Publications

Fuller DQ, Denham T, Allaby RG (2023) Plant domestication and agricultural ecologies. Current Biology 33(11):R636-R649.

Allaby RG (2023) Two domestications for grapes. Science 379:880-881.

Allaby RG, Cribdon R, Everett R, Ware R (2022) Sedimentary ancient DNA palaeoenvironmental reconstruction in the North Sea landscape. In Europe's Lost Frontiers Volume 1 Context and Methodology. eds. Gaffney V, Fitch S. Archaeopress, Oxford, pp 112-121.

Fuller DQ, Denham T, Kistler L, Stevens C, Larson G, Bogaard A, Allaby RG (2022) Progress in domestication research: Explaining expanded empirical observations. Quaternary Science Reviews 296 107737.

Ryo Ishikawa, Cristina Cobo Castilloa, Than Myint Htun, Koji Numaguchi, Kazuya Inoue, Yumi Oka, Miki Ogasawara, Shohei Sugiyama, Natsumi Takama, Chhourn Orn Chizuru Inoue, Ken-Ichi Nonomura, Robin Allaby, Dorian Q. Fuller, and Takashige Ishii (2022) A stepwise route to domesticate rice by controlling seed shattering and panicle shape. PNAS 119 (26): e2121692119.

Allaby RG, Stevens CJ, Kistler L, Fuller DQ (2022) Genetic revelations of a new paradigm of plant domestication as a landscape level process. Plant Breeding Reviews 50:321-343.

Allaby RG, Stevens CJ, Fuller DQ (2022) A novel cost framework reveals evidence for competitive selection in the evolution of complex traits during plant domestication. J. Theoretical Biology 537:111004 https://doi.org/10.1016/j.jtbi.2022.111004.

Allaby RG, Stevens CJ, Kistler L, Fuller DQ (2021) Emerging evidence of plant domestication as a landscape-level process. Trends Ecol. Evol. 37:268-279. doi: https://doi.org/10.1016/j.tree.2021.11.002.

Simon MF , Mendoza Flores JM , Liu HL , Martins MLL, Drovetski SV, Przelomska NAS , Loiselle H, Cavalcanti TB, Inglis PW, Mueller NG, Allaby RG, Freitas FO and Kistler L (2021) Phylogenomic analysis points to a South American origin of Manihot and illuminates the primary gene pool of cassava. New Phytologist doi:10.1111.nph.17743.

Bogaard A, Allaby R, Arbuckle BS, Bendrey R, Crowley S, Cucchi T, Denham T, Frantz L, Fuller D, Gilbert T, Karlsson E, Manin A, Marshall F, Mueller N, Peters J, Stépanoff C, Wedie A, Larson G (2021) Reconsidering domestication from a process archaeology perspective. World Archaeology, https://doi.ord/10.1080/00438243.2021.1954990

Mabry ME, Turner-Hissong SD, Gallagher EY, McAlvay AC, An H, Edger PP, Moore JD, Pink DAC,. Teakle GR, Stevens CJ, Barker G, Labate J, Fuller DQ, Allaby RG, Beissinger T, Decker JE, Gore MA, Pires JC (2021) The Evolutionary History of Wild, Domesticated, and Feral Brassica oleracea (Brassicaceae). Mol. Biol. Evol. 38(10):4419-4434.

Allaby RG (2021) First come first served for ancient crops. Nature Plants 7, pages 542–543. https://doi.org/10.1038/s41477-021-00926-w.

Orlando L, Allaby RG, Skoglund P, Der Sarkissian C, Stockhammer PW, Avila-Arcos M, Fu Q, Krause J, Willerslev E, Stone AC, Warinner C (2021) Ancient DNA Analysis. Nature Reviews Methods Primers 1:14.

Kistler L, Thaker HB, VanDewarker AM, Domic A, Berström A, George RJ, Harper TK, Allaby RG, Hirth K, Kennett DJ (2020) Archaelogical Central American maize genomes suggest ancient gene flow from South America. Proc. Natl. Acad. Sci. U.S.A. 117:33124-33129.

Gaffney V, Fitch S, Bates M, Ware RL, Kinnaird T, Gearey B, Hill T, Telford R, Batt C, Stern B, Whittaker J, Davies S, Ben Sharada M, Everett R, Cribdon R, Kistler L, Harris S, Kearney K, Walker J, Muru M, Hamilton D, Law M, Finlay A, Bates R, Allaby RG (2020) Multi-proxy characterisation of the Storegga tsunami and its impact on the early Holocene landscape of the southern North Sea. Geosciences 10:270 doi:10.3390/geosciences10070270

Landoni B, Viruel J, Gomez R, Allaby RG, Brennan AC, Pico, FX, Perez-Barrales R (2020) Microsatellite marker development in the crop wild relative Linum bienne using genome skimming. Applications in Plant Sciences 8 (5): e11349.

Ware RL, Garrod B, Macdonald H, Allaby RG (2020) Guano morphology has the potential to inform conservation strategies in British bats. PLoS One https://doi.org/10.1371/journal.pone.0230865.

Cribdon B, Ware R, Smith O, Gaffney V, Allaby RG (2020) PIA: More accurate taxonomic assignment of metagenomic data demonstrated in sedaDNA from the North Sea. Front. Ecol. Evol. 8:84 https://doi.org/10.3389/fevo.2020.00084.

Allaby RG (2019) Clonal crops show structural variation role in domestication. Nature Plants 5:915-916.

Smith O, Nicholson WV, Kistler L, Mace E, Clapham A, Rose P, Stevens C, Ware R, Samavedam S, Barker G, Jordan D, Fuller DQ, Allaby RG (2019) A domestication history of dynamic adaptation and genomic deterioration in Sorghum. Nature Plants 5:369-379.

Gutaker RM, Zaidem M, Fu, Y-B, Diederichsen A, Smith O, Ware R, Allaby RG (2019) Flax latitudinal adaptation at LuTFL1 altered architecture and promoted fibre production. Scientific Reports 9:976.

Kistler K, Maezumi SY, Gregorio de Souza J, Przelomska NAS, Costa FM, SmithO, Loiselle H, Ramos-Madrigal J, Wales N, Ribeiro ER, Morrison RR, Grimaldo C, Prous AP, Arriaza B, Gilbert MTP, Oliveira Freitas F, Allaby RG (2018) Multiproxy evidence highlights a complex evolutionary legacy of maize in South America Science 362:1309–1313. [download]

Allaby, R.G., Smith, O., Kistler, L. (2018). Archaeogenomics and Crop Adaptation. In: Lindqvist, C., Rajora, O. (eds) Paleogenomics. Population Genomics. Springer, Cham. https://doi.org/10.1007/13836_2018_51

Robin G. Allaby, Roselyn Ware and Logan Kistler (2018) A re-evaluation of the domestication bottleneck from archaeogenomic evidence. Evolutionary Applications 12:29-37 doi.org/10.1111/eva.12680.

Robin G. Allaby, Chris Stevens, Leilani Lucas, Osamu Maeda, Dorian Q Fuller (2017) Geographic mosaics and changing rates of cereal domestication. Phil. Trans. Roy. Soc. B 372: 20160429. http://rstb.royalsocietypublishing.org/content/372/1735/20160429

Oliver Smith, Sarah A. Palmer, Alan J. Clapham, Pamela Rose, Yuan Liu, Jun Wang, Robin G. Allaby (2017) Small RNA activity in archaeological barley shows novel germination inhibition in response to environment. Mol. Biol. Evol. 34:2555-2562 doi.org/10.1093/molbev/msx175

Claudia Payacán, Ximena Moncada, Gloria Rojas, Andrew Clarke, Kuo-Fang Chung, Robin Allaby, Daniela Seelenfreund, and Andrea Seelenfreund (2017) Molecular characterization of herbarium specimens of paper mulberry ((Broussonetia papyrifera (L.)L'Hér. ex Vent.(Moraceae)) reveals genetic diversity across the Pacific. Annals of Botany doi: 10.1093/aob/mcx062.

Zhou, Yong; Chen, Zhongxu; Cheng, Mengping; Chen, Jian; Zhu, Tingting; Wang, Rui; Liu, Yaxi; Qi, Peng-Fei; Chen, Guoyue; Jiang, Qiantao; Wei, Yu-Ming; Luo, Ming-Cheng; Nevo, Eviator; Allaby, Robin; Liu, Dengcai; Wang, Jirui ; Dvorak, Jan; Zheng, Youliang (2017) Uncovering the Dispersion History, Adaptive Evolution and Selection of Wheat in China. Plant Biotechnology Journal doi: 10.1111/pbi.12770.

Logan Kistler, Roselyn Ware, Oliver Smith, Matthew Collins and Robin G. Allaby (2017) A new model for ancient DNA decay based on paleogenomic meta-analysis. Nucleic Acids Research 45 (11): 6310-6320 doi: 10.1093/nar/gkx361.[download link]

Allaby RG, Kitchen JL, Fuller DQ (2016) Surprisingly low limits of selection in plant domestication. Evolutionary Bioinformatics 11:(S2) 41-51. [download link]

Logan Kistler, Oliver Smith, Roselyn Ware, Garry Momber, Richard Bates, Paul Garwood, Simon Fitch, Mark Pallen, Vincent Gaffney, Robin Allaby (2015) Thermal age, cytosine deamination and the veracity of 8,000 year old wheat DNA from sediments. bioArxiv (http://dx.doi.org/10.1101/032060).

Allaby RG (2015) Barley domestication: the end of a central dogma? Genome Biology 16:176.

Smith O, Momber G, Bates R, Garwood P, Fitch S, Pallen M, Gaffney V, Allaby RG (2015) Reply to comment on “Sedimentary DNA from a submerged site reveals wheat in the British Isles 8000 years ago”. Science 349: 247-b.

Smith O, Momber G, Bates R, Garwood P, Fitch S, Pallen M, Gaffney V, Allaby RG (2015) Sedimentary DNA from a submerged site reveals wheat in the British Isles 8000 years ago. Science 347: 998-1001.

Allaby RG, Kistler L, Gutaker RM, Ware R, Kitchen JL, Smith O, Clarke AC (2015) Archaeogenomic insights into the adaptation of plants to the human environment: pushing plant–hominin co-evolution back to the Pliocene. J. Human Evol. 79:150-157.

Fuller DQ, Boivin N, Castillo CC, Hoogervost T, Allaby RG (2015) The archaeobiology of the Indian Ocean translocations: Current outlines of cultural exchanges by proto-historic seafarers. In Maritime Contacts of the Past: Deciphering Connections Amongst Communities. Ed. Tripati S, Delta Book World, New Delhi.

Smith O, Clapham A, Rose P, Liu Y, Wang J, Allaby RG (2014) Genomic methylation patterns in archaeological barley show de-methylation as a time-dependent diagenetic process. Scientific Reports 4, 5559.

Allaby RG, Gutaker R, Clarke AC, Pearson N, Ware R, Palmer SA, Kitchen JL, Smith O (2014) Using archaeogenomics and computational approaches to unravel the history of local adaptation in crops. Phil. Trans. Roy. Soc. B 370: 20130377.

Gerbault P, Allaby RG, Boivin N et al. (2014) Storytelling and story testing in domestication. Proc. Natl Acad. Sci. U.S.A. 111:6159-6164.

Larson G, Piperno D, Allaby RG et al. (2014) Current perspectives and the future of domestication studies. Proc. Natl. Acad. Sci. U.S.A. 111:6139-6146.

Fuller DQ, Denham T, Arroyo-Kalin M, Lucas L, Stephens C, Qin L, Allaby RG, Purugganan MD (2014) Convergent evolution and parallelism in plant domestication revealed by an expanding archaeological record. Proc. Natl. Acad. Sci. U.S.A. 111:6147-6152.

Smith O, Clapham A, Rose P, Liu Y, Wang J, Allaby RG (2014) A complete ancient RNA genome: identification, reconstruction and evolutionary history of archaeological Barley Stripe Mosaic Virus. Scientific Reports 4, 4003; DOI:10.1038/srep04003.

Wales N., Allaby R., Willerslev E. and Gilbert M.T.P. (2013) Ancient Plant DNA. In: Elias S.A. (ed.) The Encyclopedia of Quaternary Science, vol. 2, pp. 705-715. Amsterdam: Elsevier.

Kitchen JL and Allaby RG (2013) Systems Modeling at Multiple Levels of Regulation: Linking Systems and Genetic Networks to Spatially Explicit Plant Populations. Plants 2013, 2(1), 16-49

Boivin N, Fuller DQ, Dennell R, Allaby R, Petraglia M (2013) Human Dispersal Across Diverse Environments of Asia during the Upper Pleistocene. Quaternary International 300:32-47.

Kitchen JL, Moore JD, Palmer SA, Allaby RG (2012) MCMC-ODPR: Primer design optimization using Markov- Chain Monte-Carlo sampling. BMC Bioinformatics 13:287 doi:10.1186/1471-2105-13-287

Kitchen JL and Allaby RG (2012) The limits of mean-field heterozygosity estimates under spatial extension in simulated plant populations. PLoS One 7(8): e43254. doi:10.1371/journal.pone.0043254.

Palmer SA, Clapham AJ, Rose P, Freitas F, Owen BD, Beresford-Jones D, Moore JD, Kitchen JL, Allaby RG (2012) Archaeogenomic evidence of punctuated genome evolution in Gossypium. Molecular Biology and Evolution 29(8):2031-2038.

Palmer S, Smith O, Allaby RG (2012) The Blossoming of Plant Archaeogenetics. Annals of Anatomy 194:146-156.

Fu Y-B, Diederichsen, Allaby RG (2012) Locus-specific view of flax domestication history. Ecology and Evolution 2(1):139–152.

Fuller DQ, Willcox, G, Allaby RG (2011) Cultivation and domestication had multiple origins: arguments against the core area hypothesis for the origins of agriculture in the Near East. World Archaeology 43:4, 628-652.

Fuller DQ, Willcox, G, Allaby RG (2011) Early agricultural pathways: moving outside the ‘core area’ hypothesis in Southwest Asia. J. Exp. Bot. doi:10.1093/jxb/err307

Fuller DQ, Boivin N, Hoogervorst T, Allaby R (2011) Across the Indian Ocean: the prehistoric movement of plants and animals. Antiquity 85:544-558.

Bergfjord C, Karg S, Rast-Eicher A, Nosch M-L, Mannering U, Allaby RG, Murphy BM, Holst B (2010) Comment on "30,000-Year-Old Wild Flax Fibers". Science 328:1634-b

Allaby RG (2010) Integrating the processes in the evolutionary system of domestication. Journal of Experimental Botany 61:935-944.

Allaby RG, Brown TA, Fuller DQ (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 19:151-158.

Fuller DQ, Allaby RG, Stevens C (2010) Domestication as Innovation: The entanglement of techniques, technology and chance in the domestication of cereal crops. World Archaeology 42:13-28.

Fu Y-B, Allaby RG (2010) Phylogenetic network of Linum species as revealed by non-coding chloroplast DNA sequences. Genetic Resources and Crop Evolution 57:667-677.

Palmer SA, Moore JD, Clapham AJ, Rose P, Allaby RG (2009) Archaeogenetic Evidence of Ancient Nubian Barley Evolution from Six to Two-Row Indicates Local Adaptation. Plos One 4(7): e6301. doi:10.1371/journal.pone.0006301

Brown TA, Jones MK, Powell W, Allaby RG (2009) The complex origins of domesticated crops. Trends Ecol. Evol. 24:103-109.

Fuller DQ and Allaby RG (2009) Seed Dispersal and Crop Domestication: shattering, germination and seasonality in evolution under cultivation in Fruit development and Seed Dispersal, Annual Plant Reviews Volume 38:238-295.

Allaby, R.G., Françoise R. Friedlaender, Floyd A. Reed, Kenneth K. Kidd, Judith R. Kidd, Geoffrey K. Chambers, Rodney A. Lea, Jun-Hun Loo, George Koki, Jason A. Hodgson, D. Andrew Merriwether, James L. Weber, and Jonathan S. Friedlaender. (2009) Prehistoric Pacific Population Movements. In The Global Origins and Development of Seafaring. Eds. A. Andersson, K. Boyle. MacDonald Institute Publication, Cambridge, in press.

Allaby R.G., Fuller D.Q., Brown T.A. (2008) Reply to Ross-Ibarra & Gaut: Multiple domestications do appear monophyletic if an appropriate model is used. Proceedings of the National Academy of Sciences USA pnas online: doi:10.1073/pnas.0810296105.

Allaby R.G., Fuller D.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 USA 105:13982-13986. [PDF]

Allaby R.G. (2008) The rise of plant domestication: life in the slow lane. Biologist 55:94-99.

Brown T.A., Allaby R.G. (2008) Reevaluation of the use of multilocus markers to study crop origins. In Cereal Science and Technology for Feeding Ten Billion People: Genomics Era and Beyond (ed. J.L.Molina Cano, P. Christou, A.Graner, K.Hammer, N.Jouve, B.Keller, J.M.Lasa, W.Powell, C.Royo, P.Shewry and A.M.Stanca). CIHEAM/IRTA, Zaragoza. pp19–24.

Moore, J.D., Allaby R.G. (2008) TreeMos: a high-throughput phylogenomic approach to find and visualise phylogenetic mosaicism. Bioinformatics 24(5):717-718. [PDF]

Ho, S.S.W., Kolokotronis, S.-O., Allaby R.G. (2007) Elevated substitution rates estimated from ancient DNA sequences. Biology Letters 3:702-705.

Allaby, R.G., Woodwark, M. (2007) Phylogenomic analysis reveals extensive mosaicism in the Human GPCR superfamily. Evolutionary Bioinformatics 3:155-168. [PDF]

Allaby, R.G. (2007) Origins of Plant Exploitation in the Pacific: A review. In Population Genetics, Linguistics, and Culture History in the Southwest Pacific: A Synthesis. Ed. Friedlaender, J.F., OUP.

Brown T.A., Lindsay S., and Allaby R.G. (2006) Using modern landraces of wheat to study the origins of European Agriculture. In Darwin's Harvest. Pp. 197-212. Eds. Motley, T.J., Zeregra, N., Cross, H. Columbia University Press, New York.

Allaby, R.G., Peterson, G., Merriwether, D.A., Fu, Y.-Bi (2005) Evidence of the domestication history of flax (Linum usitatissimum L.) from genetic diversity of the sad2 locus. Theor. Appl. Genet. 112: 58-65.

Merriwether, D.A., Cerchio, S., Hodgson, J., Koki, G., Allaby R., Friedlaender, F., Friedlaender, J. (2005) Ancient mitochondrial M haplogroups identified in the Southwest Pacific. Proc. Natl. Acad. Sci. USA 102:13034-13039.

Allaby R.G. and Woodwark M. (2004) Phylogenetics in the Bioinformatics Culture of Understanding. Comparative and Functional Genomics 5:128-146.[PDF]

Allaby R.G. and Brown T.A. (2004) On the use of trees and crop origins: a reply. Genome 47:621-622.

Allaby R.G. and Brown T.A. (2003) AFLP analysis and the origins of agriculture. Genome 46:448-453.[PDF]

Freitas F.O., Bendel G., Allaby R.G., and Terence A. Brown (2003) DNA from Primitive Maize Landraces and Archaeological Remains: Implications for the Domestication of Maize and its Expansion into South America. Journal of Archaeological Science 30:901-908.

Allaby R.G. and Brown T.A. (2001) Network analysis provides insights into the evolution of 5S rDNA arrays in Triticum and Aegilops. Genetics 157:1331-1341.

Allaby R.G. (2000) Wheat Domestication. Chapter 39 in Archaeogenetics: DNA and the population prehistory of Europe. Renfrew C. and Boyle K. (ed.s), MacDonald Institute publication, Cambridge.

Allaby R.G. and Brown T.A. (2000) Identification of a 5S rDNA spacer type specific to Triticum urartu and wheats containing the T. urartu genome. Genome 43:250-254.[PDF]

Allaby R.G., Banerjee M., Brown T.A. (1999). Evolution of the high molecular weight glutenin loci of the A,B,D and G genomes of wheat. Genome 42:296-307.[PDF]

Brown T.A., Allaby R.G., Sallares R., Jones G. (1998). Ancient DNA in charred wheats: taxonomic identification of mixed and single grains. Ancient Biomolecules 2:185-193.[PDF]

Allaby R.G., O’Donoghue K., Sallares R., Jones M.K., Brown T.A. (1997) Evidence for the survival of ancient DNA in charred wheat seeds from European archaeological sites. Ancient Biomolecules 1:119-129.[PDF]

Jones M.K., Brown T.A., Allaby R.G. (1997) Wheat domestication. Science 279:302-303.

Jones M.K., Brown T.A., Allaby R.G. (1996). Tracking early crops and early farmers: the potential of biomolecular archaeology. In The Origins and Spread of Agriculture and Pastoralism in Eurasia. (ed. D.R. Harris) UCL press, London

Brown K.A., Allaby R.G., Garland A.N., Brown T.A. (1996). Ancient DNA in archaeological bones and plant remains. In Proceedings of the Archaeological Sciences Conference 1991.

Sallares R., Allaby R.G., Brown T.A. (1995). PCR - based identification of wheat genomes. Molecular Ecology 4:509-514.

Allaby R.G., O’Donoghue K., Brown T.A. (1994). Glutenin alleles in modern and ancient wheat. Ancient DNA Newsletter 2:32.

Allaby R.G., Jones M.K., Brown T.A. (1994). DNA in charred wheat grains from the Iron Age hill fort at Danebury, England. Antiquity 68:126-32.

Brown T.A., Allaby R.G., Brown K.A., O’Donoghue K., Sallares R. (1994). DNA in wheat seeds from European archaeological sites. In Conservation of Plant Genes II: Intellectual property rights and DNA utilisation (eds. Adams R.P. et al) 37-46. Missouri Botanical Gardens, St.Louis.

Brown T.A., Allaby R.G., Brown K.A., O’Donoghue K., Sallares R. (1994). DNA in wheat seeds from European archaeological sites. Experientia 50:571-575.

Allaby R.G., Brown T.A. (1993). Ancient DNA in carbonised wheat seeds. Ancient DNA Newsletter. 1:18-19.

Brown T.A., Allaby R.G., Brown K.A., Jones M.K. (1993). Biomolecular archaeology of wheat: past, present and future. World Archaeology 25:64-7.