This repository contains code and data associated with the study by Miller and Stroud titled "Novel Tests of the Key Innovation Hypothesis: Adhesive Toepads in Arboreal Lizards" in Systematic Biology (https://doi.org/10.1093/sysbio/syab041). We provide the R scripts to replicate the analytical pipeline and reproduce the results we present. For any questions or inquiries, please e-mail aryehmiller(at)wustl(dot)edu.
Within the "Supplemental Tables" folder:
Supplementary Table 1 (Full_Dataset_2692_TableS1.csv): The "Full" dataset comprising 2692 species with all associated data.
Supplementary Table 2 (StandardEcologyLimbed_TableS2.csv): The "Standard" dataset comprising 2360 species with all associated data.
Supplementary Table 3 (simmap_results_TableS3.csv): Stochastic character mapping results.
Supplementary Table 4 (fitPagel_TableS4.csv): Pagel's test for evolutionary correlation results across all datasets.
Supplementary Table 5 (SSE_TableS5.csv): SSE model log likelihoods and AIC values across all datasets.
Supplementary Table 6: corHMM model results across all datasets.
5644Species_SamplingFractionReference.csv: Dataset used to calculate sampling fractions for SSE models.
FullRelaxed_TraitAnalysis.csv: Table used in R pipeline for Full Relaxed dataset analysis.
FullStrict_TraitAnalysis.csv: Table used in R pipeline for Full Strict dataset analysis.
StandardRelaxed_TraitAnalysis.csv: Table used in R pipeline for Standard Relaxed dataset analysis.
StandardStrict_TraitAnalysis.csv: Table used in R pipeline for Standard Strict dataset analysis.
FullTree.tre: Full dataset tree used in analysis.
StandardTree.tre: Standard dataset tree used in analysis.
Supplement_MillerStroud2021_SystBiol.pdf: Supplementary figures document.