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.     

DNA AND PROTEIN RECOVERY FROM WASHED EXPERIMENTAL STONE TOOLS*

Traces of protein and DNA are preserved on stone tools used to process animals. Previous research documents the identification of protein residues from tools sonicated in 5% ammonium hydroxide, but it remains untested whether the same treatment yields useable DNA. In this study we report both DNA and protein recovery using 5% ammonium hydroxide from residues on stone tools. We extracted 13‐year‐old residues from experimentally manufactured stone tools used to butcher a single animal. We also show that surface washing procedures typically used to curate stone tools remove only a small fraction of the DNA and protein deposited during animal butchery.     

Ancient DNA provides new insights into the origin of the Chinese domestic horse

Domestic horses played a pivotal role in ancient China, but their exact origin remains controversial. To investigate the origin of Chinese domestic horses, we analyzed mitochondrial DNA (mtDNA) from 35 horse remains, aged between 4000 and 2000 years, excavated from nine archaeological sites in northern China. The Chinese ancient horses exhibited high matrilineal diversity, falling into all the seven haplogroups (A–G) observed in modern horses. These results suggest that several maternal lines were introduced into the gene pool of Chinese horses in the past. Haplogroups A and F were more prevalent in ancient horses than the other haplogroups. Interestingly, only haplogroups A and F were present in the samples older than 4000 years, while the more recent horses (between 2000 and 3000 years BP) fell into all seven haplogroups. Comparison with DNA data of present-day horses suggests that haplogroup F is like to be an ancient haplogroup of East Asian origin. These analyses also suggest that the origin of Chinese domestic horses is complex, and external mtDNA input occurred after initial domestication. Our results indicate that the Chinese ancient horses are more related to the modern Mongolian horses. Lastly, our results cannot support the previous hypothesis that early Chinese domestic horses were derived from the Przewalski horse.     

Ancestral Puebloan mtDNA in context of the greater southwest

Ancient DNA (aDNA) was extracted from the human remains of seventy-three individuals from the Tommy and Mine Canyon sites (dated to PI-II and PIII, respectively), located on the B-Square Ranch in the Middle San Juan region of New Mexico. The mitochondrial DNA (mtDNA) haplogroups of 48 (65.7%) of these samples were identified, and their frequency distributions were compared with those of other prehistoric and modern populations from the Greater Southwest and Mexico. The haplogroup frequency distributions for the two sites were statistically significantly different from each other, with the Mine Canyon site exhibiting an unusually high frequency of haplogroup A for a Southwestern population, indicating the possible influence of migration or other evolutionary forces. However, both sites exhibited a relatively high frequency of haplogroup B, typical of Southwestern populations, suggesting continuity in the Southwest, as has been hypothesized by others (8, 9, 29, 45 and 57). The first hypervariable region of twenty-three individuals (31.5%) was also sequenced to confirm haplogroup assignments and compared with other sequences from the region. This comparison further strengthens the argument for population continuity in the Southwest without a detectable influence from Mesoamerica.     

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.