Periodic Reporting for period 2 - ARAUCANA (Archaeological and Anthropological Unravelling of Chickens using Ancient DNA in Neotropical America)
Reporting period: 2022-10-01 to 2023-09-30
Neotropical America contributes over a fifth to global poultry production, yet chickens only arrived on the continent ~500 years ago. Despite this recent introduction, chickens successfully adapted to the diverse local environments and diseases and are now well-embedded within the continent’s numerous cultures. But the circumstances of their introduction in South America and their interactions with local societies remain poorly documented and much debated, whilst phenotypic and genetic characterisation of local chicken ecotypes is lacking. This dearth in knowledge is a cause for concern particularly with respect to cultural heritage, biodiversity, and food security.
The ARAUCANA project addresses this debate and important knowledge gap by combining zooarchaeology and (palaeo)genomics to investigate the cultural and genetic history of chickens in Neotropical America. Its results have shown that 1) there is currently no evidence for a pre-Columbian Polynesian introduction of chickens on the continent, and 2) wild local birds still made-up an important part of local communities’ diet throughout the last 500 years. Metagenomic analyses also revealed how changing farming practices can be the driving force behind increased virulence in poultry pathogens. Our findings have crucial implications on the timing, origins, and management practices of chickens in Neotropical America and beyond.
The ARAUCANA project addresses this debate and important knowledge gap by combining zooarchaeology and (palaeo)genomics to investigate the cultural and genetic history of chickens in Neotropical America. Its results have shown that 1) there is currently no evidence for a pre-Columbian Polynesian introduction of chickens on the continent, and 2) wild local birds still made-up an important part of local communities’ diet throughout the last 500 years. Metagenomic analyses also revealed how changing farming practices can be the driving force behind increased virulence in poultry pathogens. Our findings have crucial implications on the timing, origins, and management practices of chickens in Neotropical America and beyond.
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).
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).
The bioarchaeological and palaeogenomics data gathered and analysed through the ARAUCANA project represents a valuable source of time-stamped human-bird-environment data from Neotropical America throughout the last five centuries. It offers valuable exploitable resources to both members of the academic sphere, and stakeholders:
• Zooarchaeologists and palaeogeneticists will have access to the first ancient Neotropical American chicken zooarchaeological and genomic databases. Our complete re-revaluation of domestication pathways and dispersals of chickens in Europe, Asia, Africa, and Oceania provides solid ground for future evolutionary work on this species.
• The optimisation of an ancient DNA extraction protocol for birds will be a valuable methodological tool in future avian palaeogenomics research
• The high-resolution reference of global genomic variability in chicken populations worldwide including our ancient Neotropical American populations will be released as open source data by the Chicken Genomic Diversity Consortium. This will be particularly relevant for researchers working in poultry genomics and stakeholders for the development of their breeding programs.
• Our work raises awareness on the potential of palaeogenomics in tracing the evolutionary history and molecular basis of virulence in economically relevant pathogens. It provides time-depth on modern genomic datasets of selected pathogens which will be of interest to researchers in metagenomics, epidemiology, and animal health.
• The release of a new version of the AncientMetagenomeDir, and its tooling AMDirT, as part of a community-led project will help towards easier integration and reuse of public ancient metagenomic datasets into future analyses.
• Zooarchaeologists and palaeogeneticists will have access to the first ancient Neotropical American chicken zooarchaeological and genomic databases. Our complete re-revaluation of domestication pathways and dispersals of chickens in Europe, Asia, Africa, and Oceania provides solid ground for future evolutionary work on this species.
• The optimisation of an ancient DNA extraction protocol for birds will be a valuable methodological tool in future avian palaeogenomics research
• The high-resolution reference of global genomic variability in chicken populations worldwide including our ancient Neotropical American populations will be released as open source data by the Chicken Genomic Diversity Consortium. This will be particularly relevant for researchers working in poultry genomics and stakeholders for the development of their breeding programs.
• Our work raises awareness on the potential of palaeogenomics in tracing the evolutionary history and molecular basis of virulence in economically relevant pathogens. It provides time-depth on modern genomic datasets of selected pathogens which will be of interest to researchers in metagenomics, epidemiology, and animal health.
• The release of a new version of the AncientMetagenomeDir, and its tooling AMDirT, as part of a community-led project will help towards easier integration and reuse of public ancient metagenomic datasets into future analyses.