DOI: 10.5061/dryad.6q573n64z
title: Traditional medicinal use is linked with apparency, not specialized metabolite profiles in the order Caryophyllales

description: 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) by searching scientific literature until no
 new medicinal uses were recovered. We then tested for phylogenetic
 clustering of uses using a “hot nodes" approach. To test potential
 non-metabolite drivers of medicinal use, like how often humans encounter a
 species (apparency), we repeated the analysis using only North American
 species across the entire order and performed phylogenetic generalized
 least squares regression (PGLS) with occurrence data from the Global
 Biodiversity Information Facility (GBIF). We hypothesized families with
 tyrosine-enriched metabolism would show clustering of different types of
 medicinal use compared to phenylalanine-enriched metabolism. Instead,
 wide-ranging, apparent clades in Polygonaceae and Amaranthaceae are
 overrepresented across nearly all types of medicinal use. Our results
 suggest that apparency is a better predictor of medicinal use than
 metabolite profile, although metabolism type may still be a contributing
 factor.
description: # 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 nhx format for use in
 Ethnobot.vis.nhx.) * NoAmOutput.tre - Phylocom output of North American
 analysis of all medicinal use categories of Cook (1995) (requires
 separation by category and conversion to nhx format for use in
 Ethnobot.vis.nhx.) * NoAm.tre - Guide tree trimmed to North American
 families using GBIF.R * ptrim.tre - Guide tree trimmed to selected
 families for global analysis using GBIF.R * Whole_phylo.tre - Whole guide
 tree as taken from Smith et al, (2018), publicly available
 () *Trees that require
 conversion to nhx can be quickly converted in BBedit by deleting all
 information apart from the relevant tree, and using search and replace to
 replace "[%note = 'string:SIG(MORE or LESS)']" with
 "&&NHX:XN=SIG(MORE or LESS)]" #### CSV or TSV files: *
 Full_ethnobot_survey.csv - The complete untrimmed, uncategorized
 literature search of selected global families (taxonomy not reconciled).
 Each row represents a species' uses as pulled from one source. Column
 A is the family and species name as given in the source paper. Column B is
 the medicinal uses given in that paper. Column C represents the country,
 region, or culture of study in the source paper. Column D is the URL or
 title used to access the source paper. * Ethnosample_geo_trimmed.csv - The
 trimmed (to match tree) and categorized dataset for use in
 Ethnobot.vis.nhx.R. Taxonomy is reconciled. Columns C-M detail if a use
 category for a species has been reported in the header region. *
 GeneralNoAmSample.csv - North American species categorized as
 "Medicinal" or "Non-Medicinal for use in PGLS in
 Ethnobot.vis.nhx.R" * NoAmApparency.csv - counts of occurrence data
 of North American species generated by GBIF.R * North_American_Sample.csv
 - Phylocom input for the North American analysis of all medicinal
 categories (Integer column is required for Phylocom to run, it has no
 bearing on analysis) Also needed as the data input for GBIF.R, North
 American Caryophyllales species downloadable from
 GBIF(). Download and name
 "North_America.csv" for use in GBIF.R script.