Inferring Allele Frequency Trajectories from Ancient DNA Indicates That Selection on a Chicken Gene Coincided with Changes in Medieval Husbandry

A team of international scientists led by the University of Oxford has combined ancient DNA analyses with statistical modelling to pinpoint the timing of the selection for traits associated with modern chickens. They found that medieval Christians who fasted may have played a part in producing less aggressive farm birds. 

The team found that traits linked with reduced aggression and an ability to live in confined, smaller spaces with other birds emerged about 1000 AD in the European Middle Ages. These strong selection pressures coincided with an era in which Christians had widespread influence on what people should eat, including edicts that enforced fasting and the exclusion of four-legged animals from the menu. The paper  suggests religious edicts that allowed people to eat chickens and eggs during fasts, coupled with increasing urbanisation, may have driven the evolution of modern domesticated chickens. The findings are published in the journal, Molecular Biology and Evolution.1

Illustration from Romance of Alexander, one sumptuous book of the Middle Ages, shows chickens roasting on a spit
Illustration from Romance of Alexander, one sumptuous book of the Middle Ages, shows chickens roasting on a spit © University of Oxford

Inferring Allele Frequency Trajectories from Ancient DNA Indicates That Selection on a Chicken Gene Coincided with Changes in Medieval Husbandry Practices 

Liisa Loog,  Mark G. Thomas,  Ross Barnett,  Richard Allen,  Naomi Sykes, Ptolemaios D. Paxinos,  Ophélie Lebrasseur,  Keith Dobney,  Joris Peters,  Andrea Manica, Greger Larson  and Anders Eriksson

Mol Biol Evol msx142.
DOI: https://doi.org/10.1093/molbev/msx142

Published: 02 May 2017

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.

Keywords: ancient DNA, selection, Bayesian analyses, TSHR, BCDO2, domestication.