The human mitochondrial DNA (mtDNA) variation has been the subject of countless studies that have allowed to expand the genetic and phylogeographic knowledge on the European populations. In Western Europe, Italy with its peculiar geophysical characteristics has been a crossroads for human migration and, over time, has become the perfect environment for the complex internal dynamics. The high genomic diversity, higher than in other European regions, is the result of numerous inputs that have shaped the gene pool of its populations, starting from the Upper Paleolithic, and created its current genetic structure. In this context, Sicily represents one of the main islands of the Mediterranean Sea, characterized by a variety of archaeological records, material culture and traditions that reflect the history of migrations and populations interactions at least from late Paleolithic. The oldest human remains excavated in the island have been dated to 14,000 BCE. Subsequently, complex demographic and cultural dynamics influenced the genomic landscape of Sicily at different levels; however, the impact of these migrations on the genomic structure of Sicilian populations over time is largely unknown. In an attempt to decipher this complex scenario recent archaeogenomic studies were performed through the analysis of ancient mitogenomes, dated from late Paleolithic (12,750 BCE) to IronAge (300 BCE). We retrieved and revised these data compiling a dataset of 118 ancient mitogenomes. Moreover, to obtain a present-day snapshot of the mitochondrial variation, we eventually produced a novel dataset of 182 modern mitogenomes from individuals currently living in the nine provinces of Sicily. We also developed a standardized computational approach for an accurate quality assessment of modern and ancient mitogenome reads to obtain two datasets of ancient and modern mitogenomes, comparable in terms of sequence quality and phylogenetic resolution, able to provide a more precise assessment of the distribution of genetic mitochondrial variability in Sicily from Paleolithic to present times. This quality check allowed us to remove 15 ancient and 14 modern mtDNA sequences. These similar percentages of exclusion, around 10%, testify to the improvement of ancient DNA workflows. To perform a diachronic comparison between the two datasets, the 113 ancient and 168 modern high-quality mitogenomes were phylogenetically classified into 66 and 134 different haplogroups and sub-haplogroups. This plethora of lineages alone testifies to a complex genetic history with multiple genetic inputs. As expected, a prevalent origin of the mitochondrial lineages from Western Eurasia (>80%) has been identified. They could be brought into the island by Late Glacial hunter-gathers re-expanding from glacial refuge areas who were later followed by Neolithic farmers moving from the Near East, mostly across the Mediterranean Sea, and by herders from Caucasian steppes during the Bronze Age. It is worth mentioning that some lineages point to migrations from Greece before the Hellenic period. Very intriguing is the connection with the African continent. Even if the first lineages of African origin sporadically appeared during the Bronze (one L3) and Iron (one U6) Ages, they became much more frequent only in modern mitogenomes among (~20%). Therefore, it is likely that most of them arrived in rather recent historical times, including the Romanization period, the Arab conquest of Sicily, or even during the period of the Atlantic slave trade, as attested by lineages of sub-Saharan origin. Finally, we have highlighted a significant degree of structured genetic variation from a female perspective, testified by differential geographic distributions of mtDNA lineages since Iron Age up to the present time.
La variabilità del DNA mitocondriale umano (mtDNA) è stata oggetto di innumerevoli studi che hanno permesso di ampliare le conoscenze genetiche e filogeografiche riguardo le popolazioni europee. In Europa occidentale, l'Italia, con le sue peculiari caratteristiche geofisiche, è stata un crocevia di migrazioni umane e, nel tempo, è diventata un ambiente perfetto per complesse dinamiche interne. L'elevata diversità genomica, maggiore rispetto a quella di altre regioni europee, è il risultato di numerosi input che, a partire dal Paleolitico superiore, hanno plasmato il pool genetico delle sue popolazioni e hanno creato la sua attuale struttura genetica. In questo contesto, la Sicilia rappresenta una delle principali isole del Mediterraneo, caratterizzata da un’ampia varietà di reperti archeologici, culture materiali e tradizioni, che riflettono la storia delle migrazioni e delle interazioni tra le popolazioni almeno dal tardo Paleolitico. I più antichi resti umani dell'isola sono stati datati al 14.000 a.C. Successivamente, complesse dinamiche demografiche e culturali hanno influenzato il contesto genomico della Sicilia a diversi livelli; tuttavia, l'impatto di queste migrazioni sulla struttura genomica delle popolazioni siciliane nel tempo è in gran parte sconosciuto. Nel tentativo di decifrare questo complesso scenario, di recente sono stati condotti diversistudi archeogenomici che hanno analizzato mitogenomi antichi, datati dal tardo Paleolitico (12.750 a.C.) all'Età del Ferro (300 a.C.). Abbiamo recuperato e rielaborato questi dati compilando un dataset di 118 mitogenomi antichi. Inoltre, per ottenere un'istantanea dell’attuale variabilità mitocondriale, abbiamo prodotto un nuovo dataset di 182 mitogenomi moderni, provenienti da individui che vivono attualmente nelle nove province della Sicilia. Abbiamo anche sviluppato un approccio computazionale standardizzato per un'accurata valutazione della qualità delle analisi dei dati di sequenza per ottenere due dataset di mitogenomi moderni e antichi, comparabili in termini di qualità delle sequenze e risoluzione filogenetica, e in grado di fornire una valutazione più precisa della distribuzione della variabilità genetica mitocondriale in Sicilia dal Paleolitico a oggi. Questo controllo di qualità ci ha permesso di rimuovere 15 sequenze di mtDNA antiche e 14 moderne, in entrambi i casi circa il 10% dei totali. Percentuali di esclusione così simili testimoniano il miglioramento nei metodi di analisi del DNA antico. Per effettuare un confronto diacronico tra i due dataset, 113 mitogenomi antichi e 168 moderni, di alta qualità, sono stati classificati filogeneticamente in, rispettivamente, 66 e 134 diversi aplogruppi e sotto-aplogruppi. L’elevato numero di linee mitocondriali identificate testimonia di per se una storia genetica complessa con molteplici input. Come previsto, gli aplogruppi mitocondriali identificati hanno un’origine prevalentemente dall'Eurasia occidentale (>80%). Potrebbero essere stati portati nell'isola dai cacciatori-raccoglitori del periodo tardo glaciale, che si sono espansi dalle aree di rifugio glaciali, seguiti poi dagli agricoltori neolitici provenienti dal Vicino Oriente, soprattutto attraverso il Mar Mediterraneo, e infine dai pastori delle steppe del Caucaso durante l’Età del Bronzo. Vale la pena ricordare che alcune linee filogenetiche suggeriscono migrazioni dalla Grecia prima del periodo ellenistico. Molto interessante è il legame con il continente africano. Anche se i primi aplogruppi di origine africana sono comparsi durante l'Età del Bronzo (un individuo L3) e l’Età del Ferro (un individuo U6), sono diventati molto più frequenti solo tra i mitogenomi moderni (20%). È quindi probabile che la maggior parte sia arrivata in tempi storici piuttosto recenti, tra cui il periodo della romanizzazione, la conquista araba della Sicilia, o addirittura durante il periodo della tratta degli schiavi nell’Atlantico.
Un approfondimento della storia genetica della Sicilia tramite mitogenomi moderni e antichi
TOMMASI, ANNA
2022/2023
Abstract
The human mitochondrial DNA (mtDNA) variation has been the subject of countless studies that have allowed to expand the genetic and phylogeographic knowledge on the European populations. In Western Europe, Italy with its peculiar geophysical characteristics has been a crossroads for human migration and, over time, has become the perfect environment for the complex internal dynamics. The high genomic diversity, higher than in other European regions, is the result of numerous inputs that have shaped the gene pool of its populations, starting from the Upper Paleolithic, and created its current genetic structure. In this context, Sicily represents one of the main islands of the Mediterranean Sea, characterized by a variety of archaeological records, material culture and traditions that reflect the history of migrations and populations interactions at least from late Paleolithic. The oldest human remains excavated in the island have been dated to 14,000 BCE. Subsequently, complex demographic and cultural dynamics influenced the genomic landscape of Sicily at different levels; however, the impact of these migrations on the genomic structure of Sicilian populations over time is largely unknown. In an attempt to decipher this complex scenario recent archaeogenomic studies were performed through the analysis of ancient mitogenomes, dated from late Paleolithic (12,750 BCE) to IronAge (300 BCE). We retrieved and revised these data compiling a dataset of 118 ancient mitogenomes. Moreover, to obtain a present-day snapshot of the mitochondrial variation, we eventually produced a novel dataset of 182 modern mitogenomes from individuals currently living in the nine provinces of Sicily. We also developed a standardized computational approach for an accurate quality assessment of modern and ancient mitogenome reads to obtain two datasets of ancient and modern mitogenomes, comparable in terms of sequence quality and phylogenetic resolution, able to provide a more precise assessment of the distribution of genetic mitochondrial variability in Sicily from Paleolithic to present times. This quality check allowed us to remove 15 ancient and 14 modern mtDNA sequences. These similar percentages of exclusion, around 10%, testify to the improvement of ancient DNA workflows. To perform a diachronic comparison between the two datasets, the 113 ancient and 168 modern high-quality mitogenomes were phylogenetically classified into 66 and 134 different haplogroups and sub-haplogroups. This plethora of lineages alone testifies to a complex genetic history with multiple genetic inputs. As expected, a prevalent origin of the mitochondrial lineages from Western Eurasia (>80%) has been identified. They could be brought into the island by Late Glacial hunter-gathers re-expanding from glacial refuge areas who were later followed by Neolithic farmers moving from the Near East, mostly across the Mediterranean Sea, and by herders from Caucasian steppes during the Bronze Age. It is worth mentioning that some lineages point to migrations from Greece before the Hellenic period. Very intriguing is the connection with the African continent. Even if the first lineages of African origin sporadically appeared during the Bronze (one L3) and Iron (one U6) Ages, they became much more frequent only in modern mitogenomes among (~20%). Therefore, it is likely that most of them arrived in rather recent historical times, including the Romanization period, the Arab conquest of Sicily, or even during the period of the Atlantic slave trade, as attested by lineages of sub-Saharan origin. Finally, we have highlighted a significant degree of structured genetic variation from a female perspective, testified by differential geographic distributions of mtDNA lineages since Iron Age up to the present time.È consentito all'utente scaricare e condividere i documenti disponibili a testo pieno in UNITESI UNIPV nel rispetto della licenza Creative Commons del tipo CC BY NC ND.
Per maggiori informazioni e per verifiche sull'eventuale disponibilità del file scrivere a: unitesi@unipv.it.
https://hdl.handle.net/20.500.14239/16589