DOI: 10.5061/dryad.pk0p2ngnh
title: Phylogeny reveals non-random medicinal plant organs selection by local people in Benin

description: 1. Ethnobotany, the science of human-plant interactions, has for long
 focused on documenting the traditional knowledge that humans have
 developed and accumulated over centuries towards plant uses. However, how
 such knowledge is constructed remains poorly understood and some of the
 methodological approaches developed for this purpose have been
 criticized.  2. Here, we combine negative binomial models and
 phylogenetic comparative methods to test whether selection of medicinal
 plant species and organs by local people are non-random using data from
 Benin, a country in West Africa with roughly 3,000 plant
 species.  3. We found evidence for taxonomic and phylogenetic
 non-random selection of medicinal plants: some taxa are preferentially
 used for medicine. Our analysis uncovers that plant organs are
 also non-randomly selected for medicine. Beyond plant taxonomy, similar
 plant organs of closely related species tended to be used for similar
 treatments, because these organs are likely to have similar secondary
 chemistry. Such non-random organs selection was more apparent for plant
 organs such as roots, bark and leaves which are predicted to be more vital
 for population fitness and species persistence.  4. Collectively,
 our study suggests that the emerging non-random pattern of medicinal plant
 selection may be a consequence of heterogenous within-plant distribution
 of secondary chemistry across different organs proportionally to their
 importance to plant fitness as predicted by the optimal defence
 theory. 
description: We first digitalized the existing flora of
 Benin (Akoegninou <i>et al.</i>, 2006) to retrieve species and
 family names and build the total plants list for Benin. We verified
 binomial name changes and family classification against APG IV using The
 World Flora Online (WFO, 2021). This flora includes 2802 angiosperms from
 583 families. Second, to build the medicinal plants list for Benin, we
 obtained the most comprehensive compendium on Benin medicinal
 plants (Adjanohoun <i>et al.</i>, 1989). This compendium
 includes 507 medicinal plant species from 83 families and was commissioned
 by the French <i>Agence de Cooperation Culturelle et
 Technique</i> and developed by the best-known botanists of West
 Africa at that time. From these two (total and medicinal) plant lists, we
 build a dataset that includes for each plant family occurring in Benin,
 the total number of species and number of medicinal species. For
 phylogenetic comparative methods, we reconstructed a time-calibrated
 phylogeny for all 507 species used as medicinal in Benin. To this end, we
 compiled a matrix of 488 DNA sequences for
 the <i>matK</i> region, a marker used as DNA barcode. These
 sequences were retrieved for 488 species from GenBank/EBI and BOLD (www.boldsystem.org, accessed June 2017).  For species for which DNA sequences are missing from these public repositories, we used DNA sequences from congeneric species that have their sequences on GenBank/EBI and BOLD. Adjanohoun EJ, Adjakidje V, Ahyi MRA, Ake Assi L, Akoegninou A, d’Almeida J, Akpovo F, Bouke K, Chadare M, Cusset G, et al. 1989. Contribution aux études ethnobotaniques et floristiques en République Populaire du Bénin. Médecine traditionnelle et pharmacopée. Paris: ACCT. Koegninou A, Van der Burg WJ, van der Maesen LJG. 2006. Flore analytique du Bénin. Backhuys Publishers, Leiden.
description: This
 repository includes 7 datasets and one R script that were used for all the
 analyses and illustrations in Gaoue et al. 2021 PPP Dataset 1: Plant families from the flora of Benin with the number of total species per family and the number of medicinal plant species per family. Dataset 2: Details of the DNA sequences used for phylogenetic reconstruction of the Benin medicinal flora. This includes all GenBank/EBI and BOLD accession numbers for gene sequences. Dataset 3: Coding of plant organ selection for medicinal use. 1: an organ is selected for medicinal use; 0: the organ is not used for any medicinal use. Dataset 4: Plant genera that form clusters of species that drive phylogenetic signal in organ plant selection Dataset 5: Species classification into families that are over or under-utilized for medicinal purposes. Dataset 6: Families classification into over or under-utilized categories for medicinal purposes. Dataset 7: Phylogeny of medicinal plant species from the Benin flora. Code 1: R Script for a corrected Moerman test of non-random medicinal plant selection and phylogenetic signal test for over/under-utilization of medicinal flora and non-random plant’s organs selection.