Using ancient DNA identification and osteometric measures of archaeological Pacific salmon vertebrae for reconstructing salmon fisheries and site seasonality at Dionisio Point,British Columbia

Determining the diversity of salmon species represented in archaeological contexts is critical to understanding patterns of salmon harvesting and consumption, storage practices and seasonal patterns of resource exploitation by precontact peoples of the Northwest Coast. We present species determinations generated for salmon vertebrae from the Dionisio Point site (DgRv-003) in coastal southwestern British Columbia, a well-preserved village site that dates to between 1500 and 1300 cal BP. Molecular species identification was possible for 70 Pacific salmonid vertebral elements recovered from one excavated plankhouse at the site. Coupled with osteometric measures, we determine that residents of the plankhouse fished primarily for chum, sockeye and pink salmon, with a lesser emphasis on chinook, coho and steelhead. These results indicate a diverse fishery that likely occurred between July and December, suggesting a mid summer through winter season of occupation for the village.     

A novel method for integrated age and sex determination from archaeological cattle mandibles

Analysis of ancient cattle husbandry is compromised by the need for conventional analysis of sex and age at death to use different elements of the skeleton, usually from different individuals. We demonstrate a technique using aDNA acquired from cattle mandibles and combined with age-at-death estimation based on dental eruption in the same specimens. Application to small sample groups from two sites in Na h-Eileanan Siar (the Scottish Western Isles) show a high success rate, and demonstrates the potential for a more nuanced interpretation of ancient cattle husbandry.     

Paleopathological and Molecular Study on Two Cases of Ancient Childhood Leprosy from the Roman and Byzantine Empires

This study is based on the paleaopathology of leprosy on human skeletal remains and the detection of ancient Mycobacterium leprae DNA. Two cases of childhood leprosy were recognized. The first case was in a Roman necropolis at Martellona (Rome, Central Italy), dated to the 2nd to 3rd centuries ce . The skeleton of a child aged 4–5 years, from tomb 162, is the youngest individual in Italy from this time period, with the clear rhino‐maxillary syndrome and other bony changes indicative of leprosy. The second case from a burial at Kovuklukaya, in the Sinop region of Northern Turkey, was from the 8th to the 10th centuries, during the Byzantine era. The endocranium of a 4–5‐month‐old infant with new bone formation—an indication of chronic inflammation—was positive for M. leprae DNA. Infant and childhood leprosy is uncommon today, and there is a scarcity of information in the osteoarchaeological literature of leprosy in the past, especially in children. The significance of these cases is that it adds to an understanding of the history of the disease in the former Roman Empire. It is hoped that over time sufficient data can be obtained to understand the epidemiological dynamics and clinical evolution of leprosy from the ancient period until today. Copyright © 2012 John Wiley & Sons, Ltd.     

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.     

Low regional diversity of late cave bears mitochondrial DNA at the time of Chauvet Aurignacian paintings

The Chauvet-Pont d'Arc and Deux-Ouvertures caves, located along the Ardèche River (France), contain abundant remains of the extinct cave bear (Ursus spelaeus). Because they also display a variety of Palaeolithic anthropogenic evidences, such as the earliest charcoal drawings recorded to date (Chauvet-Pont d'Arc), and delicate engravings (Deux-Ouvertures), they offer the opportunity of studying the interaction between animals and human beings during a key period for Pleistocene species extinctions. We characterized cave bear specimens from these two sites by radiocarbon dating, stable isotopes, and mitochondrial DNA analysis. In Chauvet-Pont d'Arc, we obtained radiocarbon ages that ranged between 29,000 and 37,300 years before present (BP). The Deux-Ouvertures cave bear specimens clustered to the bottom of this time frame, returning radiocarbon ages of 27,440–30,220 years BP. Cave bear nitrogen isotope values were all compatible with a vegetarian diet. Mitochondrial DNA analysis, carried out on a highly variable domain of the control region, evidenced only two cave bear haplotypes, including a new haplotype, and a common one which largely predominated. We detected both haplotypes in Chauvet-Pont d'Arc, but only recorded the predominant one in the Deux-Ouvertures Cave. Our data put forward the surprising observation that cave bears inhabited Ardèche over a short period of time, from about 37,000 to 27,400 years BP. They were notably present during the first (Aurignacian) phase of human intrusions in Chauvet-Pont d'Arc, 30,000–32,000 years BP. This points to the possible competition for cave sites, presumably on a seasonal scale considering the cave bear habit for hibernation. During this time period, the small number of haplotypes is at variance with the extensive genetic diversity reported elsewhere for much more ancient specimens.     

Hemp in ancient rope and fabric from the Christmas Cave in Israel: talmudic background and DNA sequence identification

The “Christmas Cave”, a cave in the Qidron Valley near the Dead Sea and Qumran, has yielded a complex collection of plant-derived rope and fabric artifacts. Using polymerase chain reaction (PCR) to amplify DNA of the samples, we estimated the sizes and determined restriction patterns and base sequences of chloroplast genes, primarily rbcL (gene for the large subunit of ribulose bisphosphate carboxylase). DNA was successfully extracted from all samples, but was limited to sizes of approximately 200–300 base pairs. As expected, the DNA extracted from the samples was identified as coming primarily from flax (Linum usitatissamum L.), but two samples had a significant fraction, and all samples had at least a trace, of hemp (Cannabis sativa L.) DNA. Artifacts from the Christmas Cave were thought to date from Roman times, but it was thought possible that some could be much older. Accelerator mass spectrometry (AMS)-based ¹⁴C dating confirmed that the samples contained representatives from both the Roman and Chalcolithic periods. This paper provides a synthesis of DNA, isotope, and literary analysis to illuminate textile history at the Christmas Cave site.     

First ancient bovine DNA evidence from India: difficult but not impossible

Ancient DNA isolation from the tropical countries has been shown to be very difficult in the past. Here for the first time we have been successful in isolating ancient DNA from Indian cattle samples. We were able to obtain DNA and sequence the partial mitochondrial D-loop in 3 of the 15 bovine fossil samples ranging in age from 2000 BC to 1000 AD, and were able to further identify the most recent sample as being of Bos indicus origin. Our results on ancient DNA extraction from India will encourage other researchers in this field to carry out further studies of ancient DNA from Indian bovine samples. Our results represent the first successful extraction and amplification of bovine ancient DNA from India, and thus may pave the road for a better understanding of demographic and historical processes of cattle domestication that has taken place in this region.     

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.     

Repeat silica extraction: a simple technique for the removal of PCR inhibitors from DNA extracts

Polymerase chain reaction (PCR) inhibitors are often co-extracted with ancient DNA (aDNA) and when present make the analysis of aDNA difficult, if not impossible. In this study we review previous research on PCR inhibitors and techniques that address their co-extraction with DNA from sub-optimal samples. Additionally, we introduce a simple extraction technique, “repeat silica extraction,” that effectively removed PCR inhibitors from extracts of 7000–8000-year-old human skeletal remains from the Windover archaeological site in Florida and 700–2000-year-old human coprolites excavated from Fish Slough Cave in southern California. A series of tests on these same samples demonstrates that N-phenacylthiazolium bromide is largely ineffective, despite previously reported success using this compound as part of the DNA extraction process. We also describe a method for demonstrating the presence as well as successful removal of PCR inhibitors by use of a “positive aDNA control,” a test necessary to conclude that negative PCR amplification is the result of the absence of preserved DNA.