DOI: 10.5061/dryad.cfxpnvxfk
title: Data from: Diverging evolutionary trajectories for palm seed sizes in mainland Africa and Madagascar

description: Seed size is a trait which determines survival rates for individual plants
 and can vary as a result of numerous trade-offs. In the palm family
 (Arecaceae) today, there is great variation in seed sizes. Past studies
 attempting to establish drivers for palm seed evolution have sometimes
 yielded contradictory findings in part because modern seed size variations
 are complicated by long-term legacies, including biogeographic differences
 across lineages. Here, we examined palm seed size evolution in two
 adjacent regions (mainland Africa and Madagascar) utilizing single- and
 multi-regime Brownian Motion and Ornstein-Uhlenbeck processes. We
 explicitly take into account species’ evolutionary histories to
 investigate whether there may be shared evolutionary pressures over
 regional scales. We found that regional selection pressures do exist for
 palm seed lengths, but these pressures are distinct in mainland Africa and
 Madagascar, despite the two regions’ proximity. Our study indicates that
 evolutionary drivers may differ in these two regions, highlighting the
 importance of re-considering the widespread assumption to view mainland
 Africa and Madagascar as a single evolutionary region.
description: # Diverging evolutionary trajectories for palm seed sizes in mainland
 Africa and Madagascar
 [https://doi.org/10.5061/dryad.cfxpnvxfk](https://doi.org/10.5061/dryad.cfxpnvxfk) ## Description of the data files 1. 20_trees.RSave: Loading the RSave file into your R environment will load in a vector of integers (“run_trees”), which contains the indices for the tree topologies used in the main analysis for 20 random trees selected from Faurby et al. (2016)’s 1000-tree posterior distribution. 2. MainAnalysis_hOUwieModels.zip: These files are created as the output of running the hOUwie_models.R file. The Rsave files contain hOUwie models for each tree topology in the main analysis. These files are housed in folders corresponding to the index of the tree topology used, selected from Faurby et al. (2016)’s 1000-tree posterior distribution. All models in folders that are named “tree_#” were run hOUwie parameter values nSim = 5 and nStarts = 25. Loading the RSave files for each model will load in a houwie object (unaltered outputs from running the hOUwie() function from the OUwie package) whose variable name corresponds with the model name described in the main text Methods. We also include the models created for the sensitivity test where we tested different values of nSim and nStarts parameters on the MCC tree in the test_nSim folder. Folder names within the test_nSim folder correspond to the different combinations of nSim and nStarts values used in the sensitivity tests. 3. MainAnalysis_hOUwieOutputs.zip: These files are created as the output of running the hOUwie_results_params.R file. When loaded, the RSave files will load two variables: an avg_pars variable and a comp variable. The avg_pars variable is a data.frame object with model-averaged parameter estimates for each species (averaged by the model AICc values). This is a direct output from the getModelAvgParams() function from the OUwie package. The comp variable is a data.frame object with likelihood and AICc values for each model. The name of each RSave file corresponds to the tree topology used in the main analysis. 4. models.xlsx: summary of all models created for each tree topology. Used in hOUwie_models.R to construct parameters for hOUwie models. 5. Palm_Trait_Data.xlsx: contains fruit and seed length data for palm species in mainland Africa and Madagascar. References are listed for each fruit and seed length measurement. The trait data averages for each species are shown in the ‘Seed_Final’ and ‘Fruit_Final’ tabs. These averages were calculated using the individual rows in the ‘Mainland Africa’ and ‘Madagascar’ tabs, where each row records information on a particular species from a different reference. Blank/empty cells represent unavailable values, indicating that we were unable to find that data from that particular reference. 6. phylogenetic_signal.csv: phylogenetic signal values and associated p-values using different methods for assessing phylogenetic signal. We only look at Pagel’s lambda in the main text. Output of phylogenetic_signal_traits.R. 7. RScripts.zip: contains R scripts necessary to run analyses and create drafts of figures. 8. Supplement_hOUwieModels_species_swapped.zip: Rsave files containing hOUwie models and hOUwie outputs for the MCC tree (using parameters nSim = 100, nStarts = 25) where three species shared between the regions (*Borassus aethiopum*, *Hyphaene coriacea*, and *Raphia farinifera*) that were assigned to mainland Africa in the main text were re-assigned to Madagascar as a sensitivity test. Models were created by running the hOUwie_models.R file. They can be loaded into the R environment using the RSave files starting with “nSim100_nStarts25”, with each filename describing the model housed within that RSave file. When the RSave file is loaded, each model will load in a houwie object (unaltered output from running the hOUwie() function from the OUwie package) with a variable name corresponding with the model name described in the main text Methods. Model outputs were created by running the hOUwie_results_params.R file. They can be found in the “hOUwie_Outputs” folder, which contains an RSave file. When loaded, this file (swapped_species.Rsave) will load two variables: an avg_pars variable and a comp variable. The avg_pars variable is a data.frame object with model-averaged parameter estimates for each species (averaged by the model AICc values). This is a direct output from the getModelAvgParams() function from the OUwie package. The comp variable is a data.frame object with likelihood and AICc values for each model. These files were used to create Supplementary Figures S2-S4 and Supplementary Table S3. 9. Supplementary_Information.pdf: Supplementary Tables S1-S3 and Supplementary Figures S1-S4. ## Code/Software Files found in RScripts.zip: * Fig1A_Publication.R: plots the elevation map in Figure 1, panel A. * Fig2_Publication.R: plots the phylogeny and barplot with species’ seed lengths separately, as two different plots. These two plots are combined in Adobe Illustrator to create Figure 2. * Fig4A_Publication.R: plots the violin plot in Figure 4, panel A. * Fig4BCD_Publication.R: plots each of the panels in Figure 4, panels B, C, and D. * hOUwie_models.R: runs evolutionary models using hOUwie. Code can be edited to use a variety of different discrete and continuous models for the hOUwie models by changing the models.xlsx datasheet. Saves models that are found in the MainAnalysis_hOUwieModels.zip. * hOUwie_results_params.R: examine AICc scores and calculate parameters for different hOUwie models for each tree topology. Saves outputs that are found in the MainAnalysis_hOUwieOutputs.zip. * phylogenetic_signal_traits.R: calculate phylogenetic signal and save results for all 1000 tree topologies in Faurby et al. (2016) into phylogenetic_signal.csv file.