In the last century the study of ancient and extinct species through the identification of the genetic material preserved in ancient and historical museum samples gave life to a new research field called ancient DNA (aDNA). Since then, this field has rapidly expanded and evolved, helped by technological developments of molecular tools and cheaper sequencing costs.
From the fist quagga sample extracted in the 1980s we moved to sequencing the entire genome of several ancient human populations, woolly mammoths, ground sloths, wolves and so on from many geographical regions of the globe with the intention of revealing what it went lost in the past. In this dissertation my intention was to describe three case studies in which the analyses of ancient and historical materials helped improving our knowledge of species that went extinct both recently and thousands of years ago.
This thesis is composed of an Introduction, which includes relevant information behind the main chapters and the aim of this work, and three research chapters that represent the core of my PhD work.
In Chapter 1 of this dissertation, I applied ancient DNA techniques to generate the first genome of the extinct canid from Sardinia, the Sardinian dhole, and explored its genomic history and phylogenomic placement among Eurasian, African and North American canids.
In Chapter 2, we shifted the focus on the historical wolf population from Sicily that was eradicated at the end of the 20th century. We sequenced 4 nuclear genomes (3.8x-11.6x) and 5 mitogenomes of the only seven samples preserved in museums. We analysed them in a dataset of 153 canids to genetically characterise this population and investigate the relationship between Sicilian wolf, Pleistocene wolf, modern wolves, and modern and ancient dogs. Finally, in Chapter 3 my collaborators and I analysed two historical genomes of a mysterious bovid from Southeast Asia, the Kouprey. This population has been listed as Critically endangered, and since 1996 possibly extinct, on the IUCN Red List. The newly generated genomes were analysed alongside other Bison and Bos genomes, and we shed light on its relationship with other Southeast Asian Bos species.
Follows a last section of Conclusions and perspectives that concludes the core of this dissertation with the intention to expand this work to an evolutionary context. In particular, the aim is to demonstrate that the use of historical and ancient materials from museum collections can shed light on the origin of several species and populations that are now lost.