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.     

Sex identification from the distal fibula

This study was designed to determine whether the fibula, which is one of the least studied long bones, can provide reliable information for sexing of human bones, provided that one condition is satisfied, namely, its distal end is available for measurement. The materials consisted of the dried fibulae of 71 Japanese males and 35 females whose names, ages and sex were known. The distal end of the fibula was measured with respect to five novel dimensions that are closely related to the soft tissues that had been attached to the bone surface. Highly significant sex differences were found when all parameters examined were considered together. The differences for separate items were not, however, sufficient for sex discrimination. Discriminant analysis was performed using the five parameters and yielded the correct sex with 90. 6 per cent accuracy for the entire group of specimens. This degree of accuracy suggests the utility of the present method for sexing human bones, in particular, in osteoarchaeological situations.     

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.     

Estimating the Age and Sex of Caribou from Mandibular Measurements

Formulae for estimating the age and sex of caribou are derived from measurements taken from a control sample of caribou mandibles collected by the Canadian Wildlife Service. A robust linear relationship was found to exist between first molar crown height and age, while male and female mandibular measurements are statistically distinguishable on either side of a linear regression line. The application of these formulae to three 19th century archaeological assemblages from the western Canadian Arctic indicates their usefulness in estimating the age and sex of fossil populations, although some problems due to geographical variability remain. Tentative results indicate that traditional western Arctic Inuit were unable to exert strong control over the age and sex of the caribou they killed, perhaps because of the use of large-scale communal hunting techniques. This situation seems to have changed radically with the introduction of firearms in the 1870s.     

《小屯南地甲骨》缀合拾遗

本文试缀了三例《屯南》甲骨,并作了释文。     

Sample-specific (universal) metric approaches for determining the sex of immature human skeletal remains using permanent tooth dimensions

In this paper, three approaches for developing sample-specific sex determination methods of immature skeletal remains based on permanent tooth dimensions are proposed and tested using a sample of identified skeletons. The sample comprises adult and subadult individuals selected from the Lisbon documented skeletal collection, housed at the National Museum of Natural History in Lisbon, Portugal. Faciolingual and mesiodistal diameters were the tooth dimensions utilized. In the first approach, sex-specific logistic regression formulae based on adult tooth dimensions are developed and then used to determine the sex of the subadult sample. The second and third approaches are based on the sectioning point procedure, which uses the overall mean of a measurement (tooth diameter) collected from the sample as the discriminant criteria for determining the sex of the individuals in that sample. While in the second approach the adult overall mean of each dimension is used as the discriminant criteria for determining the sex of the subadults, in the third approach it is the subadult overall mean of each dimension that comprises the discriminant criteria that is applied back to the subadults for determining sex. Results show that the canines are the teeth with the highest sexual dimorphism and methods of sex determination based on canine dimensions provide correct allocation accuracies between 58.8% and 100% depending on the diameter and the approach that is being used. Canine faciolingual dimensions provide the best overall results. Combinations of measurements from the same and different teeth do not increase significantly the accuracy of the methods and approaches. Some of the problems of subadult sex determination methods based on adult tooth dimensions result from differing levels of sexual dimorphism between the adult and subadult segment of the sample. Mortality or cultural bias may increase or decrease the sexual dimorphism of the subadults compared to the adults. Small subadult samples utilized in this study may also raise questions regarding the accuracy of the three different sample-specific approaches. However, high consistency of results using the canine and different approaches, suggests that adult and subadult canine dimensions can be reliable sex discriminators of immature skeletal remains in archaeological samples. The major advantage of the approaches presented here is that they can be used to derive sample-specific methods and, therefore, eliminate the problem of applying morphological or metric methods to individuals originating from a population that differs from the one that contributed to the development of the method.     

The ‘invisible’ hearths: a contribution to the discernment of Mesolithic non-structured surface hearths

In the cover sand area of the NW European plain very little is known about fireplaces within Mesolithic settlement areas. Yet the frequent occurrence of burnt ecofacts (hazelnut shells and bone) and artefacts (flint and quartzite) clearly indicates the presence of (surface) hearths on nearly every campsite. Most of these hearths are non-structured and are thus barely visible in the soil. Furthermore in most spatial studies minimal effort has been made to locate these ‘invisible’ hearths as accurately as possible. This paper discusses the potential and modalities of detailed spatial analysis of burnt artefacts and ecofacts, using recently obtained archaeological and experimental evidences. It is concluded that such an analysis can offer interesting insights into the dynamics of Mesolithic hearths.     

A leprous skeleton of the 7th century from Eccles,Kent, and the present evidence of leprosy in early Britain

A male skeleton of 7th century date from the Anglo-Saxon cemetery at Eccles, Kent, is described. Certain skeletal changes associated with leprosy are manifest. The disease is discussed in its palaeopathological context and this case in relation to the few other cases of the disease hitherto diagnosed in Great Britain.     

A Discrete Variant in the Third Plantar Tarsometatarsal Joint: Patterns of Occurrence in a Prehistoric Population from West-central Illinois

A small pit in the articular surfaces of the third tarsometatarsal joint has been noted with particularly high frequency in North American Indians. This pit varies in depth, and covers most of the inferior third of the articular surfaces of the third metatarsal and the lateral cuneiform; it is accompanied by remodelling of the inferior surfaces of the bones involved. In the present study, patterns of occurrence are examined in a prehistoric skeletal population from west-central Illinois. This population is extremely well preserved, enabling a thorough examination of feet as well as hands for most individuals. The sample included 496 adults and juveniles above the age of 6 years. Of this total population, 18 per cent exhibit the variation, which occurs more frequently in females and is unrelated to size. Furthermore, 29 per cent of the individuals in which it occurs exhibit this variant only unilaterally, with no significant side differences. Various lesions, trauma and acquired or activity-related aetiologies are explored, as are the patterns of sex association, occurrence near an area of ligamentous attachment and lack of age and size association. It is hypothesized that a discrete genetic trait is represented in the third tarsometatarsal joint of this population in the form of an anomalous interosseous plantar ligament. © 1997 by John Wiley & Sons, Ltd. Int. J. Osteoarchaeol., 7 : 124–132 (1997) No. of Figures: 3. No. of Tables: 2. No. of References: 26.     

New methods for the identification of evidence for bitting on horse remains from archaeological sites

This article describes alterations to equid lower second premolars and diastemata from a series of known life history equids and a number of archaeological horse specimens from the British Iron Age. Two new methods for recording bit wear are proposed involving the analysis of the extent and morphology of enamel/dentine exposure on the anterior edge of LP2s and analysis of the extent of new bone formation and bone loss to the diastema of the mandible. It is suggested that when a bit is used on a horse it acts more frequently on the anterior margin of the LP2 than has previously been thought and that repeated contact between the bit and the LP2s and diastemata results in recognisable damage to these areas of the mouth.     

MtDNA haplotype identification of aurochs remains originating from the Czech Republic (Central Europe)

Abstract

This study presents the results of the analysis of mtDNA bone samples morphologically determined to be aurochs (Bos primigenius) from four various archaeological finds in the Czech Republic (Central Europe). The results from two of them — the Pleistocene sample from Praha-?eporyje and the Neolithic sample from Vedrovice — probably represent contamination by modern DNA. Sequences identified in the Eneolithic Kutná Hora-Denemark site (～5 thousand BP) confirm the presence of haplogroup P in the geographically partly isolated Czech basin. This finding (the first of its kind within the Czech Republic) is consistent with other published findings showing the domination of this aurochs haplogroup line in Europe. The combination of large individual size and ‘domestic’ mtDNA suggest, if inconclusively, that the Early Medieval fourth sample from Vy?ehrad could potentially represent an aurochs/domestic cattle hybrid.     

Soil chemical identification of ten thousand years of prehistoric human activity areas at the Munsungun Lake Thoroughfare,Maine

Soils on a Palaeo-Indian to historic sequence in one Maine locale are analysed for chemical enrichment. To guide excavation of four discrete sites up to 4000 m², samples are collected in grid patterns and analysed for pH, Mg, P and Ca. Concentrations of Mg point to probable hearths to define some centres of human activity on each site. These correlate well with anomalies determined independently by magnetometric survey. Excavation of anomalies provides evidence of hearths, culturally diagnostic artifacts, but also features resulting from tree-throw and drainage variation. The P and Ca results develop definition and delimitation of activity areas thus refining directions for further excavation. Since P and Ca concentrations result from substantial or sustained human occupation, they show promise for preexcavation differentiation of habitation sites from limited and specialized activity sites such as lithic chipping stations. Soil chemical analysis provides both a synchronic and diachronic preview of site perimeters, size and activity areas. The consistent site definition at the Munsungun Lake thoroughfare is useful for explaining patterns as well as locating them.     

A systematic approach to the recovery and identification of starches from carbonised deposits on ceramic vessels

Starch granules are being successfully recovered from an increasing range of artefacts. Here we present the recovery of starches from carbonised ceramic ‘foodcrusts’ from late Mesolithic–early Neolithic residues at the site of Neustadt in northern Germany. A method for investigating background loading of residues with contaminant starches is proposed by comparing interior ‘foodcrusts’ versus exterior ‘sooting’, for the purposes of eliminating samples with insignificant quantities of grains from subsequent identification procedures. The classification of starches to plant taxon is traditionally achieved by manual observations and measurement of nominal and ratio morphological variables. Here, we present a method for the automated classification of granules, using software developed in-house. The results show that when multiple granules are considered, the species selected as modern reference examples can be classified to high levels of specificity. When applied to the archaeological samples we show that wild plant resources persist in importance across the transition to agriculture, with high proportions of granule forms consistent with acorn (Quercus sp.) occurring in all samples. Hazelnut (Corylus avellana) types are less well-represented suggesting it was not an important food in the context of pottery, and may have been over-represented in the repertoire of hunter–gatherer resources. Cereals are not represented in any of the samples, supporting the notion that their adoption may have been a slow process, occurring more gradually than for other domesticated foods, or that they were not initially processed in ceramic vessels.     

Directional analysis of surface artefact distributions: a case study from the Murghab Delta, Turkmenistan

This paper investigates directional influences in the distribution of Bronze Age surface pottery in the northern Murghab Delta, Turkmenistan. Drawing upon a continuous dataset of pottery sherd counts obtained by intensive field survey, it examines the degree to which we can make sense of the archaeological processes at work in a heavily obstructed and dynamic landscape. In so doing, it makes use of two analytical methods that have rarely been used in archaeology: a) geostatistical analysis using variograms to investigate directional spatial autocorrelation in recorded sherd counts; and b) angular wavelet analysis in evaluating directional influences in the sherd distributions for particular chronological periods. While some kinds of directional influence can be identified visually, a quantitative approach is particularly useful in deconstructing such patterns. In this particular dataset, distinct but related directional processes can be identified and measured: a) the impact of the complex system of watercourses in the delta on both settlement and post-depositional processes; and b) recovery bias in the observations made during survey.     

Information obtained from the microscopic examination of cultural striations in human dentition

The surfaces of teeth from some fossil remains and archaeological samples have been examined by SEM, in order to study different types of cultural striations and to determine the archaeological information that these striations can provide. Different patterns of cultural striations are present in human samples from different sites and periods. Similar cultural striations can be interpreted in different ways, depending on the tooth in which they are present, their location in the tooth and their direction, regularity, number and width. The study of cultural striations can yield valuable information about different aspects of feeding behaviour, oral hygiene, patterns of cultural diffusion and manipulative work with teeth of past human groups. A close integration with other anthropological and archaeological data is needed and specific interpretations should be made in each case.     

Desiccated plant macrofossils from the medieval castle of Marmorera,Switzerland, with a note on the identification of leaves of Cyperaceae

Abstract

During restoration work at the medieval castle of Marmorera, Graubünden canton, Switzerland, numerous desiccated plant remains were found — in a rock crevice that was protected from precipitation by a massive rock shelter. The identification of the remains showed that the majority could not have grown at the castle, but must have been transported to the site. Many of the plants came from warmer climates and were imported from lower lying regions, indicating the position of the castle at an important transalpine route. Among the finds was a lump of grass-like leaves for which for a method of preparation and identification was developed. The leaves turned out to be of Carex species that grow in wet habitats which were probably used as litter or as bedding material.     

A dental study comparing age estimations of the human remains from the Swedish warship Vasa

The great Swedish warship Vasa capsized and sank in Stockholm harbour on her maiden voyage in 1628. The ship was raised from the seabed in 1961 and skeletal remains were recovered from at least 25 individuals, with teeth and jaws from 17 of them. The skeletal material was odontologically examined, including dental radiographs. Teeth lost both ante‐mortem and post‐mortem were recorded and variations in tooth anatomy noted. Acquired changes were recorded including enamel hypoplasia, attrition, dental caries and periodontal recession. Age estimations based on a separate odontological study, osteological changes and tooth attrition had been made in 1989. Ages were estimated additionally by three non‐destructive dental methods based on (a) the length of the apical translucent zone, (b) selected measurements both on intact teeth and from ratios on dental radiographs and (c) ratios of the length and width measurements on dental radiographs from selected teeth. Several sources of post‐mortem changes had been observed, among them vivianite in 33 teeth from four individuals. The results of the dental examination showed that few teeth had been lost ante‐mortem, there was a low caries rate and little loss of periodontal attachments. With few exceptions, there is fairly good agreement between the different methods of estimating age. Age estimates based on dental attrition were, however, significantly different from the other dental methods and age estimates calculated from apical translucency ought to be regarded with scepticism due to post‐mortem changes. The chronological ages of the victims will never be known, but age estimates based on all the age‐markers available will probably reach a fairly close approximation. Copyright © 1999 John Wiley & Sons, Ltd.     

Interpretative scenarios emerging from plant micro- and macroremains in the Iron Age site of Salut,Sultanate of Oman

The archaeobotanical research carried out in the Iron Age site of Salut (north Oman) gives insights on various interpretative scenarios: the ancient vegetation surrounding the site, oasis farming, and possible ritual practices. The landscape was dominated by dry shrublands with, among others, acacia, jujube and tamarisk that were exploited for obtaining timber and firewood. Agricultural practices mainly consisted of date palm, cereal and sesame cultivation. By comparing the datasets it was possible to assess that the date palm had various uses in this site: one hypothesis involves its offering in ceremonial practices. This third scenario suggests a new way of interpreting some of the plant remains in an archaeological site as Salut, a multipurpose site including a possibly cultic function.     

Relative and absolute dating of the human skull and skeleton from Galley Hill,Kent

Over a period of some 100 years it has gradually been accepted that the human skeletal remains found in the late nineteenth century in ancient gravels at Galley Hill, Kent are not those of early man, but are of much more recent date. This conclusion was finally verified by means of relative (N, F) and absolute (¹⁴C) dating. Here we present the results of further analysis of the remains from Galley Hill for their uranium content by a method having general application to the relative dating of fossil human and other mammalian bone.