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Phylogenetic patterns and phenotypic profiles of the species of plants and mammals farmed for food

Abstract

The origins of agriculture were key events in human history, during which people came to depend for their food on small numbers of animal and plant species. However, the biological traits determining which species were domesticated for food provision, and which were not, are unclear. Here, we investigate the phylogenetic distribution of livestock and crops, and compare their phenotypic traits with those of wild species. Our results indicate that phylogenetic clustering is modest for crop species but more intense for livestock. Domesticated species explore a reduced portion of the phenotypic space occupied by their wild counterparts and have particular traits in common. For example, herbaceous crops are globally characterized by traits including high leaf nitrogen concentration and tall canopies, which make them fast-growing species and proficient competitors. Livestock species are relatively large mammals with low basal metabolic rates, which indicate moderate to slow life histories. Our study therefore reveals ecological differences in domestication potential between plants and mammals. Domesticated plants belong to clades with traits that are advantageous in intensively managed high-resource habitats, whereas domesticated mammals are from clades adapted to moderately productive environments. Combining comparative phylogenetic methods with ecologically relevant traits has proven useful to unravel the causes and consequences of domestication.

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Fig. 1: Distribution of the abundance of food domesticates and frequency of domestication events across mammalian and angiosperm families.
Fig. 2: Phylogeographic distribution of the putative place of origin of food domesticates included in phenotypic space analyses.
Fig. 3: Phenospace occupancy of livestock and wild mammals.
Fig. 4: Phenotypic differentiation between livestock and wild mammals.
Fig. 5: Phenospace occupancy of crops and wild angiosperms.
Fig. 6: Phenotypic differentiation between crops and wild angiosperms.

Data availability

All phenotypic traits of mammalian species included in this study are available from the literature (see Methods). For plants, most data are available from the database TRY59 (https://www.try-db.org), and all original sources of TRY data are listed in Supplementary References 1. All references for data not included in TRY are available in the Supplementary References 2. Unpublished data owned by R.M. and J.M.B. are available from Supplementary Data 3. Unpublished data from the University of Sheffield database of weed functional attributes can be requested from G.J. Lists of livestock and crop taxa are available in Supplementary Table 1 and Supplementary Data 1, respectively. Phylogenetic trees used in this study are available in Supplementary Data 4. Data on geography and climate at domestication sites are available as Supplementary Data 5.

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Acknowledgements

R.M., J.C.-L. and J.M.B. were funded by grants CGL2014-56567-R, CGL2017-83855-R and PCIN-2014-053 (Ministerio de Economia y Competitividad, MINECO, Spain), and Eco-serve project (Biodiversa–FACCE, Horizon 2020, European Union). The study has been supported by the TRY initiative on plant traits (http://www.try-db.org). The TRY initiative and database is hosted, developed and maintained by J. Kattge and G. Bönisch (Max Planck Institute for Biogeochemistry, Jena, Germany). TRY is currently supported by DIVERSITAS/Future Earth and the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena -Leipzig. R.M. thanks C. F. Ingala from Universidad Rey Juan Carlos. E.E.S. thanks the FAPESP/BIOTA programme for financial support. J.K. thanks BACI (EU grant ID 640176). T.H. thanks the support of Australian Research Council (DP130013029). V.D.P. was supported by CNPq, Brazil, grant no. 307689/2014-0, K.K. was funded by the project Resilient Forests (KB-29-009-003).

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R.M. and J.M.B. designed the study and compiled the data. R.M., J.M.B., J.C.-L. and M.M.T. performed statistical analyses. R.M. and J.M.B. wrote a first draft of the paper. M.M.T., G.J., C.P.O. and C.V. extensively revised drafts. All authors contributed to the writing of, and approved, the final version.

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Correspondence to Rubén Milla.

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Supplementary information

Supplementary Information

Supplementary Methods, Supplementary Figures, Supplementary Tables, Supplementary Note, and Supplementary References of the Article.

Reporting Summary

Supplementary Data 1

List of 944 domesticated angiosperms included in this study, with information about family adscription and growth forms (herbaceous, graminoid and woody). Bold typing indicates the 181 species included in phenotypic space analyses.

Supplementary Data 2

Results of the analyses on Local Indicators of Phylogenetic Association analysis (LIPA). LIPA values for relative abundance of domesticates and domestication frequencies at family level are shown for mammals and angiosperms families.

Supplementary Data 3

Unpublished crop trait dataset of R.M. and J.M.B.

Supplementary Data 4

Phylogenetic trees used in this study.

Supplementary Data 5

Data, and sources for, wild progenitor assignment, and antiquity of domestication, for the domesticates included in phenotypic space analyses.

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Milla, R., Bastida, J.M., Turcotte, M.M. et al. Phylogenetic patterns and phenotypic profiles of the species of plants and mammals farmed for food. Nat Ecol Evol 2, 1808–1817 (2018). https://doi.org/10.1038/s41559-018-0690-4

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