As one of a limited number of biomolecules recording evolutionary events,
DNA provides an unparalleled means of investigating genetic processes. Over
three decades, ancient DNA research has matured in many ways, growing
alongside technological and methodological advancements. However, due to
DNA preservation, degradation and contamination, ancient DNA research
presents significant limitations and challenges. Until recently, it was thought
that DNA did not survive more than few hundred thousand years, and that it
was impossible to retrieve whole genome data from ancient samples
preserved under suboptimal conditions. However, experimental and analytical
methods have been developed to overcome these limitations. Rigorous
laboratory procedures, optimized capture enrichment methods coupled to
high-throughput sequencing platforms, and expanding modern reference
datasets have enabled the generation of complete ancient genomes from
numerous extinct and extant species, including humans and hominins. In
addition, the field has gradually opened the opportunity to study human
populations through history. In this thesis I have applied, tested and
investigated the performance of different ancient DNA extractions, sequencing
library preparations, and whole-genome capture enrichment methods, with the
goal of retrieving ancient genome wide data from poorly preserved
archaeological remains. Such data contributes to the study of the transatlantic
slave trade, in particular helping shed light upon the origins and diversity of
enslaved Africans. Ultimately this will help answer long-standing historical
questions and broaden our understanding of the dynamics of this contested
part of human history.English summary
As one of a limited number of biomolecules recording evolutionary events,
DNA provides an unparalleled means of investigating genetic processes. Over
three decades, ancient DNA research has matured in many ways, growing
alongside technological and methodological advancements. However, due to
DNA preservation, degradation and contamination, ancient DNA research
presents significant limitations and challenges. Until recently, it was thought
that DNA did not survive more than few hundred thousand years, and that it
was impossible to retrieve whole genome data from ancient samples
preserved under suboptimal conditions. However, experimental and analytical
methods have been developed to overcome these limitations. Rigorous
laboratory procedures, optimized capture enrichment methods coupled to
high-throughput sequencing platforms, and expanding modern reference
datasets have enabled the generation of complete ancient genomes from
numerous extinct and extant species, including humans and hominins. In
addition, the field has gradually opened the opportunity to study human
populations through history. In this thesis I have applied, tested and
investigated the performance of different ancient DNA extractions, sequencing
library preparations, and whole-genome capture enrichment methods, with the
goal of retrieving ancient genome wide data from poorly preserved
archaeological remains. Such data contributes to the study of the transatlantic
slave trade, in particular helping shed light upon the origins and diversity of
enslaved Africans. Ultimately this will help answer long-standing historical
questions and broaden our understanding of the dynamics of this contested
part of human history.