Reader TTS

ABSTRACT 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. Access through your institution Buy or subscribe This is a

preview of subscription content, access via your institution ACCESS OPTIONS Access through your institution Subscribe to this journal Receive 51 print issues and online access $199.00 per

year only $3.90 per issue Learn more Buy this article * Purchase on SpringerLink * Instant access to full article PDF Buy now Prices may be subject to local taxes which are calculated during

checkout ADDITIONAL ACCESS OPTIONS: * Log in * Learn about institutional subscriptions * Read our FAQs * Contact customer support SIMILAR CONTENT BEING VIEWED BY OTHERS DOMESTICATION OF THE

AMAZONIAN FRUIT TREE _CUPUAÇU_ MAY HAVE STRETCHED OVER THE PAST 8000 YEARS Article Open access 01 November 2023 THE _MARCHANTIA POLYMORPHA_ PANGENOME REVEALS ANCIENT MECHANISMS OF PLANT

ADAPTATION TO THE ENVIRONMENT Article Open access 17 February 2025 EARLY HUMAN SELECTION OF CROPS’ WILD PROGENITORS EXPLAINS THE ACQUISITIVE PHYSIOLOGY OF MODERN CULTIVARS Article 03 January

2024 REFERENCES * Hancock, J. F. Contributions of domesticated plant studies to our understanding of plant evolution. _Ann. Bot. (Lond.)_ 96, 953–963 (2005). CAS  Google Scholar  * Diamond,

J. Evolution, consequences and future of plant and animal domestication. _Nature_ 418, 700–707 (2002). ADS  CAS  PubMed  Google Scholar  * 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). Google Scholar  * Darwin, C. _The Variation of Animals and Plants under Domestication_

(John Murray, 1868). Google Scholar  * 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). Google Scholar  * Rindos, D. _The Origins of Agriculture: An Evolutionary Perspective_ (Academic, 1984). Google Scholar  * 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). CAS  PubMed  Google

Scholar  * Schultz, T. R. & Brady, S. G. Major evolutionary transitions in ant agriculture. _Proc. Natl Acad. Sci. USA_ 105, 5435–5440 (2008). ADS  CAS  PubMed  PubMed Central  Google

Scholar  * Farrell, B. D. et al. The evolution of agriculture in beetles (Curculionidae: Scolytinae and Platypodinae). _Evolution_ 55, 2011–2027 (2001). CAS  PubMed  Google Scholar  *

Doebley, J. F., Gaut, B. S. & Smith, B. D. The molecular genetics of crop domestication. _Cell_ 127, 1309–1329 (2006). CAS  PubMed  Google Scholar  * Burke, J. M., Burger, J. C. &

Chapman, M. A. Crop evolution: from genetics to genomics. _Curr. Opin. Genet. Dev._ 17, 525–532 (2007). CAS  PubMed  Google Scholar  * 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). Google Scholar  * 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. Google Scholar  * Harris, D. R. in _Foraging and Farming: The Evolution of Plant Exploitation_ (eds

Harris, D. R. & Hillman, G. C.) 11–26 (Routledge, 1989). Google Scholar  * Hammer, K. Das Domestikationssyndrom. _Kulturpflanze_ 32, 11–34 (1984). Google Scholar  * Smith, B. D. in

_Documenting Domestication_ (eds Zeder, M. A., Bradely, D. G., Emshwiller, E. & Smith, B. D.) 15–24 (Univ. California Press, 2006). Google Scholar  * Harlan, J. R., De Wet, J. M. J.

& Price, E. G. Comparative evolution of cereals. _Evolution_ 27, 311–325 (1973). PubMed  Google Scholar  * Zohary, D. & Hopf, M. _Domestication of Plants in the Old World_ (Oxford

Univ. Press, 2000). Google Scholar  * Baskin, C. & Baskin, J. M. _Seeds: Ecology, Biogeography and Evolution of Dormancy and Germination_ (Academic, 2001). Google Scholar  * Westoby, M.,

Leishman, M. & Lord, J. Comparative ecology of seed size and dispersal. _Phil. Trans. R. Soc. Lond. B_ 351, 1309–1317 (1996). ADS  Google Scholar  * 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). Google Scholar  * 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). ADS  Google Scholar  *

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).

Google Scholar  * 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). Google Scholar  * Crawford, G. _Paleoethnobotany of the Kameda Peninsula Jomon_ (Museum of Anthropology, Univ. Michigan, 1983). Google Scholar  * 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. ADS  CAS  PubMed  Google Scholar  * Wilke, P. J., Bettinger, R., King, T. F. & O'Connell, J. F. Harvest selection and

domestication in seed plants. _Antiquity_ 46, 203–209 (1972). Google Scholar  * Hillman, G. & Davies, M. S. Domestication rates in wild wheats and barley under primitive cultivation.

_Biol. J. Linn. Soc._ 39, 39–78 (1990). Google Scholar  * Konishi, S. et al. An SNP caused loss of seed shattering during rice domestication. _Science_ 312, 1392–1396 (2006). ADS  CAS 

PubMed  Google Scholar  * Simons, K. J. et al. Molecular characterization of the major wheat domestication gene _Q_ . _Genetics_ 172, 547–555 (2006). CAS  PubMed  PubMed Central  Google

Scholar  * 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) ADS 

Google Scholar  * Fuller, D. Q. & Harvey, E. L. The archaeobotany of Indian pulses: identification, processing and evidence for cultivation. _Environ. Archaeol._ 11, 219–246 (2006).

Google Scholar  * 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).

Google Scholar  * 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). Google Scholar  * Tanno, K. I. & Willcox, G. How fast was wild wheat domesticated? _Science_ 311, 1886 (2006). CAS  PubMed  Google Scholar  * 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). Google Scholar  * 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.

Google Scholar  * 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. CAS  PubMed  Google Scholar  * Caicedo, A. L. et al. Genome-wide patterns of nucleotide polymorphism

in domesticated rice. _PLoS Genet._ 3, 1289–1299 (2007). Google Scholar  * 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). ADS  CAS  PubMed  PubMed Central  Google Scholar  * 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) Google Scholar  * Wang, H. et al. The origin of the naked grains of maize. _Nature_ 436, 714–719

(2005). ADS  CAS  PubMed  PubMed Central  Google Scholar  * 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). ADS  CAS  PubMed  Google Scholar  * 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). Google Scholar  * DeWet, J. M. Systematics and evolution of sorghum. _Am. J. Bot._ 65, 477–484 (1978). Google Scholar  * 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).

CAS  PubMed  Google Scholar  * 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). CAS  PubMed  PubMed Central  Google Scholar  * Colledge, S. & Conolly, J. (eds) _The Origins and Spread of Domestic Plants in Southwest Asia and Europe_ (Left

Coast, 2006). Google Scholar  * Kilian, B. et al. Independent wheat B and G genome origins in outcrossing _Aegilops_ progenitor haplotypes. _Mol. Biol. Evol._ 24, 217–227 (2007). CAS  PubMed

  Google Scholar  * Skoglund, P. Diet, cooking and cosmology: interpreting the evidence of Bronze Age plant macrofossils. _Curr. Swed. Archaeol._ 7, 149–160 (1999). Google Scholar  *

Anderson, E. A. & Williams, L. Maize and sorghum as a mixed crop in Honduras. _Ann. Mo. Bot. Gard._ 41, 213–221 (1954). Google Scholar  * 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). CAS  Google Scholar  * Sakamoto, S. in _Redefining Nature: Ecology,

Culture and Domestication_ (eds Ellen, R. & Fujui, K.) 215–231 (Berg, 1996). Google Scholar  * 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). Google Scholar  * 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). CAS  PubMed  Google Scholar  * Olsen, K. M. & Purugganan, M.

D. Molecular evidence on the origin and evolution of glutinous rice. _Genetics_ 162, 941–950 (2002). CAS  PubMed  PubMed Central  Google Scholar  * 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. CAS  PubMed  PubMed Central  Google Scholar  * 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). CAS  PubMed  Google

Scholar  * Fuller, D. Agricultural origins and frontiers in South Asia: a working synthesis. _J. World Prehist._ 20, 1–86 (2006). Google Scholar  * Bogaard, A. _Neolithic Farming in Central

Europe: An Archaeobotanical Study of Crop Husbandry Practices C5500–2200_ _bc_ (Routledge, 2004). Google Scholar  * 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). Google

Scholar  * 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. Google Scholar  * Paterson, A.

H. What has QTL mapping taught us about plant domestication? _New Phytol._ 154, 591–608 (2002). CAS  PubMed  Google Scholar  * Willis, D. M. & Burke, J. Quantitative trait locus

analysis of the early domestication of sunflower. _Genetics_ 176, 2589–2599 (2007). Google Scholar  * Li, W. & Gill, B. S. Multiple genetic pathways for seed shattering in the grasses.

_Funct. Integr. Genomics_ 6, 300–309 (2006). CAS  PubMed  Google Scholar  * Cai, H. W. & Morishima, H. QTL clusters reflect character associations in wild and cultivated rice. _Theor.

Appl. Genet._ 104, 1217–1228 (2003). Google Scholar  * Peng, J. et al. Domestication quantitative trait loci in _Triticum dicoccoides_, the progenitor of wheat. _Proc. Natl Acad. Sci. USA_

100, 2489–2494 (2003). ADS  CAS  PubMed  PubMed Central  Google Scholar  * 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). Google Scholar  * 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. ADS  CAS  PubMed  Google Scholar  * Maynard-Smith, J. & Haigh, J. The hitchhiking effect of a favorable gene. _Genet. Res._ 23, 23–35 (1974). Google Scholar  * 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). ADS  CAS 

PubMed  Google Scholar  * 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). ADS  CAS  PubMed  PubMed Central  Google Scholar  * Sweeney, M. T. et al. Global dissemination of a

single mutation conferring white pericarp in rice. _PLoS Genet._ 3, 1418–1424 (2007). CAS  Google Scholar  Download references ACKNOWLEDGEMENTS 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. AUTHOR INFORMATION AUTHORS AND

AFFILIATIONS * Department of Biology and Centre for Genomics and Systems Biology, 100 Washington Square East, New York University, New York, 10003, USA Michael D. Purugganan * Institute of

Archaeology, University College London, 31–34 Gordon Square, London, WC1H 0PY, UK Dorian Q. Fuller Authors * Michael D. Purugganan View author publications You can also search for this

author inPubMed Google Scholar * Dorian Q. Fuller View author publications You can also search for this author inPubMed Google Scholar ETHICS DECLARATIONS COMPETING INTERESTS The authors

declare no competing financial interests. ADDITIONAL INFORMATION Reprints and permissions information is available at http://www.nature.com/reprints. Correspondence should be addressed to

M.D.P. ([email protected]). RIGHTS AND PERMISSIONS Reprints and permissions 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 Download citation * Published: 01 February 2009 * Issue Date: 12 February 2009 * DOI: https://doi.org/10.1038/nature07895

SHARE THIS ARTICLE Anyone you share the following link with will be able to read this content: Get shareable link Sorry, a shareable link is not currently available for this article. Copy to

clipboard Provided by the Springer Nature SharedIt content-sharing initiative