lack of early materials for scientific examination. This study reports the discovery of ICM from the Neolithic Houtaomuga Site in Northeast China and the importance in deepening our knowledge of this intriguing tradition. MATERIALS AND METHODS: Twenty-five skeletons unearthed from the Neolithic cultural Phases 1-4 in the Houtaomuga Site were visually screened for ICM features. Cranial measurements were conducted to quantify the degree of variation in the modified skulls and typical ones were computer tomography (CT) scanned to obtain a diploë structure and 3D model. RESULTS: Eleven skulls carrying signs of ICM from both sexes varying in age from juveniles to full adults were identified ranging from 12,000 BP to 5,000 BP. Three types of modification patterns were observed and most of them were of typical fronto-occipital modification pattern. In particular, there were remarkable variations in the curvature of the crania along the sagittal direction. DISCUSSION: Overall, the antiquity as well as the cultural and genetic continuity of the population in Houtaomuga Site demonstrated the earliest confirmed ICM cases from the easternmost Old World, and the longest in situ duration of ICM practice at one single Neolithic site. This circumstance largely contributes to our understanding of the origins and distribution of ICM in Eurasia and the American continent.

Diachronic changes in craniofacial morphology among the middle-late Holocene populations from Hehuang region, Northwest China.

OBJECTIVES: This study analyzes craniofacial shape variation in the Hehuang region of Northwest China within a population genetic framework, and takes a diachronic approach to explore the relationship betwee cultural discontinuity and biological continuity/discontinuity in the Hehuang region during the middle to late Holocene. MATERIALS AND METHODS: The sample comprises 76 adult skulls from five archaeological sites, ranging from 4,500 to 1,530 BP. 3D geometric morphometrics, multivariate statistics, quantitative evolutionary genetic and biodistance analyses were performed to study the diachronic variation in craniofacial morphology. Analyses were performed on two cranial modules: the face and the cranial vault, across three major diachronic groups representing the late Neolithic (LNA), the Bronze Age (BA), and the Han-Jin dynasty (HD). RESULTS: Average regional FST for both cranial modules was low, indicating relatively greater variation within diachronic groups than among them. While the LNA and BA groups did not show any significant differences in facial and vault shape, significant craniofacial shape changes were detected between the BA and HD groups. DISCUSSION: The consistent craniofacial morphology during the LNA and the BA, and the shift in morphology between the BA and the HD indicates that cultural discontinuity does not always coincide with biological discontinuity. The Hehuang population evolved in situ with few changes, despite cultural and dietary changes, until the HD when migrations from the Central Plains are associated with extra-local gene flow to the area.

The Y-chromosome haplogroup C3*-F3918, likely attributed to the Mongol Empire, can be traced to a 2500-year-old nomadic group.

The Mongol Empire had a significant role in shaping the landscape of modern populations. Many populations living in Eurasia may have been the product of population mixture between ancient Mongolians and natives following the expansion of Mongol Empire. Geneticists have found that most of these populations carried the Y-haplogroup C3* (C-M217). To trace the history of haplogroup (Hg) C3* and to further understand the origin and development of Mongolians, ancient human remains from the Jinggouzi, Chenwugou and Gangga archaeological sites, which belonged to the Donghu, Xianbei and Shiwei, respectively, were analysed. Our results show that nine of the eleven males of the Gangga site, two of the eight males of Chengwugou site and all of the twelve males of Jinggouzi site were found to have mutations at M130 (Hg C), M217 (Hg C3), L1373 (C2b, ISOGG2015), with the absence of mutations at M93 (Hg C3a), P39 (Hg C3b), M48 (Hg C3c), M407 (Hg C3d) and P62 (Hg C3f). These samples were attributed to the Y-chromosome Hg C3* (Hg C2b, ISOGG2015), and most of them were further typed as Hg C2b1a based on the mutation at F3918. Finally, we inferred that the Y-chromosome Hg C3*-F3918 can trace its origins to the Donghu ancient nomadic group.

Genetic signature of natural selection in first Americans.

When humans moved from Asia toward the Americas over 18,000 y ago and eventually peopled the New World they encountered a new environment with extreme climate conditions and distinct dietary resources. These environmental and dietary pressures may have led to instances of genetic adaptation with the potential to influence the phenotypic variation in extant Native American populations. An example of such an event is the evolution of the fatty acid desaturases (FADS) genes, which have been claimed to harbor signals of positive selection in Inuit populations due to adaptation to the cold Greenland Arctic climate and to a protein-rich diet. Because there was evidence of intercontinental variation in this genetic region, with indications of positive selection for its variants, we decided to compare the Inuit findings with other Native American data. Here, we use several lines of evidence to show that the signal of FADS-positive selection is not restricted to the Arctic but instead is broadly observed throughout the Americas. The shared signature of selection among populations living in such a diverse range of environments is likely due to a single and strong instance of local adaptation that took place in the common ancestral population before their entrance into the New World. These first Americans peopled the whole continent and spread this adaptive variant across a diverse set of environments.

Craniometric examination of Longxian and Qi Li Cun archaeological sites to assess population continuity in ancient northern China.

In this paper, population continuity and discontinuity in northern China are explored using craniometric analyses from two archaeological sites, Longxian (Warring States) and Qi Li Cun (Han Dynasty). Neither population has been previously studied. Artefactual evidence shows the individuals from Qi Li Cun were Xianbei, descendants from Mongolia. Longxian is from further south in the central plains at an earlier time, thus, we expect to observe variability between these groups. In total, 24 cranial measurements were obtained on 66 crania from these sites. Howells's cranial measurements on Anyang (42 crania) and Hainan (83 crania) Chinese samples were included for comparative purposes. Less variability is expected between Longxian and Howells's Chinese data due to geographic and temporal similarity. With closer geographic and temporal affinity with Anyang, the expectation is for Longxian and Anyang to be similar. Few statistical differences exist between Longxian and Qi Li Cun; this was supported by the similarity found through principal components analysis (PCA). Regardless of sex, canonical discriminant analysis shows clustering of Longxian and Qi Li Cun separate from those of Anyang and Hainan. Their similarity indicates the people from Longxian and Qi Li Cun likely share Mongolian ancestry. Our results, supported by other studies, suggest that despite temporal differences, Mongolians living in China during the Warring States and Han dynasty retained their cultural and genetic Mongolian identity. These data add valuable bioarchaeological information regarding the peopling of northern China during a crucial period of cultural and political change in the Early Bronze Age and Iron Age.

DNA analysis of an early modern human from Tianyuan Cave, China.

Hominins with morphology similar to present-day humans appear in the fossil record across Eurasia between 40,000 and 50,000 y ago. The genetic relationships between these early modern humans and present-day human populations have not been established. We have extracted DNA from a 40,000-y-old anatomically modern human from Tianyuan Cave outside Beijing, China. Using a highly scalable hybridization enrichment strategy, we determined the DNA sequences of the mitochondrial genome, the entire nonrepetitive portion of chromosome 21 (∼30 Mbp), and over 3,000 polymorphic sites across the nuclear genome of this individual. The nuclear DNA sequences determined from this early modern human reveal that the Tianyuan individual derived from a population that was ancestral to many present-day Asians and Native Americans but postdated the divergence of Asians from Europeans. They also show that this individual carried proportions of DNA variants derived from archaic humans similar to present-day people in mainland Asia.

Recognition of dementia in ancient China.

A search of previous records in the literatures was done to summarize the opinions for dementia in ancient China. The earliest description of dementia was traced in the Yellow emperor's internal classic, a book written 2000 years ago. Hua Tuo (AD 140-208) in Han Dynasty first denominated "dementia" in the book, Hua Tuo Shen Yi Mi Zhuan. The pathogenesis of dementia could be generalized as the insufficiency of Qi, a flowing energy; the stagnation of phlegm, a harmful liquid substance in the body; and the blood stasis, which were also regarded as therapeutic targets. Therefore, we can conclude that dementia has been recognized and investigated in traditional Chinese medicine, which is definitely before the industrial civilization era.

Art, class and gender in Joseon dynasty Korea: representations of lower-class women by the scholar-painter Yun Duseo.

This paper examines several pioneering genre paintings by the important scholar painter Yun Duseo (1668-1715), with its focus on their artistic sources which have not yet been explored so far. Painted on ramie, 'Women Picking Potherbs' is one of the most intriguing examples among Yun Duseo's oeuvre, which encompasses a broad variety of themes, including genre imagery, landscapes, portraits, dragons, and horses. Even among Yun Duseo's genre paintings, 'Women Picking Potherbs' is extraordinary, as recent scholarship regards it as the earliest independent representation of lower-class women in the history of Korean art. In particular, Yun Duseo painted two women who were working ourdoors to gather spring potherbs. In a conservative Confucian society, it was extraordinary women who were working outdoors. Hence, Yun Duseo occupies a highly important place in Korean painting. Furthermore, even though Yun Duseo came from the upper-class, he often painted images of lower class people working. It is possible that Yun Duseo was familiar with the book titled "Tian gong kai wu" (Exploitation of the Works of Nature) which was published in the 17th century. By identifying the probable body of his artistic sources in the book known as "Tian gong kai wu," it will be possible to assess the innovations and limitations found in 'Women Picking Potherbs'.

Genetic characteristics and migration history of a bronze culture population in the West Liao-River valley revealed by ancient DNA.

In order to study the genetic characteristics of the Lower Xiajiadian culture (LXC) population, a main bronze culture branch in northern China dated 4500-3500 years ago, two uniparentally inherited markers, mitochondrial DNA and Y-chromosome single-nucleotide polymorphisms (Y-SNPs), were analyzed on 14 human remains excavated from the Dadianzi site. The 14 sequences, which contained 13 haplotypes, were assigned to 9 haplogroups, and Y-SNP typing of 5 male individuals assigned them to haplogroups N (M231) and O3 (M122). The results indicate that the LXC population mainly included people carrying haplogroups from northern Asia who had lived in this region since the Neolithic period, as well as genetic evidence of immigration from the Central Plain. Later in the Bronze Age, part of the population migrated to the south away from a cooler climate, which ultimately influenced the gene pool in the Central Plain. Thus, climate change is an important factor, which drove the population migration during the Bronze Age in northern China. Based on these results, the local genetic continuity did not seem to be affected by outward migration, although more data are needed especially from other ancient populations to determine the influence of return migration on genetic continuity.

Peopling the Tibetan plateau: insights from archaeology.

Recent studies of the genome of modern Tibetans have revealed the existence of genes thought to provide an adaptive advantage for life at high elevation. Extrapolating from this discovery, some researchers now argue that a Tibetan-Han split occurred no more than 2750 yr ago. This date is implausible, and in this paper I review the archaeological data from the Tibetan plateau as one means by which to examine the veracity of this assertion. Following a review of the general state of knowledge of Tibetan prehistory, which is unfortunately only at its beginnings, I first examine the data that speak to the initial peopling of the plateau and assess the evidence that traces of their presence can be seen in modern Tibetans today. Although the data are sparse, both archaeology and genetics suggest that the plateau was occupied in the Late Pleistocene, perhaps as early as 30,000 yr ago, and that these early peoples have left a genetic signature in modern Tibetans. I then turn to the evidence for later migrations and focus on the question of the timing of the establishment of permanent settled villages on the plateau. Three areas of the plateau-northeastern Qinghai, extreme eastern Tibet, and the Yarlung Tsangpo valley-have evidence of permanent settlements dating from ca. 6500, 5900, and 3750 yr ago, respectively. These data are not consonant with the 2750 yr ago date for the split and suggest at a minimum that the plateau has been occupied substantially longer and, further, that multiple migrations at different times and from different places have created a complex mosaic of population history.

Rewriting the history of Chinese families in nineteenth-century Australia.

The nineteenth-century Chinese population in Australia was made up mostly of men, drawing many commentators to the conclusion these men faced an absence of family life, resulting in prostitution, gambling, opium use and other so-called vices. Recent research has, however, expanded and complicated our knowledge of Chinese families in New South Wales and Victoria, particularly concerning the extent to which Chinese men and white Australian women formed intimate relationships. This article traces the origins of the misconceptions about Chinese families in nineteenth-century Australia, and considers how new directions in scholarship over the past decade are providing methods for enlarging our knowledge. It argues that instead of being oddities or exceptions, Chinese-European families were integral to the story of Australia's early Chinese communities.