Traditional medicinal use is linked with apparency, not specialized metabolite profiles in the order Caryophyllales
Data files
Jan 24, 2024 version files 6.60 MB
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Combined_brain.tre
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Ethnosample_geo_trimmed.csv
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Full_ethnobot_survey.csv
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GeneralNoAmSample.csv
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Globaloutput.tre
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NoAm.tre
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NoAmApparency.csv
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NoAmOutput.tre
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North_American_Sample.csv
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ptrim.tre
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README.md
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Whole_phylo.tre
Abstract
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.
README: 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 (https://doi.org/10.5061/dryad.jf7np)
*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(https://doi.org/10.15468/dl.hxzp5v). Download and name "North_America.csv" for use in GBIF.R script.