Traditional medicinal use is linked with apparency, not specialized metabolite profiles in the order Caryophyllales

A better understanding of the relationship between plant specialized metabolism and traditional medicine has the potential to aid in bioprospecting and untangling of cross-cultural use patterns. However, given the limited information available for metabolites in most plant species, understanding medicinal use-metabolite relationships can be difficult. The order Caryophyllales has a unique pattern of lineages of tyrosine- or phenylalanine-dominated specialized metabolism, represented by mutually exclusive anthocyanin and betalain pigments, making Caryophyllales a compelling system to explore the relationship between medicine and metabolites by using pigment as a proxy for tyrosine- vs phenylalanine-dominant metabolism. We compiled a list of medicinal species in select tyrosine- or phenylalanine-dominant families of Caryophyllales (Nepenthaceae, Polygonaceae, Simmondsiaceae, Microteaceae, Caryophyllaceae, Amaranthaceae, Limeaceae, Molluginaceae, Portulacaceae, Cactaceae, and Nyctaginaceae..., , , # Traditional medicinal use is linked with apparency, not specialized metabolite profiles in the order Caryophyllales

### Files include:

#### R scripts (all previously run using R v4.3.0):

* PubMedSearch.Rmd - Code used to query for medicinal use of selected families in PubMed using the R package rentrez

* GBIF.R - Code used to trim guide tree to selected families, curate GBIF data, and further trim guide tree by region

* Ethnobot.vis.nhx.R - Code used to import phylocom output that has been converted to nhx format, and visualize results on a guide tree with region mapped on (global analysis). Code also includes PGLS analysis of the North American occurrence data (apparency)by medicinal use

#### Trees:

* Combined_brain.tre - Phylocom output of the global Mental/Nervous System Medicinal category(not in nhx format)

* Globaloutput.tre - Phylocom output of the global analysis of all medicinal use categories of Cook (1995) (requires separation by category and conversion to...