Advanced analytical diagnostics applied to human osteological remains

Le ossa antiche, recuperate dai contesti archeologici e preservati all’interno dei Musei, rappresentano una preziosa fonte di informazioni sull'alimentazione, lo stato di salute, la mobilità delle popolazioni antiche nonché sulla demografia e condizioni ambientali del passato, utili a ricercatori e accademici. A seguito dello sviluppo di moderne tecnologie delle scienze omiche, i reperti osteologici sono sempre più richiesti e questo ha comportato un aumento dell'analisi del DNA antico (aDNA). I metodi di campionamento per l'estrazione del DNA antico sono prevalentemente distruttivi e spesso possono compromettere i reperti osteologici per ulteriori future analisi o per studi in altri campi di ricerca. Oltre al campionamento invasivo e distruttivo, in condizioni di scarsa conservazione dell’osso archeologico causata da alterazioni tafonomiche e diagenetiche, il sequenziamento del DNA antico può essere un'operazione estremamente costosa. Dati gli elevati costi della procedura di sequenziamento dell'aDNA, in questo lavoro di ricerca è stato condotto uno studio analitico mediante spettroscopia a raggi infrarossi (FTIR) per sviluppare un metodo di pre-screening affidabile, veloce ed economico per determinare la presenza/assenza di molecole genetiche in un campione osseo archeologico. La spettroscopia IR è uno strumento utile in quanto è rapida, minimamente distruttiva, economica e sensibile alle variazioni delle proprietà strutturali delle componenti organiche (collagene) e inorganiche (nano cristalli di bioapatite) che costituiscono l’osso. A livello ultrastrutturale, le componenti organiche e inorganiche possono stabilire forti legami con il DNA , stabilizzandolo e determinando la sua sopravvivenza nel tempo. Da campioni archeologici (di epoche e provenienze diverse) estremamente alterati a moderne ossa fresche, abbiamo valutato la sensibilità e l'efficacia di nuovi parametri IR per caratterizzare la diagenesi subita dalle ossa tenendo in considerazioni i cambiamenti delle condizioni climatico–ambientali e di seppellimento. Il lavoro è stato esteso per esaminare le modificazioni indotte dalla diagenesi sulla struttura secondaria del collagene conservato, valutandone gli effetti sui cristalli di bioapatite. I risultati ottenuti dimostrano che il parametro IR che descrive l’ordine/disordine atomico, utilizzato in questa ricerca, è vantaggioso per il monitoraggio di variazioni minime nella struttura e nelle proprietà chimiche della bioapatite nonché indirettamente nel collagene. Questo metodo potrebbe migliorare il processo di selezione dei campioni ossei nonché la loro idoneità per analisi specifiche, ad es. analisi genetiche, paleoproteomiche e degli isotopi stabili sulla base delle analisi spettrali. Viene qui proposto inoltre un modello predittivo funzionale con i parametri infrarossi utilizzati, al fine di determinare il parametro più predittivo per la prensenza/assenza di DNA, utile per ridurre i costi delle analisi genetiche. Dai dati ottenuti, la qualità/quantità di aDNA risulterebbe non essere determinabile a causa dell'influenza di fattori ambientali locali.Ancient bone tissues, recovered from archaeological contexts and preserved within the Museums, represent a valuable source of information on health, diet, mobility of ancient populations as well as on demographics and environmental conditions of the past, useful for researchers and academics. Following the development of modern technologies of omic sciences, osteological finds are increasingly requested and this has led to an increase in the analysis of ancient DNA (aDNA). Sampling methods for ancient DNA extraction are predominantly destructive and may often compromise osteological findings for further future analysis or for studies in other research fields. In addition to invasive and destructive sampling, in poor conservation conditions of the archaeological bone caused by taphonomic and diagenetic alterations, the sequencing of ancient DNA can be an extremely expensive operation. Given the high costs of the aDNA sequencing procedure, an analytical study by means of infrared spectroscopy (FTIR) was conducted in this research work to develop a reliable, fast and inexpensive pre-screening method to determine presence/absence of genetic molecules in an archaeological bone sample. Infrared spectroscopy is a useful tool fast, minimally destructive, inexpensive and sensitive to changes in the structural properties of the organic (collagen) and inorganic (bioapatite nanocrystals) components that make up bone. At the ultrastructural level, the organic and inorganic components of bone may stabilize strong bounds with DNA, stabilizing it and determining its survival over time. The sensitivity and efficiency of new IR parameters was tested on fresh bones and extremely altered archaeological samples, characterized by different chronology and origin. The diagenesis undergone by the bones was characterized taking into account changes in climatic-environmental and burial conditions. The research was expanded by examining changes induced by diagenesis on the secondary structure of collagen preserved, evaluating their effects on bioapatite crystals. The results obtained demonstrate that the IR parameter used in this research, that describes the atomic order/disorder, is advantageous for monitoring minimal changes in the structure and chemical properties of bioapatite as well as indirectly in collagen. This method may improve the selection process of bone samples as well as their suitability for specific analyzes, e.g. genetic, paleo-proteomic and stable isotope analysis on the basis of infrared spectra. A functional predictive model with the infrared parameters used, in order to determine the most predictive parameter for the presence/absence of DNA, allowing to reduce the costs of genetic analyzes, was proposed here. The results obtained, shows that the quality/quantity of aDNA cannot be determined due to the influence of local environmental factors

The Genetic Origin of Daunians and the Pan-Mediterranean Southern Italian Iron Age Context.

The geographical location and shape of Apulia, a narrow land stretching out in the sea at the South of Italy, made this region a Mediterranean crossroads connecting Western Europe and the Balkans. Such movements culminated at the beginning of the Iron Age with the Iapygian civilization which consisted of three cultures: Peucetians, Messapians, and Daunians. Among them, the Daunians left a peculiar cultural heritage, with one-of-a-kind stelae and pottery, but, despite the extensive archaeological literature, their origin has been lost to time. In order to shed light on this and to provide a genetic picture of Iron Age Southern Italy, we collected and sequenced human remains from three archaeological sites geographically located in Northern Apulia (the area historically inhabited by Daunians) and radiocarbon dated between 1157 and 275 calBCE. We find that Iron Age Apulian samples are still distant from the genetic variability of modern-day Apulians, they show a degree of genetic heterogeneity comparable with the cosmopolitan Republican and Imperial Roman civilization, even though a few kilometers and centuries separate them, and they are well inserted into the Iron Age Pan-Mediterranean genetic landscape. Our study provides for the first time a window on the genetic make-up of pre-Roman Apulia, whose increasing connectivity within the Mediterranean landscape, would have contributed to laying the foundation for modern genetic variability. In this light, the genetic profile of Daunians may be compatible with an at least partial autochthonous origin, with plausible contributions from the Balkan peninsula

Anthropological analysis and paleo-demographic study of human skeletal remains from the late ancient necropolis of Biverone (4th-5th c.AD), San Stino Di Livenza (Venice, Italy)

The study of the osteological collections preserved at the Museum of Anthropology – University of Padua coming from archaeological excavations dated to the end of 19th and 20th century, is a great opportunity to disseminate still unpublished anthropological data. The aim of this work was the analysis through modern anthropological methodology of the human skeletal remains brought to light in 1983 at the necropolis of Biverone, municipality of San Stino di Livenza (Venice, Northeast Italy). The site, close to Livenza River, began its decadence in the Late Ancient period (4th-5th c. AD) as a result of regional morphological variations and barbarian invasions, that caused an important local depopulation

Anthropological analysis and paleo-demographic study of human skeletal remains from the late ancient necropolis of Biverone (4th-5th c.AD), San Stino Di Livenza (Venice, Italy)

The study of the osteological collections preserved at the Museum of Anthropology – University of Padua coming from archaeological excavations dated to the end of 19th and 20th century, is a great opportunity to disseminate still unpublished anthropological data. The aim of this work was the analysis through modern anthropological methodology of the human skeletal remains brought to light in 1983 at the necropolis of Biverone, municipality of San Stino di Livenza (Venice, Northeast Italy). The site, close to Livenza River, began its decadence in the Late Ancient period (4th-5th c. AD) as a result of regional morphological variations and barbarian invasions, that caused an important local depopulation

Ancient genomes reveal structural shifts after the arrival of Steppe-related ancestry in the Italian Peninsula

Across Europe, the genetics of the Chalcolithic/Bronze Age transition is increasingly characterized in terms of an influx of Steppe-related ancestry. The effect of this major shift on the genetic structure of populations in the Italian Peninsula remains underexplored. Here, genome-wide shotgun data for 22 individuals from commingled cave and single burials in Northeastern and Central Italy dated between 3200 and 1500 BCE provide the first genomic characterization of Bronze Age individuals (n = 8; 0.001–1.2× coverage) from the central Italian Peninsula, filling a gap in the literature between 1950 and 1500 BCE. Our study confirms a diversity of ancestry components during the Chalcolithic and the arrival of Steppe-related ancestry in the central Italian Peninsula as early as 1600 BCE, with this ancestry component increasing through time. We detect close patrilineal kinship in the burial patterns of Chalcolithic commingled cave burials and a shift away from this in the Bronze Age (2200–900 BCE) along with lowered runs of homozygosity, which may reflect larger changes in population structure. Finally, we find no evidence that the arrival of Steppe-related ancestry in Central Italy directly led to changes in frequency of 115 phenotypes present in the dataset, rather that the post-Roman Imperial period had a stronger influence, particularly on the frequency of variants associated with protection against Hansen’s disease (leprosy). Our study provides a closer look at local dynamics of demography and phenotypic shifts as they occurred as part of a broader phenomenon of widespread admixture during the Chalcolithic/Bronze Age transition