Archaeological genetics: a preliminary overview of the Iron Age Italian population

Recent studies suggest that Italian population shows a higher degree of internal genomic variability than other European populations. This scenario is the result of complex demographic dynamics, dating back mainly from Late Palaeolithic and Neolithic, but also dating to Metal Ages. In fact, numerous population movements occurred between the Mediterranean basin and the Middle East during the Metals Ages, a period that has determined the transformation of the first social organizations in ancient civilizations. During the 1st millennium BC, Italy appeared as a patchwork of different peoples, either whose origin remain still largely unresolved (e.g. Ligures, Veneti and, Etruscans), or that are known to have originated from specific migration processes (e.g. Celts in North-Western Italy; Greeks and Phoenician-Punic in Southern Italy, Sardinia, and Sicily). In this thesis, I focused my attention on the Italian Iron Age period, in particular on the ancient ‘Piceni’ (Case Study I) and ‘Punic’ (Case Study II) populations, and I analysed the ancient DNA (aDNA) of skeletal remains coming from the Novilara necropolis located in Central Italy (Case Study I), and from Tharros (Capo San Marco - Sardinia, IT) and Lilybaeum (Corso Gramsci - Sicily, IT) necropolises (Case Study II). I have applied different aDNA protocols and methods in order to obtain ancient mitochondrial DNA (HVS-I) (Case Study I and II) or complete genome (Case Study II). This research provides a pioneering survey on the ancient genetic diversity of Italy, contributing to disentangle the migration patterns and the relationships between ancient and presentday populations of the Mediterranean basin

Izostanak mutacija humanoga interferon alfa-2b gena u radnika kronično izloženih ionizirajućem zračenju

Individuals chronically exposed to low-level ionising radiation (IR) run the risk of harmful and long-term adverse health effects, including gene mutations and cancer development. The search for reliable biomarkers of IR exposure in human population is still of great interest, as they may have a great implementation potential for the surveillance of occupationally exposed individuals. In this context, and considering previous literature, this study aimed to identify mutations in the human interferon alpha-2b (hIFNα-2b) as a potential biomarker of occupational chronic low-dose IR exposure linking low-IR exposure to the effects on haematopoiesis and reduced immunity. The analysis was performed in the genomic DNA of 51 uranium miners and 38 controls from Kazakhstan, and in 21 medical radiology workers and 21 controls from Italy. hIFNα-2b gene mutations were analysed with the real-time polymerase chain reaction (PCR) or Sanger sequencing. However, none of the investigated workers had the hIFNα-2b mutation. This finding highlights the need for further research to identify biomarkers for early detection of health effects associated with chronic low-dose IR exposure.Kronična izloženost niskim razinama ionizirajućega zračenja povezana je s rizikom od dugoročnih štetnih posljedica za zdravlje, što obuhvaća i mutacije gena te nastanak raka. U tijeku je potraga za pouzdanim biopokazateljima izloženosti ionizirajućem zračenju u ljudi, budući da njihova primjena može značajno unaprijediti praćenje profesionalno izloženih osoba. U tom smislu, a s obzirom na ranija saznanja, cilj je ovoga istraživanja bio utvrditi mutacije gena za proizvodnju humanoga interferona alfa-2b (hIFNα-2b gena) kao mogućega biopokazatelja profesionalne kronične izloženosti niskim dozama ionizirajućega zračenja, koje je usto povezano s djelovanjem na hematopoezu i pad imuniteta. Analiziran je genomski DNA 51 rudara u rudnicima uranija te 38 kontrolnih ispitanika iz Kazahstana, odnosno genomski DNA 21 zdravstvenoga radnika na radiologiji i 21 kontrolnoga ispitanika iz Italije. Mutacije hIFNα-2b gena utvrđivane su metodom lančane reakcije polimerazom u stvarnom vremenu (engl. real-time PCR) odnosno sekvenciranjem prema Sangeru, ali se pokazalo da niti jedan radnik nije imao niti jednu od deset traženih mutacija toga gena. Stoga ne preostaje drugo nego i dalje tražiti pouzdane biopokazatelje za rano otkrivanje štetnih zdravstvenih učinaka povezanih s kroničnom izloženosti niskim dozama ionizirajućega zračenja

Old wild wolves: ancient DNA survey unveils population dynamics in Late Pleistocene and Holocene Italian remains

Background The contemporary Italian wolf (Canis lupus italicus) represents a case of morphological and genetic uniqueness. Today, Italian wolves are also the only documented population to fall exclusively within the mitochondrial haplogroup 2, which was the most diffused across Eurasian and North American wolves during the Late Pleistocene. However, the dynamics leading to such distinctiveness are still debated. Methods In order to shed light on the ancient genetic variability of this wolf population and on the origin of its current diversity, we collected 19 Late Pleistocene-Holocene samples from northern Italy, which we analyzed at a short portion of the hypervariable region 1 of the mitochondrial DNA, highly informative for wolf and dog phylogenetic analyses. Results Four out of the six detected haplotypes matched the ones found in ancient wolves from northern Europe and Beringia, or in modern European and Chinese wolves, and appeared closely related to the two haplotypes currently found in Italian wolves. The haplotype of two Late Pleistocene samples matched with primitive and contemporary dog sequences from the canine mitochondrial clade A. All these haplotypes belonged to haplogroup 2. The only exception was a Holocene sample dated 3,250 years ago, affiliated to haplogroup 1. Discussion In this study we describe the genetic variability of the most ancient wolf specimens from Italy analyzed so far, providing a preliminary overview of the genetic make-up of the population that inhabited this area from the last glacial maximum to the Middle Age period. Our results endorsed that the genetic diversity carried by the Pleistocene wolves here analyzed showed a strong continuity with other northern Eurasian wolf specimens from the same chronological period. Contrarily, the Holocene samples showed a greater similarity only with modern sequences from Europe and Asia, and the occurrence of an haplogroup 1 haplotype allowed to date back previous finding about its presence in this area. Moreover, the unexpected discovery of a 24,700-year-old sample carrying a haplotype that, from the fragment here obtained, falls within the canine clade A, could represent the oldest evidence in Europe of such dog-rich clade. All these findings suggest complex population dynamics that deserve to be further investigated based on mitochondrial or whole genome sequencing

Dinamiche di popolamento a Tharros in et\ue0 punica. Analisi archeogenetiche preliminari dei reperti osteologici della tomba A2 della necropoli meridionale di Capo San Marco

Several human osteological remains were found in the burial called \u201cGrave A2\u201d, which was discovered during the archaeological campaign (2014) at the southern Punic necropolis of Tharros. In this paper, through the ancient DNA (aDNA) analysis of the first hypervariable segment (HVS-I) of the mitochondrial DNA (mtDNA), we tried to define the ethnic origin and possible kinship relationship between the individuals buried, as well as to determine genetic affinities with current human populations of the Mediterranean Area. Durante la campagna di scavo del 2014 presso la necropoli meridionale punica di Tharros \ue8 stata individuata una sepoltura, denominata Tomba A2, all\u2019interno della quale sono stati rinvenuti diversi reperti osteologici umani. Nel presente lavoro, si \ue8 cercato di definire attraverso l\u2019analisi del DNA antico (aDNA), e in particolare attraverso lo studio della prima regione ipervariabile (HVS-I) del DNA mitocondriale (mtDNA), l\u2019origine etnica e le eventuali relazioni di parentela degli inumati sepolti, nonch\ue9 determinare le affinit\ue0 genetiche conpopolazioni moderne dell\u2019area mediterranea

Genetic variability of CYP2D6, CYP2B6, CYP2C9 and CYP2C19 genes across the Italian Peninsula

Background: Environmental conditions and past migratory events may have shaped genetic heterogeneity of clinically relevant enzymes involved in the phase I metabolism of the most common therapeutic drugs. Aim: To investigate the genetic variability of CYP2D6, CYP2B6, CYP2C19 and CYP2C9 across the Italian Peninsula, by sampling only ancestrally and geographically homogeneous individuals from northern, central and southern Italy. Subjects and methods: A total of 25 SNPs were genotyped in 174 unrelated Italian individuals by means of multiplex PCR and minisequencing reactions. CYP2D6 genotypic data were used to predict phenotypes and the phylogenetic relationships among reconstructed haplotypes were represented by means of a Median Joining Network. Results: Pairwise Fisher Exact tests revealed significant differences between northern and southern Italy in the distribution of CYP2C19 genotypes, with the CYP2C19*2 allele appearing over-represented in northern Italy. Likewise, significant differences in the distribution of CYP2D6 genotypes (*4/*3, *4/*4 and *6/*4) responsible for the poor metabolizer phenotype were observed in northern with respect to both central and southern Italy. Conclusions: The north\u2013south structuring pattern showed by CYP2D6 and CYP2C19 underline how a deeper knowledge of the geographic distribution of alleles may improve clinical practice and help to avoid hypothetical bias in drug trials

Multiple selective events at the PRDM16 functional pathway shaped adaptation of western European populations to different climate conditions

Several studies highlighted the role of climate in shaping many human evolutionary processes. This occurred even in relatively recent times, having affected various human phenotypic traits, among which metabolic processes that orchestrate absorption and accumulation of substances to maintain energy homeostasis, that is critical for the survival of individuals in high energy-expenditure environments. To date, most researches have focalized on detection of climatic influence on SNPs' frequency in populations exposed to extreme environmental conditions or by comparing variation patterns between populations from different continents. In this study, we instead explored the genetic background of distinct western European human groups at loci involved in nutritional and thermoregulation processes, to test whether patterns of differential local adaptation to environmental conditions could be appreciated also at a lower geographical scale. Taking advantage from the 1000 Genomes Project data, genetic information for 21 genes involved in nutritional and thermoregulation processes was analysed for three western European populations. The applied Anthropological Genetics methods pointed to appreciable differentiation between the examined groups especially for the PRDM16 gene. Moreover, several neutrality tests suggested that balancing selection has acted on different regions of the gene in people from Great Britain, as well as that more recent positive selection could have also targeted some PRDM16 SNPs in Finn and Italian populations. These series of adaptive footprints are plausibly related to climate variability in both ancient and relatively recent times. Since this locus is involved in thermoregulation mechanisms and adipogenesis, local adaptations mediated by a pathway related to the brown adipose tissue activity could have evolved in response to changing cold temperature exposures of such populations

Between Anthropology, Genetics and Obstetrics: a Study of Potential Childbirth Deaths from the Hospital Cemetery of Forl\uec Campus (18th Century)

In 2014 an archaeological area dated between the 17th and the 18th centuries and located in the historical downtown of the city of Forl\uec (FC), in Northern Italy, offered the possibility to retrieve and study a huge amount of burials, some of which contained perinatal individuals buried in the same grave with adults. The location of this archaeological site (identified as \u201cForl\uec Campus\u201d), near the area of the ancient city hospital, generated the idea that this site could have been the hospital cemetery in the 18th century. The possibility to study the bisome burials, represented by an adult and a perinatal individual, coupled with the period to which they date, make this sample of particularly interest. In fact, since prehistoric times, pregnancy, labor, birth and obstetrics have been women\u2019s field

Pope Leo XII\u2019s death: the twist to a longstanding dispute by novel historical documents and paleopathographic analysis

Although the practice of autopsy on the Pope\u2019s corpse was performed from the 16 century, autopsy reports are only rarely analysed, and never with the aim of investigating the real causes of the death from a concomitant medical and th historical point of view. Here, for the frst time, we report on the discovery of new unpublished documents from the Vatican Secret Archives and their investigation by a scientifc and inter-disciplinary approach. This analysis allows us to draw new conclusions on the true cause of Leo XII\u2019s mysterious death. His sudden death, that occurred on February 10 , 1829 after a short illness, particularly struck the public. Suspicions of poisoning or surgeon\u2019s guilt or inexperience and even the shadow of a venereal disease, contributed to create a \u201cblack legend\u201d on his pontifcate and death. On the contrary, the pres- ent paleopathographic analysis points toward a new conclusion. The regular use of catheterization with a silver syringe provided an easy access for bacterial superinfection, confrmed by the observed early emphysematous stage of the corpse. So, the most substantiated hypothesis concerning the cause of Leo XII\u2019s death indicates a severe form of sepsis, exacerbated by a weakened state due to chronic hemorrhoids

Pope Leo XII's death: the twist to a longstanding dispute by novel historical documents and paleopathographic analysis

Although the practice of autopsy on the Pope's corpse was performed from the 16$^{th}$ century, autopsy reports are only rarely analysed, and never with the aim of investigating the real causes of the death from a concomitant medical and historical point of view. Here, for the first time, we report on the discovery of new unpublished documents from the Vatican Secret Archives and their investigation by a scientific and inter-disciplinary approach. This analysis allows us to draw new conclusions on the true cause of Leo XII's mysterious death. His sudden death, that occurred on February 10$^{th}$, 1829 after a short illness, particularly struck the public. Suspicions of poisoning or surgeon's guilt or inexperience and even the shadow of a venereal disease, contributed to create a "black legend" on his pontificate and death. On the contrary, the present paleopathographic analysis points toward a new conclusion. The regular use of catheterization with a silver syringe provided an easy access for bacterial superinfection, confirmed by the observed early emphysematous stage of the corpse. So, the most substantiated hypothesis concerning the cause of Leo XII's death indicates a severe form of sepsis, exacerbated by a weakened state due to chronic hemorrhoids

Il lupo che venne dal freddo: i reperti di ex Cava a Filo rivelano l\u2019antica origine del lupo italiano (Canis lupus italicus, Altobello 1921) attraverso lo studio del DNA antico

L\u2019origine e l\u2019unicita\u300 genetica del lupo italiano (Canis lupus italicus) sono state oggetto di diversi studi. Recenti pubbli- cazioni descrivono la distribuzione spazio-temporale di due ecomor , uno dei quali (HG2), associato alla megafauna pleistocenica, era dominante in Eurasia e in America durante l\u2019ultimo massimo glaciale (LGM). In seguito al successivo cambiamento climatico un \u201cnuovo\u201d ecomorfo (HG1) ha sostituito i lupi preesistenti in Nord America, ed e\u300 divenuto progressivamente dominante in Eurasia. La popolazione italiana attuale e\u300 l\u2019unica sopravvissuta interamente riferibile all\u2019ecomorfo antico, ma le dinamiche che hanno portato a questa situazione non sono ben de nite. I reperti di ex Cava a Filo (16 campioni, datati da circa 25000 a circa 17400 anni fa) sono stati analizzati allo scopo di confrontare una regione del DNA mitocondriale con sequenze antiche e moderne di lupi e cani. Dai risultati emergono analogie con lupi antichi dell\u2019Europa settentrionale e della Beringia, lupi moderni e anche cani primitivi e recenti. Alcuni campioni mostrano una notevole similitudine con i lupi italiani contemporanei. I lupi preistorici di ex Cava a Filo, associati a bisonti e megaceri, appartenevano solo alla popolazione riferita a HG2, caratterizzata da una maggiore variabilita\u300 e in continuita\u300 con la situazione attuale. Presumibilmente l\u2019ondata migratoria dei lupi con HG1 non ha raggiunto l\u2019Italia in numeri signi cativi, facendo della penisola italiana l\u2019ultimo rifugio di un\u2019antica popolazione di lupo un tempo di usa nell\u2019intero emisfero nord