BEING A TREE CROP INCREASES THE ODDS OF EXPERIENCING YIELD DECLINES IRRESPECTIVE OF POLLINATOR DEPENDENCE
- 1. Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA), Universidad Nacional del Comahue-CONICET, Pasaje Gutierrez 1415, 8400 San Carlos de Bariloche, Río Negro, Argentina.
- 2. Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan 5 Carlos, Tulipán s/n, 28933 Móstoles, Spain
Description
Marcelo A. Aizen, Gabriela R. Gleiser, Thomas Kitzberger, Ruben Milla. Being a tree crop increases the odds of experiencing yield declines irrespective of pollinator dependence (to be submitted to PCI)
Data and R scripts to reproduce the analyses and the figures shown in the paper. All analyses were performed using R 4.0.2.
Data
1. FAOdata_21-12-2021.csv
This file includes yearly data (1961-2020, column 8) on yield and cultivated area (columns 6 and 10) at the country, sub-regional, and regional levels (column 2) for each crop (column 4) drawn from the United Nations Food and Agriculture Organization database (data available at http://www.fao.org/faostat/en; accessed July 21-12-2021). [Used in Script 1 to generate the synthesis dataset]
2. countries.csv
This file provides information on the region (column 2) to which each country (column 1) belongs. [Used in Script 1 to generate the synthesis dataset]
3. dependence.csv
This file provides information on the pollinator dependence category (column 2) of each crop (column 1).
4. traits.csv
This file provides information on the traits of each crop other than pollinator dependence, including, besides the crop name (column1), the variables type of harvested organ (column 5) and growth form (column 6). [Used in Script 1 to generate the synthesis dataset]
5. dataset.csv
The synthesis dataset generated by Script 1.
6. growth.csv
The yield growth dataset generated by Script 1 and used as input by Scripts 2 and 3.
7. phylonames.csv
This file lists all the crops (column 1) and their equivalent tip names in the crop phylogeny (column 2). [Used in Script 2 for the phylogenetically-controlled analyses]
8.phylo137.tre
File containing the phylogenetic tree.
Scripts
1. dataset
This R script curates and merges all the individual datasets mentioned above into a single dataset, estimating and adding to this single dataset the growth rate for each crop and country, and the (log) cumulative harvested area per crop and country over the period 1961-2020.
2. analyses
This R script includes all the analyses described in the article’s main text.
3. figures
This R script creates all the main and supplementary figures of this article.
4. lme4_phylo_setup
R function written by Li and Bolker (2019) to carry out phylogenetically-controlled generalized linear mixed-effects models as described in the main text of the article.
References
Li, M., and B. Bolker. 2019. wzmli/phyloglmm: First release of phylogenetic comparative analysis in lme4- verse. Zenodo. https://doi.org/10.5281/zenodo.2639887.