Ancient DNA in human bone remains from Pompeii archaeological site

Bioarchaeological and palaeogenomic portrait of two Pompeians that died during the eruption of Vesuvius in 79 AD

The archaeological site of Pompeii is one of the 54 UNESCO World Heritage sites in Italy, thanks to its uniqueness: the town was completely destroyed and buried by a Vesuvius’ eruption in 79 AD. In this work, we present a multidisciplinary approach with bioarchaeological and palaeogenomic analyses of two Pompeian human remains from the Casa del Fabbro. We have been able to characterize the genetic profile of the first Pompeian’ genome, which has strong affinities with the surrounding central Italian population from the Roman Imperial Age. Our findings suggest that, despite the extensive connection between Rome and other Mediterranean populations, a noticeable degree of genetic homogeneity exists in the Italian peninsula at that time. Moreover, palaeopathological analyses identified the presence of spinal tuberculosis and we further investigated the presence of ancient DNA from Mycobacterium tuberculosis. In conclusion, our study demonstrates the power of a combined approach to investigate ancient humans and confirms the possibility to retrieve ancient DNA from Pompeii human remains. Our initial findings provide a foundation to promote an intensive and extensive paleogenetic analysis in order to reconstruct the genetic history of population from Pompeii, a unique archaeological site.

Bone Diagenesis and its Implication for Disease Diagnosis: The Relevance of Bone Microstructure Analysis for the Study of Past Human Remains

When bone is exposed to the burial environment it may experience structural changes induced by multiple agents. The study of postmortem alterations is important to differentiate decomposition phenomena from normal physiological processes or pathological lesions, as well as to assess bone tissue quality. Microscopy is of great utility to evaluate the integrity of bone microstructure and it provides significant data on long-term bone decomposition. A total of 18 human bone sections (eight archeological and ten retrieved from an identified skeletal collection) were selected for analysis under plane light and polarized light. The aim of this exploratory study was to analyze the impact of diagenesis and taphonomy on the bone microstructure, as well as on the differential diagnosis of pathological conditions. The results showed that the microscopy approach to bone tissues contributed materially as an aid in the detailed description of the main diagenetic changes observed. It showed that gross inspection does not provide a realistic assessment of bone tissue preservation, which can impact in the characterization of lesions present and subsequent disease diagnosis. Therefore, researchers should continue to consider the application of histological techniques if the aim is to comprehend tissue integrity and its association with decomposition or disease.

The origin of bacteria responsible for bioerosion to the internal bone microstructure: Results from experimentally-deposited pig carcasses

It is unclear whether the principal forms of bioerosion that are often found within the internal microstructure of human bone are produced by intrinsic gut microbiota or exogenous bacteria from the soil. The aim of this study was to attempt to resolve this issue through the histological analysis of bone sampled from experimentally-deposited domestic pig (Sus scrofa) carcasses. Confirmation of either scenario will dictate how patterns of bone bioerosion can be used in reconstructions of taphonomic events. The results should also reveal the post mortem processes that promote the survival of bone biomolecules as well as the histomorphological structures that can be used in forensic identifications of human remains. Twelve pig carcasses were differentially buried and sub-aerially exposed for one year at Riseholme, Lincolnshire, U.K. Their femora were examined after one year using thin section light microscopy to investigate the patterns of microscopic bioerosion. The distribution and extent of degradation observed within the microstructures of the pig femora were consistent with bacterial bioerosion. The early occurrence of bioerosion within the Riseholme samples suggested that enteric putrefactive bacteria are primarily responsible for characteristic internal bone bioerosion. The distribution of bioerosion amongst the buried/unburied and stillborn/juvenile pig remains also supported an endogenous model. Bone from stillborn neonatal carcasses always demonstrated immaculate histological preservation due to the intrinsic sterility of newborn infant intestinal tracts. Bioerosion within the internal microstructure of mature bone will reflect the extent to which the skeletal element was exposed to putrefaction. Bone histology should be useful in reconstructing early taphonomic events. There is likely to be a relationship between post mortem processes that deny enteric gut bacteria access to internal bone microstructures and the survival of biomolecules.

Preamplification procedure for the analysis of ancient DNA samples

In ancient DNA studies the low amount of endogenous DNA represents a limiting factor that often hampers the result achievement. In this study we extracted the DNA from nine human skeletal remains of different ages found in the Byzantine cemetery of Abdera Halkidiki and in the medieval cemetery of St. Spiridion in Rhodes (Greece). Real-time quantitative polymerase chain reaction (qPCR) was used to detect in the extracts the presence of PCR inhibitors and to estimate the DNA content. As mitochondrial DNA was detected in all samples, amplification of nuclear targets, as amelogenin and the polymorphism M470V of the transmembrane conductance regulator gene, yielded positive results in one case only. In an effort to improve amplification success, we applied, for the first time in ancient DNA, a preamplification strategy based on TaqMan PreAmp Master Mix. A comparison between results obtained from nonpreamplified and preamplified samples is reported. Our data, even if preliminary, show that the TaqMan PreAmp procedure may improve the sensitivity of qPCR analysis.

Association between ancient bone preservation and dna yield: a multidisciplinary approach

Ancient molecular typing depends on DNA survival in archaeological bones. Finding valuable tools to predict DNA presence in ancient samples, which can be measured prior to undertaking a genetic study, has become an important issue as a consequence of the peculiarities of archaeological samples. Since the survival of DNA is explained by complex interrelations of multiple variables, the aim of the present study was to analyze morphological, structural, chemical, and biological aspects of a set of medieval human bones, to provide an accurate reflection of the state of preservation of the bony components and to relate it with DNA presence. Archaeological bones that yielded amplifiable DNA presented high collagen content (generally more than 12%), low racemization values of aspartic acid (lesser than 0.08), leucine and glutamic acid, low infrared splitting factor, small size of crystallite, and more compact appearance of bone in the scanning electron micrographs. Whether these patterns are characteristic of ancient bones or specific of each burial site or specimen requires further investigation.

Sex determination of Joseon people skeletons based on anatomical, cultural and molecular biological clues

Sex determination is very integral to examinations conducted by anatomists on human skeletons discovered in the archaeological field. In Korea, as in other countries, cultural or anatomical information has been the tool of first resort in making such determinations. In cases in which anatomical examination has revealed only borderline characteristics, PCR-based analysis of X/Y-chromosome genes has been employed. Even so, there are as yet very few reports on how accurately the respective results correspond with each other. In this study on 34 examined medieval Korean skeletons, 11 (32.3%) showed perfectly matching results for the three methods of sex determination. In the cases in which the cultural and anatomical findings were discordant, the amelogenin assay corroborated either the former or the latter. Although we must admit the relatively limited role of aDNA analysis, when only very small amounts of amplifiable DNA remain, we believe that the amelogenin assay can be very meaningful to Korean anatomists when employed in adjunct to conventional anatomically or culturally based sex determination.

Ancient DNA and family relationships in a Pompeian house

Archaeological, anthropological and pathological data suggest that thirteen skeletons found in a house at the Pompeii archaeological site, dated to 79 A.D., belong to one family. To verify this and to identify the relationships between these individuals, we analyzed DNA extracted from bone specimens. Specifically, hypervariable segment 1 (HVS1) of the human mitochondrial DNA (mtDNA) control region was amplified in two overlapping polymerase chain reactions and the sequences were compared to the revised Cambridge Reference Sequence. As independent controls, other polymorphic sites in HVS1, HVS2 and in the coding region were analyzed. We also amplified some short tandem repeats of the thirteen specimens. This study revealed that six of the thirteen individuals are indeed closely related.

Novel methods of molecular sex identification from skeletal tissue using the amelogenin gene

Sex identification from skeletal material is of vital importance in order to reconstruct the demographic variables of an individual in forensic genetics and ancient DNA (aDNA) analysis. When the use of conventional methods of sex identification are impossible, molecular analysis of the X and Y chromosomes provides an expedient solution. Two novel systems of molecular sex identification suitable for skeletal material using the amelogenin gene are described, beginning in intron 2-3, spanning exon 3 and ending in intron 3-4. This area was optimal for sexing, as it includes 14 sex-specific polymorphic regions in addition to an indel (insertion or deletion of nucleotides). Once optimised and working with 100% efficiency on the controls, these procedures were applied to a collection of miscellaneous archaeological skeletons (ex situ) sourced from the Raymond Dart Collection of Human Skeletons (Dart Collection). This collection was used to optimise these techniques for skeletal remains derived from an archaeological context. These methods produced 46.66% sex results for the ex situ sample, which is within the normal range for aDNA studies. These new techniques are optimal for sex identification, with both the inherent control of isolating many sex-specific features and combined with the use of sensitive micro-fluidic electrophoresis.

Genetic analysis on Tuoba Xianbei remains excavated from Qilang Mountain Cemetery in Qahar Right Wing Middle Banner of Inner Mongolia

Sixteen sequences of the hypervariable segment I (HVS-I, 16039-16398) in mtDNA control region from ancient Tuoba Xianbei remains excavated from Qilang Mountain Cemetery were analyzed. In which, 13 haplotypes were found by 25 polymorphic sites. The haplotype diversity and nucleotide diversity were 0.98 and 0.0189, respectively, and the mean of nucleotide number differences was 6.25. Haplogroup analysis indicates these remains mainly belong to haplogroup C (31.25%) and D (43.75%). According to the published data were considered, we can suggest that the Tuoba Xianbei presented a close genetic affinity to Oroqen, Outer Mongolian and Ewenki populations, especially Oroqen.

Methods to improve the yield and quality of DNA from dried and processed figs

We describe here a molecular method that can be used to detect genome traits of a given horticultural item at each stage from the farm to the market. We developed a procedure to extract and amplify by PCR DNA obtained from complex matrixes, such as dried figs and fig jam. Few fragmented DNA molecules can be recovered from food products. However, we were able to increase the yield of PCR reactions by successfully applying an enzymatic repair protocol to retrieved DNA.

Young adult mortality following severe physiological stress in childhood: skeletal evidence

Numerous studies report that early childhood biological stress impairs health in later adulthood. Overwhelmingly these studies are based on modern data, when health conditions are quite good by historical standards. Potentially much can be learned by examining the relationship within populations that lived under enormous pressure, enduring life expectancies less than one-half of those found in industrial countries of the late twentieth century. This paper uses the skeletal remains of over 3000 individuals who lived in the Western Hemisphere as long as 6000 years ago to probe the connection between several markers of early childhood stress and survival from approximately age 15 to 30. In a logit model with explanatory variables that control for sex and ethnicity, the probability of survival was systematically 7.6 percentage points less among individuals with two or more hypoplasias, 3.9 percentage points less for those with cribra orbitalia or porotic hyperostosis, and 4.6 percentage points less for individuals stunted by 20 cm in height. The paper compares these findings with those from studies on modern data and concludes with suggestions for research.

2000 Year-old ancient equids: an ancient-DNA lesson from pompeii remains

Ancient DNA extracted from 2000 year-old equine bones was examined in order to amplify mitochondrial and nuclear DNA fragments. A specific equine satellite-type sequence representing 3.7%-11% of the entire equine genome, proved to be a suitable target to address the question of the presence of aDNA in ancient bones. The PCR strategy designed to investigate this specific target also allowed us to calculate the molecular weight of amplifiable DNA fragments. Sequencing of a 370 bp DNA fragment of mitochondrial control region allowed the comparison of ancient DNA sequences with those of modern horses to assess their genetic relationship. The 16S rRNA mitochondrial gene was also examined to unravel the post-mortem base modification feature and to test the status of Pompeian equids taxon on the basis of a Mae III restriction site polymorphism.

Ancient DNA as a multidisciplinary experience

Investigation into DNA from archeological remains offers an inestimable tool for unraveling the history of humankind. However, a series of basic and technical difficulties renders the analysis of ancient DNA (aDNA) molecules troublesome, depending either on their own peculiar characteristics or on the complexity of processes affecting the bone matrix over time, all compromising the preservation of ancient DNA. This review underlines the contribution of many different disciplines, in particular molecular biology and genetics, to overcome these obstacles. The role of each expertise is illustrated to appropriately address the questions arising in aDNA investigations.

Sexual dimorphism in the robusticity of long bones of infants and young children

It is difficult to determine the sex of subadult skeletal remains because there is a little sexual dimorphism present pre-pubertally. In a historic sample of 24 children aged 0-4 years from St. Mary's Anglican Church,Marion, South Australia, the robustness of femora and of humeri was correlated with sexually dimorphic mandibular morphology. Ratios of midshaft circumference to diaphyseal length of humeri and femora and the ratio of minimum circumference to diaphyseal length of the humerus showed correlation with sex determined by mandibular morphology, male indices being greater than the female ones. The humerus midshaft circumference index showed the greatest difference between sexes (P value=0.0002). The results need confirmation on known-sex skeletal remains, but for the moment this robusticity dimorphism seems to be a new discovery for osteological practice.

Enzymatic repair of selected cross-linked homoduplex molecules enhances nuclear gene rescue from Pompeii and Herculaneum remains

Ancient DNA (aDNA) samples extracted from the bone remains of six equids buried by the Vesuvius eruption in 79 AD were investigated to test pre-amplification and enzymatic repair procedures designed to enhance the rescue of nuclear genes. The extracts, which proved all positive for Equidae mtDNA amplification, proved positive only four times out of 18 when tested for single-copy Equidae nuclear genes (epsilon globin, p53 and gamma interferon). Pre-amplification did not change the number of retrieved aDNA sequences but 10 times out of 14 enzymatic repair restored the amplifiability of the genes analysed, proving that repair increases the rate of successful rescue from 22 to alpha(lambda)mu(omicron)sigma(tau) 80%. These findings support the hypothesis that some of these cross-linked aDNA molecules, which are not completely separated when DNA is extracted under denaturing conditions, become homoduplex substrates for Pol I and/or T4 ligase action upon renaturation. aDNA authenticity is proved by the homology of the nucleotide sequences of loci tested to the corresponding modern Equidae sequences. Data also indicate that cross-linked homoduplex molecules selected by denaturation of the extract are repaired without any chimera formation. The general features of aDNA amplification with and without denaturation and enzymatic repair are discussed.

Detection of DNA in ancient bones using histochemical methods

We describe histochemical techniques for detecting DNA within the osteocytic lacunae of ancient bones. The bones examined were fragments of femurs from two human individuals found in the Pompeian C. I. Polybius house and fragments of metacarpals from two horses (Equus sp.) found in the Pompeian "Casti Amanti" house. Both buildings were buried by the 79 A. D. Vesuvius eruption. Fragments of femurs from a modern horse, a modern swine and a modern amphibian also were studied as controls. Some bone sections were stained with two different DNA-specific fluorochromes, 4'-'6-diamidino-2-phenylindole (DAPI) and chromomycin A3 (CMA), while others were stained by the Feulgen reaction. All of the techniques gave a positive reaction within the osteocytic lacunae. Histological analysis of the undecalcified, ground and unstained sections agreed well with results of bone sections stained with either the fluorochromes or the Feulgen reaction. Bones showing good histology also were positive by our DNA-specific stain. Histochemical and histological analyses correlated well with the success of DNA extraction and amplification. Using conventional DNA-specific histochemical techniques in conjunction with histological analysis can be useful in the study of DNA extracted from ancient bone remains while reducing both the amount of time and cost.