Inferring Allele Frequency Trajectories from Ancient DNA Indicates That Selection on a Chicken Gene Coincided with Changes in Medieval Husbandry Practices
Open accessAbstract
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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An ancient DNA study shows how two strong sweeps in the domestic chicken, at TSHR and BCO2, both were selected much later than early domestication.
“For example, an ancient DNA study shows how two strong sweeps in the domestic chicken, at TSHR and BCO2, both were selected much later than early domestication (Flink et al. 2014; Loog et al. 2017).”
From The neural crest cell hypothesis: no unified explanation for domestication (2021) · cites this paper as Loog et al. 2017
The Results section dates strong selection at TSHR to around 920 AD, long after early domestication. For BCDO2, the Results say that the start of selection is poorly resolved and that its allele frequency rose only marginally before recent Asian gene flow; the paper therefore does not establish a second strong, late sweep. (LLM, conf=0.90)
Experimental — accuracy not yet measuredThroughout much of early medieval Europe, poultry farming likely benefited from the spread of Christianity, and chickens were also associated with early monastic contexts in Ireland.
“Throughout much of early medieval Europe, poultry farming likely benefited from the spread of Christianity (78), and chickens were also associated with early monastic contexts in Ireland (SI Appendix, Table S2).”
From The biocultural origins and dispersal of domestic chickens (2022) · cites this paper as [78]
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Bača, M. (2021) · Historický časopis · doi:10.31577/histcaso.2022.70.3.5
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Černý, V., Hofmanová, Z., & Květina, P. (2017) · Archeologické rozhledy · doi:10.35686/ar.2017.20
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Lyu, W., Dai, X., Beaumont, M., Yu, F., & He, Z. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.07.10.548348
Huang, X., Otecko, N. O., Peng, M., Weng, Z., Li, W., Chen, J., Zhong, M., Zhong, F., Jin, S., Geng, Z., et al. (2020) · Figshare · doi:10.6084/m9.figshare.12160245
Huang, X., Otecko, N. O., Peng, M., Weng, Z., Li, W., Chen, J., Zhong, M., Zhong, F., Jin, S., Geng, Z., et al. (2020) · Figshare · doi:10.6084/m9.figshare.12160293
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Huang, X., Otecko, N. O., Peng, M., Weng, Z., Li, W., Chen, J., Zhong, M., Zhong, F., Jin, S., Geng, Z., et al. (2020) · Figshare · doi:10.6084/m9.figshare.12160236
Huang, X., Otecko, N. O., Peng, M., Weng, Z., Li, W., Chen, J., Zhong, M., Zhong, F., Jin, S., Geng, Z., et al. (2020) · Figshare · doi:10.6084/m9.figshare.12160254
Huang, X., Otecko, N. O., Peng, M., Weng, Z., Li, W., Chen, J., Zhong, M., Zhong, F., Jin, S., Geng, Z., et al. (2020) · Figshare · doi:10.6084/m9.figshare.12160299
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Additional file 2 of Galbase: a comprehensive repository for integrating chicken multi-omics data
Fu, W., Wang, R. Y., Xu, N., Wang, J., Li, R., Nanaei, H. A., Nie, Q., Zhao, X., Han, J., Yang, N., et al. (2022) · Figshare · doi:10.6084/m9.figshare.19759724
Yin, Z., Li, X., Sun, Y.-X., Smith, J., Hincke, M. T., Yang, N., & Hou, Z. (2023) · Figshare · doi:10.6084/m9.figshare.24892832
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Additional file 3 of Galbase: a comprehensive repository for integrating chicken multi-omics data
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Hamerow, H., Bogaard, A., Charles, M., Forster, E., Holmes, M., McKerracher, M., Ramsey, C. B., Stroud, E., & Thomas, R. M. (2025) · doi:10.1093/9780191988905.002.0005
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Hamerow, H., Bogaard, A., Charles, M., Forster, E., Holmes, M., McKerracher, M., Ramsey, C. B., Stroud, E., & Thomas, R. M. (2025) · doi:10.1093/9780191988905.003.0003
Hamerow, H., Bogaard, A., Charles, M., Forster, E., Holmes, M., McKerracher, M., Ramsey, C. B., Stroud, E., & Thomas, R. M. (2025) · doi:10.1093/9780191988905.003.0002
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Hamerow, H., Bogaard, A., Charles, M., Forster, E., Holmes, M., McKerracher, M., Ramsey, C. B., Stroud, E., & Thomas, R. M. (2025) · doi:10.1093/9780191988905.003.0001
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Hamerow, H., Bogaard, A., Charles, M., Forster, E., Holmes, M., McKerracher, M., Ramsey, C. B., Stroud, E., & Thomas, R. M. (2025) · doi:10.1093/9780191988905.005.0004
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Zhang, Y., Day, J. P., Lirintzi, M., Ji, J., Tregaskes, C. A., Carneiro, M., Alves, J. M., Strive, T., Kaufman, J., & Jiggins, F. M. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2532064123
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Additional file 4 of Galbase: a comprehensive repository for integrating chicken multi-omics data
Fu, W., Wang, R., Xu, N., Wang, J., Li, R., Nanaei, H. A., Nie, Q., Zhao, X., Han, J., Yang, N., et al. (2022) · Figshare · doi:10.6084/m9.figshare.19759730
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Additional file 1 of Large-scale genomic analysis reveals the genetic cost of chicken domestication
Wang, M.-S., Zhang, J.-J., Guo, X., Li, M., Meyer, R., Ashari, H., Zheng, Z.-Q., Wang, S., Peng, M.-S., Jiang, Y., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14788353
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Genome-wide analysis reveals domestication selection signals in Bashang long-tail chickens
Liang, Y., Yu, B., Zhou, R.-L., & Li, X. (2026) · British Poultry Science · doi:10.1080/00071668.2025.2593634
Sant, J., Jenkins, P. A., Koskela, J., & Spanò, D. (2026) · BMC Bioinformatics · doi:10.1186/s12859-026-06576-z
- Authors
- Loog, L., Thomas, M. G., Barnett, R., Allen, R., Sykes, N., Paxinos, P. D., Lebrasseur, O., Dobney, K., Peters, J., Manica, A., Larson, G., & Eriksson, A.
- Affiliations
- University of Cambridge (GB)
- University College London (GB)
- University of Oxford (GB)
- University of Nottingham (GB)
- Ludwig-Maximilians-Universität München (DE)
- University of Liverpool (GB)
- Bavarian Natural History Collections (DE)
- Guy's Hospital (GB)
- Corresponding author
- Loog, Liisa
- Larson, Greger
- Eriksson, Anders
- ORCID
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-05-02
- Volume
- 34
- Issue
- 8
- Pages
- 1981-1990
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- PMC
- PMC5850110
- OpenAlex
- W2607157138
- Cited by
- 82
- References
- 35
- Citations by year
- 2026: 4 · 2025: 21 · 2024: 5 · 2023: 6 · 2022: 8 · 2021: 12 · 2020: 7 · 2019: 11 · 2018: 4 · 2017: 4
- FWCI
- 6.52
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Molecular Biology and Evolution (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Research Portal (King's College London) (submittedVersion, cc-by)
- UCL Discovery (University College London) (submittedVersion)
- Apollo (University of Cambridge) (submittedVersion, cc-by)
- Apollo (cc-by)
- Funders
- Natural Environment Research Council (NE/K005243/1, NE/K003259/1)
- Wellcome Trust (100719/Z/12/Z)
- Leverhulme Trust (RP2011-R-045)
- Arts and Humanities Research Council (AH/L006979/1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- chickens, natural selection, TSHR, oviposition, aggression, food preferences, gene flow, chicken domestication, ancient DNA
- MeSH terms
- DNA, Ancient, Alleles, Animals, Animal Husbandry, Animals, Domestic, Bayes Theorem, Breeding, Chickens, DNA, Mitochondrial, Gene Frequency, Poultry, Receptors, Thyrotropin, Selection, Genetic, Sequence Analysis, DNA, Dioxygenases
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