Ancient DNA in archaeological wheat grains: preservation conditions and the study of pre-Hispanic agriculture on the island of Gran Canaria (Spain)

The recovery of ancient DNA from archaeological wheat samples under different preservation conditions was assessed using a number of genetic markers. It was possible to amplify nuclear DNA from desiccated grains but not from charred. The desiccated grain was from a pre-Hispanic grain silo in Gran Canaria and showed excellent DNA preservation, enabling the amplification of the ribosomal DNA markers IGS and ITS, the upstream region of the HMW-glutenin locus and single-locus nuclear microsatellites. Our results demonstrated the presence of both durum and bread wheat in an assemblage of naked grain. We were also able to identify different genotypes in durum wheat and compare these with extant landraces, providing insights into the agrarian practices of the ancient Canarians and the origin of their crops.     

Osteometric and molecular sexing of cattle metapodia

Sex identification of skeletal remains based on morphology is a common practice in Zooarchaeology. Knowledge of the sex distribution of slaughtered or hunted animals may help in the interpretation of e.g. hunting or breeding strategies. Here we investigate and evaluate several osteometric criteria used to assess sex of cattle (Bos taurus) metapodia using molecular sex identification as a control of the metric data. The bone assemblage used to assess these new criteria derives from the Eketorp ringfort in the southern parts of Öland Island in Sweden. One hundred metapodia were selected for molecular analysis of sex and we were able to genetically identify the sex of 76 of these elements. The combined results of the molecular and osteometric analyses confirm a significant size difference between females and males for several measurements for both metacarpals (Mc) and metatarsals (Mt). Our results show that some measurements are applicable for metapodials. These measurements include the slenderness indices such as the Mennerich’s index 1 and 3, as well as the distal breadth (Bd), the breadth between the articular crests (Bcr), and the maximum breadth of the lateral trochlea (BFdl). We show that they can be used for sexing of both metacarpals and metatarsals. The latter measurements offer an opportunity to study fragmented elements and thus a higher number of elements may be utilized for morphological sexing of archaeological bones. Size comparisons of Mc and Mt may also aid in the separation of bulls and oxen.     

Minimally destructive DNA extraction from archaeological artefacts made from whale baleen

Here we demonstrate the successful extraction and amplification of target species DNA from artefacts made of whale baleen collected from excavations of past palaeo-Eskimo and Inuit cultures in Greenland. DNA was successfully extracted and amplified from a single baleen bristle of 1.5 cm length dated based on archaeological context to the period of the Saqqaq culture, more than 4000 years ago and following decades of storage at room temperature at the National Museum. The results reveal ancient baleen in archaeological material as a potential source of DNA that can be used for population genetic studies. We conclude that genetic investigation of historical baleen collections can contribute to our knowledge of the prehistoric population genetics of baleen whales, for example by quantifying the impact of modern whaling on the genetic diversity of bowhead whales.     

TRUTH IN THE BONES: RESOLVING THE IDENTITY OF THE FOUNDING ELITE THOROUGHBRED RACEHORSES

Our multidisciplinary study of historic Thoroughbred horses solves two long‐running mysteries in racing history. Eclipse, the greatest racehorse ever known, never lost a race. His skeleton is housed in the Royal Veterinary College, London; however, there is controversy over its authenticity. The 1880 Epsom Derby was won by Bend Or. In one of the great controversies of Thoroughbred racing, the owners of Bend Or were accused of swapping him with another horse, Tadcaster, whose maternal pedigree was more prestigious. Bend Or's skeleton resides at the Natural History Museum, in London. Eclipse and Tadcaster were both extremely popular at stud, and the vast majority of racehorses today are descendents. We compared mitochondrial DNA haplotypes of living and historic Thoroughbred skeletons, including those of Eclipse and Bend Or. Additionally, we compared skeletal morphometrics of Eclipse's skeleton with measurements taken at autopsy. Carbon and nitrogen stable isotopes of a range of skeletal elements were compared in order to establish that the Eclipse skeleton was that of a single horse. Our multidisciplinary data suggest that the putative skeleton is consistent with that of Eclipse. In contrast, mitochondrial DNA haplotype sharing indicated that the skeleton known as Bend Or is most probably that of Tadcaster.     

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.