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Crop Origins and Phylo Food: A database and a phylogenetic tree to stimulate comparative analyses on the origins of food crops
Global Ecology and Biogeography ( IF 6.4 ) Pub Date : 2020-01-13 , DOI: 10.1111/geb.13057
Rubén Milla 1
Affiliation  

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.

中文翻译:

作物起源和 Phylo Food:一个数据库和一个系统发育树,以促进对粮食作物起源的比较分析

动机:关于野生粮食作物起源的知识丰富但支离破碎,这阻碍了宏观生态学方法来解决作物起源的系统地理学和历史的长期问题。所含变量的主要类型: (a) 粮食作物品种综合清单;(b) 关于古代栽培(最早的栽培和驯化书面记录)、采集的主要用途器官和生长形式的各种连续和分类描述的数据;(c) 作物野生祖先来源的特性、地理分布和当前气候;( d )粮食作物的时间校准分子系统发育(Phylo Food v 1.0)。空间位置和谷物:全球。全球生物多样性信息设施 (GBIF) 源数据库中野生祖先地理记录的空间准确性各不相同。WorldClim 数据以 2.5 分钟(赤道约 4.5 公里)空间分辨率检索。时间周期和谷物:估计栽培年代的时间准确性因来源而异,但测量单位是几年前的。系统发育树的规模是数百万年前的。主要分类和测量水平:开花植物。其中,粮食作物866种,野生祖先901种。大多数信息是在物种级别检索的。然而,野生祖先的地理分布是从野外特定物种个体观察的 GBIF 记录中获得的。软件格式:Crop Origins v 1.0 和 Phylo Food v 1。0 在本文的支持信息中以压缩文件的形式提供。压缩文件包含一个。使用 Crop Origins 数据库 v 1.0 的 .csv 文件,a。tre 文件的 Newick 格式为 Phylo Food v 1.0,这两种资源的元数据和文献源文件,以及用于构建 Phylo Food v 1.0 的 R 代码。资源也存放在 https://rubenmilla.github.io/Crop_Origins_Phylo,并将定期更新。
更新日期:2020-01-13
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