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

Abstract

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.

Genome-wide genetic structure and selection signatures for color in 10 traditional Chinese yellow-feathered chicken breeds

“…We also describe the genetic structure and molecular background of the distinguished color phenotype of these chickens. YFCs are a traditional nutritional and commercial mainstay for millions of people living in China and its purlieus, and are believed to have contributed to the recent breeding of European chickens [5]. Next generation sequencing has augmented scientific research into the molecular foundations of various complex phenotypic poultry traits such as body size in chicken [15], body size and plumage color in ducks [17], as well as maturation and plumage color in domestic quails [18], among others.…”

Learning the properties of adaptive regions with functional data analysis

“…There are a number of potential applications of our methodological framework. For one, it is possible to naturally extend SURFDAWave to incorporate genomic data from ancient samples, and several recent studies have employed ancient DNA to directly examine temporal allele frequency fluctuations to identify positively-selected loci (e.g., Bollback et al, 2008;Ludwig et al, 2009;Mathieson et al, 2015;Fehren-Schmitz and Georges, 2016;Schraiber et al, 2016;Loog et al, 2017). SURFDAWave's framework would allow examination of changes in the spatial distribution of genetic diversity over time by incorporating information from ancient genomes of a single population at various time points throughout history, and summarizing patterns of variation using two-dimensional wavelet bases.…”

Morphological diversity of integumentary traits in fowl domestication: Insights from disparity analysis and embryonic development

“…[4][5][6][7] The main ancestor of domestic chicken is the red junglefowl (Gallus gallus), but a contribution from at least two other Gallus species (Grey junglefowl: Gallus sonneratii and Sri Lankan junglefowl: Gallus lafayetii) has been postulated. [8][9][10] Several "domestication centres" of chicken have been identified in South and South-East Asia. 11 The number of chicken breeds is estimated as hundreds, and varieties count in the thousands, 12 but there is no international commission or standard that regulates the naming and definition of all breeds.…”

“…A proposed earlier event of domestication around 8000 bce in northern China, based on mtDNA analysis, remains debated . The main ancestor of domestic chicken is the red junglefowl ( Gallus gallus ), but a contribution from at least two other Gallus species (Grey junglefowl: Gallus sonneratii and Sri Lankan junglefowl: Gallus lafayetii ) has been postulated . Several “domestication centres” of chicken have been identified in South and South‐East Asia .…”