The first peopling of the Americas and the genetic structure of current inhabitants after the admixture with other populations are largely debated and studied. To add more information to this complex scenario, the work presented in this thesis aims to explore and characterize the genetic peculiarities of South American people, with a specific focus on the Chilean population. Due to its distinctive extension along the “Southern Cone” (name used to refer to the South American region covered by Chile, Argentina and Uruguay), different territorial morphologies can be found moving from the north to the south of the country. Chile is a long and narrow strip of land stretched between the Andes to the east and the Pacific Ocean to the west. This peculiar position along the Pacific Coast of South America and down the western side of the Southern Cone made it a mandatory path for the first Americans who reached the archaeological site of Monte Verde about 15 kya. The combination of this original footprint with a rich set of historical events and social dynamics, particularly during colonial times, had the potential to shape in a unique way the distribution of genetic variation of Chilean populations. The molecular target of this thesis work has been the mitochondrial DNA (mtDNA), a uniparental matrilineal marker widely used in population genetics. We sequenced and analysed 44 complete mitogenomes from randomly selected (and unrelated) individuals living at different latitudes of the country, from the north to the southernmost regions. Basically, this is the first representative population dataset that allowed for an unbiased reconstruction of the genetic history of Chile from a female perspective. The majority of the mtDNA profiles presented an Indigenous origin (75.00%) and have been classified within the four pan-American lineages (A2, B2, C1 and D1) plus D4h3a, another founding haplogroup present nowadays only in South America. The age estimates of the most represented sub-haplogroups (B2b, B2i2, C1b13, D1g) and the archaeogenomic comparison with the dataset of ancient mitogenomes, dated more than one thousand years ago (kya), helped us to relate these contemporary Chilean lineages to the first Indigenous groups that moved into the Southern Cone about 15 kya. Moreover, haplogroup matches with the most ancient remains excavated from archeological sites located on both coasts of the continent, confirm the hypothesis that at least one part of the earlier Indigenous groups followed a dual migration route in South America. On the other hand, the prevalence of younger ancient DNA samples matching typical Chilean haplogroups could also testify for more recent demographic events related to the Pacific coast. We were also able to identify the genetic traces of the colonial period that began in 1520 Common era (CE) in Chile with the Spanish domination. A significant African component (15.91%) was found in our samples, while the remaining haplotypes were mostly of European origin (9.09%). It is evident from our mtDNA perspective that the slave trade involved various routes from Africa and that probably more recent (still unclear) demographic events created a differential distribution of sub-Saharan haplogroups between different areas of Chile, maintaining a prevalence in the southern regions. Finally, a comparison with preliminary results on autosomal DNA points to a sex-bias in the colonization process, with a greater African maternal legacy in Chile, as previously reported for other countries of Central and South America. These findings reflect our need to evaluate how, and on which scientific and historic bases, sex-differentiated mobility and mixture impacted cultural as well as biological survival in the Americas since colonial times.
Il primo popolamento delle Americhe e l’attuale struttura genetica del doppio continente sono stati ampiamente discussi e studiati. Per aggiungere più informazioni a questo complesso scenario, lo scopo di questo lavoro è stato quello di esplorare e delineare le caratteristiche genetiche delle popolazioni del Sud America, con un focus specifico sulla popolazione del Cile. Grazie alla sua estensione latitudinale si possono riscontrare diverse morfologie territoriali, da nord a sud. Il Cile occupa infatti una striscia di terra lunga e stretta che si estende tra le Ande a est e l'Oceano Pacifico a ovest. Questa particolare posizione, lungo la costa pacifica del Sud America e lungo il lato occidentale del Cono meridionale, ne ha fatto un passaggio obbligato per i primi gruppi indigeni che raggiunsero Monte Verde 15 mila anni fa. La combinazione di questa impronta genetica originale con una serie di eventi storici e dinamiche sociali, soprattutto durante il periodo coloniale, ha avuto modo di modellare in maniera unica la distribuzione della variazione genetica delle popolazioni cilene. Il target molecolare di questa analisi è stato il DNA mitocondriale, un marcatore uniparentale a trasmissione materna ampiamente usato nella genetica di popolazione. Abbiamo sequenziato e analizzato 44 mitogenomi completi di individui selezionati casualmente (non imparentati tra loro) provenienti da diverse località della nazione cilena, dal nord fino alle regioni meridionali. In pratica, questo è il primo dataset rappresentativo della popolazione cilena che permette una ricostruzione realistica (senza bias di campionamento) della storia genetica del Cile dal punto di vista materno. La maggior parte dei profili mitocondriali presenta un’origine indigena (75.00%), venendo classificati all’interno dei quattro macro-aplogruppi pan-Americani (A2, B2, C1 e D1) più il D4h3a, un altro aplogruppo fondatore presente al giorno d’oggi solo in Sud America. Le età stimate dei sotto-aplogruppi più frequenti (B2b, B2i2, C1b13, D1g) e il confronto (archaeogenomico) con il dataset di genomi antichi disponibili, datati più di mille anni fa, ci hanno permesso di mettere in relazione queste linee cilene attuali con i primi gruppi indigeni che si sono insediati nella regione dell’estremo Cono meridionale circa 15 mila anni fa. Inoltre, il fatto che gli aplogruppi trovati corrispondano con quelli di campioni antichi ricavati da siti archeologici localizzati in entrambe le coste del continente conferma l’ipotesi che almeno una parte dei primi gruppi indigeni ha seguito una “doppia rotta di migrazione” in Sud America. Allo stesso tempo, la prevalenza di campioni antichi “più giovani” con tipici aplogruppi cileni potrebbe testimoniare eventi demografici più recenti collegati alla costa pacifica. Inoltre, siamo stati in gradi di identificare tracce genetiche del periodo coloniale, iniziato nel 1520 CE (Common Era) in Cile con la dominazione spagnola. Una forte componente africana (15.91%) è stata riscontrata nei nostri campioni, mentre i restanti aplotipi si sono dimostrati soprattutto di origine europea (9.09%). Dalla prospettiva mitocondriale si evince che la tratta degli schiavi ha coinvolto rotte differenti dall’Africa e che probabilmente eventi demografici più recenti (non ancora ben noti) hanno definito una distribuzione differenziale di aplogruppi sub-sahariani tra le diverse aree del Cile, con una particolare prevalenza nelle regioni meridionali. Infine, un confronto con risultati preliminari relativi al DNA autosomico suggerisce un “sex-bias” nel processo coloniale, con maggiore eredità materna di origine africana in Cile, come precedentemente identificato anche in altre regioni dell’America centro-meridionale. Questi risultati sottolineano la necessità di valutare l'impatto (scientifico e storico) della diversa mobilità di uomini e donne per le popolazioni indigene sin dall'epoca coloniale.
La variabilità mitocondriale del Cile inquadrata nel contesto archeogenomico del Sud America
RAFFANTI, LUCA
2019/2020
Abstract
The first peopling of the Americas and the genetic structure of current inhabitants after the admixture with other populations are largely debated and studied. To add more information to this complex scenario, the work presented in this thesis aims to explore and characterize the genetic peculiarities of South American people, with a specific focus on the Chilean population. Due to its distinctive extension along the “Southern Cone” (name used to refer to the South American region covered by Chile, Argentina and Uruguay), different territorial morphologies can be found moving from the north to the south of the country. Chile is a long and narrow strip of land stretched between the Andes to the east and the Pacific Ocean to the west. This peculiar position along the Pacific Coast of South America and down the western side of the Southern Cone made it a mandatory path for the first Americans who reached the archaeological site of Monte Verde about 15 kya. The combination of this original footprint with a rich set of historical events and social dynamics, particularly during colonial times, had the potential to shape in a unique way the distribution of genetic variation of Chilean populations. The molecular target of this thesis work has been the mitochondrial DNA (mtDNA), a uniparental matrilineal marker widely used in population genetics. We sequenced and analysed 44 complete mitogenomes from randomly selected (and unrelated) individuals living at different latitudes of the country, from the north to the southernmost regions. Basically, this is the first representative population dataset that allowed for an unbiased reconstruction of the genetic history of Chile from a female perspective. The majority of the mtDNA profiles presented an Indigenous origin (75.00%) and have been classified within the four pan-American lineages (A2, B2, C1 and D1) plus D4h3a, another founding haplogroup present nowadays only in South America. The age estimates of the most represented sub-haplogroups (B2b, B2i2, C1b13, D1g) and the archaeogenomic comparison with the dataset of ancient mitogenomes, dated more than one thousand years ago (kya), helped us to relate these contemporary Chilean lineages to the first Indigenous groups that moved into the Southern Cone about 15 kya. Moreover, haplogroup matches with the most ancient remains excavated from archeological sites located on both coasts of the continent, confirm the hypothesis that at least one part of the earlier Indigenous groups followed a dual migration route in South America. On the other hand, the prevalence of younger ancient DNA samples matching typical Chilean haplogroups could also testify for more recent demographic events related to the Pacific coast. We were also able to identify the genetic traces of the colonial period that began in 1520 Common era (CE) in Chile with the Spanish domination. A significant African component (15.91%) was found in our samples, while the remaining haplotypes were mostly of European origin (9.09%). It is evident from our mtDNA perspective that the slave trade involved various routes from Africa and that probably more recent (still unclear) demographic events created a differential distribution of sub-Saharan haplogroups between different areas of Chile, maintaining a prevalence in the southern regions. Finally, a comparison with preliminary results on autosomal DNA points to a sex-bias in the colonization process, with a greater African maternal legacy in Chile, as previously reported for other countries of Central and South America. These findings reflect our need to evaluate how, and on which scientific and historic bases, sex-differentiated mobility and mixture impacted cultural as well as biological survival in the Americas since colonial times.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.
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https://hdl.handle.net/20.500.14239/11898