DOI: 10.5061/dryad.bvq83bkdx
title: Data from: The sequential direct and indirect effects of mountain uplift, climatic niche and floral trait evolution on diversification dynamics in an Andean plant clade

description: Why and how organismal lineages radiate is commonly studied through either
 assessing abiotic factors (biogeography, geomorphological processes,
 climate) or biotic factors (traits, interactions). Despite increasing
 awareness that both abiotic and biotic processes may have important joint
 effects on diversification dynamics, few attempts have been made to
 quantify the relative importance and timing of these factors, and their
 potentially interlinked direct and indirect effects, on lineage
 diversification. We here combine assessments of historical biogeography,
 geomorphology, climatic niche, vegetative and floral trait evolution to
 test whether these factors jointly, or in isolation, explain
 diversification dynamics of a Neotropical plant clade (Merianieae,
 Melastomataceae). After estimating ancestral areas and disparification
 over time in climate and trait space, we employ Phylogenetic Path Analyses
 as a synthesis tool to test eleven hypotheses on the individual direct and
 indirect effects of these factors on diversification rates. We find
 strongest support for interlinked effects of colonization of the uplifting
 Andes during the mid-Miocene and rapid abiotic climatic niche evolution in
 explaining a burst in diversification rate in Merianieae. Within Andean
 habitats, later disparification in floral trait space allowed for the
 exploitation of wider pollination niches (i.e., shifts from bee to
 vertebrate pollinators), but did not affect diversification rates. Our
 approach of including both vegetative and floral trait evolution, rare in
 assessments of plant diversification in general, highlights important
 pre-adaptations to mountain colonization, specifically woody habit and
 larger flowers. Overall, and in concert with the idea that ecological
 opportunity is a key element of evolutionary radiations, our results
 suggest that a combination of rapid niche evolution and pre-adapted traits
 were critical for the exploitation of newly available niche space in the
 Andes in the mid-Miocene. Further, our results emphasize the importance of
 incorporating both abiotic and biotic factors into the same analytical
 framework if we aim to quantify the relative and interlinked effects of
 these processes on diversification.
description: phylogenetic hypothesis for Merianieae stems from Reginato et al.
 2022 (https://doi.org/10.1007/978-3-030-99742-7_4) and was pruned to 139 species for which we could score floral trait data floral trait data stems from Dellinger et al. 2021 (https://doi.org/10.1111/nph.17390) vegetative trait data (growth form, leaf area, leaf thickness, leaf margin) was collected for this study from herbarium specimens and descriptions climatic niche data was collected by extracting bioclimatic variables (from Chelsa v2) at carefully pruned gbif occurrence records all analyses are based on these four basic datasets; for several phylogenetic analyses, we used scores from morphospace analyses and diversification estimates, all of which can be obtained through the R scripts we have provided on Zenodo the only other software you will need if you want to obtain initial diversification rates for Merianieae (which we have provided as .csv which you can readily open in R) is BAMM, which you will need to run through your computer's command line as specified here: http://bamm-project.org/
description: Applications needed to run the scripts: RStudio/R
description: DATASETS AND CODES FOR DELLINGER ET AL. MERIANIEAE DIVERSIFICATION updated
 08/31/2023: Please note that we have organized the R scripts and
 corresponding source files in separate folders to facilitate the process
 of re-analyses; some of these include datasets that you can produce
 yourself from the initial datasets provided on Dryad; we here first
 describe the initial datasets provided, and then list the files you will
 find in the different folders on Zenodo that will allow you to run the
 analyses Please refer to our extensive Supplementary Information for
 details on the analyses, justfications for parameter choices and further
 explanations on the different factor levels included in the vegetative and
 floral trait datasets. DATASETS ON DRYAD floraltraits.csv vegtraits.csv
 meri139\_extracted.csv Marcelo\_meris.tre VARIABLES IN DATASETS ON DRYAD
 Meri139\_extracted.csv: r: row names, matching tip labels on the phylogeny
 species: species names long: median decimal longitude of occurrence lat:
 median decimal latitude of occurrence elevation: median elevation of
 species b1: bioclim variable 1 b2: bioclim variable 2 b3: bioclim variable
 3 b4: bioclim variable 4 b5: bioclim variable 5 b6: bioclim variable 6 b7:
 bioclim variable 7 b8: bioclim variable 8 b9: bioclim variable 9 b10:
 bioclim variable 10 b11: bioclim variable 11 b12: bioclim variable 12 b13:
 bioclim variable 13 b14: bioclim variable 14 b15: bioclim variable 15 b16:
 bioclim variable 16 b17: bioclim variable 17 b18: bioclim variable 18 b19:
 bioclim variable 19 n: N-content of soil tc: cloud cover x: species names
 matching phylogeny vegraits.csv: (NAs in cell values mean missing data)
 species: Species names growth.form: tree/shrub/liana etc, from the
 literature and herbarium vouchers (following Schulmann & Hyvönen
 2005) blade.area: measured on 3 herbarium specimens/species using the
 software TraitEx [numeric] leaf.margin: serrate, entire, ...; from the
 literature and herbarium vouchers (following Schulmann & Hyvönen
 2005) leaf.thickness: lamina texture, from the literature and herbarium
 vouchers (following Schulmann & Hyvönen 2005, but extended)
 floraltraits.csv: for detailed descriptions of characters and criteria for
 trait classification see Dellinger et al. 2019, New Phytologist and
 Dellinger et al. 2021, New Phytologist, (NAs in cell values mean missing
 data) species: Species names x: tip labels from phylogeny
 confirmed.pollinator: pollinators when empirically documented
 estimated\_pollinator: pollinators as estimated through Random Forest
 analyses in Dellinger et al. 2021, New Phytologist confirmed.reward.type:
 reward type, evaluated on fresh flowers in the field and ethanol-preserved
 material pollen.expulsion: Pollen expulsion mechanism - evaluated on fresh
 flowers in the field and ethanol-preserved material
 positioning.of.info.flower: Inflorescence extended from foliage or not?
 orientation.of.flower: Orientation of flowers in inflorescence - evaluated
 on photos and herbarium specimens and considering the majority of flowers
 petal.lenth..mm.: Petal length – numeric (mm). measured from the base of
 the petal to the tip corolla.shape: Corolla shape (bowl shaped, open,
 reflexed, ....) – assessed at mid-anthesis (thus excluding opening buds
 (which at first will all resemble cupule/funnel shapes) and senescent
 flowers (which will have opened more in certain species)). evaluated on
 photos. ethanol-preserved material and herbarium vouchers corolla.colour:
 Corolla colour - evaluated on photos. in the field. and derived from
 species descriptions and herbarium labels corolla.contrast.stamens:
 Contrast between petal color and stamen color (as assessed through human
 eye) stamen.shape.dimorphism: evaluated on photos, ethanol-preserved
 material, drawings, species descriptions and herbarium vouchers
 level.of.anther.pore: height of the anther pores relative to the style
 length, evaluated on ethanol-preserved material, photos and herbarium
 vouchers stamen.secondary.dorsal.appendage: evaluated on ethanol-preserved
 material. herbarium vouchers. drawings and species descriptions
 stamen.appendage.shape: Shape of primary stamen appendage (e.g., bulbous,
 crown shaped, ...)– evaluated on ethanol-preserved material, herbarium
 vouchers, drawings and species descriptions
 stamen.location.of.connection.thecae.connective: Location of thecae on
 connective – evaluated on ethanol-preserved material, herbarium vouchers,
 drawings and species descriptions stamen.location.of.thecal.end: whether
 thecal end is offset or not stamen.anther.shape: evaluated on
 ethanol-preserved material. herbarium vouchers, drawings and species
 descriptions recurving.of.anther..abaxial.adaxial: evaluated on
 ethanol-preserved material. herbarium vouchers, drawings and species
 descriptions stamen.adaxial.thecal.wall: thecal wall structure (smooth,
 ruminate, crumpled), evaluated on ethanol-preserved material, herbarium
 vouchers, drawings and species descriptions stamen.number.of.pores:
 numeric stamen.location.of.pore: apical/ventral/dorsal – evaluated on
 ethanol-preserved material, herbarium vouchers, drawings and species
 descriptions stamen.colour.appendage: colour of stamen appendage
 stamen.contrast.app.thec: colour contrast between stamen appendages and
 thecae gynoecium.relation.style.corolla: Relative position of stigma and
 corolla (flower viewed from the side) – evaluated on ethanol-preserved
 material. herbarium vouchers. drawings and species descriptions
 gynoecium.style.curvature.new: Style curvature – evaluated on
 ethanol-preserved material, herbarium vouchers, drawings and species
 descriptions <br> FOLDERS ON ZENODO FOR ANALYSES
 1\_morphospaces\_disparity.R - Datasets & skripts floraltraits.csv
 - floral traits for 139 Merianieae species vegtraits.csv - vegetative
 traits for 139 Merianieae species Meri139\_extracted.csv - bioclimatic
 variables for 139 Merianieae species Marcelo\_meris.tre - molecular
 phylogenetic hypothesis for Merianieae, extracted from Reginato et al.
 2022 1\_morphospaces\_disparity.R - Climatic, vegetative and floral space
 analyses, calculations of disparity and calculations of disparity through
 time 2\_biogeo - Datasets & skripts biogeo.data - data of
 Merianieae species with biogeographic areas dispersal\_matrix.txt -
 dispersal matrix for Merianieae Marcelo\_Meris.tre - phylogeny
 timeperiods.txt - time periods for time-stratified analyses biogeobears.R
 - skript for biogeogbears models and model comparison nicer\_plot.R -
 nicer plot for the large number of species 3\_paleoenvironmental\_BD -
 skripts Diversification analyses\_consensus.R - script adapted for
 Merianieae from Boschman & Condamine 2022 - the source files and
 paleoenvironmental data used are available in their publication
 4\_BAMM\_DR\_ClaDS - skripts ClaDS.R - script for estimating
 species-specific diversification rates using ClaDS2 DR\_statistic.R -
 script for estimating the DR statistic BAMM.txt - script for estimating
 diversification rate shifts through BAMM in bamm (through the command
 line) BAMM\_postprocess.R - script for processing BAMM run, assessing
 convergence of MCMC chain and plotting results 5\_OU\_models PCflor.csv -
 PC values of floral morphospace vegPC12.csv - PC values of vegetative
 morphospace Meri139\_clim13.csv - PC values of climatic niche space
 OUestimation.R - script for running OU models without an a-priori
 hypothesis on trait evolution, and testing three specific hypotheses
 6\_PhyloRidgeRegression PCflor.csv - values from floral morphospace (axes
 1-3) vegPC12.csv - values from vegetative morphospace Meri139\_clim13.csv
 - values from climatic morphospace RidgeRegression.R - script for
 calculation of evolutionary rate of the different trait spaces
 7\_PhylogeneticPathAnalyses pathdata.csv - dataset including the ClaDS2
 speciation rates, rates of climtaic, vegetative and floral niche
 evolution, as well as biogeographic background and clade ages
 DR\_rates.csv - rates from DR statistic bamm\_rates.csv - rates from BAMM
 PPA\_03.R - script for setting up and running phylogenetic path analyses