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Unifying Domestication and Evolution through Ancient DNA

Final Report Summary - UNDEAD (Unifying Domestication and Evolution through Ancient DNA)

The goal of UNDEAD was to leverage the power of newly emerging DNA sequencing technologies to questions related to the origins of three key animal domesticates: dogs, pigs, and chickens. We have since collected, extracted, and analysed DNA derived from more than 4,500 individuals spanning the last 30,000 years. Our primary motivations have been to combine high-resolution genomic data sets with information pertaining to the archaeological context of the ancient animal remains to understand when, where, and how many times each of these three species became closely associated with people as part of a domestication process.
We have focussed primarily on uncovering the spatiotemporal pattern of genomic change, and by analysing the ancient DNA data alongside modern individuals, we have also developed novel insights into process of domestication itself. By combining these insights, we have developed a deeper and more sophisticated empirical and theoretical understanding of animal domestication.

For dogs, the ancient DNA of dozens of individuals spanning the past 10,000 years has revealed deep, and early population divergences between lineages of dogs that then later met and mixed again as people moved across the Northern and Southern continents. Our genomic sequencing revealed a completely unknown, and now virtually extinct, population of dogs in North America that likely arrived with people, only to be replaced when Europeans arrived into the Americas with their own dogs. Through our collaborations we have several ongoing projects involving global patterns of dog genomics through time, the most exciting of which are revealing the tight correlation with specific human cultures as well as the genes those people selected for in their own dogs.

By assessing dozens of ancient genomes of pigs spanning the last 10,000 years, we have revealed a near complete nuclear turnover in domestic pigs. Derived from Near Eastern wild boar, domestic pigs first arrive in Europe as part of the Neolithic migration of people. From that point on, domestic pigs interbred with local European wild boar, and over a period of 3,000 years the Near Easter fraction of their genomes were replaced by European ancestry. We are following up this study by investigating similar patterns of genomic turnover as people travelled with their pigs in Asia and into the Pacific.

Modern chicken populations are virtually fixed for a gene called TSHR which is associated with reduced aggression and faster onset of egg laying as well as the ability to survive and reproduce in close proximity to other chickens. Given its ubiquity, this gene was originally thought to be selected for at the beginning of the process of chicken domestication. By analysing the TSHR variants in ancient chickens over the past 2,000 years in Europe, we were able to show that the increase in selection for the modern domestic variant only started 1,000 years ago, coincident with a cultural shift in food preferences associated with religious fasting rituals. We are currently analysing more than 15 complete ancient chicken genomes alongside several hundred mitochondrial genomes in the context of modern chicken genomes representing global wild and domestic populations.