Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Crop origins explain variation in global agricultural relevance

Nature Plants volume 7, pages 598–607 (2021)Cite this article

Subjects

Abstract

Human food production is dominated globally by a small number of crops. Why certain crops have attained high agricultural relevance while others have remained minor might partially stem from their different origins. Here, we analyse a dataset of 866 crops to show that seed crops and species originating from seasonally dry environments tend to have the greatest agricultural relevance, while phylogenetic affinities play a minor role. These patterns are nuanced by root and leaf crops and herbaceous fruit crops having older origins in the aseasonal tropics. Interestingly, after accounting for these effects, we find that older crops are more likely to be globally important and are cultivated over larger geographical areas than crops of recent origin. Historical processes have therefore left a pervasive global legacy on the food we eat today.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Learn more

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Global production of food crops included in FAOSTAT.
Fig. 2: Predictors of the antiquity of cultivation.
Fig. 3: Phylogenetic structure of crop antiquity.
Fig. 4: Probability that a crop is major or minor as a function of crop antiquity and climate.
Fig. 5: Global production as a function of crop origins and crop type.
Fig. 6: Phylogenetic structure of global production.

Data availability

All data used in this paper are publicly available at https://github.com/rubenmilla/Crop_Origins_Phylo and http://www.fao.org/faostat/en.

Code availability

The analyses carried out in this paper did not require the development of custom code. Functions were run as provided by the R packages mentioned in Methods.

References

  1. FAOSTAT: Crops (FAO, 2109); http://www.fao.org/faostat/en/#data/QC

  2. Mottet, A. et al. Livestock: on our plates or eating at our table? A new analysis of the feed/food debate. Glob. Food Sec. 14, 1–8 (2017).

    Article  Google Scholar 

  3. Prescott-Allen, R. & Prescott-Allen, C. How many plants feed the world? Conserv. Biol. 4, 365–374 (1990).

    Article  Google Scholar 

  4. Crittenden, A. N. & Schnorr, S. L. Current views on hunter-gatherer nutrition and the evolution of the human diet. Am. J. Phys. Anthropol. 162, 84–109 (2017).

    Article  PubMed  Google Scholar 

  5. Khoury, C. K. et al. Origins of food crops connect countries worldwide. Proc. R. Soc. B 283, 20160792 (2016).

    Article  PubMed Central  Google Scholar 

  6. Poisot, T., Canard, E., Mouquet, N. & Hochberg, M. E. A comparative study of ecological specialization estimators. Methods Ecol. Evol. 3, 537–544 (2012).

    Article  Google Scholar 

  7. Ray, D. K., Mueller, N. D., West, P. C. & Foley, J. A. Yield trends are insufficient to double global crop production by 2050. PLoS ONE 8, e66428 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Khoury, C. K. et al. Increasing homogeneity in global food supplies and the implications for food security. Proc. Natl Acad. Sci. USA 111, 4001–4006 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Renard, D. & Tilman, D. National food production stabilized by crop diversity. Nature 571, 257–260 (2019).

    Article  CAS  PubMed  Google Scholar 

  10. Newton, A. C., Johnson, S. N. & Gregory, P. J. Implications of climate change for diseases, crop yields and food security. Euphytica 179, 3–18 (2011).

    Article  Google Scholar 

  11. Hawkesworth, S. et al. Feeding the world healthily: the challenge of measuring the effects of agriculture on health. Philos. Trans. R. Soc. B 365, 3083–3097 (2010).

    Article  Google Scholar 

  12. Popkin, B. M. Technology, transport, globalization and the nutrition transition food policy. Food Policy 31, 554–569 (2006).

    Article  Google Scholar 

  13. Spengler III, R. N. Fruit from the Sands: The Silk Road Origins of the Foods We Eat (Univ. of California Press, 2019).

  14. Vaughan, J. & Geissler, C. The New Oxford Book of Food Plants (Oxford Univ. Press, 2009).

  15. Purugganan, M. D. & Fuller, D. Q. The nature of selection during plant domestication. Nature 457, 843–848 (2009).

    Article  CAS  PubMed  Google Scholar 

  16. Wang, L. et al. The interplay of demography and selection during maize domestication and expansion. Genome Biol. 18, 215 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  17. Milla, R., Bastida, J. M., Turcotte, M. M. & Al, E. Phylogenetic patterns and phenotypic profiles of the species of plants and mammals farmed for food. Nat. Ecol. Evol. 2, 1808–1817 (2018).

    Article  PubMed  Google Scholar 

  18. Ellis, E. C., Klein Goldewijk, K., Siebert, S., Lightman, D. & Ramankutty, N. Anthropogenic transformation of the biomes, 1700 to 2000. Glob. Ecol. Biogeogr. 19, 589–606 (2010).

    Google Scholar 

  19. Xu, C., Kohler, T. A., Lenton, T. M., Svenning, J.-C. & Scheffer, M. Future of the human climate niche. Proc. Natl Acad. Sci. USA 117, 11350–11355 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Harlan, J. R. Crops and Man (ASA, 1992).

  21. Blumler, M. A. et al. in The Origins and Spread of Agriculture and Pastoralism in Eurasia (ed. Harris, D. R.) 25–50 (Smithsonian Institution Press, 1996).

  22. Hancock, J. F. Plant Evolution and the Origin of Crop Species (CABI, 2012).

  23. Harlan, J. R. The Living Fields: Our Agricultural Heritage (Cambridge Univ. Press, 1998).

  24. Lombardo, U. et al. Early Holocene crop cultivation and landscape modification in Amazonia. Nature 581, 190–193 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Denham, T. et al. The domestication syndrome in vegetatively propagated field crops. Ann. Bot. 125, 581–597 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  26. Meyer, R. S., DuVal, A. E. & Jensen, H. R. Patterns and processes in crop domestication: an historical review and quantitative analysis of 203 global food crops. New Phytol. 196, 29–48 (2012).

    Article  PubMed  Google Scholar 

  27. Milla, R. Crop origins and phylo food: a database and a phylogenetic tree to stimulate comparative analyses on the origins of food crops. Glob. Ecol. Biogeogr. 29, 606–614 (2020).

    Article  Google Scholar 

  28. Larson, G. et al. Current perspectives and the future of domestication studies. Proc. Natl Acad. Sci. USA 111, 6139–6146 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Esquinas-Alcázar, J. Protecting crop genetic diversity for food security: political, ethical and technical challenges. Nat. Rev. Genet. 6, 946–953 (2005).

    Article  PubMed  Google Scholar 

  30. Clement, C. R. 1492 and the loss of Amazonian crop genetic resources. I. The relation between domestication and human population decline. Econ. Bot. 53, 188–202 (1999).

    Article  Google Scholar 

  31. Webb, C. O., Ackerly, D. D., McPeek, M. A. & Donoghue, M. J. Phylogenies and community ecology. Annu. Rev. Ecol. Syst. 33, 475–505 (2002).

    Article  Google Scholar 

  32. Tauger, M. B. Agriculture in World History (Routledge, 2013).

  33. Futuyma, D. J. & Moreno, G. The evolution of ecological specialization. Annu. Rev. Ecol. Syst. 19, 207–233 (1988).

    Article  Google Scholar 

  34. Forister, M. L., Dyer, L. A., Singer, M. S., Stireman, J. O. III & Lill, J. T. Revisiting the evolution of ecological specialization, with emphasis on insect–plant interactions. Ecology 93, 981–991 (2012).

    Article  CAS  PubMed  Google Scholar 

  35. Colles, A., Liow, L. H. & Prinzing, A. Are specialists at risk under environmental change? Neoecological, paleoecological and phylogenetic approaches. Ecol. Lett. 12, 849–863 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  36. McKinney, M. L. & Lockwood, J. L. Biotic homogenization: a few winners replacing many losers in the next mass extinction. Trends Ecol. Evol. 14, 450–453 (1999).

    Article  CAS  PubMed  Google Scholar 

  37. Richerson, P. J., Boyd, R. & Bettinger, R. L. Was agriculture impossible during the Pleistocene but mandatory during the Holocene? A climate change hypothesis. Am. Antiq. 66, 387–411 (2001).

    Article  Google Scholar 

  38. Mueller, U. G. & Rabeling, C. A breakthrough innovation in animal evolution. Proc. Natl Acad. Sci. USA 105, 5287–5288 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Schultz, T. R. & Brady, S. G. Major evolutionary transitions in ant agriculture. Proc. Natl Acad. Sci. USA 105, 5435–5440 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Mueller, U. G., Scott, J. J., Ishak, H. D., Cooper, M. & Rodrigues, A. Monoculture of leafcutter ant gardens. PLoS ONE 5, e12668 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  41. Kingsbury, N. Hybrid, the History and Science of Plant Breeding (Univ. of Chicago Press, 2009).

  42. Food Outlook—Biannual Report on Global Food Markets: June 2020 (FAO, 2020).

  43. van Kleunen, M. et al. Economic use of plants is key to their naturalization success. Nat. Commun. 11, 3201 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  44. Li, T. et al. Domestication of wild tomato is accelerated by genome editing. Nat. Biotechnol. 36, 1160–1163 (2018).

    Article  CAS  Google Scholar 

  45. Siddique, K. H. M., Li, X. & Gruber, K. Rediscovering Asia’s forgotten crops to fight chronic and hidden hunger. Nat. Plants 7, 116–122 (2021).

    Article  PubMed  Google Scholar 

  46. Lancaster, L. T. Host use diversification during range shifts shapes global variation in Lepidopteran dietary breadth. Nat. Ecol. Evol. 4, 963–969 (2020).

  47. Milla, R. Crop Origins and Phylo Food (GitHub, accessed 1 December 2020); https://github.com/rubenmilla/Crop_Origins_Phylo

  48. Global Biodiversity Information Facility (GBIF, 2018); https://www.gbif.org

  49. Fick, S. E. & Hijmans, R. J. WorldClim 2: new 1-km spatial resolution climate surfaces for global land areas. Int. J. Climatol. 37, 4302–4315 (2017).

    Article  Google Scholar 

  50. Paradis, E., Claude, J. & Strimmer, K. {APE}: analyses of phylogenetics and evolution in R language. Bioinformatics 20, 289–290 (2004).

    Article  CAS  PubMed  Google Scholar 

  51. Martin, A. R. et al. Regional and global shifts in crop diversity through the Anthropocene. PLoS ONE 14, e0209788 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. The Plant List Version 2 (2013); http://www.theplantlist.org/

  53. Cayuela, L., la Cerda, Í. G., Albuquerque, F. S. & Golicher, D. J. taxonstand: an R package for species names standardisation in vegetation databases. Methods Ecol. Evol. 3, 1078–1083 (2012).

    Article  Google Scholar 

  54. Beres, B. L. et al. A systematic review of durum wheat: enhancing production systems by exploring genotype, environment, and management (Gx Ex M) synergies. Front. Plant. Sci. 11, 568657 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  55. Paradis, E. in Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology (ed. Garamszegi, L. Z.) 3–18 (Springer, 2014).

  56. Pagel, M. Inferring the historical patterns of biological evolution. Nature 401, 877–884 (1999).

    Article  CAS  PubMed  Google Scholar 

  57. Revell, L. J. phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol. 3, 217–223 (2011).

    Article  Google Scholar 

  58. de Villemereuil, P. & Nakagawa, S. in Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology (ed. Garamszegi, L. Z.) 287–304 (Springer, 2014).

  59. Keck, F., Rimet, F., Bouchez, A. & Franc, A. phylosignal: an R package to measure, test, and explore the phylogenetic signal. Ecol. Evol. 6, 2774–2780 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  60. Bush, S. E. et al. Unlocking the black box of feather louse diversity: a molecular phylogeny of the hyper-diverse genus Brueelia. Mol. Phylogenet. Evol. 94, 737–751 (2016).

    Article  PubMed  Google Scholar 

  61. R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2018).

  62. Fox, J. & Weisberg, S. An R Companion to Applied Regression (Sage, 2019).

  63. Grafen, A. & Hamilton, W. D. The phylogenetic regression. Philos. Trans. R. Soc. Lond. B 326, 119–157 (1989).

    Article  CAS  Google Scholar 

  64. Pinheiro, J., Bates, D., DebRoy, S., Sarkar, D. & R Development Core Team. nlme: Linear and nonlinear mixed effects models. R package version 3.1-142 (2020).

  65. Ives, A. R. & Garland, T. Jr. Phylogenetic logistic regression for binary dependent variables. Syst. Biol. 59, 9–26 (2009).

    Article  PubMed  Google Scholar 

Download references

Acknowledgements

This study has been supported by grant nos. CGL2014-56567-R and CGL2017-83855-R (Ministerio de Economia y Competitividad, MINECO, Spain) and REMEDINAL TE (Comunidad de Madrid). J. María Iriondo, P. García-Palacios and M. Delgado-Baquerizo provided valuable comments to earlier versions of this work. We thank the GBIF (https://www.gbif.org/) and WordClim (https://worldclim.org/data/bioclim.html) initiatives for providing geographic and climate data.

Author information

Authors and Affiliations

  1. Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Móstoles, Spain

    Rubén Milla

  2. Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK

    Colin P. Osborne

Authors
  1. Rubén Milla
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Colin P. Osborne
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

R.M. and C.P.O. conceived the study. R.M. analysed data and wrote a first draft of the manuscript. R.M. and C.P.O. contributed to subsequent rounds of writing and gave the approval for submission of the final version.

Corresponding author

Correspondence to Rubén Milla.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Peer review information Nature Plants thanks Robin Allaby, Itay Mayrose and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Information

Supplementary Figs. 1–5 and Tables 1–6.

Reporting Summary

Supplementary Data 1

Results of local indicators of phylogenetic association analysis (LIPA) analyses.

Supplementary Data 2

Loadings of WordClim variables on the two PCA axes shown in Supplementary Fig. 5 and used as climate-at-origin variables in the main text.

Rights and permissions

Reprints and Permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Milla, R., Osborne, C.P. Crop origins explain variation in global agricultural relevance. Nat. Plants 7, 598–607 (2021). https://doi.org/10.1038/s41477-021-00905-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41477-021-00905-1

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing