Methodological strategies to assess the degree of bone preservation for ancient DNA studies.

BACKGROUND: Archaeological bones contain only small amounts of DNA due to post-mortem DNA degradation and the changes endogenous DNA is subjected to during diagenesis. An important step before undertaking such time-consuming and costly analyses as ancient DNA investigation is to predict the presence of DNA in ancient samples. To date, the leading screening method has been amino acid racemization; however, other analytical techniques can also be used to assess the degree of bone preservation. AIM: The aim of the present study was to relate the presence of DNA with bone preservation in order to select samples potentially suitable for ancient DNA analysis. SUBJECTS AND METHODS: Bones collected from several archaeological sites, different locations (cave, rockshelter or sub divo) and diachronic periods were selected for analytical and spectroscopic analysis in order to correlate bone tissue preservation with the presence of DNA. Different techniques were combined to assess the degree of preservation of organic and inorganic components. RESULTS: As determined by different analytical methods, preservation of the inorganic component was best associated with the presence of DNA. CONCLUSION: Evaluation of the bone preservation state may be an efficient step to predict the presence of DNA in ancient samples prior to aDNA analysis.

Population dynamic of the extinct European aurochs: genetic evidence of a north-south differentiation pattern and no evidence of post-glacial expansion.

BACKGROUND: The aurochs (Bos primigenius) was a large bovine that ranged over almost the entirety of the Eurasian continent and North Africa. It is the wild ancestor of the modern cattle (Bos taurus), and went extinct in 1627 probably as a consequence of human hunting and the progressive reduction of its habitat. To investigate in detail the genetic history of this species and to compare the population dynamics in different European areas, we analysed Bos primigenius remains from various sites across Italy. RESULTS: Fourteen samples provided ancient DNA fragments from the mitochondrial hypervariable region. Our data, jointly analysed with previously published sequences, support the view that Italian aurochsen were genetically similar to modern bovine breeds, but very different from northern/central European aurochsen. Bayesian analyses and coalescent simulations indicate that the genetic variation pattern in both Italian and northern/central European aurochsen is compatible with demographic stability after the last glaciation. We provide evidence that signatures of population expansion can erroneously arise in stable aurochsen populations when the different ages of the samples are not taken into account. CONCLUSIONS: Distinct groups of aurochsen probably inhabited Italy and northern/central Europe after the last glaciation, respectively. On the contrary, Italian and Fertile Crescent aurochsen likely shared several mtDNA sequences, now common in modern breeds. We argue that a certain level of genetic homogeneity characterized aurochs populations in Southern Europe and the Middle East, and also that post-glacial recolonization of northern and central Europe advanced, without major demographic expansions, from eastern, and not southern, refugia.

Genealogical discontinuities among Etruscan, Medieval, and contemporary Tuscans.

The available mitochondrial DNA (mtDNA) data do not point to clear genetic relationships between current Tuscans and the Bronze-Age inhabitants of Tuscany, the Etruscans. To understand how and when such a genetic discontinuity may have arisen, we extracted and typed the mtDNAs of 27 medieval Tuscans from an initial sample of 61, spanning a period between the 10th and 15th century AD. We then tested by serial coalescent simulation various models describing the genealogical relationships among past and current inhabitants of Tuscany, the latter including three samples (from Murlo, Volterra, and Casentino) that were recently claimed to be of Etruscan descent. Etruscans and medieval Tuscans share three mitochondrial haplotypes but fall in distinct branches of the mitochondrial genealogy in the only model that proved compatible with the data. Under that model, contemporary people of Tuscany show clear genetic relationships with Medieval people, but not with the Etruscans, along the female lines. No evidence of excess mutation was found in the Etruscan DNAs by a Bayesian test, and so there is no reason to suspect that these results are biased by systematic contamination of the ancient sequences or laboratory artefacts. Extensive demographic changes before AD 1000 are thus the simplest explanation for the differences between the contemporary and the Bronze-Age mtDNAs of Tuscany. Accordingly, genealogical continuity between ancient and modern populations of the same area does not seem a safe general assumption, but rather a hypothesis that, when possible, should be tested using ancient DNA analysis.

Lorenzo Lotto's painting materials: an integrated diagnostic approach.

This paper presents the results of a comprehensive diagnostic investigation carried out on five paintings (three wood panels and two paintings on canvas) by Lorenzo Lotto, one of the most significant artists of the Italian Renaissance in the first half of 16th century. The paintings considered belong to 1508-1522 period, corresponding to the most significant years of Lotto's evolution. A wide array of non-invasive (reflectance spectrometry and X-ray fluorescence) and micro-invasive analytical techniques (optical microscopy, scanning electron microscopy with energy dispersive spectroscopy, micro-FTIR spectroscopy, micro-Raman spectroscopy, gas chromatography coupled with mass spectrometry and high performance liquid chromatography coupled with photodiode array detection and mass spectrometry) were applied in order to provide a large set of significant data, limiting as much as possible the sampling. This study has proved that Lotto's painting palette was typical of Venetian practice of that period, but some significant peculiarities emerged: the use of two kinds of red lakes, the addition of calcium carbonate and colourless powdered glass, the latter frequently found in pictorial and ground layers. Moreover, the integrated investigation showed that Lotto's technique was sometimes characterized by the use of coloured priming and multi-layer sequences with complex mixtures. Chromatographic analyses allowed to identify in all specimens: azelaic, palmitic and stearic acids, generally referring to the presence of drying oils. The extension of additional non-invasive examination to about 50 paintings by the same author, spanning from 1505 to around 1556, helped to verify the evolution in the use of some pigments, such as the yellow ones, where Pb-Sb yellow was used alongside Pb-Sn yellow.

Raman microspectrometric investigation of wall paintings in S. Giovanni Evangelista Abbey in Parma: a comparison between two artists of the 16th century.

Micro-Raman spectroscopy, combined with gas chromatography and ultra-violet fluorescence photography, was used to study some wall paintings in the S. Giovanni Evangelista Abbey in Parma, Italy. The restoration of some painted chapels enabled a comparison between two painters of the 16th century: Parmigianino (Girolamo Francesco Maria Mazzola, 1503-1540) and Michelangelo Anselmi (1492?-1556?). Micro-Raman spectroscopy determined the palette used by the artists, leading to the identification of different white, yellow, red, brown, green, blue and black pigments. Some pigments are evidence of later restorations. Gas chromatography combined with mass spectroscopy revealed the presence of organic binding media and enabled to distinguish between fresco and secco paintings.

Presence and racemisation of amino acids in calcium oxalate patinas. A case study from the Baptistery in Parma, Italy.

The organic material present in oxalate patinas, collected from the stone external surfaces of the Baptistery in Parma (Italy), was analysed by GC-MS. The high racemisation levels determined for several specific amino acids indicate that microbial activity could contribute to the formation and modification of the organic material leading to the calcium oxalate patinas.

Cleaning painted surfaces: evaluation of leaching phenomenon induced by solvents applied for the removal of gel residues.

Cleaning is one of the most important, delicate, and at the same time controversial processes in the conservation treatment of paintings. Although a strict definition of cleaning would be the removal of dirt, grime, or other accretions (surface cleaning), in the conservation field, cleaning is used in the broader meaning to include thinning/removing altered or "unwanted layers" of materials without damaging or altering the physicochemical properties of the surfaces to be preserved. The cleaning of unvarnished paintings is one of the most critical issues that are currently discussed. Several studies exist regarding different cleaning tools, such as gels, soaps, enzymes, ionic liquids, and foams, as well as various dry methods and lasers, but only a few have been performed on the risk associated with the use of water and organic solvents for the cleaning treatments in relation to the original paint binder. The aim of the study is to verify analytically the behavior of water gelling agents during cleaning treatments and the interaction of the following elements: water or organic solvents applied for the removal of gel residues with the original lipid paint binder. For this purpose, the study was conducted on a fragment of canvas painting (sixteenth to seventeenth century) of Soprintendenza per i Beni Storici, Artistici ed Etnoantropologici del Friuli Venezia Giulia (Superintendence for the Historical, Artistic and Ethno-anthropological Heritage of Friuli Venezia Giulia), Udine by means of Fourier transform infrared spectroscopy, gas chromatography/mass spectrometry, and scanning electron microscopy.

Organic materials in the wall paintings in Pompei: a case study of Insula del Centenario.

BACKGROUND: The present research concerns the Roman wall paintings preserved at Insula del Centenario (IX, 8), the important Pompeian block situated in the Regio IX, along Via di Nola. RESULTS: The aims of this research are two: to verify the presence of lipidic and proteinaceous material to spread the pigments, and to identify organic matter in painting materials owing to previous restoration works. The samples collected from the wall paintings of different rooms have been investigated by Fourier Transform Infrared Spectroscopy (FT-IR), and Gas Chromatography/ Mass Spectrometry (GC/MS). CONCLUSIONS: The analytical results show that these Roman wall paintings were realized without the use of lipidic and proteinaceous materials, supposedly in fresco technique. Moreover, it was detected that wax, egg, and animal glue were used in previous restoration works for protective purpose and to restore the wall paintings to their original brilliant colours.

Green pigments of the Pompeian artists' palette.

Green colored samples on wall paintings and green powder from a pigment pot found in Pompeii area are investigated by micro-Raman, FT-IR and, for one sample, SEM-EDX. To obtain the green color, green earths and malachite were used, together with mixture of Egyptian blue and yellow ochre. The mineralogical identification of the green earths has been attempted through the comparison of the vibrational features, discriminating between celadonite and glauconite spectra. Traces of a modern synthetic pigment containing copper phthalocyanine were found in a fresco fragment.

A 28,000 years old Cro-Magnon mtDNA sequence differs from all potentially contaminating modern sequences.

BACKGROUND: DNA sequences from ancient specimens may in fact result from undetected contamination of the ancient specimens by modern DNA, and the problem is particularly challenging in studies of human fossils. Doubts on the authenticity of the available sequences have so far hampered genetic comparisons between anatomically archaic (Neandertal) and early modern (Cro-Magnoid) Europeans. METHODOLOGY/PRINCIPAL FINDINGS: We typed the mitochondrial DNA (mtDNA) hypervariable region I in a 28,000 years old Cro-Magnoid individual from the Paglicci cave, in Italy (Paglicci 23) and in all the people who had contact with the sample since its discovery in 2003. The Paglicci 23 sequence, determined through the analysis of 152 clones, is the Cambridge reference sequence, and cannot possibly reflect contamination because it differs from all potentially contaminating modern sequences. CONCLUSIONS/SIGNIFICANCE: The Paglicci 23 individual carried a mtDNA sequence that is still common in Europe, and which radically differs from those of the almost contemporary Neandertals, demonstrating a genealogical continuity across 28,000 years, from Cro-Magnoid to modern Europeans. Because all potential sources of modern DNA contamination are known, the Paglicci 23 sample will offer a unique opportunity to get insight for the first time into the nuclear genes of early modern Europeans.

Genetic variation in prehistoric Sardinia.

We sampled teeth from 53 ancient Sardinian (Nuragic) individuals who lived in the Late Bronze Age and Iron Age, between 3,430 and 2,700 years ago. After eliminating the samples that, in preliminary biochemical tests, did not show a high probability to yield reproducible results, we obtained 23 sequences of the mitochondrial DNA control region, which were associated to haplogroups by comparison with a dataset of modern sequences. The Nuragic samples show a remarkably low genetic diversity, comparable to that observed in ancient Iberians, but much lower than among the Etruscans. Most of these sequences have exact matches in two modern Sardinian populations, supporting a clear genealogical continuity from the Late Bronze Age up to current times. The Nuragic populations appear to be part of a large and geographically unstructured cluster of modern European populations, thus making it difficult to infer their evolutionary relationships. However, the low levels of genetic diversity, both within and among ancient samples, as opposed to the sharp differences among modern Sardinian samples, support the hypothesis of the expansion of a small group of maternally related individuals, and of comparatively recent differentiation of the Sardinian gene pools.

Genetic analysis of the skeletal remains attributed to Francesco Petrarca.

We report on the mitochondrial DNA (mtDNA) analysis of the supposed remains of Francesco Petrarca exhumed in November 2003, from the S. Maria Assunta church, in Arquà Padua (Italy) where he died in 1374. The optimal preservation of the remains allowed the retrieval of sufficient mtDNA for genetic analysis. DNA was extracted from a rib and a tooth and mtDNA sequences were determined in multiple clones using the strictest criteria currently available for validation of ancient DNA sequences, including independent replication. MtDNA sequences from the tooth and rib were not identical, suggesting that they belonged to different individuals. Indeed, molecular gender determination showed that the postcranial remains belonged to a male while the skull belonged to a female. Historical records indicated that the remains were violated in 1630, possibly by thieves. These results are consistent with morphological investigations and confirm the importance of integrating molecular and morphological approaches in investigating historical remains.

Ancient biomolecules from deep ice cores reveal a forested southern Greenland.

It is difficult to obtain fossil data from the 10% of Earth's terrestrial surface that is covered by thick glaciers and ice sheets, and hence, knowledge of the paleoenvironments of these regions has remained limited. We show that DNA and amino acids from buried organisms can be recovered from the basal sections of deep ice cores, enabling reconstructions of past flora and fauna. We show that high-altitude southern Greenland, currently lying below more than 2 kilometers of ice, was inhabited by a diverse array of conifer trees and insects within the past million years. The results provide direct evidence in support of a forested southern Greenland and suggest that many deep ice cores may contain genetic records of paleoenvironments in their basal sections.

The origin of European cattle: evidence from modern and ancient DNA.

Cattle domestication from wild aurochsen was among the most important innovations during the Neolithic agricultural revolution. The available genetic and archaeological evidence points to at least two major sites of domestication in India and in the Near East, where zebu and the taurine breeds would have emerged independently. Under this hypothesis, all present-day European breeds would be descended from cattle domesticated in the Near East and subsequently spread during the diffusion of herding and farming lifestyles. We present here previously undescribed genetic evidence in contrast with this view, based on mtDNA sequences from five Italian aurochsen dated between 7,000 and 17,000 years B.P. and >1,000 modern cattle from 51 breeds. Our data are compatible with local domestication events in Europe and support at least some levels of introgression from the aurochs in Italy. The distribution of genetic variation in modern cattle suggest also that different south European breeds were affected by introductions from northern Africa. If so, the European cattle may represent a more variable and valuable genetic resource than previously realized, and previous simple hypotheses regarding the domestication process and the diffusion of selected breeds should be revised.

Evidence for a genetic discontinuity between Neandertals and 24,000-year-old anatomically modern Europeans.

During the late Pleistocene, early anatomically modern humans coexisted in Europe with the anatomically archaic Neandertals for some thousand years. Under the recent variants of the multiregional model of human evolution, modern and archaic forms were different but related populations within a single evolving species, and both have contributed to the gene pool of current humans. Conversely, the Out-of-Africa model considers the transition between Neandertals and anatomically modern humans as the result of a demographic replacement, and hence it predicts a genetic discontinuity between them. Following the most stringent current standards for validation of ancient DNA sequences, we typed the mtDNA hypervariable region I of two anatomically modern Homo sapiens sapiens individuals of the Cro-Magnon type dated at about 23 and 25 thousand years ago. Here we show that the mtDNAs of these individuals fall well within the range of variation of today's humans, but differ sharply from the available sequences of the chronologically closer Neandertals. This discontinuity is difficult to reconcile with the hypothesis that both Neandertals and early anatomically modern humans contributed to the current European gene pool.

The Etruscans: a population-genetic study.

The origins of the Etruscans, a non-Indo-European population of preclassical Italy, are unclear. There is broad agreement that their culture developed locally, but the Etruscans' evolutionary and migrational relationships are largely unknown. In this study, we determined mitochondrial DNA sequences in multiple clones derived from bone samples of 80 Etruscans who lived between the 7th and the 3rd centuries b.c. In the first phase of the study, we eliminated all specimens for which any of nine tests for validation of ancient DNA data raised the suspicion that either degradation or contamination by modern DNA might have occurred. On the basis of data from the remaining 30 individuals, the Etruscans appeared as genetically variable as modern populations. No significant heterogeneity emerged among archaeological sites or time periods, suggesting that different Etruscan communities shared not only a culture but also a mitochondrial gene pool. Genetic distances and sequence comparisons show closer evolutionary relationships with the eastern Mediterranean shores for the Etruscans than for modern Italian populations. All mitochondrial lineages observed among the Etruscans appear typically European or West Asian, but only a few haplotypes were found to have an exact match in a modern mitochondrial database, raising new questions about the Etruscans' fate after their assimilation into the Roman state.