Sex identification of ancient DNA samples using a microfluidic device

A microfluidic device has been developed for the sex identification of ancient DNA samples and works by manipulating liquids within an environment of micrometer dimensions. In this work a range of microfluidic DNA extraction methods were evaluated for their compatibility with ancient DNA samples, and the use of streptavidin-coated super paramagnetic particles to isolate biotin-labeled abasic sites within damaged DNA was shown to be the most reproducible. Polymerase chain reaction-based DNA amplification was possible on the microfluidic device when less than 50 pg of template DNA was added. As a proof-of-principle, powdered bone samples were analysed using the integrated methodology developed. Following conventional capillary gel electrophoresis, two out of the three samples produced positive amplification results and were successfully identified as female. These sex identifications were corroborated by independent Amelogenin, anthropological and Y chromosome analysis. The work reported here is the first step in the development of a complete miniaturized microfluidic system that would enable on-site ancient DNA analysis.     

A DNA test for sex identification in cattle confirms osteometric results

It is of vital importance to be able to sex identify cattle remains to understand the strategies and importance of cattle husbandry in an ancient society. This is usually done from osteoarchaeological assemblages and often relies on measurements of metapodials. The breadth measurement of the distal trochlea is considered an easy way to identify the sex. Bones from males appears to be easily distinguishable from female counterparts, although it has been complicated to find an external control for the morphological results. Here we investigate the reliability of these particular morphometrics for sex identifying cattle bones with molecular genetics. We use a sex discriminating single nucleotide polymorphism in the ZFXY gene and we apply it to DNA from the bones. To keep the fragment size short and suitable for ancient DNA we base the test on a SNP. The test confirms the osteological sex identification in all cases were DNA could be retrieved. This molecular method can also be used when no fragments suitable for osteological sex identification can be found or when the measurements are non-conclusive.     

Accurate sex identification of ancient human remains using DNA shotgun sequencing

Accurate identification of the biological sex of ancient remains is vital for critically testing hypotheses about social structure in prehistoric societies. However, morphological methods are imprecise for juvenile individuals and fragmentary remains, and molecular methods that rely on particular sex-specific marker loci such as the amelogenin gene suffer from allelic dropout and sensitivity to modern contamination. Analyzing shotgun sequencing data from 14 present-day humans of known biological sex and 16 ancient individuals from a time span of 100 to ∼70,000 years ago, we show that even relatively sparse shotgun sequencing (about 100,000 human sequences) can be used to reliably identify chromosomal sex simply by considering the ratio of sequences aligning to the X and Y chromosomes, and highlight two examples where the genetic assignments indicate morphological misassignment. Furthermore, we show that accurate sex identification of highly degraded remains can be performed in the presence of substantial amounts of present-day contamination by utilizing the signature of cytosine deamination, a characteristic feature of ancient DNA.     

Ancient DNA investigation of prehistoric salmon resource utilization at Keatley Creek,British Columbia,Canada

This study applied ancient DNA techniques to achieve accurate species identifications for the archaeological salmon remains recovered from the prehistoric pithouse village of Keatley Creek in British Columbia, Canada. Previous archaeological studies indicate that economic stratification within the community might have resulted in differential access to some preferred salmon species, such as sockeye and chinook. Unambiguous ancient DNA species identification now makes it possible to more accurately address the issue of early salmon resource utilization in the region. This study analyzed 60 salmon remains from two specialized structures and two residential structures in order to identify any species differences among bony salmon remains found within the structure. Although high success rates (over 90%) were obtained for ancient DNA tests, only three species (chinook, sockeye and coho salmon) were identified from the remains. Pink salmon was not identified among the tested sample, despite the fact that it was originally assumed to be a staple species for the site's native inhabitants. The absence of pink salmon in our sample significantly altered the picture of early salmon fishing activities in the region. As a result, the effects of economic stratification on differential access to the remaining so-called preferred species of sockeye and chinook within the four structures studied were not as dramatic as previously thought, although differences among the structures could still be observed.     

馆藏纸质书画文物上霉菌的分离与鉴定

霉菌污染会影响馆藏纸质书画的保存和展示。对书画污染菌进行分离及鉴定,有助于提高文物霉变防治工作的针对性,进而提高防治效果。本研究利用传统的纯培养法从遭受霉菌污染的馆藏纸质书画表面分离得到8株霉菌,通过形态特征观察和r DNA转录间隔区序列ITS(Internal Transcribed Spacer)测序分析。结果表明:8株霉菌分属于曲霉属(Aspergillus)、根霉属(Rhizopu)和木霉属(Trichoderma)。研究结果可为馆藏纸质书画文物防霉剂的研发和文物霉菌的综合防治提供靶标和依据。     

《推定儿女法》与中古辨胎术

《推定儿女法》为俄藏黑水城出土金代占卜类写本文献,其文本来源于《孙子算经》,特殊性在于通过算术方法并结合阴阳五行思想卜算胎儿性别。以《推定儿女法》为代表的祈男辨胎思想和孕育信仰曾长期流行于中国古代社会,是研究古代社会民生与民间信仰的珍贵资料。在历史发展过程中,《推定儿女法》逐渐渗透到医学与命理学文本书写中,反映了阴阳五行思想主导下,中国古代数术、巫术与医学思想的相互影响与交流融合。     

Sex Identification in Some Putative Infanticide Victims from Roman Britain Using Ancient DNA

Previous study of infant burials has suggested that infanticide was routinely practised during the Roman period in Britain. This, together with the observation that there is an adult sex imbalance in favour of males at many Romano-British cemetery sites, has raised the question of female infanticide. We attempted to investigate this possibility by identifying sex in some infant skeletons from Romano-British contexts using ancient DNA (aDNA) techniques. Of 31 individuals sampled, sex identification was successful in 13, of which nine were males and four females. These results are discussed in the light of previous work on DNA-based seeking of infant burials.     

天津博物馆文物库房部分文物与囊匣中霉菌的分离与鉴定

馆藏文物中的书画、古籍、档案、纺织品和竹木漆器等有机质文物,常常受到霉菌的破坏。为了解文物库房有机质文物中霉菌病害现状,寻找适合的防治方法,利用显微形态观察和分子生物学方法,对四个库房内文物材料与囊匣上滋生的霉菌进行采样、培养、分离和鉴定。实验分离出的14株菌株通过形态观察和分子生物学鉴定为6个属,包括毛壳菌属(Chaetomium)、畸枝霉属(Malbranchea)、曲霉属(Aspergillus)、派伦霉属(Peyronellaea)和枝孢属(Cladosporium)等,其中毛壳菌属数量最多,曲霉属次之,多数为能对文物产生危害的常见菌种,亟待采取有效防治措施。实验结果可为今后霉菌的防治工作提供依据。     

Identification of ancient textiles from Yingpan,Xinjiang, by multiple analytical techniques

Various extraordinary textiles were excavated from a graveyard at Yingpan, Xinjiang, on the middle route of the ancient Silk Road. Applications of western motifs and designs to traditional Chinese textiles led to the emergence of compound woven textiles with central Asian characters. For a better understanding of the cultural exchanges and textile trade between the West and the East in ancient times, identifications of archaeological fibres and dyes were carried out for various funerary textile objects by using multiple analytical techniques, such as high performance liquid chromatography with photodiode detection, optical microscopy, scanning electronic microscopy (SEM), and Fourier transform infrared spectroscopy (FT-IR). Fibre identifications were performed for 35 archaeological textile samples, and the results showed that the ancient textiles were mostly made from Bombyx mori silk and wool. The SEM and FT-IR experimental results revealed that these ancient textiles remained morphologically intact due to the special (very dry) climate in Xinjiang, but noticeably degraded at the molecular level due to long time thermo-ageing and/or biodegradation. The principal colouring matters, such as alizarin, purpurin, indigotin and luteolin, were respectively characterised for nine archaeological textile samples. The yellow dyestuffs derived from luteolin-based plants were assumed to have been imported to China from the Middle East and Western Asia through the Silk Road.     

Flax look‐alikes: Pitfalls of ancient plant fibre identification

Plant fibres have been used since ancient times in numerous applications ranging from nets and basketry to textiles for clothing. A proper identification of plant fibre remains in archaeological excavations provides important information about resource exploitation and agriculture. In order to identify plant fibres, a series of fibre features—cross‐section diameter, lumen diameter, dislocations (nodes), cross markings, cross‐section shape and lumen shape—have been defined and characteristic traits of these features for different fibre types established. How suitable these traits really are for fibre identification has been a matter of debate. To resolve this issue, we have performed a systematic investigation of typical textile bast fibres: flax, nettle and hemp. We have investigated cross‐section diameter, lumen diameter, dislocations (nodes) and cross markings using standard compound, white light transmission microscopy. Our investigations show that all the traits that are considered characteristic for one type of plant fibre can also, on occasion, be found in other types. This demonstrates that an investigation of the traits listed above is not sufficient to ensure a correct identification of the plant fibre material; in particular, when only a small amount of material is available. This is often the case in archaeological excavations.     

Radio – Ulnar Weight Index — is it a Useful Criterion for Sex Identification of the Human Skeleton?

Sex identification of human long bones has been studied by several investigators. Measurements of the radius and the ulna have also been reported as an indicator of sex by reference to separate parameters and/or to combinations of the parameters of a single bone. This study was designed to determine whether the radius and the ulna can provide reliable information for the sexing of human bones, as can the lower leg bones, if the forearm measurements include the weight index of the two bones as a parameter. The materials consisted of the dried radii and ulnae of 20 recently deceased Japanese males and 20 similar females. Almost all the dimensions exhibited statistically significant sex differences. The radio–ulnar weight index did not, however, differ between the sexes. In discriminant analysis, the rate of correct sex discrimination based on distances between various pairs of points was not improved by the inclusion of the radio–ulnar weight index. Therefore, the radio–ulnar weight index cannot be recommended as a parameter for the sexing of human bones.     

Differentiation of archaeological ivory and bone materials by micro-PIXE/PIGE with emphasis on two Upper Palaeolithic key sites: Abri Pataud and Isturitz,France

The exact identification of the raw material used for ancient bone objects is the basis to understand the manner in which humans in ancient times chose the medium for the manufacture of objects. The material identification is not trivial in the case of highly modified surfaces – worked by man or degraded by diagenesis. Even if bone materials are morphologically quite different, they show in general a very similar chemical composition. Nevertheless, slight differences can be observed in their chemical composition on minor and trace level. These variations may be used as a marker of their exact nature, when other means such as morphological observations are limited. A large data base was built up by analysing different modern and archaeological osseous materials in order to define chemical markers for the identification of the raw materials used to manufacture objects.Micro-Proton Induced X-ray and Gamma-ray Emission (micro-PIXE/PIGE) was chosen to analyse the different bone materials as a non-invasive method is generally required for the study of ancient worked osseous objects. These analyses were performed at the particle accelerator AGLAE installed at the laboratory of the C2RMF, Paris.This paper presents the results obtained on about 150 objects made of different bone materials dating from the Palaeolithic to today and coming from various archaeological sites, mainly in France. Some chemical markers seem to be characteristic, such as the magnesium to calcium ratio for well preserved ivory on one hand and the fluorine content versus strontium to calcium ratio for bones of marine mammals on the other hand. The limits of this approach and the different parameters to consider for an identification of ancient bone and ivory material based on this method are particularly discussed in the case of Palaeolithic material from Abri Pataud and Isturitz, France.     

A Bioarchaeological and Biogeochemical Study of Warfare and Mobility in Andahuaylas,Peru (ca. ad 1160–1260)

Warfare impacts how people and populations can move about the landscape. Ethnographers have posited that internal warfare, conflict that takes place within a single society, is strongly associated with female abduction. In contrast, external warfare, combat between different societies, is often accompanied by the in‐migration of men for purposes of defence. To test this assertion, we evaluate human remains from one of the most violent eras in Andean prehistory, the Late Intermediate Period (ad 1000–1400). In the south‐central highlands of Andahuaylas, Peru, this era witnessed the coalescence of two formidable polities, the Chanka and the Quichua. Ethnohistoric accounts describe internal warfare among the Chanka and external warfare between the Quichua and their neighbours. In this study, bioarchaeological and biogeochemical methods are marshalled to elucidate ancient patterns of violence and mobility with greater nuance. We employ strontium isotope analysis of tooth enamel apatite to inform on residential origin, and we reconstruct patterns of violent conflict through analysis of cranial trauma. In all, 265 crania were excavated from 17 cave ossuaries at two Chanka sites and one Quichua site. Data were collected on age, sex and cranial modification—an indicator of social identity and cranial trauma. A representative subsample of molars from 34 individuals subjected to strontium isotope analysis demonstrates that among the Chanka, violence was significantly directed towards social groups within society, marked by modified crania. The presence of two nonlocal women with signs of increased morbidity and mistreatment points to possible mobility‐by‐abduction. In contrast, among the Quichua, men have significantly more trauma, and wounds are concentrated on the anterior. Trauma on women is lower, nonlethal, and concentrated on the posterior. This divergent pattern is commonly observed in external warfare (raids and community defence), where men face attackers and women escape them. The presence of two nonlocal men supports a mobility model of strategic in‐migration. In sum, osteological and isotopic data sets are shown to reveal divergent life‐course experiences not captured by the archaeological data or historic records alone. Copyright © 2014 John Wiley & Sons, Ltd.     

Hyperostosis Frontalis Interna and sex identification of two skeletons from the Early Middle Ages necropolis of Vicenne‐Campochiaro (Molise,Italy)

Lesions attributable to Hyperostosis Frontalis Interna (HFI) were examined in two skulls (from graves 100 and 113) from the Early Middle Ages necropolis of Vicenne‐Campochiaro (Molise, Italy). Both skeletons were of older individuals and it was difficult to sex them using standard anthropological methods. We discuss the sex identification of the skeletons in relation to the presence of HFI, as well as the usefulness of this pathological condition as a sex marker, underlining the importance of the relationship between palaeopathological and clinical‐forensic studies. Our study is a further contribution to the case history of HFI in osteoarchaeological material. Copyright © 2006 John Wiley & Sons, Ltd.     

古代残留物分析在考古中的应用

动植物是人类社会发展的重要基石,它的利用是人类适应、改造和征服自然的物质基础,古代社会的方方面面都与之相关,因而动植物及其制品的残留物分析能提供古代社会丰富的信息。残留物分析重点在于从残留物中提取有机物。利用科学检测手段进行定性定量分析来判断残留物来源,从而了解古代动植物的加工、利用和相关载体的功能等。本文从DNA、淀粉粒、蛋白质、脂类、炭化物和酒等六个方面简要介绍了残留物分析的方法和进展,希望能促进残留物分析在中国的开展．     

Sex work and exclusion in the tourist districts of Salvador,Brazil

Salvador, capital of the state of Bahia, in the Northeastern region of Brazil, is composed of racialized, gendered, and sexualized spaces in which certain people are welcome, while others are marginalized and excluded. Praça da Sé, in the Centro Histórico, is a major site of both the local commercial sex industry and the tourist industry in Salvador. With their public visibility in sites heavily frequented by tourists, sex workers in Salvador reveal how sexuality is public, politically contested, economically charged, and, most significantly, racialized. If, as Tom Boellstorff argues, ‘globalization resignifies the meaning of place rather than making place irrelevant’ (2007, 23), how does one then study racialized sexualities in the context of the globalized tourism industry? How do class, space, and race influence practices of sex work and sex tourism in Salvador? This article offers a critical analysis of racialized sexualities in the study of the sexual economies of tourism in Salvador. I conceptualize Salvador as a ‘site of desire’ (Manderson and Jolly 1997) where issues of socioeconomic inequality, racism, and sexism coexist alongside celebratory affirmations of Afro-Brazilian cultural production in Salvador. This article explores how the touristic cityscape of Salvador is divided into carefully demarcated zones where class and race are crucial factors in determining who ‘belongs’ and who is ‘out of place.’     

Beware the Springbok in Sheep’s Clothing: How Secure Are the Faunal Identifications upon Which We Build Our Models?

Lively debate surrounds the introduction of non-indigenous domestic livestock to southern Africa. Despite disagreements regarding process, the archaeological community agrees, with unusual unanimity, on the broad chronology. Indeed, the certainty with which the timing is known (admittedly within the limits of radiocarbon dating) has been celebrated, because with these underpinning data in hand, issues of process can be explored in a serious and empirically grounded manner. Recently published ancient DNA (aDNA) research in southern Africa now calls into question the reliability of many faunal identifications upon which this debate rests. These data build on earlier ecological data, suggesting that some faunal identifications at sites crucial to the debate may be unreliable. A number of morphologically identified domesticate bones were chosen for aDNA sequencing to explore the relationships among southern Africa’s early domestic stock. Unfortunately, a large proportion yielded DNA sequences indicating a wild origin. This led us to consider the potential scale of the problem and the implications for existing models regarding the introduction of herding to the subcontinent. The issue may originate largely from the optimistic identification of specimens retaining too few key morphological markers. We acknowledge that reconstructions of the past are likely to be biased by discarding potential zooarchaeological data through overly conservative identification. We argue, however, that the potential ramifications of building models on unreliable data are far greater than those of being forced to acknowledge gaps in our data and are calling for further research.     

Functionality and Morphology: Identifying <Emphasis Type="Italic">Si</Emphasis> Agricultural Tools from Among Hemudu Scapular Implements in Eastern China

Most Chinese archaeologists assume that the scapular implements used in the Hemudu culture in eastern China (7000–5000 BP) were the si agricultural implements (tools for breaking ground and turning soils over to assist in seeding) recorded in ancient Chinese literatures and, accordingly, assume the Hemudu culture was a farming society. However, ethnographic and historical literatures worldwide have suggested inconclusive functions for similar implements. We conducted a range of experiments under realistic conditions, including hide and plant processing and earth-working, followed by use-wear analysis, to identify the functions of the Hemudu scapular implements. The results suggest that no more than half of the implements were employed as si and that their penetrability and durability were rather limited. These findings help explain why Hemudu should not be labeled as a farming society. Through experimentation and use-wear analysis, we produced relatively large datasets that make a significant contribution to the identification of soil-derived wear patterns on bone tools. We also included quantitative measurements of soil properties to ensure similarities in use contexts between our experimental and archaeological analogies in order to reach reliable functional identifications. Our approaches and results, therefore, provided a solid base for re-evaluating previous research as well as building a standardized database of scientific value for future evaluation and adjustment, even if that future research is done in isolation and in different soil contexts.     

Further developments in molecular sex assignment: a blind test of 18th and 19th century human skeletons

The identification of sex in human remains recovered from archaeological locations is important in order to understand the social and biological structure of past societies, and to reconstruct past population demographic events. Sex determination is usually based on morphological traits of the skeletons, with the drawback that most methods do not apply to juveniles and require well preserved remains. In cases where morphological methods cannot be used, or are ambiguous, methods of molecular sexing systems are an alternative. In this methodological study we tested and validated the accuracy and usefulness of a molecular sexing method based on the amelogenin gene using pyrosequencing. We did this in a double blind study of documented 18th and 19th century human remains.