Plant domestication is an outstanding example of plant–animal co-evolution and is a far richer model for studying evolution than is generally appreciated. There have been numerous studies to identify genes associated with domestication, and archaeological work has provided a clear understanding of the dynamics of human cultivation practices during the Neolithic period. Together, these have provided a better understanding of the selective pressures that accompany crop domestication, and they demonstrate that a synthesis from the twin vantage points of genetics and archaeology can expand our understanding of the nature of evolutionary selection that accompanies domestication.
This is a preview of subscription content
Subscribe to Journal
Get full journal access for 1 year
only $3.90 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Tax calculation will be finalised during checkout.
Get time limited or full article access on ReadCube.
All prices are NET prices.
Hancock, J. F. Contributions of domesticated plant studies to our understanding of plant evolution. Ann. Bot. (Lond.) 96, 953–963 (2005).
Diamond, J. Evolution, consequences and future of plant and animal domestication. Nature 418, 700–707 (2002).
Darwin, C. On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life (John Murray, 1859).
Darwin, C. The Variation of Animals and Plants under Domestication (John Murray, 1868).
Darwin, C. & Wallace, A. R. On the tendency of species to form varieties; and on the perpetuation of varieties and species by natural means of selection. J. Proc. Linn. Soc. (Zool.) 3, 46–50 (1858).
Rindos, D. The Origins of Agriculture: An Evolutionary Perspective (Academic, 1984).
Zeder, M. A., Emshwiller, E., Smith, B. D. & Bradley, D. G. Documenting domestication: the intersection of genetics and archaeology. Trends Genet. 22, 139–155 (2006).
Schultz, T. R. & Brady, S. G. Major evolutionary transitions in ant agriculture. Proc. Natl Acad. Sci. USA 105, 5435–5440 (2008).
Farrell, B. D. et al. The evolution of agriculture in beetles (Curculionidae: Scolytinae and Platypodinae). Evolution 55, 2011–2027 (2001).
Doebley, J. F., Gaut, B. S. & Smith, B. D. The molecular genetics of crop domestication. Cell 127, 1309–1329 (2006).
Burke, J. M., Burger, J. C. & Chapman, M. A. Crop evolution: from genetics to genomics. Curr. Opin. Genet. Dev. 17, 525–532 (2007).
Kislev, M. E., Nadel, D. & Carmi, I. Epipalaeolithic cereal and fruit diet at Ohalu II, Sea of Galilee, Israel. Rev. Palaeobot. Palyn. 73, 161–166 (1992).
Fuller, D. Q. Contrasting patterns in crop domestication and domestication rates: recent archaeobotanical insights from the Old World. Ann. Bot. (Lond.) 100, 903–924 (2007). This paper synthesizes and compares quantitative data for morphological change across time from archaeologically dated subfossil crop remains.
Harris, D. R. in Foraging and Farming: The Evolution of Plant Exploitation (eds Harris, D. R. & Hillman, G. C.) 11–26 (Routledge, 1989).
Hammer, K. Das Domestikationssyndrom. Kulturpflanze 32, 11–34 (1984).
Smith, B. D. in Documenting Domestication (eds Zeder, M. A., Bradely, D. G., Emshwiller, E. & Smith, B. D.) 15–24 (Univ. California Press, 2006).
Harlan, J. R., De Wet, J. M. J. & Price, E. G. Comparative evolution of cereals. Evolution 27, 311–325 (1973).
Zohary, D. & Hopf, M. Domestication of Plants in the Old World (Oxford Univ. Press, 2000).
Baskin, C. & Baskin, J. M. Seeds: Ecology, Biogeography and Evolution of Dormancy and Germination (Academic, 2001).
Westoby, M., Leishman, M. & Lord, J. Comparative ecology of seed size and dispersal. Phil. Trans. R. Soc. Lond. B 351, 1309–1317 (1996).
Hillman, G. C. in Village on the Euphrates: From Foraging to Farming at Abu Hureyra (eds Moore, A. M. T., Hillman, G. C. & Legge, A. J.) 327–398 (Oxford Univ. Press, 2000).
Hillman, G. C., Hedges, R., Moore, A. M. T., Colledge, S. & Pettitt, P. New evidence of Late Glacial cereal cultivation at Abu Hureyra on the Euphrates. Holocene 11, 383–393 (2001).
Fuller, D. Q. et al. Presumed domestication? Evidence for wild rice cultivation and domestication in the fifth millennium bc of the Lower Yangtze region. Antiquity 81, 316–331 (2007).
Zhao, Z. The Middle Yangtze region in China is one place where rice was domesticated: phytolith evidence from the Diaotonghuan Cave, Northern Jaingxi. Antiquity 72, 885–897 (1998).
Crawford, G. Paleoethnobotany of the Kameda Peninsula Jomon (Museum of Anthropology, Univ. Michigan, 1983).
Li, C. B., Zhou, A. L. & Sang, T. Rice domestication by reducing shattering. Science 311, 1936–1939 (2006). This paper reports the first molecular isolation of a loss-of-shattering gene in a cereal crop species, a trait that is the hallmark of domestication in seed crops.
Wilke, P. J., Bettinger, R., King, T. F. & O'Connell, J. F. Harvest selection and domestication in seed plants. Antiquity 46, 203–209 (1972).
Hillman, G. & Davies, M. S. Domestication rates in wild wheats and barley under primitive cultivation. Biol. J. Linn. Soc. 39, 39–78 (1990).
Konishi, S. et al. An SNP caused loss of seed shattering during rice domestication. Science 312, 1392–1396 (2006).
Simons, K. J. et al. Molecular characterization of the major wheat domestication gene Q . Genetics 172, 547–555 (2006).
Liu, L., Lee, G.-A., Jiang, L. & Zhang, J. Evidence for the early beginning (c. 9000 cal. bp) of rice domestication in China: a response. Holocene 17, 1059–1068 (2007)
Fuller, D. Q. & Harvey, E. L. The archaeobotany of Indian pulses: identification, processing and evidence for cultivation. Environ. Archaeol. 11, 219–246 (2006).
D'Andrea, A. C., Kahlheber, S., Logan, A. L. & Watson, D. J. Early domesticated cowpea (Vigna unguiculata) from Central Ghana. Antiquity 81, 686–698 (2007).
D'Ennequin, M. L. T., Toupance, B., Robert, T., Godelle, B. & Gouton, P. H. Plant domestication: a model for studying the selection of linkage. J. Evol. Biol. 12, 1138–1147 (1999).
Tanno, K. I. & Willcox, G. How fast was wild wheat domesticated? Science 311, 1886 (2006).
Zheng, Y., Sun, G. & Chen, X. Characteristics of the short rachillae of rice from archaeological sites dating to 7000 years ago. Chin. Sci. Bull. 52, 1654–1660 (2007).
Willcox, G., Fornite, S. & Herveux, L. Early Holocene cultivation before domestication in northern Syria. Veg. Hist. Archaeobot. 17, 313–325 (2008). This paper reports assemblages of morphologically wild cereals and early weed assemblages from two sites that indicate that wheat and barley were cultivated for more than 1,000 years before morphological domestication.
Wright, S. et al. The effects of artificial selection of the maize genome. Science 308, 1310–1314 (2005). This paper reports a genome-wide screen for genes that display a signature of positive selection associated with crop domestication and diversification.
Caicedo, A. L. et al. Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genet. 3, 1289–1299 (2007).
Eyre-Walker, A., Gaut, R. L., Hilton, H., Feldman, D. L. & Gaut, B. S. Investigation of the bottleneck leading to the domestication of maize. Proc. Natl Acad. Sci. USA 95, 4441–4446 (1998).
Iltis, H. Homeotic sexual translocations and the origin of maize (Zea mays, Poaceae): a new look at an old problem. Econ. Bot. 54, 7–42 (2000)
Wang, H. et al. The origin of the naked grains of maize. Nature 436, 714–719 (2005).
Dorweiler, J., Stec, A., Kermicle, J. & Doeble, J. Teosinte-glume-architecture — a genetic locus controlling a key step in maize evolution. Science 262, 233–235 (1993).
Harlan, J. R. & Stemler, A. B. in The Origins of African Plant Domestication (eds Harlan, J. R., De Wet, J. M. J. & Stemler, A. B.) 465–478 (Mounton, 1976).
DeWet, J. M. Systematics and evolution of sorghum. Am. J. Bot. 65, 477–484 (1978).
Giles, R. & Brown, T. GluDy allele variations in Aegilops tauschii and Triticum aestivum: implications for the origins of hexaploid wheats. Theor. Appl. Genet. 112, 1563–1572 (2006).
Gu, Y. Q. et al. Types and rates of sequence evolution at the high-molecular-weight glutenin locus in hexaploid wheat and its ancestral genomes. Genetics 174, 1493–1504 (2006).
Colledge, S. & Conolly, J. (eds) The Origins and Spread of Domestic Plants in Southwest Asia and Europe (Left Coast, 2006).
Kilian, B. et al. Independent wheat B and G genome origins in outcrossing Aegilops progenitor haplotypes. Mol. Biol. Evol. 24, 217–227 (2007).
Skoglund, P. Diet, cooking and cosmology: interpreting the evidence of Bronze Age plant macrofossils. Curr. Swed. Archaeol. 7, 149–160 (1999).
Anderson, E. A. & Williams, L. Maize and sorghum as a mixed crop in Honduras. Ann. Mo. Bot. Gard. 41, 213–221 (1954).
Bradbury, L. M. T., Henry, R. J., Jin, Q., Reinke, R. F. & Waters, D. L. E. A perfect marker for fragrance genotyping in rice. Mol. Breed. 16, 279–283 (2005).
Sakamoto, S. in Redefining Nature: Ecology, Culture and Domestication (eds Ellen, R. & Fujui, K.) 215–231 (Berg, 1996).
Yoshida, S. in Vegeculture in Eastern Asia and Oceania (eds Yoshida, S. & Matthews, P.) 31–44 (Japan Center for Area Studies, National Museum of Ethnology, Osaka, 2002).
Hirano, H. Y., Eiguchi, M. & Sano, Y. A single base change altered the regulation of the waxy gene at the posttranscriptional level during the domestication of rice. Mol. Biol. Evol. 15, 978–987 (1998).
Olsen, K. M. & Purugganan, M. D. Molecular evidence on the origin and evolution of glutinous rice. Genetics 162, 941–950 (2002).
Olsen, K. M. et al. Selection under domestication: evidence for a sweep in the rice waxy genomic region. Genetics 173, 975–983 (2006). This paper reports the characterization of a selective sweep in the waxy gene, which underlies the origin and spread of sticky rice.
Fukunaga, K., Kawase, M. & Kato, K. Structural variation in the waxy gene and differentiation in foxtail millet (Setaria italica (L.) P. Beauv.): implications for multiple origins of the waxy phenotype. Mol. Genet. Genomics 268, 214–222 (2002).
Fuller, D. Agricultural origins and frontiers in South Asia: a working synthesis. J. World Prehist. 20, 1–86 (2006).
Bogaard, A. Neolithic Farming in Central Europe: An Archaeobotanical Study of Crop Husbandry Practices C5500–2200 bc (Routledge, 2004).
Kreuz, A., Marinova, E., Schafer, E. & Wiethold, J. A comparison of Early Neolithic crop and weed assemblages from the Linearbankeramik and the Bulgarian Neolithic culture: differences and similarities. Veg. Hist. Archaeobot. 14, 237–258 (2005).
Colledge, S., Conolly, J. & Shennan, S. The evolution of Neolithic farming from SW Asian origins to NW European limits. Eur. J. Archaeol. 8, 137–156 (2005). This paper provides a quantitative analysis of crop assemblages and shows the role of selection and drift in the creation of a suitable crop package for new environments.
Paterson, A. H. What has QTL mapping taught us about plant domestication? New Phytol. 154, 591–608 (2002).
Willis, D. M. & Burke, J. Quantitative trait locus analysis of the early domestication of sunflower. Genetics 176, 2589–2599 (2007).
Li, W. & Gill, B. S. Multiple genetic pathways for seed shattering in the grasses. Funct. Integr. Genomics 6, 300–309 (2006).
Cai, H. W. & Morishima, H. QTL clusters reflect character associations in wild and cultivated rice. Theor. Appl. Genet. 104, 1217–1228 (2003).
Peng, J. et al. Domestication quantitative trait loci in Triticum dicoccoides, the progenitor of wheat. Proc. Natl Acad. Sci. USA 100, 2489–2494 (2003).
Fan. C. et al. GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor. Appl. Genet. 112, 1164–1171 (2006).
Prethepha, P. The fragrance (fgr) gene in natural populations of wild rice (Oryza rufipogon Griff.). Genet. Resour. Crop Evol. 56, 13–18 (2009).
Wang, R. L., Stec, A., Hey, J., Lukens, L. & Doebley, J. The limits of selection during maize domestication. Nature 398, 236–239 (1999). This paper describes the cloning of the maize tb1 gene, the first domestication gene cloned in a cereal crop, and discusses a selective sweep at the promoter region.
Maynard-Smith, J. & Haigh, J. The hitchhiking effect of a favorable gene. Genet. Res. 23, 23–35 (1974).
Clark, R. M., Linton, E., Messing, J. & Doebley, J. F. Pattern of diversity in the genomic region near the maize domestication gene tb1 . Proc. Natl Acad. Sci. USA 101, 700–707 (2004).
Palaisa, K., Morgante, M., Tingey, S. & Rafalski, A. Long-range patterns of diversity and linkage disequilibrium surrounding the maize Y1 gene are indicative of an asymmetric selective sweep. Proc. Natl Acad. Sci. USA 101, 9885–9890 (2004).
Sweeney, M. T. et al. Global dissemination of a single mutation conferring white pericarp in rice. PLoS Genet. 3, 1418–1424 (2007).
We thank K. Olsen and S. Colledge for critical reading of the manuscript. Work in the Purugganan laboratory is funded in part by a grant from the National Science Foundation Plant Genome Research Program.
The authors declare no competing financial interests.
Reprints and permissions information is available at http://www.nature.com/reprints.
Correspondence should be addressed to M.D.P. (firstname.lastname@example.org).
About this article
Cite this article
Purugganan, M., Fuller, D. The nature of selection during plant domestication. Nature 457, 843–848 (2009). https://doi.org/10.1038/nature07895
Nature Communications (2022)
Nature Communications (2022)
Selective signatures and high genome-wide diversity in traditional Brazilian manioc (Manihot esculenta Crantz) varieties
Scientific Reports (2022)
Microbial Ecology (2022)