Investigating patterns of animal domestication using ancient DNA

Abstract

Animal domestication is a continuous but nonlinear evolutionary process that follows different paths (trajectories) of human-animal relationships. These paths vary in structure and intensity over time and include processes like human intentionality (such as control and taming of wild animals), directed selection on behavioral and phenotypic traits and characters, human-mediated movement of domestic herds across space (migration), wild-domestic admixture, and adaptation. Because domestic animals are continuously shaped through complex interaction of these processes, gaining a better understanding of where, when and how these took place helps clarifying human prehistory and the practice and process of domestication.
Studies of modern and ancient DNA (aDNA) have recently disentangled the history of several domestic species. These studies have often shown that domestication processes were far more complex than previously thought, often encompassing more than one independent domestication event, and continuously shaped by migration and admixture. Importantly, ancient DNA studies have convincingly demonstrated that inferring the past (for example, where, when and how domestication and selection took place) from the present (modern contemporary domesticates) is biased by comparatively recent events such as modern breed formation. Ancient DNA is therefore a key component in the reconstruction of where, when and how animal domestication took place.
This thesis aims to shed new light on pig and chicken domestication by analysing ancient DNA extracted from archaeological specimens from Europe and the Near and Middle East. First, I find that pig domestication took place over a much wider temporal and geographical range than previously thought, and secondly that the current reference framework for inferring where and when pigs were domesticated (wild boar mitochondrial phylogeography) must be revised. In addition, I find that genetic variation in modern domestic chickens, to a great extent, is the result of recent rather than ancient events of admixture and strong human driven selection. Overall, these finds strengthen the presumption that genetic signatures in modern contemporary populations often provide misleading estimates of their ancient history. Across genes and species, therefore, this thesis demonstrates the effectiveness of using ancient DNA for resolving a range of different aspects of human prehistory and animal domestication.