DOI: 10.25338/b85938
title: Data from: Macroevolution of floral scent chemistry across radiations of male euglossine bee-pollinated plants

description: Floral volatiles play key roles as signaling agents that mediate
 interactions between plants and animals. Despite their importance, few
 studies have investigated broad patterns of volatile variation across
 groups of plants that share pollinators, particularly in a phylogenetic
 context. The “perfume flowers”, Neotropical plant species exhibiting
 exclusive pollination by male euglossine bees in search of chemical
 rewards, present an intriguing system to investigate these patterns due to
 the unique function of their chemical phenotypes as both signaling agents
 and rewards. We leverage recently-developed phylogenies and knowledge of
 biosynthesis along with decades of chemical ecology research to
 characterize axes of variation in the chemistry of perfume flowers, as
 well as understand their evolution at finer taxonomic scales. We detect
 pervasive chemical convergence, with many species across families
 exhibiting similar volatile phenotypes. Scent profiles of most species are
 dominated by compounds of either the phenylpropanoid or terpenoid
 biosynthesis pathways, while terpenoid compounds drive more subtle axes of
 variation. We find recapitulation of these patterns within two independent
 radiations of perfume flower orchids, in which we further detect evidence
 for rapid evolution of divergent floral chemistries, consistent with the
 putative importance of scent in the process of adaptation and speciation.
description: We built a database of floral perfume chemical composition, as
 well as pollinator identity, for any angiosperm pollinated by
 perfume-collecting male euglossine bees. Both published and unpublished
 data from the literature and from collaborators were used to build this
 database. For the published data, a literature search in ISI Web of
 Science and Scopus using the following search terms was conducted: (“scent
 plant” OR “perfume plant” OR “VOC” OR “volatile” OR “scent reward* plant”
 OR “perfume reward* flower” OR “scent reward* flower” OR “perfume reward*
 flower) AND (eugloss* OR “orchid bee”). In addition to this search, we
 screened the reference list of all obtained articles to check for works
 not obtained from the literature search. Only studies using headspace
 analyses were used. Following compilation of perfume data in a single
 database, we searched for the CAS number of individual floral perfume
 compounds in the online database (https://webbook.nist.gov/chemistry/cas-ser.html). Based on the number, we checked for possible synonyms. Compounds included more than once were then merged. Following data curation, we excluded compounds present in relative proportions below 1% of each species’ perfume to avoid biased sampling of rare compounds with more sensitive technology in recent years. This also allowed us to compare studies that elected to characterize compounds below 1% as “trace” without providing further quantitative information. Species with less than 70% of their total perfume blends resolved were then excluded from the dataset. The resulting chemical matrix was then re-standardized such that the sum of relative proportions within each species was 1.
description: ## Perfume flower dataset Scent data from male euglossine bee-pollinated
 plants, in addition to pollinator information The zipped folder contains 5
 folders. Apart from the "Raw_data" folder, each folder contains
 all the data and source code required to run the primary R script.
 Analyses were run in R version 4.2.1 with the following packages: dplyr v.
 1.1.2 tidyr v. 1.3.0 ggplot2 v. 3.4.2 compositions v. 2.0.6 ggpubr v.
 0.6.0 pez v. 1.2.4 dendextend v. 1.17.1 ecodist v 2.0.9 ape v. 5.7.1
 geomorph v. 4.0.5 phytools v. 1.5.1 geiger v. 2.0.11 phylogram v. 2.1.0
 picante v. 1.8.2 chemodiv v. 0.2.0 webchem v. 1.2.0 ChemmineR v. 3.48.0
 fmcsR v. 1.38.0 fBasics v. 4022.94 ade4 v. 1.7.22 Cells with NA refer to
 cases where formulae used to calculate values are unable to do so due to
 some inherent property of the data (e.g. when only 1 compound is present,
 diversity metrics are not possible to calculate). These values are removed
 from analyses when diversity metrics are used as predictors. ##
 Description of scripts and datasets within each folder **Raw_data: raw
 data used for the analyses prior to filtering** 1. Plant_pollinator.csv -
 csv of plant species with pollinator info and scent data; each row
 corresponds to a plant species - pollinator combination (so if a given
 plant has multiple pollinators, it occupies as many rows as its total
 number of pollinators). * "plantspecies" corresponds to plant
 species in a plant-pollinator combination * "plantfamily"
 corresponds to the family the plant is in * "plantgenus"
 corresponds to the genus the plant is in * "beespecies"
 corresponds to a bee pollinator of the plant * "beegenus"
 corresponds to the bee genus ("Eg" = Euglossa, "Ag" =
 Aglae, "Ex" = Exaerete, "El" = Eulaema, "Ef"
 = Eufriesea") * all other columns correspond to compounds present in
 the plant's perfume, with values ranging from 0 to 100 corresponding
 to the percentage of the compound in the total blend 2.
 plant_VOC_averages_all.csv - csv of all plant species with scent data;
 each row corresponds to a species while columns correspond to compounds;
 values range from 0 to 100, corresponding to the percentage of the
 compounds in the blend **Chemodiv_analyses: Data and script to generate
 the chemodiv distancematrices used for downstream analyses** Files in this
 folder include: 1. chemodivscript.R - Primary R script to generate
 chemical distance matrices used in downstream analyses in other
 subfolders. 2. cleaneddataset_with_features_FINAL.csv - csv of plant
 species with their chemical traits after filtering out spp with less than
 70% of their total scent profile resolved and standardizing such that
 values correspond to proportions, in addition to some other features for
 exploratory plotting * "Family" corresponds to the family the
 plant is in * "SuborFam" correspond to the subfamily the plant
 is in, if it is an orchid, or the family if not * "richness"
 corresponds to the total number of compounds * "aroprop"
 corresponds to the proportion of the perfume comprised of aromatic
 compounds * "monoprop" corresponds to the proportion of the
 perfume comprised of monoterpenoid compounds * "terpprop"
 corresponds to the proportion of the perfume comprised of all terpenoid
 compounds * "sesprop" corresponds to the proportion of the
 perfume comprised of sesquiterpenoid compounds * "faprop"
 corresponds to the proportion of the perfume comprised of fatty acid
 derivative compounds * "carprop" corresponds to the proportion
 of the perfume comprised of carotenoid compounds * "broadclass"
 corresponds to the broad chemical class of the plant ("T" =
 terpenoid-dominated, "AT" = mix of aromatic and terpenoid,
 "A" = aromatic-dominated, "F" = fatty acid
 derivative-dominated) * "most_abundant" corresponds to the most
 abundant compound in the blend * "ses_jac" corresponds to
 standard effect size calculated using jaccard distances *
 "ses_bray" corresponds to standard effect size calculated using
 Bray-curtis distances 3. R Compound Properties - csv of compounds present
 in the dataset with their InChiKey and SMILES code for chemodiv
 **Analyses_with_full_dataset: data and scripts to perform analysesacross
 all species** Files in this folder include: 1. Broad_patterns_Final.R -
 Primary R script used to generate biosynthetic distances using the method
 of Junker 2018, Chemoecology, generate ordinations, and perform
 correlative analyses of axes of variation with specific chemical traits.
 2. SI1_sourceFunctions_BioSynDist_copy.R - Source code from Junker 2018,
 Chemoecology, to generate biosynthetic distances among species 3.
 Coded.csv - csv containing taxonomic information * "Family"
 corresponds to the family the plant is in * "SuborFam"
 correspond to the subfamily the plant is in, if it is an orchid, or the
 family if not 4. compoundxproperty_sorted_filtered - csv where rows
 correspond to compounds present in dataset and columns correspond to
 biosynthetic pathways and functional group information. Entries are coded
 1 or 0 based on presence / absence 5.
 master_VOC_averages_no_poll_cleaned.csv - csv where rows correspond to
 species present in dataset while columns correspond to different compounds
 present after data filtering, and values correspond to percentage (0 to
 100) 6. diversity_metrics_chemodiv.csv - csv of chemical diversity metrics
 generated from the chemodivscript * finger_funchill corresponds to
 functional Hill diversity of compounds calculated using the
 "fingerprint" scheme * finger_hill corresponds to Hill diversity
 of compounds calculated using the "fingerprint" scheme *
 fmcs_funchill corresponds to functional Hill diversity of compounds
 calculated using the "fMCS" scheme * fmcs_hill corresponds to
 Hill diversity of compounds calculated using the "fMCS" scheme
 7. fingerprintdisdata_full.csv - csv of distance matrix from
 "fingerprints" scheme in chemodiv 8. fmcsdisdata_full.csv - csv
 of distance matrix from "fMCS" scheme in chemodiv
 **Pollinator_analyses: data and scripts for performing analysesinvolving
 pollinators** Files in this folder include: 1. pollinator_analyses_FINAL.R
 - Primary R script to perform correlative tests between chemical traits
 and pollinators using chemical distance matrices generated earlier. 2.
 dataset_with_everything.csv - csv containing filtered chemical traits, PCO
 scores, and chemodiv metrices generated from
 "Analyses_with_full_dataset" 3.
 master_VOC_regions_20220224_edited - csv where rows correspond to plant
 species and columns correspond to pollinator species. *
 "plantspecies" corresponds to plant species in a
 plant-pollinator combination * "plantfamily" corresponds to the
 family the plant is in * "plantgenus" corresponds to the genus
 the plant is in * "beespecies" corresponds to a bee pollinator
 of the plant * "beegenus" corresponds to the bee genus
 ("Eg" = Euglossa, "Ag" = Aglae, "Ex" =
 Exaerete, "El" = Eulaema, "Ef" = Eufriesea") *
 all other columns correspond to compounds present in the plant's
 perfume, with values ranging from 0 to 100 corresponding to the percentage
 of the compound in the total blend 4. complete_AE_Plant.tre - most general
 phylogeny of plants within the dataset 5. euglossine_tree.tree -
 euglossine bee phylogeny (Ramirez et al. 2011). 6.
 fingerprintdisdata_full.csv - csv of distance matrix from
 "fingerprints" scheme in chemodiv 7. fmcsdisdata_full.csv - csv
 of distance matrix from "fMCS" scheme in chemodiv 8.
 myscheme_full.csv - csv of distance matrix from "simple" scheme
 using Junker 2018 method produced in "Analyses_with_full_datset"
 **Phylogenetic_analyses: data and scripts for performing
 phylogeneticcomparative methods** Files in this folder include: 1.
 Phylogenetic_Comparative_FINAL.R - Primary R script for calculating
 phylogenetic signal and disparity through time in two separate clades. 2.
 Adams_function.r - R source code to calculate phylogenetic signal 3.
 complete_AE_Plant.tre - most general phylogeny of plants within the
 dataset 4. euglossine_tree.tree - euglossine bee phylogeny (Ramirez et al.
 2011). 5. cattreeforanalyses.tre - complete_AE_Plant.tre pruned to just
 the Catasetinae 6. stantreeforanalyses.tre - complete_AE_Plant.tre pruned
 to just the Stanhopeinae 7. bigtreechemodataset_new.csv - csv containing
 scent data for all species in the dataset with phylogenetic information.
 Rows correspond to species while the first 167 columns correspond to
 compounds, with values representing relative proportion of that compound
 in the species' blend. Other columns: * "Family"
 corresponds to the family the plant is in * "SuborFam"
 correspond to the subfamily the plant is in, if it is an orchid, or the
 family if not * "richness" corresponds to the total number of
 compounds * "aroprop" corresponds to the proportion of the
 perfume comprised of aromatic compounds * "monoprop" corresponds
 to the proportion of the perfume comprised of monoterpenoid compounds *
 "terpprop" corresponds to the proportion of the perfume
 comprised of all terpenoid compounds * "sesprop" corresponds to
 the proportion of the perfume comprised of sesquiterpenoid compounds *
 "faprop" corresponds to the proportion of the perfume comprised
 of fatty acid derivative compounds * "carprop" corresponds to
 the proportion of the perfume comprised of carotenoid compounds *
 "linearmono" corresponds to the proportion of the perfume
 comprised of linear monoterpenoid compounds * "ringedmono"
 corresponds to the proportion of the perfume comprised of ringed
 monoterpenoid compounds * "cineolecasette" corresponds to the
 proportion of the perfume comprised of cineole casette compounds *
 "carvones" corresponds to the proportion of the perfume
 comprised of carvones compounds * "broadclass" corresponds to
 the broad chemical class of the plant ("T" =
 terpenoid-dominated, "AT" = mix of aromatic and terpenoid,
 "A" = aromatic-dominated, "F" = fatty acid
 derivative-dominated) * "most_abundant" corresponds to the most
 abundant compound in the blend * "ses_jac" corresponds to
 standard effect size calculated using jaccard distances *
 "ses_bray" corresponds to standard effect size calculated using
 Bray-curtis distances * finger_funchill corresponds to functional Hill
 diversity of compounds calculated using the "fingerprint" scheme
 * finger_hill corresponds to Hill diversity of compounds calculated using
 the "fingerprint" scheme * fmcs_funchill corresponds to
 functional Hill diversity of compounds calculated using the
 "fMCS" scheme * fmcs_hill corresponds to Hill diversity of
 compounds calculated using the "fMCS" scheme * pcoa1_full
 corresponds to values of PCo 1 for the species calculated using the
 "simple" scheme * pcoa2_full corresponds to values of PCo 2 for
 the species calculated using the "simple" scheme * pcoa3_full
 corresponds to values of PCo 3 for the species calculated using the
 "simple" scheme * pcoa4_full corresponds to values of PCo 4 for
 the species calculated using the "simple" scheme * pcoa1_finger
 corresponds to values of PCo 1 for the species calculated using the
 "fingerprint" scheme * pcoa2_finger corresponds to values of PCo
 2 for the species calculated using the "fingerprint" scheme *
 pcoa3_finger corresponds to values of PCo 3 for the species calculated
 using the "fingerprint" scheme * pcoa4_finger corresponds to
 values of PCo 4 for the species calculated using the
 "fingerprint" scheme * pcoa1_fmcs corresponds to values of PCo 1
 for the species calculated using the "fMCS" scheme * pcoa2_fmcs
 corresponds to values of PCo 2 for the species calculated using the
 "fMCS" scheme * pcoa3_fmcs corresponds to values of PCo 3 for
 the species calculated using the "fMCS" scheme * pcoa4_fmcs
 corresponds to values of PCo 4 for the species calculated using the
 "fMCS" scheme 8. Catchemodataset_new.csv - csv containing
 filtered scent data for the Catasetinae. See bigtreechemodataset
 description for column meanings 9. Stanchemodataset_new.csv - csv
 containing filtered scent data for the Stanhopeinae. See
 bigtreechemodataset description for column meanings