Persistence and decay of the intestinal microbiota's DNA in glacier mummies from the Alps

The study of the DNA of ancient microorganisms in human remains represents one of the newest and most promising branches of molecular archaeoanthropology. Despite the growing number of papers addressing this subject, however, the analysis of ancient bacterial DNA is still a contentious issue. The indigenous microbiota of the gastrointestinal tract of man represents a community characterized by relative constancy in species composition and proportion. As a model system, we studied the preservation of the intestinal microbiota DNA in two naturally freeze-dried human mummies found on the Alps. This kind of mummy is an ideal subject for ancient DNA investigations. The first is a male body historically dated 1918 A.D. while the second is the famous Tyrolean Iceman (3.350–3.100 B.C.). The screening of bacterial 16S rRNA gene libraries from colon samples of the two mummies (49 clones for the 1918 mummy, 119 clones for the Iceman) showed that the characteristic composition of the intestinal microbiota of man (Alpha-, Beta-, Gammaproteobacteria, Bacteroides, Clostridia) is still kept in the library from the recent mummy while the Iceman's library is almost entirely composed by the DNA of clostridia. Comparison of the intestinal data with those from the literature describing the screening of 16S rRNA gene libraries from other parts of the Iceman's body and from permafrost specimens indicates that the changes in library composition may partly be attributed to the proliferation of clostridia inside the corpses, as described in forensic literature, and partly to the differential persistence of the DNA of gram-negative bacteria and endospore-former low-GC gram-positive bacteria. The present results contribute to the issue of the authentication of claims of pathogen DNA identification in archaeological human remains.     

Palaeopathological and palaeogenetic study of 13 cases of developmental dysplasia of the hip with dislocation in a historical population from southern France

Dislocation of the hip can be consecutive to developmental dysplasia of the hip that is linked to a complex set of genetic and mechanical factors. The purpose of this report is to describe 13 cases of complete dysplastic hip dislocation observed in the skeletal remains of nine women exhumed from an historical gravesite dating from the 5th to 17th centuries in southern France. Despite the size of this palaeopathological series, which is the largest study published to date, findings indicate that the prevalence of hip dislocation in this historical sample was still lower than in some French areas at the beginning of the 20th century. Mitochondrial DNA sequencing demonstrated possible kinship only between two women, i.e. one who died in the period from the 11th to 13th centuries and another who died in the period from the 16th to 17th centuries. It is suggested that the tight swaddling of young infants in France up to the end of the 19th century could have been a predisposing factor for this highly debilitating disorder. Copyright © 2006 John Wiley & Sons, Ltd.     

The application of ancient DNA analysis to identify neolithic caprinae: a case study from the site of Hatoula,Israel

The evidence for wild sheep (Ovis orientalis) in archaeological sites from the southern Levant is examined through the application of ancient DNA analysis to specimens from the Pre‐Pottery Neolithic A (8300–7500 uncal. BC) site of Hatoula, Israel. The results indicate that at least one of the bones from this site, previously identified as sheep, is in fact goat. To date this is the earliest faunal sample to have yielded DNA in the region. This study highlights the problems in applying morphological criteria to distinguish between caprine species, and illustrates how ancient DNA analysis can serve as a powerful tool in resolving questions of species attribution. Copyright © 2003 John Wiley & Sons, Ltd.     

A first prehistoric case of tuberculosis from Britain

A likely case of tuberculosis in an Iron Age human burial from Dorset, England is described. Osteological examination and biomolecular study support the diagnosis. A radiocarbon determination indicates a date range for the burial of BC 400–230. This case represents the earliest reported case of tuberculosis from Britain, and indicates that the disease was present here prior to the Roman invasion. Copyright © 2003 John Wiley & Sons, Ltd.     

DNA of Mycobacterium leprae detected by PCR in ancient bone

We report the extraction and amplification of DNA of Mycobacterium leprae, from ancient skeletal material. The significance of the extraction of ancient bacterial DNA is discussed, as are future directions of research into ancient disease.     

The molecular palaeoecology of geese: identification of archaeological goose remains using ancient DNA analysis

The remains of six species of geese are commonly recovered from archaeological sites in Britain dating from the Saxon and later periods. However, identification of this material to species level is hampered by a lack of morphological variation and a large overlap in size. To address this issue we obtained DNA sequence data for a section of the mitochondrial cytochrome b gene from modern samples of each species, and successfully identified several DNA markers for Branta species. No markers were found within the cytochrome b gene for the genus Anser. Ancient DNA techniques were then used to recover DNA from goose bones excavated from two archaeological sites. The DNA sequences enabled identification of Barnacle goose (Branta leucopsis) from one site and confirmed the presence of Anser species at another. © 1998 John Wiley & Sons, Ltd.     

Molecular identification and characterization of Mycobacterium tuberculosis complex in ancient Egyptian mummies

A considerable number of molecular studies have provided evidence for the presence of Mycobacterium tuberculosis complex (MTB) DNA in ancient skeletal and mummified material. Moreover first studies on the differentiation of sub‐types of the MTB (M. tuberculosis, M. bovis, M. africanum, M. microti, M. canettii) have successfully been performed on ancient tissue samples. In our present study we extend previous analyses and investigate bone and soft tissue samples from 118 ancient Egyptian mummies and skeletons from the Pre‐ to Early Dynastic site of Abydos and different tomb complexes in Thebes West, which were built and used between the Middle and New Kingdom until the Late Period (c. 2050–500 BC). The samples were tested for the presence of MTB DNA and further identified by spoligotyping. Twenty‐six samples provided molecular evidence for the presence of ancient mycobacterial DNA by amplification of a 123 base pair fragment of the repetitive element IS6110. Out of the 26 positive samples, 12 provided a complete spoligotyping signature, which was compared to an international database. Ten further cases showed an incomplete, patchy hybridization pattern, while in four cases no spoligotyping signature could be obtained. Interestingly, they all show either a M. tuberculosis or M. africanum pattern, but none revealed a M. bovis specific pattern. In the material from a Middle Kingdom tomb (used exclusively between c. 2050–1650 BC) several samples revealed a M. africanum type specific spoligotyping signature, while samples from later periods provided patterns typical for M. tuberculosis. This study clearly shows that spoligotyping can be used for the characterization of members of the MTB in historic tissue samples. In addition, our results do not support the theory that M. tuberculosis originated from the M. bovis type. Copyright © 2004 John Wiley & Sons, Ltd.     

Rapid loss of endogenous DNA in pig bone buried in five different environments

The rate at which endogenous DNA from differently prepared (butchered, boiled and baked) compact pig bones degrades in five different Danish terrestrial and marine environments over 12 months was investigated. Although > 70% of the estimated endogenous mtDNA is lost after just four weeks of exposure, no cytosine deamination of DNA was recognised. A correlation between the presence of oxygen and the amount of preserved DNA was observed. The results provide valuable information on the interaction between the endogenous DNA and the depositional environment in the early stages of bone diagenesis, which can be a support in the interpretation of the initial diagenetic pathways of archaeological bone.     

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.