Crop Origins and Phylo Food: A database and a phylogenetic tree to stimulate comparative analyses on the origins of food crops

Abstract

Motivation Knowledge on the origins of food crops in the wild is abundant but fragmentary and unconsolidated, which hinders macroecological approaches to long-standing questions on the phylogeography and history of crop origins.

Main types of variable contained (a) Comprehensive checklist of crop species cultivated for food; (b) data on diverse continuous and categorical descriptors of antiquity of cultivation (earliest written records of cultivation and of domestication), organ harvested for primary use, and growth form; (c) identities, geographic distribution and current climate at the origin of crops’ wild progenitors; (d) a time-calibrated molecular phylogeny (Phylo Food v 1.0) of food crops.

Spatial location and grain Global. Spatial accuracy of geographic records for wild progenitors varies among Global Biodiversity Information Facility (GBIF) source databases. WorldClim data were retrieved at 2.5 min (approximately 4.5 km at the equator) spatial resolution.

Time period and grain Temporal accuracy of estimation of cultivation antiquity varies among sources, but unit of measurements is years ago. The scale of the phylogenetic tree is millions of years ago.

Major taxa and level of measurement Flowering plants. Specifically, 866 species of food crops and 901 species of wild progenitors. Most information was retrieved at the species level. However, geographic occurrence of wild progenitors was obtained from GBIF records of observations of individuals of a given species in the field.

Software format Crop Origins v 1.0 and Phylo Food v 1.0 are provided as zipped files in the Supporting Information of this paper. The zipped files contain a. csv file with v 1.0 of the Crop Origins database, a. tre file with Newick format as Phylo Food v 1.0, metadata and literature sources files for both resources, and R code used to build Phylo Food v 1.0. The resources are also deposited, and will be regularly updated, at https://rubenmilla.github.io/Crop_Origins_Phylo