A new miniSTR heptaplex system for genetic fingerprinting of ancient DNA from archaeological human bone

The analysis of short tandem repeats (STRs) is a useful tool in various contexts of ancient DNA research. Main applications are the reconstruction of kinship, identification, and authentication. Here we describe a short amplicon autosomal short tandem repeat (miniSTR) heptaplex system for the amplification of D13S317, D21S11, D18S51, TH01, D5S818, FGA and Amelogenin from highly degraded DNA as an inexpensive alternative to commercially available kits. All primers were newly designed and the amplicon length of all systems is less than 200 bp, with the exception of some rare alleles in the FGA and D21S11 systems. To validate the suitability of this system for typing STRs from human specimens with low DNA preservation we systematically tested it on 20 skeletal samples from four archaeological sites representing different burial environments and time spans since death. Finally, to test the sensitivity of the heptaplex system, we analyzed serial dilutions of control DNA and ancient DNA extracts. Using the system we were able to reproducibly obtain full STR profiles, down to a concentration of 0.06 ng DNA. Even with 0.004 ng DNA partial profiles could be amplified. The accumulated power of discrimination for the six selected STR loci is 0.99999984, plus the option of genetic sex determination through Amelogenin. The tests conducted prove that the system presented is efficient and especially suited for cases where STRs have to be typed and sex has to be assessed from human specimens with highly degraded DNA.     

Diet and death in times of war: isotopic and osteological analysis of mummified human remains from southern Mongolia

This study presents the results of an isotopic analysis of nine naturally mummified individuals—three adults, two adolescents, one juvenile, and three infants—recovered from the Hets Mountain Cave site in southern Mongolia, where they had been secondarily deposited. All of the individuals show evidence of violent perimortem trauma, but no skeletal indicators of nutritional or disease-related stress. Multi-isotopic data (δ¹³C, δ¹⁵N, δ¹⁸O, ⁸⁷Sr/⁸⁶Sr, and ²⁰ⁿPb/²⁰⁴Pb) were characterized in multiple tissues from each individual when possible, in order to reconstruct diet composition and residential origin at different points in life. Specifically, δ¹³C and δ¹⁵N in bone carbonate and collagen (N = 8) and hair keratin (N = 4) were coupled with enamel carbonate δ¹⁸O and δ¹³C (N = 3) and enamel ⁸⁷Sr/⁸⁶Sr, and ²⁰ⁿPb/²⁰⁴Pb (N = 3) to assess diet and residential mobility in relation to skeletal indicators of health and trauma. Results are consistent with a persistence of mixed C₃/C₄ pastoral subsistence and general stability of diet composition over the life course, in contrast to contemporary accounts of widespread famine and a dependence on grains imported from China throughout the region. However, results also suggest that at least some individuals may have migrated to this region of southern Mongolia from elsewhere during life, meaning that their dietary isotopic profiles may not represent local subsistence patterns near the Hets Mountain Cave site. Overall, these results speak to the utility of life course oriented multi-isotopic analysis in complementing more top-down historical analyses in understanding variation in subsistence, nutrition, and migration in regions undergoing significant political and economic turmoil.     

Molecular and morphological analyses of avian eggshell excavated from a late thirteenth century earth oven

Using ancient DNA (aDNA) extracted from eggshell of the extinct moa (Aves: Dinornithiformes) we determined the species composition and number of eggs found in a late thirteenth century earth oven feature at Wairau Bar (South Island, New Zealand) – one of New Zealand’s most significant archaeological sites. Mitochondrial and nuclear DNA signatures confirmed this oven feature contained fragments of at least 31 moa eggs, representing three moa genera: Emeus; Euryapteryx; Dinornis. We demonstrate through the genetic identification of 127 moa eggshell fragments that thickness is an unreliable character for species assignment. We also present a protocol for assessing the preservation likelihood of DNA in burnt eggshell. This is useful because eggshell fragments found in archaeological contexts have often been thermally modified, and heat significantly increases DNA fragmentation. Eggshell is widely used in radiocarbon dating and stable isotope research, this study showcases how aDNA can also add to our knowledge of eggshell in both archaeological and palaeoecological contexts.     

Histomorphometric analysis of bone tissue from a neolithic skeleton

The histomorphometric analysis of neolithic bone tissue from the radiomorphometricly unaffected 9th thoracic vertebral body of a 20–25 year old man showed significantly elevated bone volume in comparison to the contemporary findings (BV/TV, 28.72% versus 20%). Also the number of trabeculae was clearly higher (Tb.N.: 17.7 cm versus 5.4 cm). The mean width (Tb.Th.) of the plate-shaped trabeculae was 160 μm and 180 μm. Thus, they were significantly wider than current normal findings of 120 μm. These results show a structural, obviously multifactual caused degeneration of spongy bone within the last 6200 years, representing a relatively short period in relation to evolutionary criteria. With regards to the irretrievable loss of preserved bone substance the indication to histomorphometric diagnostic has to be restricted; tissue sampling is only to happen after the carrying-out of all possible non-invasive methods of investigation as well as a comprehensive photo and film documentation. Observing these conditions further fundamental findings for the evolution of bone tissue can be expected through histomorphometry.     

Mitochondrial DNA from 3000-year old chickens at the Teouma site,Vanuatu

Chickens were part of the Lapita cultural complex, transported into and through the Pacific by prehistoric colonists; as such they can be used as a proxy for tracking prehistoric migration and interaction. The Lapita site of Teouma in Vanuatu is well known for the recovery of complete dentate stamped pots and a cemetery containing the largest collection of Lapita period skeletons ever found. Chicken bones recovered from these excavations provide the first ancient DNA sequences from any commensal organism directly associated with a Lapita context. The ancient mtDNA sequences obtained from two Teouma chicken bones are compared with previously published archaeologically derived ancient DNA sequences to extend our understanding of the spread of chickens in Pacific prehistory. The results also show that the haplogroup E signature was present in very early populations of chickens transported into Remote Oceania. This study also adds to the suite of available data relating to isotopic signatures for commensal animals during the early settlement of Vanuatu and may reveal a different diet for Teouma chickens than those from other early prehistoric assemblages in the Pacific.     

Biofilm growth in human skeletal material from ancient Mesopotamia

Investigators have long recognised the effects of microbial activity on archaeological bone. These investigators, however, have focused on single or groups of microbes rather than on complex microbial aggregates such as biofilms, a focus that has affected our understanding of archaeological bone biodeterioration. In this paper, we report on the investigation of a biofilm in archaeological human bone from the site of Tell Leilan, Syria (2900–1900 BCE). Scanning electron microscopy indicated that the biofilm is characterised by single cells and microcolonies of bacteria and fungi, as well as calcite crystals that were all embedded within extracellular polymeric substances. Using culture techniques and DNA sequencing, we isolated and identified several microbes from the biofilm including Amycolatopsis sp., Penicillium chrysogenum, Aspergillus sp., Chaetomium sp., and Cladosporium sp. Having characterised the Leilan biofilm, we are now closer to understanding the complex process of bone biodeterioration in archaeological bone collections.     

Raman microprobe analysis of stucco samples from the buildings of Maya Classic Copan

Micro-Raman spectroscopy has been applied to painted stucco samples from three buildings at the Maya site of Copan, Honduras. The buildings, Clavel (AD 450–550), Ani (AD550–650) and Structure 10L-22 (AD730,) date from three phases of the Classic Period (AD400–820) acropolis construction. The red pigment has been identified as haematite and the stucco as a mixture of calcite particles dispersed throughout a calcite based lime wash stucco. The physical structure of the stucco changed through time, indicating a refining of production techniques over this period. By combining Micro-Raman spectroscopy with other micro-ATR infrared spectroscopy and environmental scanning electron microscopy a detailed investigation of the materials and production techniques used to decorate these buildings has been made. Differences in the mineralogy of the red pigment used on each building indicate a different geological pigment source for each period.     

Charcoal analysis and dendrology: data from archaeological sites in north-western France

During the last 15 years, charcoal analysis of archaeological sites in north-western France has been carried out in conjunction with systematic and detailed dendrological examination. By considering these extrinsic criteria in association with the analytical results, palaeo-ethnographic and palaeo-environmental information can be obtained. The charcoals are classically identified under the microscope on the basis of their cellular structure. This examination is associated with an observation of the ligneous structure on transverse sections using a binocular lens. When charcoal fragments are large enough, the growth ring widths are measured. Tree ring curvature is also noted. Finally, alteration by fusion or radial cracks, the presence of fungal hyphae, and insect degradation are also recorded. Results are thus obtained on the nature of fuel used in domestic fireplaces and kilns. The selection of timbers and their catchment areas are also revealed. The average width of the growth rings in oak charcoal from domestic hearths coming from about forty sites in north-western France shows a significant increase from 6000 to 2000 BP. There is a similar increase in the number of heliophilic taxa used from the Neolithic to the Iron Age. This implies that the environment became more and more open because of use by society. The interpretation of the dendrology results applied to charcoal analyses is obtained through a convergence of criteria. Thus, charcoal analysis can provide more than just an identification of the species used, and can yield fundamental information on the interaction of society with the environment.     

“汉代城市和聚落考古与汉文化国际学术研讨会”纪要

城市是一个国家或地区的政治、文化中心和经济管理、军事指挥中心,是人类文明的集中体现,对古代城址进行发掘和研究历来是考古学的基本内容及重要任务之一。聚落一般指人们聚居的地方,是生产、生活等各种活动的空间及场所。广义的聚落包括城市,     

Immunological diagnosis of multiple myeloma in a medieval bone

An inhibition enzyme-linked immunosorbent assay using monoclonal antibodies has been used to confirm the diagnosis of IgA type multiple myeloma in a small fragment (< 10 g) of cranium from a medieval female. Further testing by sodium dodecyl sulphate-polyacrylamide gel electrophoresis and immunoblotting showed that the IgA was mainly polymeric, suggesting that the individual would have suffered from a hyperviscosity syndrome. This is the first time that immunological assays have been used to diagnose multiple myeloma in ancient human tissue and have permitted speculation on associated clinical symptoms.     

Neutron activation analysis of stone from the Chadron Formation and a Clovis Site on the Great Plains

Cryptocrystalline silicates from the Chadron Formation were widely used by prehistoric human groups in the Great Plains of North America. There are two documented quarry areas: Flattop Butte in Colorado and the White River Badlands of South Dakota. Cryptocrystalline silicates from these sources are visually indistinguishable, making it difficult to determine the sources of artefacts found at archaeological sites. In this investigation, neutron activation analysis is used to distinguish the two sources. This technique also identifies lithic material from the Clovis-age Eckles site in Kansas as being from Flattop Butte.     

Confocal laser scanning microscopy: a flexible tool for simultaneous polarization and three-dimensional fluorescence imaging of archaeological compact bone

Wide-field polarized light and epifluorescence microscopy have been used to enhance analysis of archaeological bone tissue, providing information on bone formation, modeling, pathology, preservation, age estimation, and biomechanics. Though valuable, these techniques are limited by their inability to remove out-of-focus light and view multiple levels of a sample, restricting our understanding of the three-dimensional (3-D) microarchitecture of compact bone. Modern technological advances, such as microscopic computerized tomography, allow increasing resolution in 3-D bone imaging, but do not allow fluorescence labeling or polarized-light analysis. Confocal laser scanning microscopy (CLSM) is a valuable tool for 3-D histology. However, its application to the study of compact bone is lacking, especially in archaeological and forensic sciences. The current study investigated CLSM as a tool for fluorescence and polarized-light microscopy of archaeological compact bone in order to demonstrate its advantages. Standard techniques and CLSM are compared in their suitability for imaging well preserved archaeological bones from the Dakhleh Oasis, Egypt. CLSM's high resolution, multi-channel, two- and three-dimensional capabilities augment the flexibility and creativity of compact bone imaging and have the potential to increase the accuracy of quantitative medical and anthropological histomorphometric techniques. CLSM is specifically suggested as a useful tool for the investigation of ancient bone fluorescence caused by the presence of tetracycline and/or other fluorochromes.     

In situ oxygen isotope micro-analysis of faunal material and human teeth using a SHRIMP II: a new tool for palaeo-ecology and archaeology

A Sensitive High Resolution Ion MicroProbe (SHRIMP II) has been used to make high spatial resolution in situ micro-analyses of oxygen isotopes in fish otoliths, and teeth from fossil herbivores and a Neanderthal. Large intra-tooth variations in the oxygen isotopic composition (up to 9‰) were observed in the enamel of herbivores from the Neanderthal fossil site of Payre, consistent with preservation of seasonal cyclicity. The range of isotopic compositions observed in Neanderthal tooth enamel was much smaller (∼3‰), possibly the result of a longer enamel maturation time averaging out variability. An archaeological otolith from a Preceramic site in Northern Peru exhibited marked changes in δ¹⁸O over life, due either to the fish occasionally migrating from the sea to a lower salinity habitat, or to short-lived rises in sea water temperature. A fish otolith from Australia's Willandra Lakes World Heritage Area showed clear seasonal variations, but also a general trend towards isotopically heavier and more saline water, as indicated by higher δ¹⁸O and Sr/Ca values resulting from increased evaporation. The results of these case studies are compared to results of oxygen isotope analysis using more conventional methods and demonstrate the ability of the SHRIMP II to provide precise high spatial resolution in-situ oxygen isotope analyses of a variety of biogenic materials. This approach has major advantages over conventional methods. It can provide rapid, micro-scale isotopic analyses of sub-permil precision without the need for chemical preparation of the sample.     

唐宋墓葬出土陀罗尼经咒及其民间信仰

唐宋墓葬中出土有一种陀罗尼经咒,它往往以特殊的佩戴方式与死者伴出。通过对考古出土的这类材料进行综合研究,认为其与唐宋时期持明密教在中土的流行有关,同时也与中国传统文化中的咒术、避邪等方术相互结合,形成唐宋之际民间信仰的一种新的表现形式。     

Methods for the extraction of archaeological features from very high-resolution Ikonos-2 remote sensing imagery,Hisar (southwest Turkey)

Archaeological research in the territory of Sagalassos is a multidisciplinary project covering scientific disciplines traditionally linked to archaeology and also new technologies such as very high-resolution remote sensing with sufficient radiometric and spatial resolution (<2.5 m). This paper focuses on the evaluation of GIS-, pixel- and object-based techniques for automatic extraction of archaeological features from Ikonos-2 satellite imagery, which are then compared to a visual interpretation of ancient structures. The study was carried out on the unexcavated archaeological site of Hisar (southwest Turkey). Although all techniques are able to detect archaeological structures from Ikonos-2 imagery, none of them succeed in extracting features in a unique spectral class. Various landscape elements, including archaeological remains, can be automatically classified when their spectral characteristics are different. However, major difficulties arise when extracting and classifying archaeological features such as wall remnants, which are composed of the same material as the surrounding substrate. Additionally, archaeological structures do not have unique shape or colour characteristics, which can make the extraction more straightforward. In contrast to automatic extraction methods, a simple visual interpretation performs rather well. The methods presented in this paper can be applied with variable success to archaeological structures composed of the same material as the surrounding substrate, which is often the case.     

Extended depth of focus image for phytolith analysis

This paper proposes a new phytolith analysis method by extended depth of focus technology. The extended depth of focus image is sharp throughout by the image processing of a series of photos, while each acquisition of the original photo will be compromised and show certain parts of the specimen in and out of focus. Consequently, the extended depth of focus image is suitable for computer-assisted morphometrics analysis. Meanwhile, the extended depth of focus image can be used for three-dimensional reconstruction images. Experiments on rice husk multi-cell panel show that the three-dimensional reconstruction image method can reconstruct multiple double-peaked phytoliths at one time. We also measure the parameters of multiple double-peaked phytoliths from the reconstructed three-dimension image. Comparative experiments show that the reconstructed three-dimensional image is precise enough for rice identification. Based on the above experiments, we recommend the extended depth of focus method as a promising tool in phytolith research.     

DNA analysis of archaeological sheep remains from China

Recent research has thrown considerable light on the history of the domestic sheep, but has not extended to ancient sheep specimens. In the present study, ancient DNA analysis was carried out on eight archaeological sheep remains recovered from Erlitou archaeological site in Henan Province (ca. 2100–1800 B.C.) to explore the genetic structure of ancient sheep and the phylogenetic relationship between ancient and modern sheep. We analyzed the control region sequences and coding regions of mitochondrial DNA from the remains by direct sequencing and restriction fragment length polymorphism analysis, respectively. Our results reveal that all ancient sheep belong to lineage A defined by modern sheep sequences. Phylogenetic analysis shows that neither argali (Ovis ammon) nor urial (Ovis vignei) mtDNA is closely related to Erlitou ancient sheep. In addition, our results suggest that ancient DNA analysis can serve as a powerful tool in tracing prehistoric population movement.     

Effects of site lithology on geochemical signatures of human occupation in archaeological house plans in the Netherlands

This study presents the application of multi-element soil analyses (X-ray fluorescence spectroscopy and inductively coupled plasma optical emission spectroscopy of 1 M HCl extracts) to grid samples from 3 archaeological house plans embedded in sandy clays, clays and sands to assess effects of site lithology on geochemical signatures of human occupation.     

Geochemical composition of source obsidians from Kenya

Here we provide a reference resource to archaeologists interested in the sources of obsidian in Kenya, through electron microprobe analyses of 194 obsidian samples from 90 localities. Averaged analyses of each sample and eleven published analyses are categorized into 84 compositional groups of which only about 21 are known to have been used to produce artifacts, possibly because studies of artifactual material in the region are lacking. We also provide trace element analyses determined by XRF and LA-ICP-MS for these same obsidians. In northern Kenya 27 distinct compositions of obsidian have been found, including some of Miocene age, but the source of the most abundant obsidian found in archaeological sites in this part of Kenya remains obscure. The Baringo region contains at least 13 varieties of low-silica obsidian. The Naivasha–Nakuru region contains an abundance of obsidian with 38 compositional types recognized, and is the only region in Kenya apart from the Suregei (northern Kenya) that contains rhyolitic obsidian. Nine compositionally distinct types of obsidian are known from southern Kenya. Although Kenyan obsidians span the compositional range from phonolite to rhyolite, low-silica, nepheline-normative obsidians occur only south of 1°N latitude. One obsidian type, the Lukenya Hill Group, appears to have been derived from a regionally extensive ash flow tuff with a distribution of over 8000 km². From previous studies it is known that obsidians of lowest (Mundui) and highest iron content were used for tool manufacture, as were some obsidians (e.g., Kisanana) with the highest alkali content, and obsidians with both high (Njorowa) and low (Kisanana) silica content.     

Ancient DNA in human bones from Neolithic and Bronze Age sites in Greece and Crete

Attempts were made to detect ancient DNA (aDNA) in samples of 88 human skeletons from eight Neolithic and Bronze Age sites in Greece and Crete. Ancient DNA was absent in specimens from Nea Nikomedia, Lerna, Karaviádena (Zakro), Antron Grave Circle A and Mycenae Grave Circle A. For each of three skeletons from Antron Grave Circle B that were sampled, polymerase chain reactions (PCRs) gave products for nuclear but not mitochondrial DNA, but amplicon yield was low and inconsistent with replicate PCRs failing to give reproducible results. With specimens from Mycenae Grave Circle B, evidence for mitochondrial aDNA was obtained for four of the 22 skeletons that were studied, and at Kouphovouno evidence for mitochondrial and/or nuclear aDNA was obtained with eight of the 20 skeletons that were examined. We conclude that, although aDNA might be present in some Eastern Mediterranean skeletons from later centuries of the Bronze Age, it is not commonly found in material from this period and is likely to be absent from older material.