Dataset DOI: 10.5061/dryad.7h44j104b

Description of the data and file structure

This README file was generated on 14-03-2025 by Erika Paez Vargas

This dataset, integral to our research paper, contains crucial data for understanding our key findings. It includes phylogenetic analysis data and results, raw data used to assess mimicry pattern evolution along with their R scripts, as well as supplementary materials and appendix data.

Files and variables

Below is a summary of the included files:

1. Phylogenetic and dating analyses

Folder: Paez_et_al_SYEN_PhylogeneticAnalyses_R1.zip

This folder contains the dataset and results of the topological tests, molecular phylogenetic and dating analyses.

• AU_test folder: the files and results to perform topological tests and ML analyses under IQ-TREE (v3.0.1).

• BEAST folder: the files to perform molecular dating analyses (using Bayesian relaxed clocks) using BEAST software package (v1.10.4), and results. 
• IQTREE - gene tree analyses folder: files to perform molecular phylogenetic analyses per gene under IQTREE ( IQ-TREE v3.0.1), and tree file results for 1 mitochondrial gene and 15 nuclear genes.
• IQTREE2 - unconstrained folder: files to perform ML analyses under IQTREE (v2.2.2.7) with all subspecies included.

2. Reconstruction of the evolution of mimicry wing colour patterns

Folder: Paez_et_al_SYEN_mimpatt_evol_datasets_R1.zip

This folder contains the raw datasets and the tree file to perform all the analyses for the mimicry pattern evolution.

• Adelpha.pattern_list.txt: raw data for the ancestral state reconstruction analysis.

• Adelpha_Adelphina_Limenitis.txt: raw data for the ancestral state reconstruction analysis (Limenitidinae).
• Adelpha_node_states.txt: raw data for the ancestral state reconstruction analysis (Adelpha + Adelphina)
• lowland_Adelpha_node_states.txt: raw data for the ancestral state reconstruction analysis (only Adelpha)
• Adelpha_phylo.nwk: phylogenetic tree used in the ancestral state reconstruction analysis.
• Adelpha_tip_data.txt: raw data for the ancestral state reconstruction analysis.
• Adelpha_macroecol_traits.txt: raw data for the macroecological traits analyses using Phylogenetic Generalized Linear Models (PGLS).
• Adelpha_tip_data_Dstat.txt: raw data for the phylogenetic signal analysis (D-statistic).
• Adelpha_traits_plgs_2024: It summarizes ecological and evolutionary traits of various species in a dataset, with each row representing a different species (e.g., A.abia, A.abyla, etc.). This can be used to explore patterns in mimicry, niche breadth, geographic distribution, and evolutionary rates across species.

3. Electronic supplementary materials

Folder: Paez_et_al_SYEN_ESM_0309

• Figure S1: Estimation of ancestral character states for mimicry colour patterns in Adelpha + Adelphina + Limenitis showed that IPHICLUS colour pattern was most likely to be the state of the common ancestor of the Neotropical limenitidines Adelpha and Adelphina species.
• Figure S2: Estimation of ancestral character states for mimicry colour patterns only in Adelpha (lowland) species showed that IPHICLUS colour pattern was most likely to be the state of the common ancestor.
• Figure S3: A comparison of tree topologies from recent molecular phylogenetic studies, simplified to clades relevant to generic classification.

• Table S1: List of sequences including Voucher and GenBank accession numbers for the sixteen gene fragments.

• Table S2: Partition scheme inferred by the Modelfinder analysis of the specimen-level dataset.
• Table S3: Results of the AU-tests carried out with IQ-TREE.
• Table S4: Results for mimicry rate evolution analyses.
• Table S5: Summary of relevant limenitidine taxa included within recent molecular phylogenetic studies, a suggested generic-level classification, type species of genera, and inferred ages of genera from the present study.

4. Appendix files

Folder: Paez_et_al_SYEN__Appendix_R1.zip

This folder contains appendix files:

• Appendix S1: Details on generation of the transcriptomic data
• Appendix S2: Explanation for the calculation of the distribution maps for Adelpha species and macroecological traits.
• Appendix S3: Macroecological traits raw dataset.;

Code/software

All mimicry pattern evolution analyses were performed using R software.

1. Programs needed:

   • BayesTraits v4.0

     Pagel, M., Meade, A., & Barker, D. (2004). Bayesian estimation of ancestral character states on phylogenies. Systematic Biology, 53(5), 673–684. https://doi.org/10.1080/10635150490522232

   • BEAST v1.10.4

     Suchard, M. A., Lemey, P., Baele, G., Ayres, D. L., Drummond, A. J., & Rambaut, A. (2018). Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evolution, 4(1), vey016.

   • Codoncode Aligner (v3.7.1.1, CodonCode Corporation, http://www.codoncode.com/)

   • IQ-TREE v2.2.2.7

     Minh, B. Q., Schmidt, H. A., Chernomor, O., Schrempf, D., Woodhams, M. D., von Haeseler, A., & Lanfear, R. (2020). IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Molecular Biology and Evolution, 37(5), 1530–1534. https://doi.org/10.1093/molbev/msaa015

   • ModelFinder

     Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A., & Jermiin, L. S. (2017). ModelFinder: fast model selection for accurate phylogenetic estimates. Nature Methods, 14(6), 587–589. https://doi.org/10.1038/nmeth.4285

   • Sequence Capture Processor (SECAPR) pipeline (http://htmlpreview.github.io/?https://github.com/AntonelliLab/seqcap_processor/blob/master/docs/documentation/main_doc.html)

   • Tracer v1.7.2

     Rambaut, A., Drummond, A. J., Xie, D., Baele, G., & Suchard, M. A. (2018). Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Systematic Biology, 67(5), 901–904. https://doi.org/10.1093/sysbio/syy032

2. Analysis Scripts:

   Folder: Paez_et_al_SYEN_scripts_pattern_evolution_R1.zip

   All anaylses were performed using R software. 

   • R-ASRPLOT_2025: Script for Ancestral State Reconstruction analyses of wing colour patterns
   • R-D_stat_2025: Script for D statistics analyses
   • R-PGLS_2025: Script for PGLS. wing colour pattern rates of evolution correlated to macroecological traits. 
   • R-TipRatesEvol_2025: Script for wing colour pattern evolution analyses 

3. Loaded packages for R scripts:

   • ade4

     Thioulouse J, Dray S, Dufour A, Siberchicot A, Jombart T, Pavoine S (2018). Multivariate Analysis of Ecological Data with ade4. Springer. doi:10.1007/978-1-4939-8850-1

   • ape

     Paradis E, Schliep K. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics. 2019;35(3):526–8.

   • caper

     Orme, D., Freckleton, R.P., Thomas, G.H., Petzoldt, T., Fritz, S. & Isaac, N. (2013) Caper: Comparative analyses of phylogenetics and evolution in R. R package version 0.5.2

   • dplyr

     Wickham H, François R, Henry L, Müller K, Vaughan D (2023). dplyr: A Grammar of Data Manipulation. R package version 1.1.4, https://CRAN.R-project.org/package=dplyr.

   • geiger

     Pennell, M. W., J. M. Eastman, G. J. Slater, J. W. Brown, J. C. Uyeda, R. G. FitzJohn, M. E. Alfaro, and L. J. Harmon {2014} geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees. Bioinformatics, 30, 2216-2218

   • ggimage

     Yu G (2023). _ggimage: Use Image in 'ggplot2'_. R package version 0.3.

   • ggplot2

     H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2016.

   • ggtree

     Guangchuang Yu. Using ggtree to visualize data on tree-like structures. Current Protocols in Bioinformatics, 2020, 69:e96. doi: 10.1002/cpbi.96

   • ggtreeExtra

     S Xu, Z Dai, P Guo, X Fu, S Liu, L Zhou, W Tang, T Feng, M Chen, L Zhan, T Wu, E Hu, Y Jiang, X Bo, G Yu. ggtreeExtra: Compact visualization of richly annotated phylogenetic data. Molecular Biology and Evolution 2021, 38(9):4039-4042. doi: 10.1093/molbev/msab166

   • MASS

     Venables, W. N. & Ripley, B. D. (2002) Modern Applied Statistics with S. Fourth Edition. Springer, New York. ISBN 0-387-95457-0

   • mvtnorm

     Genz A, Bretz F (2009). Computation of Multivariate Normal and t Probabilities, series. Lecture Notes in Statistics. Springer-Verlag, Heidelberg. ISBN 978-3-642-01688-2.

   • phangorn

     Schliep K.P. 2011. phangorn: phylogenetic analysis in R. Bioinformatics, 27(4) 592-593

   • phytools

     Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

   • picante

     S.W. Kembel, P.D. Cowan, M.R. Helmus, W.K. Cornwell, H. Morlon, D.D. Ackerly, S.P. Blomberg, and C.O. Webb. 2010. Picante: R tools for integrating phylogenies and ecology. Bioinformatics 26:1463-1464

   • RColorBrewer

     Neuwirth E (2022).  RColorBrewer: ColorBrewerpalettes. R package version 1.1-3https://CRAN.R-project.org/package=RColorBrewer

   • reshape2

     Hadley Wickham (2007). Reshaping Data with the reshape Package. Journal of Statistical Software, 21(12), 1-20. URL http://www.jstatsoft.org/v21/i12/

   • scales

     Wickham H, Pedersen T, Seidel D (2025). scales: Scale Functions for Visualization. Rpackage version 1.4.0, https://CRAN.R-project.org/package=scales.

   • tidyr

     Wickham H, Vaughan D, Girlich M (2024). tidyr: Tidy Messy Data. package version 1.3.1https://CRAN.R-project.org/package=tidyr.

   • TreePar

     Stadler T (2015). TreePar: Estimating Birth and Death Rates Based on Phylogenies. R package version 3.3

   • TreeSim

     Stadler T (2019).  TreeSim: Simulating Phylogenetic Trees. R package version 2.4. https://CRAN.R-project.org/package=TreeSim

Access information

Other publicly accessible locations of the data:

• Genbank

Data was derived from the following sources:

• NA