The ARAUCANA zooarchaeological database comprises 11 bird assemblages from Neotropical American archaeological sites ranging from the 16th to the 20th century CE. Based upon comprehensive reference collections, the analyses conducted on the full avifaunal assemblage (n=580 bones) highlighted the close osteological resemblance between chickens and Tinamous (indigenous birds). Interestingly, chickens rarely made up more than half the bird assemblages, which implies local wild birds continued to play a significant role in the diet. Following these observations, we reviewed the species authenticity of the earliest chicken bones identified in South America and found no evidence for a Polynesian introduction prior to the arrival of the Europeans.
Mitochondrial genome analysis on 15 samples further supports a European introduction, whilst 12 samples were selected for whole genome sequencing to investigate the ancestry of South American chicken populations. The generation of data is still pending, but will be mapped against the comprehensive genome database compiled and processed by the Chicken Genomic Diversity Consortium once the latter is made available. Indeed, this high-resolution reference of global genomic variability is essential to accurately interpret our data, ensures that our data will be analysed and processed according to the state-of-the-art, and will be released together with all other consortium data as open source data, which will considerably enhance the potential and inclusion of our own data for future research.
To contextualise our findings, we reviewed the biocultural history of chickens in Eurasia, Africa and Oceania with our collaborators G. Larson, L. Frantz, and J. Peters. Our comprehensive study revealed that the earliest unequivocal domestic chicken bones originate from the Neolithic site of Ban Non Wat in central Thailand, and date to 1650-1250 BCE. This implies a domestication a few millennia younger than previously asserted, and which may have been linked to the arrival of dry-rice agriculture in the region. Furthermore, the reassessment revealed no proof that chickens reached Europe prior to the 8th century BCE. This considerably revises our understanding of chicken domestication and dispersal across the western world. It also provides a crucial contextual framework against which we can interpret the ARAUCANA results.
Through our collaboration with G. Larson, L. Frantz, A. Smith and S. Fiddaman, we leveraged the shotgun-sequenced genomic data of our extensive ancient European chicken and Neotropical American chicken datasets and have identified a pathogen of particular economic importance to the poultry industry. The data helps establish its evolutionary history and how changing farming practices have led to its increased virulence. Through hands-on training in metagenomics, we have also identified the earliest Equine Herpesvirus 4 case dating to 3,900 years ago and found in the Southeastern Urals. Our work provided the first temporal calibration for the evolutionary tree of EHV4 viruses.
Outputs and dissemination of the project and its results include 11 manuscripts, with six as lead author and five as co-author. These include three published (PNAS, Cytogenetic and Genome Research), one accepted (Science), two in review (Virus Evolution, F1000Research), one near submission (Conference proceedings) and four in preparation. The research was presented at 14 international conferences and seminars, and was picked up by numerous media outlet including several French popular science magazines, two radio shows and a podcast. Several outreach activities with schools and members of the general public also took place, whilst the project and its results were also presented to the Syndicat National des Accouveurs (France).
