Assessing the distribution of African Palaeolithic sites: a predictive model of collagen degradation

In order to assess the distribution of African Palaeolithic sites and hominin remains, we need an understanding of the factors that may affect the preservation of archaeological material in the fossil record. One of the main factors that is thought to affect seriously the global distribution of fossil remains is taphonomy, but it would seem that taphonomic processes may themselves be overprinted by collagen degradation.The rate of collagen loss is highly temperature dependent, and it has been shown that bone is more likely to be preserved in areas of lower temperature and so lower collagen loss. Hence, it would be expected that fossil fauna remains would be distributed in areas of low collagen loss, i.e. low temperature. Conversely, lithics will not be subject to a temperature bias in their preservation. We have tested this hypothesis through the use of archaeological material.Our results show that the distributions of both lithic and faunal assemblages are non-random across the African continent, with all archaeological sites being found in areas of relatively low collagen degradation. This implies that bone collagen degradation is not the only factor affecting the distribution of African Palaeolithic sites and hominin remains. We suggest that the site distribution is not a reflection of bias in excavation history, but is a real phenomenon reflecting hominin habitat choice.     

Comparative human and deer (Odocoileus virginianus) taphonomy at the Richards site,Ohio

The Richards site is attributed to the Philo phase of the Fort Ancient tradition of the Ohio Valley area. Human skeletal material from the site shows evidence of peri‐ and post‐mortem taphonomic changes, including cut marks, burning and fracturing. Previous analyses have discussed explanations for these changes, including secondary burial, ritual destruction and cannibalism. Researchers have theorised that, allowing for differences in anatomy among species, humans and animals butchered for the same purpose (consumption) will show similar patterns of taphonomic changes associated with butchery. The human remains at the Richards Site were disposed in general midden pits containing mixed cultural debris and faunal remains. White‐tailed deer (Odocoileus virginianus) constitutes approximately 60% of all the faunal bone, indicating that it was a major food resource. To test a cannibalism explanation, a comparative analysis of human‐induced taphonomy in human and deer skeletal remains was performed, using chi‐square and odds ratio tests. If humans were being used as a food resource, the pattern of butchery seen would mirror that of the deer. The analysis described here compares the patterns of treatment and disposal of human and deer skeletal elements at the Richards site, to test whether both species were used as food resources. Similar types of evidence for human‐induced taphonomic changes, including cutting, chopping, burning and breakage, can be seen in both species. However, results indicate that, in general, human remains show much more evidence of perimortem treatment than do deer remains. In fact, the common odds ratio for perimortem treatment in all bones is 3.25, indicating that a human bone is 3.25 times as likely as a deer bone to be affected by burning, cutting or chopping. This probably indicates that perimortem treatment of humans was greater than that necessary simply for butchering for consumption. Copyright © 2005 John Wiley & Sons, Ltd.     

Pick the Right Pocket. Sub‐sampling of Bone Sections to Investigate Diagenesis and DNA Preservation

Many archaeological bones display a heterogeneous degradation pattern. Highly degraded bones could contain pockets of well‐preserved bone, harbouring good quality DNA. This dichotomy may explain why the relationships between global bone preservation parameters such as histological integrity, bone mineral crystallinity or collagen yield, and bulk DNA preservation/amplification success rate have been found to be at best, weak to moderate. In this pilot study, we explore whether or not a more localised approach will highlight a stronger relationship between diagenetic parameters and DNA preservation. This study includes a detailed histological characterisation of bone diagenesis in sub‐areas of three bone samples. Regions of the same bone, which displayed differential degrees of preservation or type of diagenesis were sampled for further analysis and both genetic (small scale Illumina MiSeq sequencing) and chemical (Fourier‐transform infrared spectrometric analysis) analyses were performed. The aim was to investigate how bone diagenetic processes relate to DNA preservation at a higher resolution than in previous studies. This is key in order to improve DNA analytical success rates. The expected relationship between bone and DNA preservation (retrieved endogenous DNA) was observed and the results corroborate previous work that DNA preservation is linked to the integrity of bone collagen and mineral. The results further suggest that non‐biological diagenetic alterations such as etching and the presence of mineral infiltrations and inclusions have a negative effect on DNA preservation/extraction. Copyright © 2016 John Wiley & Sons, Ltd.     

Taphonomy and zooarchaeology of the Upper Palaeolithic cave of Dzudzuana,Republic of Georgia

We present the results of a detailed taphonomic and zooarchaeological study of the faunal remains from the Upper Palaeolithic layers of Dzudzuana Cave, Republic of Georgia. This study presents the first carefully analysed Upper Palaeolithic faunal assemblage from the southern Caucasus and thus serves as a significant point of reference for inter‐regional studies of Upper Palaeolithic subsistence in Eurasia. A series of intra‐site taphonomic comparisons are employed to reconstruct the depositional history of the bone assemblages within the different occupational phases at the site and to investigate subsistence, meat procurement and bone‐processing strategies. Caucasian tur (Capra caucasica), aurochs (Bos primigenius) and steppe bison (Bison priscus) were the major prey species throughout the Upper Palaeolithic. Their frequencies do not change significantly over time, and nor does bone preservation vary by layer. The assemblage is characterised by significant density‐mediated biases, caused by both human bone‐processing behaviours and in situ post‐burial bone attrition. Bone marrow extraction produced large numbers of unidentified bone fragments, many exhibiting green bone fractures. The density and size of bone assemblages and the extent of fragmentation indicate that Dzudzuana Cave was repeatedly occupied by Upper Palaeolithic foragers over many years. Skeletal part representation and butchery marks from all stages of carcass processing suggest that prey occasionally underwent field butchery. Intra‐site taphonomic comparisons highlight uniform patterns of cultural and economic behaviours related to food procurement and processing strategies. Copyright © 2007 John Wiley & Sons, Ltd.     

Urban small vertebrate taphonomy: a case study from Anglo–Scandinavian York

Sampling of deposits at the Queens Hotel site, York, produced a substantial number of small terrestrial vertebrate remains from the Anglo–Scandinavian features. By studying bone surface modification, fragmentation and skeletal completeness as taphonomic indicators, it was possible to demonstrate that the assemblage had resulted from two very different modes of accumulation and deposition. Refuse pits situated within the boundaries of the tenements had acted as accumulators of the fragmented and abraded small mammal and amphibian bones that existed as a sub‐surface death assemblage within the local environment. In contrast, the excellent preservation and skeletal completeness of numerous frogs recovered from the basal fill of a wooden well could be accounted for by their direct entry into the burial environment as a result of pit‐fall trapping. This paper also discusses the implications that the temporal and spatial variation in deposition demonstrated by the micro‐faunal remains has for the reconstruction of local ecological and environmental conditions within this site, and for other such sites. Copyright © 2001 John Wiley & Sons, Ltd.     

Estimating the magnitude of data asymmetry in palaeozoological biogeography

Palaeozoological data are asymmetrical because they indicate the presence of a species in the area in which its remains are recovered, but the absence of remains is not necessarily evidence for the absence of a species. It is impossible to measure the magnitude of data asymmetry with respect to biogeography, but the magnitude can be estimated. The proportion of sites in an area where a species is known to occur that have not produced remains of that species is an estimate of counter‐ubiquity. The proportion of identified faunal remains in an area where a species is known to occur that do not represent that species is another estimate of data asymmetry. Bivariate plots of the number of sites in an area that have produced remains of a taxon against the total number of faunal remains identified in the area indicate that data asymmetry can be estimated as the inverse of sample size. More sites and more identified faunal remains tend to produce more occurrences of a species, so more sites and more identified faunal remains will tend to provide a database that is not only more accurate but also less asymmetrical with respect to the geographical range of a species. Copyright © 2007 John Wiley & Sons, Ltd.     

Using microscopy to improve a diagnosis: an isolated case of tuberculosis‐induced hypertrophic osteopathy in archaeological dog remains

The use of histology to estimate age, understand taphonomic history and diagnose disease in human skeletal and mummified remains is a well‐known method. Even though non‐human animals experience stress and disease similar to humans, microscopy is rarely applied to faunal remains to obtain a diagnosis. Histological results from a 16^th‐century Iroquoian dog which had previously been diagnosed by macroscopic and molecular methods with tuberculosis‐induced hypertrophic osteopathy (HPO) are presented here. Comparisons indicate that canid microscopic skeletal manifestations of HPO are reminiscent of human alterations caused by this condition. In addition, the microscopy reveals an aggressive form of HPO that was chronic in nature which could not be identified by either macroscopic or molecular methods. By providing an extension to the original diagnosis, the impact of a chronic case of tuberculosis is discussed. This study helps to emphasise the utility of palaeohistopathology in both biological anthropology and zooarchaeology, as it allows for a deeper discussion of the manifestation of HPO and the impact of tuberculosis on both dogs and humans. Copyright © 2008 John Wiley & Sons, Ltd.     

Stable isotope analysis of prehistoric populations from the cemeteries of the Middle and Lower Dnieper Basin,Ukraine

This paper presents the results of new stable isotopes (carbon and nitrogen) analysis of human, faunal and fish remains from thirteen cemeteries from the Middle and Lower Dnieper Basin, Ukraine. The results are integrated with earlier analyses, undertaken solely on human samples, in order to provide a comprehensive overview of subsistence across the Upper Palaeolithic through to Eneolithic periods in this region. This is the first time that a combined sample of human, faunal and fish remains has been studied in order to interpret subsistence strategies across these periods in Ukraine. The total dataset comprises 113 samples of human, faunal and fish remains, 59 of which include new analyses of faunal and fish remains that have not previously been made available for study (Table 1). The analysis of the faunal and fish remains allows for a consideration of trophic levels which indicates that the consumption of freshwater fish occurs from the Epipalaeolithic period onwards. Whilst the majority of the cemeteries and the individuals therein cluster in relatively tight groups, there is a significant offset between the human and faunal samples due to the consumption of freshwater resources. The fish samples analysed in the study appear to exhibit a relatively random distribution when compared to the other samples analysed. In general, freshwater resources remain significant through until the end of the Neolithic period and into the Eneolithic period at the sites investigated.     

Taphonomy,life history,and human exploitation of Rhinoceros sinensis at the Middle Pleistocene site of Panxian Dadong,Guizhou, China

Rhinoceros remains are commonly found in Chinese Pleistocene archaeological localities. This study examines the characteristics of the Rhinoceros sinensis sample from Panxian Dadong, a karst cave in the mountains of western Guizhou province, with a mammalian fauna in association with stone artefacts and human remains from the late Middle Pleistocene (MIS 6‐8). The distribution of skeletal elements shows a predominance of foot (metapodial and phalanges) and lower limb (carpals and tarsals) bones, while the dental age‐at‐death profile, constructed using dental eruption and tooth wear data, is characterised by a high frequency of prime age adult teeth. There is little taphonomic evidence for the involvement of non‐human carnivores or natural agencies in the formation of the faunal assemblage. Instead, it appears that human activities were responsible for the unexpected prevalence of prime age adults. Copyright © 2008 John Wiley & Sons, Ltd.     

Understanding faunal contexts of a complex Tell: Tel Dor, Israel, as a case study

The complex stratigraphy of the large Levantine tells and the complexity of human behavior that took place on them, poses a major challenge in understanding site formation processes and their reflection in the faunal remains. We studied the contextual deposition of faunal remains in Tel Dor, as a model for complex tell sites, and the possibility of using faunal remains as a tool to distinguish between context types. In addition, we asked how can we use this knowledge to elucidate site formation processes. Our results demonstrate that most loci defined in the field as primary refuse or purposive disposal are indeed different from the loci defined as secondary refuse. Different types of contexts can be differentiated, to a degree, from one another based upon multivariate analysis of faunal remains. Statistical as well as spatial analyses may help elucidate site formation processes and the use of space. Bones can, and in many cases do, reflect primary activities. Lumping zooarchaeological data into a single ‘assemblage’, as done in most zooarchaeological studies today causes major loss of information. Consideration of the specific location of faunal remains can be used as further indication for context identity and for understanding specific activities in a site, with care this can be done even in complex sites such as the ‘urban mounds’ of the Levant.     

Assessing the reliability of pRIA for identifying ancient proteins from archaeological contexts

The use of immunological techniques for identifying the origin of proteins and inferring foodstuffs exploited by prehistoric occupations has been conducted for several decades. Cases of experimental laboratory and archaeological studies have shown the potential of these techniques for reliable results. However, very few of these case studies employ archaeological sites that have excellent preservation and high-resolution spatial contexts between identifiable faunal remains, features, and stone tools. We present an assessment of the identification reliability of one immunological technique, protein radioimmunoassay (pRIA), using faunal remains and stone tools from two sites from arctic and subarctic contexts. The results of this research indicate that, even in contexts with excellent preservation, the identifications produced by the pRIA technique are subject to misidentification and cross-reactions due to diagenetic alteration of proteins. We propose a higher minimum reaction value (percent binding of labeled antibody) that mitigates these effects, and renders the pRIA results more reliable for ancient, poorly preserved organic remains.     

Age‐at‐Death Estimates from a Disarticulated,Fragmented and Commingled Archaeological Battlefield Assemblage

Estimation of age‐at‐death is an important and challenging part of any investigation of human remains. Extensive research has been undertaken on this subject as demographic information contributes much to bioarchaeological and forensic work. Disarticulated, fragmentary and commingled human remains occur from a wide range of spatial and temporal contexts, and estimation of age‐at‐death can be particularly challenging in these collections. This study evaluated the impact of preservation on techniques that might be applied and their relative utility, using human remains from the site of the Smith's Knoll associated with the Battle of Stoney Creek, a War of 1812 collection from Ontario Canada with some supporting documentary evidence on age‐at‐death. Features assessed were the pubic symphysis, auricular surface and epiphyseal fusion in the innominate. An age‐at‐death estimate was produced for 16 out of 19 individuals considered; the highest minimum number of individuals (MNI) was 24 (right radius) from 2701 identifiable fragments. The pubic symphysis made no contribution to construction of a demographic profile, but as has been suggested previously epiphyseal fusion was useful in this respect. Results demonstrate that previous statements regarding preservation of the auricular surface and its utility in fragmented and poorly preserved collections need to be carefully evaluated. Although 129 fragments of innominate were recorded just one had an auricular surface and post auricular area that could be fully assessed. Transition Analysis was easier to apply than techniques developed previously, and findings from this study suggest that use of the forensic prior distribution could assist in assessment of battlefield assemblages. These results raise some valuable points that need to be considered in any future attempts to improve age‐at‐death estimates using the auricular surface, and important questions regarding expectations for estimation of age‐at‐death in disarticulated, fragmented and commingled collections of human bone. Copyright © 2015 John Wiley & Sons, Ltd.     

Taphonomic evidence for site formation processes at fort Christanna

Fort Christanna was an early eighteenth century Indian trading post on the western frontier of Virginia. This paper describes and interprets the faunal remains recovered during three seasons of excavation at the site. Taxonomic and body part representation are examined to gain insight into diet on the frontier, food provisioning at the fort, and the relationship between the fort's occupants and the neighbouring Indian settlement. These interpretations are limited by the poor preservation apparent in the faunal assemblage. The patterning of a variety of different surface modifications is explored to understand the taphonomic history of the assemblage. These characteristics of the assemblage seem to be related largely to the bone refuse disposal practices of the fort's occupants, and thus give important insight into a crucial aspect of the site formation processes.     

灵宝西坡遗址动物骨骼的收集与整理

本文介绍了河南灵宝西坡遗址动物骨骼的收集与整理过程 ,并重点对收集方法和埋藏因素对动物遗存的影响作了评估。结果表明 ,自然和生物因素对骨骼埋藏过程的影响较小 ,而人为因素的影响比较显著。不同的收集方法对出土骨骼的绝对数量和重量有直接影响 ,但用相对比例分析主要动物的骨骼发现率 ,能够减小不同收集方法造成的差异     

Adipocere Inside Nineteenth Century Femora: The Effect of Grave Conditions.

Adipocere has, infrequently, been reported from archaeological contexts normally on the external surface of bodies. In contrast to those cases, this study focuses on a white, powdery and greasy substance found inside two right human femora during sampling. These samples were obtained from two identified individuals buried in the late 19th century, who were exhumed from a rock‐cut and a brick‐lined grave in a steeply sloping graveyard with wet soil conditions. Both individuals were buried in coffins. Fourier transform infrared spectroscopy was used to test the composition of the substances, and both were found to conform to the spectrum of adipocere. This is likely to be a breakdown product of the fats in bone marrow in an anaerobic, moist environment mediated by bacteria. None of the other individuals (n = 6) buried in similar graves displayed evidence of adipocere; this includes those whose femora were in a similar state of preservation (n = 4). Contemporaneous data on precipitation for the month of burials do not highlight any obvious trends, but one of the individuals was found in a water‐logged grave. The similar preservation of other femora buried in brick‐lined graves highlights the interplay of multiple factors in the formation and degradation of adipocere. More importantly, it demonstrates differential preservation, which may impact on DNA and other biomolecular research. Furthermore, this adds to the limited data currently available on adipocere found in archaeological contexts. Copyright © 2013 John Wiley & Sons, Ltd.     

Faunal remains from the Islamic fort at Luluyyah (Sharjah,UAE)

Knowledge about human subsistence and the role of animal economy in the Islamic period of south‐east Arabia is still sketchy. The analysis of faunal remains from the coastal fort at Luluyyah (Sharjah, UAE), dated to the late thirteenth and early fourteenth century CE, provides some information. People depended on marine resources and domestic animals, a trait observable in the region since the Neolithic. Livestock breeding was not particularly developed. Judging by the distribution of their skeletal remains, the animals were slaughtered at the fort, implying that they either lived there or reached it alive.     

Bone Preservation and Ancient DNA: The Application of Screening Methods for Predicting DNA Survival

Given the technical difficulties associated with ancient DNA research, any methods that help to identify samples that will yield amplifiable DNA will be of great value. This study examined the relationships between gross preservation, histological preservation, bone size and the ability to amplify short fragments of mitochondrial DNA in 323 goose humeri from the Anglo-Saxon site at Flixborough. Bone size was not a good predictor of the presence of amplifiable DNA, but there was a significant association between both gross and histological preservation and DNA survival. This suggests that it is worthwhile to preferentially select morphologically well-preserved bones for ancient DNA studies. Our results with ancient avian bone mirror those previously obtained with mammalian archaeological bone, although the relationship between DNA survival and histological preservation was stronger for the latter.     

The hunted hunter: the capture of a lion (Panthera leo fossilis) at the Gran Dolina site,Sierra de Atapuerca,Spain

Many Pleistocene caves and rock shelters contain evidence of carnivore and human activities. For this reason, it is common to recover at these sites faunal remains left by both biological agents. In order to explain the role that carnivores play at the archaeological sites it is necessary to analyse several elements, such as the taxonomical and skeletal representation, the age profiles, the ratio of NISP to MNI, the anthropogenic processing marks on the carcasses (location and purpose of cutmarks and burning and bone breakage patterns), carnivore damage (digested bones, location and frequencies of toothmarks and bone breakage), length of the long bones, frequencies of coprolites and vertical distribution of the faunal remains, inter alia. From this, the documentation of carnivores in a faunal assemblage with a clear anthropogenic component can be understood from three main phenomena: (1) the carnivores as accumulators and the use of the site as a den; (2) carnivores as scavengers of hominid refuse and; (3) carnivores as hominids’ prey. Of these three phenomena, the last one is the least documented at the Middle Pleistocene sites. From this perspective, here we present the case of the anthropogenic use of a lion (Panthera leo fossilis) from level TD10-1 of Gran Dolina (MIS 9, Sierra de Atapuerca, Burgos, Spain). The lion bone remains show signs of direct interaction between this big cat and human groups that occupied Gran Dolina in these chronologies. From this perspective, the aim of this paper is to contribute to the knowledge of the role developed by large carnivores in the anthropogenic contexts and to provide data on human use of these predators at the European Middle Pleistocene sites.     

COMPLEX RELATIONSHIPS BETWEEN MITOCHONDRIAL AND NUCLEAR DNA PRESERVATION IN HISTORICAL DNA EXTRACTS*

‘Historical’ DNA obtained from specimens preserved in natural history collections has proven useful for addressing a wide variety of questions, such as the spread of domesticated species or changes in genetic diversity. With the development of high‐throughput sequencing techniques, there is an increasing focus on acquiring genetic information encoded by single‐copy nuclear DNA from historical DNA extracts. The development of efficient techniques to determine the level of nuclear DNA preservation in candidate specimens is necessary to maximize the data obtained from these analyses. Although current evidence suggests that a sample's mitochondrial DNA preservation predicts its nuclear DNA preservation, we show that the relationships between mitochondrial and nuclear DNA preservation are complex.     

State of preservation of polymorphic plasma proteins recovered from ancient human bones

Protected by the mineral matrix, bone proteins are capable of surviving inhumation periods of several hundreds or thousands of years in soil. While the preservation of the bone matrix protein, collagen I, is the prerequisite for a variety of archaeometric approaches, such as radiocarbon dating and the reconstruction of palaeodiet by stable isotope analysis, little is known about both the rate and state of preservation of non‐collagenous proteins. We succeeded in the isolation, electrophoretic separation (SDS‐PAGE, IEF) and immunological detection (radial immunodiffusion, IEF immunoblotting and ELISA) of plasma proteins preserved in archaeological human bones. However, sample preparation and electrophoretic methods had to be adapted to the specific demands of these aged proteins, since they are not only degraded and fragmented but also cross‐linked to other organic components, either indigenous to the bone or to contaminants from the burial environment. Complex decomposition phenomena are responsible for the altered mode of migration of aged proteins through a gel. After isoelectric focusing, the ancient proteins mainly concentrate below pH 4.45 in the pH‐gradient. Thus, highly negatively charged protein components have a better chance of preservation in bone after death. Isoelectric focusing with subsequent immunoblotting of ancient protein samples revealed protein patterns which showed marked charge‐modifications in comparison with those of modern human plasma proteins due to protein degradation (e.g. α₂‐HS‐glycoprotein and α₁‐antitrypsin). Nevertheless, in combination with different immunological analyses, previous results concerning the selective enrichment of α₂‐HS‐glycoprotein in bone compared with other plasma glycoproteins could be confirmed. Copyright © 1999 John Wiley & Sons, Ltd.