Animal domestication was one of the most important transitions in human history, beginning with the long-term association between hunter–gatherers and wolves more than 15,000 years. This long term association with people resulted in new selective pressures which led to substantial biological changes in animal species (e.g. behavior, appearance, circadian rhythm etc.), as well as in people (e.g. via spread of zoonotic disease etc). Genomic data obtained from modern domestic animals can be used to address questions about the geographical and temporal origins as well as to understand the strength and consequences of these selective pressures on the genome. Genomic information obtained from living animals, however, provides only a contemporary snapshot of a long-term evolutionary process. Domestic species have also dramatically changed in less than a century, e.g. chicken growth rate has tripled in the last 50 years and cranial shape variation across modern dog breeds now exceeds the range of differences observed across the entire order of Carnivora. This makes it difficult to make inferences about domestication based solely on the analyses of modern population data. In the past decade, novel molecular techniques have enabled access to genetic information from past populations (palaeogenomics). This has allowed us to obtain genomes of animals and that of the pathogens they were infected with, using DNA extracted from ancient skeletal remains, found at archeological and palaeontological sites. Palaeogenomics allows us to generate genomic time series, and answer questions related to the origin and the spread of domestic populations across the globe, to assess how animals adapted to the myriad of environments in which they were introduced, or to better understand ancient events of zoonoses.
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