Data and code from: Functional traits drive speciation in tropical palms through complex interactions between genome size, adaptation and allometry
Data files
May 08, 2026 version files 1.46 MB
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README.md
5.45 KB
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RSPB-2025-3116.zip
1.45 MB
Abstract
Speciation shapes biodiversity, yet why some lineages diversify faster than others remains unclear. Theory predicts that traits promote ecological speciation through adaptation, but their evolvability (‘trait flexibility’) may be impacted by allometric and genomic constraints. Here we test this by integrating phylogenetic, trait and genome size data for palms (Arecaceae) – a large pantropical family (>2,600 species) with 167-fold variation in certain traits (e.g., fruit size) and 60-fold genome size variation. Using structural equation modelling, we test three hypotheses: trait evolution promotes speciation (H1: trait flexibility hypothesis), and, speciation and trait evolution rates are constrained by allometry (H2: allometric constraint hypothesis) and genome size (H3: large genome constraint hypothesis). We detected seven major speciation rate shifts during ~110-million-years of palm evolution. Tip-derived speciation rates increased with faster evolution in leaf size and plant height, supporting H1, whereas correlated evolution between all traits indirectly influenced speciation, supporting H2. Large genomes decreased plant height and stem diameter evolution rates, supporting H3, but the genome size-speciation association was sensitive to phylogenetic autocorrelation. Our findings illustrate how the interplay between genome size, allometry and trait evolvability affect speciation, emphasizing the importance of holistic approaches for uncovering general mechanisms driving speciation throughout the Tree of Life.
Dataset DOI: 10.5061/dryad.dz08kpscf
File: RSPB-2025-3116.zip
Description of the data and file structure
This repository contains data and scripts used in Bhadra et al. “Trait evolution drives speciation through complex interactions between genome size, adaptation and allometry” (Proceedings of the Royal Society B; DOI: 10.1098/rspb) to investigate the relationships between trait evolution, genome size, and speciation rates in palms.
Detailed methodological descriptions are provided in the Methods section of the associated publication.
This repository consists of the following folders and files:
Main folder
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Folder BAMM_speciation_rate: contains
(i) R script for BAMM analyses of speciation rate (BAMM_speciation rate.R)
(ii) Control file (PalmDiv_control.txt) to run BAMM in console
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Folder BAMM_trait_evolution_rate: contains
(i) R script for BAMM analyses for trait evolution rates (BAMM_trait_evolution_rate.R)
(ii) Trait data files FruitAL.txt (Average length of the fruit in centimeter), LeafBL.txt (Maximum length of the blade in meter), StemSH.txt (Maximum stem height in meter) and, StemSD.txt (Maximum stem diameter in centimeter). Each file has two columns - first with species name and second with the respective trait data derived from Kissling et al. (2019). Data to be used with R script.
(iii) Control files to run BAMM in console (FruitAL_control.txt, LeafBL_control.txt, StemSH_control.txt and StemSD_control.txt).
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Folder ClaDS_speciation_rate_Julia: contains
(i) Julia scripts for ClaDS speciation rates analyses (ClaDS_speciation_rate_Julia.txt)
(ii) R scripts for ClaDS speciation rates analyses (ClaDS_speciation_rate_JuliaResultAnalyses.R)
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DR_speciation_rate.R: R script to calculate DR speciation rate
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PGLS.R: R script for phylogenetic generalized least squares analyses
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SEM.R: R script for structural equation modelling
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SEM_loop.R: R script for repeated SEM analyses to test phylogenetic robustness
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Table_S2.csv: Dataset of the estimated rates of speciation and trait evolution of each species; data to be used with R script. This table presents a detailed dataset derived from our analyses, including estimates of speciation rate (in lineages per million years) using three methods: BAMM (Palm_Speciation_BAMM), ClaDS (Palm_Speciation_ClaDS) and DR (Palm_Speciation_DR), measured from the MCC phylogenetic tree. Trait evolution rates (in lineages per million years) derived using BAMM are included (FruitSize_Rate, StemDiameter_Rate, PlantHeight_Rate, LeafSize_Rate). The compiled genome size data in Gbp/1C (GenomeSize_Gbp/1C) from published resources (Pellicer and Leitch, 2020; Schley et al., 2022). Columns labelled BAMM1 to BAMM100 represent speciation rates measured from 100 constrained, posterior phylogenetic trees (Faurby et al., 2016) using BAMM. For consistency, nomenclature of Faurby et al. (2016) was used in our analyses. For taxonomic clarity, the accepted species names (Species_name_WCVP) according to the World Checklist of Vascular Plants (WCVP) are also included, along with their corresponding taxonomic status (taxon_status_WCVP). The higher order classification (Subfamily, Tribe and Genus) is also included.
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tree.nex: Phylogenetic information of palms represented as maximum clade credibility (MCC) tree derived from the published all-evidence supertree of palms (Faurby et al., 2016); data to be used with R script.
Code/software
All analyses were conducted using R (version ≥ 4.0) with the provided scripts. BAMM needs to be installed from the website (http://bamm-project.org/settingup.html) and run in console. ClaDS analyses was performed in Julia (version ≥ 1.0) and the output was subsequently processed in R. Required packages and dependencies are specified within the individual scripts. Users should set the working directory appropriately before running the scripts.
References
- Faurby S, Eiserhardt WL, Baker WJ, Svenning J-C. An all-evidence species-level supertree for the palms (Arecaceae). Molecular Phylogenetics and Evolution. 2016;100:57-69. [https://doi.org/10.1016/j.ympev.2016.03.002]
- Kissling WD, Balslev H, Baker WJ, Dransfield J, Göldel B, Lim JY, Onstein RE, Svenning J-C. PalmTraits 1.0, a species-level functional trait database of palms worldwide. Scientific Data. 2019;6(1):178. [https://doi.org/10.1038/s41597-019-0189-0]
- Pellicer J, Leitch IJ. The Plant DNA C-values database (release 7.1): An updated online repository of plant genome size data for comparative studies. New Phytologist. 2020;226(2):301-5. [https://doi.org/10.1111/nph.16261]
- Schley RJ, Pellicer J, Ge X-J, Barrett C, Bellot S, Guignard MS, Novák P, Suda J, Fraser D, Baker WJ, Dodsworth S, Macas J, Leitch AR, Leitch IJ. The ecology of palm genomes: Repeat-associated genome size expansion is constrained by aridity. New Phytologist. 2022;236(2):433-46. [https://doi.org/10.1111/nph.18323]
Contact
Sreetama Bhadra (Email: sreetama.bhadra@gmail.com)
Please refer to the Methods section of the published article.
