Ancient DNA supports lineage replacement in European dog gene pool: insight into Neolithic southeast France

We report palaeogenetic analysis of domesticated dog (Canis familiaris) remains excavated from three archaeological sites from southeast France and dating from Middle Neolithic. Ancient DNA analysis was attempted on teeth and bone samples taken from 11 dogs. Three 266-base-pair fragments of the mitochondrial genome Hypervariable Region I (HVR-I) could be retrieved and revealed two haplotypes belonging to HVR-I lineage C. These three sequences were compared to the sequences of Swedish and Italian Neolithic dogs and permitted to confirm that clade C was largely represented all over Western Europe during this period. One haplotype defined in Neolithic French dog was observed for the first time in Canis mtDNA, underlining the loss of mitochondrial diversity in Europe since the Neolithic. Finally, these results point out mitochondrial lineage replacement in Europe, since lineage C represents only 5% of extant European dogs. Altogether, these results support the proposition that palaeogenetic studies are essential for the reconstruction of the past demographic history and the domestication process of dogs.     

Phylogeographic analysis of barley DNA as evidence for the spread of Neolithic agriculture through Europe

Results of analyses of the photoperiod response gene (PPD-H1) and simple sequence repeats (SSRs) in modern landraces of cultivated barley were used as evidence for the mechanism of agricultural spread in Neolithic Europe. In particular, we explored the usefulness of considering adaptive genes as indicators of past selective pressures acting on crops, during their spread through Europe. In some areas, such as the Alpine region, Britain and Scandinavia, we have evidence to suggest that the adaptation of crops to certain climatic conditions may have contributed to the timing of agricultural spread. At the northern fringes of Europe, and in higher altitude locations in central Europe, the introduction of more suitably adapted cereals may have facilitated successful agriculture to trigger agricultural expansion. This research opens up the possibility of investigating other genetic adaptations to climate, which would permit a fuller evaluation of the relative contributions of climate/crop and forager/farmer interactions in the process of agricultural spread.     

Ancient DNA typing shows that a Bronze Age mummy is a composite of different skeletons

Excavations at Cladh Hallan, a Bronze Age-Iron Age settlement on South Uist in the Outer Hebrides off the west coast of Scotland, revealed the skeletons of two adults, a sub-adult and a child buried beneath the foundations of three roundhouses. Osteological and isotopic evidence has shown that the male adult skeleton is a composite made up of parts of at least three different individuals. To test the hypothesis that the female skeleton was also a composite we examined ancient DNA from four of its components: the skull, mandible, right humerus and right femur. Seven polymerase chain reactions (PCRs) were attempted, these covering positions 15,996–16,420, 16–132 and 232–368 of the mitochondrial DNA hypervariable I and II regions. Three PCRs were successful for each sample and a total of 55 sequences were obtained from the cloned products. After exclusion of possible contaminating sequences, the remaining 34 were compared. It was concluded that the mandible, humerus and femur come from different individuals. Insufficient data were obtained to draw conclusions regarding the origin of the skull. The presence of two composite skeletons at Cladh Hallan indicates that the merging of identities may have been a deliberate act, perhaps designed to amalgamate different ancestries into a single lineage.     

Forensics and fortification in South African self-captivity

ABSTRACT

This essay considers how residential security and forensic genetics in South Africa open ways to think about captivity as something that the relatively privileged embrace to delineate a safe inside from a threatening outside. Captivity functions here as a means to entrench privilege and guarantee its protection.     

Aspects of ancient Greek trade re-evaluated with amphora DNA evidence

Ancient DNA trapped in the matrices of ceramic transport jars from Mediterranean shipwrecks can reveal the goods traded in the earliest markets. Scholars generally assume that the amphora cargoes of 5th-3rd century B.C. Greek shipwrecks contained wine, or to a much lesser extent olive oil. Remnant DNA inside empty amphoras allows us to test that assumption. We show that short ∼100 nucleotides of ancient DNA can be isolated and analyzed from inside the empty jars from either small amounts of physical scrapings or material captured with non-destructive swabs. Our study material is previously inaccessible Classical/Hellenistic Greek shipwreck amphoras archived at the Ministry of Culture and Tourism Ephorate of Underwater Antiquities in Athens, Greece. Collected DNA samples reveal various combinations of olive, grape, Lamiaceae herbs (mint, rosemary, thyme, oregano, sage), juniper, and terebinth/mastic (genus Pistacia). General DNA targeting analyses also reveal the presence of pine (Pinus), and DNA from Fabaceae (Legume family); Zingiberaceae (Ginger family); and Juglandaceae (Walnut family). Our results demonstrate that amphoras were much more than wine containers. DNA shows that these transport jars contained a wide range of goods, bringing into question long-standing assumptions about amphora use in ancient Greece. Ancient DNA investigations open new research avenues, and will allow accurate reconstruction of ancient diet, medicinal compounds, value-added products, goods brought to market, and food preservation methods.     

Neolithic Hedgehogs (Erinaceus europaeus) from the Island of Gotland show early contacts with the Swedish mainland

Previous research probing early migrations and contacts in the Baltic Sea area is characterized by the analysis of different chronologies and subsistent strategies on all sides of the Sea. Several studies performed on artifact typology, ceramics, grave rituals and physical anthropology ended with varying results. Although the question of human origins remains inconclusive, in this study, we rely on the phylogeography of an animal associated with humans to elucidate findings regarding prehistoric human migration and contacts.Hedgehogs, along with other fauna on Gotland, were brought over to the island by humans. We examined hedgehog mitochondrial DNA from the Pitted Ware Culture (Middle Neolithic). The genetic signatures of the animals on the island were investigated to determine the animal’s origin.From the 23 bones originally examined, twelve bones from all five locations studied yielded reliable results and resembled published extant Erinaceus europaeus sequences from Sweden, Norway and Denmark. We postulate that a western heritage for the Neolithic hedgehogs on Gotland indicates early human contact with the Swedish mainland.     

An Analysis Of Mitochondrial Dna From The Pakhomovskaya Population Of The Late Bronze Age,Western Siberia

This article presents the results of an analysis of mitochondrial DNA extracted from bone samples from Stary Sad – a burial ground representing the eastern variant of the Late Bronze Age Pakhomovskaya culture in the Baraba forest-steppe, Western Siberia. Comparison with mitochondrial DNA data from earlier populations of the region and also with archaeological facts, points to the origins of the Pakhomovskaya people. Certain components of their gene pool were evidently derived from the local pre-Andronovo populations, others from the actual Andronovo (Fedorovka) population and also from later immigrants. In this article an integrative reconstruction based on biological and cultural facts is proposed.     

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.     

Species identification of archaeological dung remains: A critical review of potential methods

Abstract

Dung, macroscopically recognisable as such or not, can more commonly be found in archaeological contexts than is perhaps realised. Up to now, identification of dung to the species which produced it is usually either tenuous, or is not possible. However, species identification can be very informative and is necessary before any further studies can be conducted on the dung, for example on health and hygiene in the past and palaeoecology. This study presents a review of potential methods by which species identifications of archaeological dung can be undertaken. Criteria for identification can be divided into three broad categories: morphometric features of the dung; the content of dung and contextual evidence. Overall, the chances of a precise identification are high; however, a combination of different criteria and techniques will often be necessary to establish a secure identification. Moreover, preservation issues may exclude the application of some criteria while several criteria require more research and the expansion of reference collections of recent material. The overall aim is to move towards standardised methods for species identification of archaeological dung.     

DNA FROM HUMAN ANCIENT BACTERIA: A NOVEL SOURCE OF GENETIC EVIDENCE FROM ARCHAEOLOGICAL DENTAL CALCULUS

We report a molecular methodology to obtain and analyse ancient bacterial DNA from archaeological dental calculus. Recent and archaeological DNA samples, as old as 4000 bp , were successfully extracted and amplified with species‐specific PCR primers. We propose this approach in order to: detect the presence of specific bacterial species infecting past human populations; compare the composition of ancient oral microbiomes among human populations; and analyse the genetic variability and covariation of bacteria and human host populations. Genomic analysis of bacteria from dental calculus is a promising source of evidence for palaeopathological and micro‐evolutionary studies, focused either on micro‐organisms or their human hosts.