Journal Article

Allaby, Robin G., Stevens, Chris J. and 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 . 111004. doi:10.1016/j.jtbi.2022.111004

Allaby, Robin G., Stevens, Chris J., Kistler, Logan and Fuller, Dorian Q. (2022) Emerging evidence of plant domestication as a landscape-level process. Trends in Ecology & Evolution, 37 (3). pp. 268-279. doi:10.1016/j.tree.2021.11.002

Simon, Marcelo F., Mendoza, J Moises F., Liu, Hsiao-Lei, Martins, Márcio 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, Fábio and 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. doi:10.1111/nph.17743

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. and Pires, J. Chris (2021) The evolutionary history of wild, domesticated, and feral Brassica oleracea (Brassicaceae). Molecular Biology and Evolution, 38 (10). pp. 4419-4434. doi:10.1093/molbev/msab183

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, Aurélie, Marshall, Fiona, Mueller, Natalie, Peters, Joris, Stépanoff, Charles, Weide, Alexander and Larson, Greger (2021) Reconsidering domestication from a process archaeology perspective. World Archaeology, 53 (1). pp. 56-77. doi:10.1080/00438243.2021.1954990

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. and Warinner, Christina (2021) Ancient DNA analysis. Nature Reviews Methods Primers, 1 (1). 14. doi:10.1038/s43586-020-00011-0

Kistler, Logan, Thakar, Heather B., VanDerwarker, Amber M., Domic, Alejandra, Bergström, Anders, George, Richard J., Harper, Thomas K., Allaby, Robin G., Hirth, Kenneth and 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. doi:10.1073/pnas.2015560117

(2020) Multi-proxy characterisation of the Storegga tsunami and its impact on the early holocene landscapes of the southern North Sea. Geosciences, 10 (7). 270. doi:10.3390/geosciences10070270

Landoni, Beatrice, Viruel, Juan, Gómez, Rocio, Allaby, Robin G., Brennan, Adrian C., Picó, F. Xavier and Pérez‐Barrales, Rocio (2020) Microsatellite marker development in the crop wild relative Linum bienne using genome skimming. Applications in Plant Sciences, 8 (5). e11349. doi:10.1002/aps3.11349

Ware, Roselyn, Garrod, Benjamin, Macdonald, Hannah and Allaby, Robin G. (2020) Guano morphology has the potential to inform conservation strategies in British bats. PLoS One, 15 (4). e0230865. doi:10.1371/journal.pone.0230865

Cribdon, Becky, Ware, Roselyn, Smith, Oliver, Gaffney, Vincent and 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 . 84. doi:10.3389/fevo.2020.00084

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. and Allaby, Robin G. (2019) A domestication history of dynamic adaptation and genomic deterioration in Sorghum. Nature Plants, 5 (4). pp. 369-379. doi:10.1038/s41477-019-0397-9

Allaby, Robin G., Ware, Roselyn and Kistler, Logan (2019) A re-evaluation of the domestication bottleneck from archaeogenomic evidence. Evolutionary Applications, 12 (1). pp. 29-37. doi:10.1111/eva.12680

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 and Allaby, Robin G. (2018) Multiproxy evidence highlights a complex evolutionary legacy of maize in South America. Science, 362 (6420). pp. 1309-1313. doi:10.1126/science.aav0207

Gutaker , Rafal M. , Zaidem, Maricris, Fu, Yong-Bi , Diederichsen, Axel, Smith, Oliver, Ware, Roselyn and Allaby, Robin G. (2018) Flax latitudinal adaptation at LuTFL1 altered architecture and promoted fiber production. Scientific Reports, 9 (976). doi:10.1038/s41598-018-37086-5

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 and Zheng, Youliang (2018) Uncovering the dispersion history, adaptive evolution and selection of wheat in China. Plant Biotechnology Journal, 16 (1). pp. 280-291. doi:10.1111/pbi.12770

Allaby, Robin G., Stevens, Chris, Lucas, Leilani, Maeda, Osamu and Fuller, Dorian Q. (2017) Geographic mosaics and changing rates of cereal domestication. Philosophical Transactions of the Royal Society B: Biological Sciences, 372 (1735). 20160429. doi:10.1098/rstb.2016.0429

Smith, Oliver , Palmer, Sarah A., Clapham, Alan J., Rose, Pamela, Liu, Yuan, Wang, Jun and 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. doi:10.1093/molbev/msx175

Payacan, Claudia, Moncada, Ximena, Rojas, Gloria, Clarke, Andrew C., Chung, Kuo-Fang, Allaby, Robin G., Seelenfreund, Daniela and 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. doi:10.1093/aob/mcx062

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

Allaby, Robin G., Kitchen, James and Fuller, Dorian Q. (2016) Surprisingly low limits of selection in plant domestication. Evolutionary Bioinformatics (2). pp. 41-51. doi:10.4137/EBO.S33495

Smith, Oliver, Momber, G., Bates, R., Garwood, P., Fitch, S., Pallen, Mark J., Gaffney, V. and 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). p. 247. doi:10.1126/science.aab2062

Smith, Oliver , Momber, G., Bates, R., Garwood, P., Fitch, S., Pallen, Mark J., Gaffney, V. and Allaby, Robin G. (2015) Sedimentary DNA from a submerged site reveals wheat in the British Isles 8000 years ago. Science, Volume 347 (Number 6225). pp. 998-1001. doi:10.1126/science.1261278

Allaby, Robin G., Kistler, Logan, Gutaker, Rafał M., Ware, Roselyn, Kitchen, James, Smith, Oliver and 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, Volume 79 . pp. 150-157. doi:10.1016/j.jhevol.2014.10.014

Allaby, Robin G., Gutaker, Rafał M., Clarke, Andrew C., Pearson, Neil, Ware, Roselyn, Palmer, Sarah A., Kitchen, James and 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, Volume 370 (Number 1660). Article number 20130377. doi:10.1098/rstb.2013.0377

Smith, Oliver , Clapham, Alan J., Rose, Pam, Liu, Yuan, Wang, Jun and Allaby, Robin G. (2014) Genomic methylation patterns in archaeological barley show de-methylation as a time-dependent diagenetic process. Scientific Reports, Volume 4 . Article number 5559. doi:10.1038/srep05559

Fuller, D. Q., Denham, T., Arroyo-Kalin, M., Lucas, L., Stevens, C. J., Qin, L., Allaby, Robin G. and 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, Volume 111 (Number 17). pp. 6147-6152. doi:10.1073/pnas.1308937110

(2014) Current perspectives and the future of domestication studies. Proceedings of the National Academy of Sciences of the United States of America, Volume 111 (Number 17). pp. 6139-6146. doi:10.1073/pnas.1323964111

(2014) Storytelling and story testing in domestication. Proceedings of the National Academy of Sciences of the United States of America, Volume 111 (Number 17). pp. 6159-6164. doi:10.1073/pnas.1400425111

Smith, Oliver , Clapham, Alan J., Rose, Pam, Liu, Yuan, Wang, Jun and Allaby, Robin G. (2014) A complete ancient RNA genome : identification, reconstruction and evolutionary history of archaeological Barley Stripe Mosaic Virus. Scientific Reports, Volume 4 . Article number 4003. doi:10.1038/srep04003

Boivin, Nicole, Fuller, Dorian Q., Dennell, Robin, Allaby, Robin G. and Petraglia, Michael D. (2013) Human dispersal across diverse environments of Asia during the Upper Pleistocene. Quaternary International, Volume 300 . pp. 32-47. doi:10.1016/j.quaint.2013.01.008

Kitchen, James and Allaby, Robin G. (2013) Systems modeling at multiple levels of regulation : linking systems and genetic Networks to spatially explicit plant populations. Plants, Volume 2 (Number 1). pp. 16-49. doi:10.3390/plants2010016

Palmer, Sarah A., Clapham, A. J., Rose, P., Freitas, F. O., Owen, B. D., Beresford-Jones, D., Moore, Jonathan D., Kitchen, James and Allaby, Robin G. (2012) Archaeogenomic evidence of punctuated genome evolution in Gossypium. Molecular Biology and Evolution, Volume 29 (Number 8). pp. 2031-2038. doi:10.1093/molbev/mss070

Kitchen, James and Allaby, Robin G. (2012) The limits of mean-field heterozygosity estimates under spatial extension in simulated plant populations. PLoS ONE, Vol.7 (No.8). e43254. doi:10.1371/journal.pone.0043254

Fuller, Dorian Q., Willcox, G. and 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. doi:10.1093/jxb/err307

Fu, Yong-Bi, Diederichsen, Axel and Allaby, Robin G. (2012) Locus-specific view of flax domestication history. Ecology and Evolution, Vol.2 (No.1). pp. 139-152. doi:10.1002/ece3.57

Kitchen, James, Moore, Jonathan D., Palmer, Sarah A. and Allaby, Robin G. (2012) MCMC-ODPR : primer design optimization using Markov Chain Monte Carlo sampling. BMC Bioinformatics, Vol.13 (No.1). p. 287. doi:10.1186/1471-2105-13-287

Palmer, Sarah A., Smith, Oliver and Allaby, Robin G. (2012) The blossoming of plant archaeogenetics. Annals of Anatomy, Vol.194 (No.1). pp. 146-156. doi:10.1016/j.aanat.2011.03.012

Fuller, Dorian Q., Boivin, Nicole, Ph. D., Hoogervorst, Tom and 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 and 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. doi:10.1080/00438243.2011.624747

Fu, Yong-Bi and 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. doi:10.1007/s10722-009-9502-7

Fuller, Dorian Q., Allaby, Robin G. and 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. doi:10.1080/00438240903429680

Allaby, Robin G. (2010) Integrating the processes in the evolutionary system of domestication. Journal of Experimental Botany, Vol.61 (No.4). pp. 935-944. doi:10.1093/jxb/erp382

Palmer, Sarah A., Moore, Jonathan D., Clapham, Alan J., Rose, Pamela and 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). e6301. doi:10.1371/journal.pone.0006301

Brown, T. A., Jones, Martin K., Powell, Wayne and 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. doi:10.1016/j.tree.2008.09.008

Allaby, Robin G., Fuller, Dorian Q. and 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. doi:10.1073/pnas.0803780105

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. and Allaby, Robin G. (2008) TreeMos : a high-throughput phylogenomic approach to find and visualize phylogenetic mosaicism. Bioinformatics, Vol.24 (No.5). pp. 717-718. doi:10.1093/bioinformatics/btn027

Ho, Simon Y. W., Kolokotronis, Sergios-Orestis and Allaby, Robin G. (2007) Elevated substitution rates estimated from ancient DNA sequences. Biology Letters, Vol.3 (No.6). pp. 702-705. doi:10.1098/rsbl.2007.0377

Allaby, Robin G. and Woodwark, Mathew (2007) Phylogenomic analysis reveals extensive phylogenetic mosaicism in the Human GPCR Superfamily. Evolutionary Bioinformatics, Vol.3 . pp. 357-370.

Journal Item

Allaby, Robin G. (2021) First come, first served for ancient crops. Nature Plants, 7 (5). pp. 542-543. doi:10.1038/s41477-021-00926-w

Allaby, Robin G. (2019) Clonal crops show structural variation role in domestication. Nature Plants, 5 (9). pp. 915-916. doi:10.1038/s41477-019-0515-8

Bergfjord, C., Karg, S., Rast-Eicher, A., Nosch, M. -L., Mannering, U., Allaby, Robin G., Murphy, B. M. and Holst, B. (2010) Comment on "30,000-year-old wild flax fibers". Science, Vol.328 (No.5986). 1634 . doi:10.1126/science.1186345

Allaby, Robin G., Brown, T. A. and 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, Vol.19 (No.2). pp. 151-158. doi:10.1007/s00334-009-0232-8

Brown, T. A., Jones, Martin K., Powell, Wayne and Allaby, Robin G. (2009) The complex origins of domesticated crops in the Fertile Crescent. Trends in Ecology & Evolution, Vol.24 (No.2). pp. 103-109. doi:10.1016/j.tree.2008.09.008

Allaby, Robin G., Fuller, Dorian Q. and 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, Vol.105 (No.49). E106-E106. doi:10.1073/pnas.0810296105

Dataset

Kistler, Logan, Thakar, Heather B., VanDerwarker, Amber M., Domic, Alejandra, Bergström, Anders, George, Richard J., Harper, Thomas K., Allaby, Robin G., Hirth, Kenneth and Kennett, Douglas J. (2021) Data for Archaeological Central American maize genomes suggest ancient gene flow from South America. [Dataset]