Ancient DNA provides an opportunity to infer the drivers of natural selection by linking allele frequency changes to temporal shifts in environment or cultural practices. However, analyses have often been hampered by uneven sampling and uncertainties in sample dating, as well as being confounded by demographic processes. Here, we present a Bayesian statistical framework for quantifying the timing and strength of selection using ancient DNA that explicitly addresses these challenges. We applied this method to time series data for two loci: TSHR and BCDO2, both hypothesised to have undergone strong and recent selection in domestic chickens. The derived variant in TSHR, associated with reduced aggression to conspecifics and faster onset of egg laying, shows strong selection beginning around 1,100 years ago, coincident with archaeological evidence for intensified chicken production and documented changes in egg and chicken consumption. To our knowledge, this is the first example of preindustrial domesticate trait selection in response to a historically attested cultural shift in food preference. For BCDO2, we find support for selection, but demonstrate that the recent rise in allele frequency could also have been driven by gene flow from imported Asian chickens during more recent breed formations. Our findings highlight that traits found ubiquitously in modern domestic species may not necessarily have originated during the early stages of domestication. In addition, our results demonstrate the importance of precise estimation of allele frequency trajectories through time for understanding the drivers of selection.

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Stable isotope analysis of human remains has been used to address long-standing debates regarding the speed and degree to which the introduction of farming transformed diet. In Europe, this debate has centered on northern and Atlantic regions with much less attention devoted to the arrival of farming across the Mediterranean. This study presents carbon and nitrogen stable isotope analyses of collagen from 19 human and 37 faunal remains from eight sites in the Apulia and Marche regions of south-eastern and central Italy, dating to the early phases of agricultural adoption during the first half of the 6th Millennium BC. Where collagen preservation permitted, sulfur stable isotope analysis was also performed. Overall, there was significant isotopic variation between the different geographic regions, although there was also considerable uncertainty in interpreting these data, especially given heterogeneous isotope values for fauna from site to site. By considering isotope data from each region separately, it was noticeable that the degree of carbon isotope enrichment in humans compared to fauna was higher for individuals buried near the coast, consistent with increased marine consumption. Coastal individuals also had higher sulfur isotope values. Nitrogen isotope values were very variable between individuals and regions and, in some cases, were consistent with very high plant food consumption. Overall, early "farmers" in south-east and central Italy consumed a wide range of foods, including marine, and had much more variable stable isotope values than those observed in central and northern Europe during this period, perhaps indicating a different mode for agricultural adoption.