Ancient DNA analysis of desiccated wheat grains excavated from a Bronze Age cemetery in Xinjiang

Wheat has been one of the most important crop in Eurasia since the Neolithic period. Understanding the spread of wheat cultivation is crucial to understanding the spread of agriculture as a whole and the interactions between prehistoric populations across the Eurasian continent. However, the routes by which wheat cultivation spread eastwards have been poorly understood to date, due to the scarcity of plant remains recovered from archaeological sites. Desiccated wheat grains excavated from the Xiaohe cemetery in Xinjiang, and dated to the early Bronze Age, show excellent DNA preservation. Here we present an ancient DNA (aDNA) analysis of wheat (Triticum sp.) grains excavated from Xiaohe and provide the first definitive evidence for bread wheat in China during the Bronze Age. The nuclear ribosomal DNA internal transcribed spacer regions (ITS1 and ITS2) and the intergenic spacer region (IGS) were amplified. The IGS region within the D genome of wheat has a 71 bp insertion that is absent from corresponding regions in the A and B genomes. The results showed that the Xiaohe wheat showed most sequence similarity to hexaploid bread wheat (Triticum aestivum), including the characteristic insertion into the D genome. The presence of bread wheat at the Xiaohe cemetery is discussed in relation to it having spread into Xinjiang by the Bronze Age, providing new insight into the origins of bread wheat in East Asia.     

Ancient-DNA reveals an Asian type of Mycobacterium leprae in medieval Scandinavia

Leprosy is a chronic infection of the skin and peripheral nerves caused by the pathogen Mycobacterium leprae. Its impact on human populations and societies of the past as well as its phylogeographic patterns around the world – at least in modern times – has been well documented. This slow growing bacterium has been shown to exist in distinct ‘SNP types’ that occur in relatively defined parts of the globe. The routes that the disease followed in the past are, however, still uncertain. This study of ancient-DNA typing of archaeological human remains from Sweden dated to early Medieval times provides genetic evidence that a transmission of M. leprae ‘SNP subtype’ 2G – found mainly in Asia – took or had already taken place at that time from the Middle East to Scandinavia. This finding is unique in the history of leprosy in Europe. All human specimens from this continent – both modern and ancient – that have been tested to date showed that the one responsible for the infection strains of M. leprae belong to ‘SNP type’ 3, whereas our results show that there were some European populations that were hosts to bacteria representing ‘SNP type’ 2 of the species as well.     

Ancient DNA analysis on Clonorchis sinensis eggs remained in samples from medieval Korean mummy

In the present study, Clonorchis sinensis (C. sinensis) ancient DNA (aDNA) was successfully extracted from human remains discovered in a tomb dating to the medieval Joseon dynasty of Korea. The presence of C. sinensis eggs was confirmed by microscopic observation, after which a PCR-based aDNA analysis was performed using primer sets designed for the amplification of nuclear ribosomal internal transcribed spacer 1 (ITS1), 2 (ITS2) and mitochondrial cytochrome c oxidase 1 (CO1) genes. The sequences obtained were 100% homologous to some contemporary C. sinensis gene sequences reported from Korea and other East Asian countries. We believe that the results of our analysis expand the temporal and geographical scopes of research on the history of C. sinensis infection in different human populations.     

Clarifying prehistoric parasitism from a complementary morphological and molecular approach

This paper reports an approach to the identification of prehistoric parasitic infection, which integrates traditional morphological methods with molecular methods. The approach includes the strengths of each method while mitigating the limitations. Demonstrating the efficacy of this approach, we provide a case study from a 1400 year old desiccated fecal sample from La Cueva de los Muertos Chiquitos, archaeological site, near Rio Zape, Durango, Mexico. Traditionally prepared microscope slides were processed via microscopy and tentative ascarids were identified. Information regarding the parasites' developmental stage was recorded. DNA was then extracted directly from the slide material. From this DNA extract, a small segment of the 18S ribosomal RNA gene variant that is specific to Ascaris, and its phylogenetically close relatives, was targeted for PCR amplification and sequencing. Phylogenetic analysis of the DNA sequence best matched a member of physalopterids, rather than ascarids, with a single exception of a match to Contracaecum spiculigerum. Subsequent extractions, amplifications and sequencing of the original rehydrated coprolite material confirmed these results. The C. spiculigerum sequence represented a phylogenetic anomaly and subsequent analysis determined the sequence was an error in the BLAST database, likely attributable to misidentification of juvenile specimens prior to sequencing and submission. Physaloptera are a difficult genus to identify morphologically and can carry major health burdens. They may be underreported in humans, in part, because of morphological similarities to the more common human parasites belonging to ascarids. We conclude that integrating traditional morphological methods with molecular methods can help resolve this issue, in both contemporary and prehistoric populations.     

Ancient DNA reveals a major genetic change during the transition from hunting economy to reindeer husbandry in northern Scandinavia

The timing and origin of reindeer domestication has been highly debated. Recent molecular analyses show several mitochondrial lineages of domestic reindeer across Eurasia suggesting different origins of Fennoscandian and Siberian domestic reindeer. In order to investigate the origin of domestic Fennoscandian reindeer, we sequenced a mitochondrial control region fragment of 68 ancient reindeer remains from archaeological sites in Finnmark, the major county for extant reindeer husbandry in Norway, spanning from ca. BC 3400 to AD 1800. The majority of the Stone and Iron Age reindeer assemblages in Finnmark are from settlements in the eastern part of the county, in the Varangerfjord area. The reindeer remains from these settlements show affiliation to the large and complex Beringian haplotype cluster, found in extant reindeer from the Kola Peninsula to north-eastern Russia. A distinct haplotype shift is observed in the late medieval period, when the typical haplotype signatures of extant domestic Fennoscandian reindeer appeared in coastal regions of both eastern and western Finnmark. These haplotypes were not found among the Stone and Iron Age wild reindeer samples of Finnmark, suggesting that this population was not ancestral to extant domestic reindeer of Fennoscandia.     

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.     

DISTINGUISHING AMBER AND COPAL CLASSES BY PROTON MAGNETIC RESONANCE SPECTROSCOPY

Fossilized resin, or amber, has been examined from 120 worldwide sources by 1D and 2D proton magnetic resonance spectroscopy in solution. These spectra fall into five categories, corresponding to the classes already established by mass spectrometry and carbon‐13 magnetic resonance spectroscopy. The wide availability of this technique provides a straightforward method to classify amber rapidly and inexpensively.     

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.     

Ancient DNA typing of archaeological pig remains corroborates historical records

The recent increase in both the abundance and taxonomic range of DNA sequence data in public repositories makes it possible to determine the maternal origin of lineages of faunal archaeological material by characterizing its mitochondrial DNA. Among the most commonly represented taxa are domesticated animals, for which extensive genetic characterization has revealed high levels of genetic diversity and (in at least some cases) strong phylogeographic clustering. Such information has significant implications not only for characterizing important aspects of the occupation history of archaeological sites, but also in providing novel insights into colonisation history and the scale and scope of trade and exchange networks. This can be done through studying the origins and dispersal of proxy organisms such as commensal and domesticated animals, as well as economically important wild fauna. To illustrate this approach, we compare historical records of maritime movement of people and pigs from two sites on Lord Howe Island, Australia, to phylogeographic results of DNA extracted from pig bones.