Job Title
Professor
Department
Life Sciences
Phone
Ext 75059
Email
Web Link
Research Interests
Key interest areas: plant evolutionary genetics; evolution of plant domestication; molecular archaeobotany; molecular anthropology; phylogenomics; software design for population dynamics and molecular evolution.
In my group we are interested in the evolutionary dynamics associated with the plant domestication process on several levels of organization: the gene, the genome, the population and the selective environment in which the population exists. We utilize genetic information directly from both archaeological and modern samples, and develop bioinformatic approaches for high throughput analysis. We also work closely with the archaeology community. Our empirical work is balanced by a theoretical approach, through computational biology, in which we study the complex evolutionary system which gives rise to the patterns of genetic diversity we observe. Using this in vitro and in silico two-pronged approach we wish to answer questions about where crops come from, and how plants such as crops become locally adapted to environmental conditions. Such information may help us in the future to produce crops which are better adapted to a wider range of conditions: the key to a sustainable future is to understand the past.
Biography
PhD, University of Manchester Institute of Science and Technology, 1996
BSc Hons, King's College London, 1991
Fellow of the Linnean Society
Fellow of the Society of Biologists
Associate Editor, PLosOne Journal
Associate Editor, Archaeological and Anthropological Sciences
- Allaby, Robin G., Stevens, Chris J., Fuller, Dorian Q., 2022. A novel cost framework reveals evidence for competitive selection in the evolution of complex traits during plant domestication. Journal of Theoretical Biology, 537
- 'Simon, Marcelo F., 'Mendoza, J Moises F., 'Liu, Hsiao-Lei, 'Martins, M?rcio Lacerda Lopes, 'Drovetski, Sergei V., 'Przelomska, Natalia A. S., 'Loiselle, Hope, 'Cavalcanti, Taciana B., 'Inglis, Peter W, 'Mueller, Natalie G., 'Allaby, Robin G., 'de Oliveira Freitas, F?bio, 'Kistler, Logan, 2022. 'Phylogenomic analysis points to a South American origin of Manihot and illuminates the primary gene pool of cassava. The New Phytologist, 233 (6), pp. 534-545
- 'Allaby, Robin G., 'Stevens, Chris J., 'Kistler, Logan, 'Fuller, Dorian Q., 2022. 'Emerging evidence of plant domestication as a landscape-level process. Trends in Ecology & Evolution, 37 (3), pp. 268-279
- 'Ishikawa, Ryo, 'Castillo, Cristina Cobo, 'Htun, Than Myint, 'Numaguchi, Koji, 'Inoue, Kazuya, 'Oka, Yumi, 'Ogasawara, Miki, 'Sugiyama, Shohei, 'Takama, Natsumi, 'Orn, Chhourn, 'Inoue, Chizuru, 'Nonomura, Ken-Ichi, 'Allaby, Robin G., 'Fuller, Dorian Q., 'Ishii, Takashige, 2022. 'A stepwise route to domesticate rice by controlling seed shattering and panicle shape. Proceedings of the National Academy of Sciences of the United States of America, 119 (26)
- Mabry, Makenzie E., Turner-Hissong, Sarah D., Gallagher, Evan Y., McAlvay, Alex C., An, Hong, Edger, Patrick P., Moore, Jonathan D., Pink, David A. C., Teakle, Graham R., Stevens, Chris J., Barker, Guy C., Labate, Joanne, Fuller, Dorian Q., Allaby, Robin G., Beissinger, Timothy, Decker, Jared E., Gore, Michael A., Pires, J. Chris, 2021. The evolutionary history of wild, domesticated, and feral Brassica oleracea (Brassicaceae). Molecular Biology and Evolution
- Orlando, Ludovic, Allaby, Robin G., Skoglund, Pontus, Der Sarkissian, Clio, Stockhammer, Philipp W., Ávila-Arcos, María C., Fu, Qiaomei, Krause, Johannes, Willerslev, Eske, Stone, Anne C., Warinner, Christina, 2021. Ancient DNA analysis. Nature Reviews Methods Primers, 1 (1)
- 'Bogaard, Amy, 'Allaby, Robin G., 'Arbuckle, Benjamin S., 'Bendrey, Robin, 'Crowley, Sarah, 'Cucchi, Thomas, 'Denham, Tim, 'Frantz, Laurent, 'Fuller, Dorian, 'Gilbert, Tom, 'Karlsson, Elinor K., 'Manin, Aur?lie, 'Marshall, Fiona, 'Mueller, Natalie, 'Peters, Joris, 'St?panoff, Charles, 'Weide, Alexander, 'Larson, Greger, 2021. 'Reconsidering domestication from a process archaeology perspective. World Archaeology, 53 (1), pp. 56-77
- Cribdon, Becky, Ware, Roselyn, Smith, Oliver, Gaffney, Vincent, Allaby, Robin G., 2020. PIA : more accurate taxonomic assignment of metagenomic data demonstrated on sedaDNA from the North sea. Frontiers in Ecology and Evolution, 8
- Landoni, Beatrice, Viruel, Juan, Gómez, Rocio, Allaby, Robin G., Brennan, Adrian C., Picó, F. Xavier, Pérez-Barrales, Rocio, 2020. Microsatellite marker development in the crop wild relative Linum bienne using genome skimming. Applications in Plant Sciences, 8 (5)
- Ware, Roselyn, Garrod, Benjamin, Macdonald, Hannah, Allaby, Robin G., 2020. Guano morphology has the potential to inform conservation strategies in British bats. PLoS One, 15 (4)
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Gaffney, Vincent, Fitch, Simon, Bates, Martin, Ware, Roselyn, Kinnaird, Tim, Gearey, Benjamin, Hill, Tom, Telford, Richard, Batt, Cathy, Stern, Ben, Whittaker, John, Davies, Sarah, Sharada, Mohammed Ben, Everett, Rosie, Cribdon, Rebecca, Kistler, Logan, Harris, Sam, Kearney, Kevin, Walker, James, Muru, Merle et al (Select to open full list), 2020. Multi-proxy characterisation of the Storegga tsunami and its impact on the early holocene landscapes of the southern North Sea. Geosciences, 10 (7)
- Kistler, Logan, Thakar, Heather B., VanDerwarker, Amber M., Domic, Alejandra, Bergström, Anders, George, Richard J., Harper, Thomas K., Allaby, Robin G., Hirth, Kenneth, Kennett, Douglas J., 2020. Archaeological Central American maize genomes suggest ancient gene flow from South America. Proceedings of the National Academy of Sciences of the United States of America, 117 (52), pp. 33124-33129
- Allaby, Robin G., Ware, Roselyn, Kistler, Logan, 2019. A re-evaluation of the domestication bottleneck from archaeogenomic evidence. Evolutionary Applications, 12 (1), pp. 29-37
- Smith, Oliver, Nicholson, William V., Kistler, Logan, Mace, Emma, Clapham, Alan, Rose, Pamela, Stevens, Chris, Ware, Roselyn, Samavedam, Siva, Barker, Guy C., Jordan, David, Fuller, Dorian Q., Allaby, Robin G., 2019. A domestication history of dynamic adaptation and genomic deterioration in Sorghum. Nature Plants, 5 (4), pp. 369-379
- Zhou, Yong, Chen, Zhongxu, Cheng, Mengping, Chen, Jian, Zhu, Tingting, Wang, Rui, Liu, Yaxi, Qi, Pengfei, Chen, Guoyue, Jiang, Qiantao, Wei, Yuming, Luo, Ming-Cheng, Nevo, Eviatar, Allaby, Robin G., Liu, Dengcai, Wang, Jirui, Dvorák, Jan, Zheng, Youliang, 2018. Uncovering the dispersion history, adaptive evolution and selection of wheat in China. Plant Biotechnology Journal, 16 (1), pp. 280-291
- Kistler, Logan, Maezumi, S. Yoshi, de Souza, Jonas Gregorio, Przelomska, Natalia A. S., Costa, Flaviane Malaquias, Smith, Oliver, Loiselle, Hope, Ramos-Madrigal, Jazmin, Wales, Nathan, Ribeiro, Eduardo, Morrison, Ryan R., Grimaldo, Claudia, Prous, Andre P., Arriaza, Bernardo, Gilbert, M. Thomas P., de Oliveira Freitas, Fabio, Allaby, Robin G., 2018. Multiproxy evidence highlights a complex evolutionary legacy of maize in South America. Science, 362 (6420), pp. 1309-1313
- Gutaker , Rafal M., Zaidem, Maricris, Fu, Yong-Bi, Diederichsen, Axel, Smith, Oliver, Ware, Roselyn, Allaby, Robin G., 2018. Flax latitudinal adaptation at LuTFL1 altered architecture and promoted fiber production. Scientific Reports, 9 (976)
- Payacan, Claudia, Moncada, Ximena, Rojas, Gloria, Clarke, Andrew C., Chung, Kuo-Fang, Allaby, Robin G., Seelenfreund, Daniela, Seelenfreund, Andrea, 2017. Phylogeography of herbarium specimens of asexually propagated paper mulberry [Broussonetia papyrifera (L.) L'Hér. ex Vent. (Moraceae)] reveals genetic diversity across the Pacific. Annals of Botany, 120 (3), pp. 387-404
- Smith, Oliver, Palmer, Sarah A., Clapham, Alan J., Rose, Pamela, Liu, Yuan, Wang, Jun, Allaby, Robin G., 2017. Small RNA activity in archaeological barley shows novel germination inhibition in response to environment. Molecular Biology and Evolution, 34 (10), pp. 2555-2562
- Kistler, Logan, Ware, Roselyn, Smith, Oliver, Collins, Matthew, Allaby, Robin G., 2017. A new model for ancient DNA decay based on paleogenomic meta-analysis. Nucleic Acids Research, 45 (11), pp. 6310-6320
- Allaby, Robin G., Stevens, Chris, Lucas, Leilani, Maeda, Osamu, Fuller, Dorian Q., 2017. Geographic mosaics and changing rates of cereal domestication. Philosophical Transactions of the Royal Society B: Biological Sciences, 372 (1735)
- Allaby, Robin G., Kitchen, James, Fuller, Dorian Q., 2016. Surprisingly low limits of selection in plant domestication. Evolutionary Bioinformatics, pp. 41-51
- Allaby, Robin G., Kistler, Logan, Gutaker, Rafal M., Ware, Roselyn, Kitchen, James, Smith, Oliver, Clarke, Andrew C., 2015. Archaeogenomic insights into the adaptation of plants to the human environment : pushing plant?hominin co-evolution back to the Pliocene. Journal of Human Evolution, 79, pp. 150-157
- Smith, Oliver, Momber, G., Bates, R., Garwood, P., Fitch, S., Pallen, Mark J., Gaffney, V., Allaby, Robin G., 2015. Response to comment on "Sedimentary DNA from a submerged site reveals wheat in the British Isles 8000 years ago". Science, 349 (6245), pp. 247-247
- Smith, Oliver, Momber, G., Bates, R., Garwood, P., Fitch, S., Pallen, Mark J., Gaffney, V., Allaby, Robin G., 2015. Sedimentary DNA from a submerged site reveals wheat in the British Isles 8000 years ago. Science, 347 (6225), pp. 998-1001
- Smith, Oliver, Clapham, Alan J., Rose, Pam, Liu, Yuan, Wang, Jun, Allaby, Robin G., 2014. A complete ancient RNA genome : identification, reconstruction and evolutionary history of archaeological Barley Stripe Mosaic Virus. Scientific Reports, 4
- Smith, Oliver, Clapham, Alan J., Rose, Pam, Liu, Yuan, Wang, Jun, Allaby, Robin G., 2014. Genomic methylation patterns in archaeological barley show de-methylation as a time-dependent diagenetic process. Scientific Reports, 4
- Allaby, Robin G., Gutaker, Rafal M., Clarke, Andrew C., Pearson, Neil, Ware, Roselyn, Palmer, Sarah A., Kitchen, James, Smith, Oliver, 2014. Using archaeogenomic and computational approaches to unravel the history of local adaptation in crops. Philosophical Transactions of the Royal Society B: Biological Sciences, 370 (1660)
- Fuller, D. Q., Denham, T., Arroyo-Kalin, M., Lucas, L., Stevens, C. J., Qin, L., Allaby, Robin G., Purugganan, M. D., 2014. Convergent evolution and parallelism in plant domestication revealed by an expanding archaeological record. Proceedings of the National Academy of Sciences of the United States of America, 111 (17), pp. 6147-6152
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Gerbault, P., Allaby, Robin G., Boivin, N., Rudzinski, A., Grimaldi, I. M., Pires, J. C., Climer Vigueira, C., Dobney, K., Gremillion, K. J., Barton, L., Arroyo-Kalin, M., Purugganan, M. D., Rubio de Casas, R., Bollongino, R., Burger, J., Fuller, D. Q., Bradley, D. G., Balding, D. J., Richerson, P. J., Gilbert, M. T. P. et al (Select to open full list), 2014. Storytelling and story testing in domestication. Proceedings of the National Academy of Sciences of the United States of America, 111 (17), pp. 6159-6164
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Larson, G., Piperno, D. R., Allaby, Robin G., Purugganan, M. D., Andersson, L., Arroyo-Kalin, M., Barton, L., Climer Vigueira, C., Denham, T., Dobney, K., Doust, A. N., Gepts, P., Gilbert, M. T. P., Gremillion, K. J., Lucas, L., Lukens, L., Marshall, F. B., Olsen, K. M., Pires, J. C., Richerson, P. J. et al (Select to open full list), 2014. Current perspectives and the future of domestication studies. Proceedings of the National Academy of Sciences of the United States of America, 111 (17), pp. 6139-6146
- Boivin, Nicole, Fuller, Dorian Q., Dennell, Robin, Allaby, Robin G., Petraglia, Michael D., 2013. Human dispersal across diverse environments of Asia during the Upper Pleistocene. Quaternary International, 300, pp. 32-47
- Kitchen, James, Allaby, Robin G., 2013. Systems modeling at multiple levels of regulation : linking systems and genetic Networks to spatially explicit plant populations. Plants, 2 (1), pp. 16-49
- Palmer, Sarah A., Clapham, A. J., Rose, P., Freitas, F. O., Owen, B. D., Beresford-Jones, D., Moore, Jonathan D., Kitchen, James, Allaby, Robin G., 2012. Archaeogenomic evidence of punctuated genome evolution in Gossypium. Molecular Biology and Evolution, 29 (8), pp. 2031-2038
- Fuller, Dorian Q., Willcox, G., Allaby, Robin G., 2012. Early agricultural pathways : moving outside the 'core area' hypothesis in Southwest Asia. Journal of Experimental Botany, Vol.63 (No.2), pp. 617-633
- Fu, Yong-Bi, Diederichsen, Axel, Allaby, Robin G., 2012. Locus-specific view of flax domestication history. Ecology and Evolution, Vol.2 (No.1), pp. 139-152
- Kitchen, James, Moore, Jonathan D., Palmer, Sarah A., Allaby, Robin G., 2012. MCMC-ODPR : primer design optimization using Markov Chain Monte Carlo sampling. BMC Bioinformatics, Vol.13 (No.1)
- Palmer, Sarah A., Smith, Oliver, Allaby, Robin G., 2012. The blossoming of plant archaeogenetics. Annals of Anatomy, Vol.194 (No.1), pp. 146-156
- Kitchen, James, Allaby, Robin G., 2012. The limits of mean-field heterozygosity estimates under spatial extension in simulated plant populations. PLoS ONE, Vol.7 (No.8)
- Fuller, Dorian Q., Boivin, Nicole, Ph. D., Hoogervorst, Tom, Allaby, Robin G., 2011. Across the Indian Ocean : the prehistoric movement of plants and animals. Antiquity, Vol.85 (No.328), pp. 544-558
- Fuller, Dorian Q, Willcox, George, Allaby, Robin G., 2011. Cultivation and domestication had multiple origins: arguments against the core area hypothesis for the origins of agriculture in the Near East. World Archaeology, Vol. 43 (No. 4), pp. 628-652
- Allaby, Robin G., 2010. Integrating the processes in the evolutionary system of domestication. Journal of Experimental Botany, Vol.61 (No.4), pp. 935-944
- Fu, Yong-Bi, Allaby, Robin G., 2010. Phylogenetic network of Linum species as revealed by non-coding chloroplast DNA sequences. Genetic Resources and Crop Evolution, Vol.57 (No.5), pp. 667-677
- Fuller, Dorian Q., Allaby, Robin G., Stevens, Chris, 2010. Domestication as innovation : the entanglement of techniques, technology and chance in the domestication of cereal crops. World Archaeology, Vol.42 (No.1), pp. 13-28
- Palmer, Sarah A., Moore, Jonathan D., Clapham, Alan J., Rose, Pamela, Allaby, Robin G., 2009. Archaeogenetic evidence of ancient Nubian barley evolution from six to two-row indicates local adaptation. PLoS ONE, Vol.4 (No.7)
- Allaby, Robin G., Fuller, Dorian Q., Brown, T. A., 2008. The genetic expectations of a protracted model for the origins of domesticated crops. Proceedings of the National Academy of Sciences of the United States of America, Vol.105 (No.37), pp. 13982-13986
- Allaby, Robin G., 2008. The rise of plant domestication : life in the slow lane. Biologist, Vol.55 (No.2), pp. 94-99
- Moore, Jonathan D., Allaby, Robin G., 2008. TreeMos : a high-throughput phylogenomic approach to find and visualize phylogenetic mosaicism. Bioinformatics, Vol.24 (No.5), pp. 717-718
- Brown, T. A., Jones, Martin K., Powell, Wayne, Allaby, Robin G., 2008. The complex origins of domesticated crops in the Fertile Crescent. Trends in Ecology & Evolution, Vol.24 (No.2), pp. 103-109
- Ho, Simon Y. W., Kolokotronis, Sergios-Orestis, Allaby, Robin G., 2007. Elevated substitution rates estimated from ancient DNA sequences. Biology Letters, Vol.3 (No.6), pp. 702-705
- Allaby, Robin G., Woodwark, Mathew, 2007. Phylogenomic analysis reveals extensive phylogenetic mosaicism in the Human GPCR Superfamily. Evolutionary Bioinformatics, Vol.3, pp. 357-370
- Kistler, Logan, Thakar, Heather B., VanDerwarker, Amber M., Domic, Alejandra, Bergström, Anders, George, Richard J., Harper, Thomas K., Allaby, Robin G., Hirth, Kenneth, Kennett, Douglas J., 2021. Data for Archaeological Central American maize genomes suggest ancient gene flow from South America. Data Dryad
- Allaby, Robin G., 2021. First come, first served for ancient crops. Nature Plants, Nature Publishing Group, pp. 542-543
- Allaby, Robin G., 2019. Clonal crops show structural variation role in domestication. Nature Plants, Nature Publishing Group, pp. 915-916
- Allaby, Robin G., Brown, T. A., Fuller, Dorian Q., 2010. A simulation of the effect of inbreeding on crop domestication genetics with comments on the integration of archaeobotany and genetics: a reply to Honne and Heun. Vegetation History and Archaeobotany, Springer, pp. 151-158
- Bergfjord, C., Karg, S., Rast-Eicher, A., Nosch, M. -L., Mannering, U., Allaby, Robin G., Murphy, B. M., Holst, B., 2010. Comment on "30,000-year-old wild flax fibers". Science, American Association for the Advancement of Science
- Brown, T. A., Jones, Martin K., Powell, Wayne, Allaby, Robin G., 2009. The complex origins of domesticated crops in the Fertile Crescent. Trends in Ecology & Evolution, Elsevier, pp. 103-109
- Allaby, Robin G., Fuller, Dorian Q., Brown, T. A., 2008. Reply to Ross-Ibarra and Gaut : Multiple domestications do appear monophyletic if an appropriate model is used. Proceedings of the National Academy of Sciences of the United States of America, National Academy of Sciences, pp. E106-E106
| Title | Funder | Award start | Award end |
|---|---|---|---|
| Central England NERC Training Alliance 2 (CENTA2) Doctoral Training Programme | NERC | 01 Oct 2019 | 30 Sep 2027 |
| Tracking the altitudinal adaptation of Andean maize using archaeogenomics | NERC | 04 Jul 2022 | 03 Jul 2025 |
| LinnéSys: Systematics Research Fund for Annabelle De Vries | Linnean Society, The | 01 Jul 2021 | 30 Jun 2022 |
| Europe's Lost Frontiers: exploring climate change, settlement and colonisation of the submerged landscapes of the North Sea basin using ancient DNA, seismic mapping and complex systems modelling | European Research Council (ERC) | 01 Dec 2015 | 30 Nov 2021 |
| MICROWINE - Microbial metagenomics and the modern wine industry (Marie Curie ITN) | European Commission | 01 Jul 2015 | 30 Jun 2018 |
| Wine through the nubian ages | National Geographic Society | 01 Dec 2017 | 31 Mar 2018 |
| Bioengineering Brazilian indigenous crop diversity into peanuts for a changing climate | Royal Academy of Engineering | 15 Jan 2016 | 31 Aug 2017 |
| Zika virus ? harnessing the powers of molecular and device engineering to counter a global threat | EPSRC | 01 Jun 2016 | 31 Mar 2017 |
| An archaeogenomic survey of maize biodiversity and evolution in South America | STFC | 15 Sep 2016 | 14 Mar 2017 |
| Archaeogenomics of Sorghum domestication and adaptation | NERC | 06 Jan 2014 | 05 Jan 2017 |
| Strategic Environmental Science Capital Call | NERC | 01 Jan 2014 | 30 Jun 2014 |
| Collaboration on a study to examine a small number of genetic loci in samples of banana (Musa spp.), taro (Colocasia esculenta) and yam (Dioscorea spp.) to establish population affiliations | Monash University | 02 Jan 2012 | 31 Dec 2012 |
| Elucidating the genetic expectations of protracted crop domestication | Leverhulme Trust | 01 Oct 2009 | 30 Sep 2012 |
| Was Barley Locally Adapted to Ancient Nubia | NERC | 05 Jan 2009 | 04 Jan 2012 |
| SEALINKS - Tracing taro and other crop movements from island SE Asia to Africa | EU | 01 Jun 2010 | 30 Nov 2011 |
| Agricultural Origins in Southwest Asia: The pace of transition | University of Manchester | 01 Oct 2007 | 30 Sep 2010 |
| IF0174 Identification of candidate genes for resource-use-efficiency by genome-wide association mapping in Arabidopsis thaliana | Department for Environment, Food and Rural Affairs | 01 Oct 2008 | 31 Mar 2009 |
| New Investigator Award - Origins and evolution of ancient Egyptian cotton tracked by paleogenomics | NERC | 01 Aug 2007 | 31 Jul 2008 |
