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
Data files
Sep 06, 2023 version files 16.28 KB
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Marcelo_Meris.tre
8.19 KB
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README.md
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Abstract
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.
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
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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
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/
Applications needed to run the scripts: RStudio/R