Caitlin Cherryh

March 2024

This github repository contains scripts used to:

1. Estimate trees from 14 empirical phylogenetic datasets with 26 models of substitution
2. Estimate constrained trees for 5 alternate topologies of the Metazoan tree
3. Apply the MAST model to evaluate a multi-tree model for the Metazoan taxa

If you replicate any part of these analyses or use functions from these scripts, please cite this repository.

• Scripts
  • All scripts necessary to completely replicate this analysis are included in the code/ folder
  • Each script includes an overview, a list of necessary parameters or file paths, and a list of software necessary to run that script
• Output
  • Contains output .csv files generated throughout the project
    • Cherryh_MAST_metazoa_taxa_collation.csv: table of the name and clade of each species in each dataset
    • alignment_dimensions.csv: number of sites and taxa in each alignment
• Trees
  • Maximum Likelihood trees
    • Contains all 364 trees generated throughout this process (14 datasets, 26 models of substitution)
  • Hypothesis trees
    • Constrained maximum likelihood trees
• Taxa reconciliation
  • Table used to make taxa names consistent across datasets
• Conda enviroment
  • The environment.yml file is included to replicate the conda environment used for this project

1. Download and install the software programs necessary to repeat these analyses:
   • IQ-Tree2
2. Estimate trees
   • Estimate maximum likelihood trees with standard IQ-Tree protein models and profile mixture (PM) models in IQ-Tree using the script 01_estimate_all_trees_parallel.R
   • Estimate trees with the posterior mean site frequency (PMSF) in IQ-Tree using the script 01_estimate_PMSF_trees.R
   • To rename tips in all trees to be consistent across datasets, use the script util_tree_processing.R
3. Estimate constrained trees using the best models of evolution in each class using the script 02_estimate_hypothesis_trees.R
4. Apply the mixture of trees model using the script 03_TreeMixtures.R
5. Format output csvs using the script 04_reformat_output_dataframes.R
6. Plot results using the scripts 05_plots.R and 05_plots_5trees.R

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• Borowiec, M.L., Lee, E.K., Chiu, J.C., Plachetzki, D.C., 2015. Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa. BMC Genomics 16, 987. https://doi.org/10.1186/s12864-015-2146-4

• Chang, E.S., Neuhof, M., Rubinstein, N.D., Diamant, A., Philippe, H., Huchon, D., Cartwright, P., 2015. Genomic insights into the evolutionary origin of Myxozoa within Cnidaria. Proceedings of the National Academy of Sciences 112, 14912. https://doi.org/10.1073/pnas.1511468112

• Dunn, C.W., Hejnol, A., Matus, D.Q., Pang, K., Browne, W.E., Smith, S.A., Seaver, E., Rouse, G.W., Obst, M., Edgecombe, G.D., Sørensen, M.V., Haddock, S.H.D., Schmidt-Rhaesa, A., Okusu, A., Kristensen, R.M., Wheeler, W.C., Martindale, M.Q., Giribet, G., 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452, 745–749. https://doi.org/10.1038/nature06614

• Feuda, R., Dohrmann, M., Pett, W., Philippe, H., Rota-Stabelli, O., Lartillot, N., Wörheide, G., Pisani, D., 2017. Data repository for “Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals.” https://doi.org/10.1016/j.cub.2017.11.008

• Laumer, C.E., Fernández, R., Lemer, S., Combosch, D., Kocot, K.M., Riesgo, A., Andrade, S.C.S., Sterrer, W., Sørensen, M.V., Giribet, G., 2019a. Revisiting metazoan phylogeny with genomic sampling of all phyla. Proceedings of the Royal Society B: Biological Sciences 286, 20190831. https://doi.org/10.1098/rspb.2019.0831

• Laumer, C.E., Fernández, R., Lemer, S., Combosch, D., Kocot, K.M., Riesgo, A., Andrade, S.C.S., Sterrer, W., Sørensen, M.V., Giribet, G., 2019b. Data from: Revisiting metazoan phylogeny with genomic sampling of all phyla. https://doi.org/10.5061/DRYAD.293KP3D

• Laumer, C.E., Gruber-Vodicka, H., Hadfield, M.G., Pearse, V.B., Riesgo, A., Marioni, J.C., Giribet, G., 2018a. Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias. eLife 7, e36278. https://doi.org/10.7554/eLife.36278

• Laumer, C.E., Gruber-Vodicka, H., Hadfield, M.G., Pearse, V.B., Riesgo, A., Marioni, J.C., Giribet, G., 2018b. Data from: Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias. https://doi.org/10.5061/DRYAD.6CM1166

• Li, Y., Shen, X.-X., Evans, B., Dunn, C.W., Rokas, A., 2020. Data repository for “Rooting the animal tree of life.” https://doi.org/10.6084/m9.figshare.13122881.v1

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• Nosenko, T., Schreiber, F., Adamska, M., Adamski, M., Eitel, M., Hammel, J., Maldonado, M., Müller, W.E.G., Nickel, M., Schierwater, B., Vacelet, J., Wiens, M., Wörheide, G., 2013a. Deep metazoan phylogeny: when different genes tell different stories. Molecular Phylogenetics and Evolution 67, 223–233. https://doi.org/10.1016/j.ympev.2013.01.010

• Nosenko, T., Schreiber, F., Adamska, M., Adamski, M., Eitel, M., Hammel, J., Maldonado, M., Müller, W.E.G., Nickel, M., Schierwater, B., Vacelet, J., Wiens, M., Wörheide, G., 2013b. Additional data to: Deep metazoan phylogeny: When different genes tell different stories. https://doi.org/10.5282/ubm/data.55

• Philippe, H., Brinkmann, H., Lavrov, D.V., Littlewood, D.T.J., Manuel, M., Wörheide, G., Baurain, D., 2011. Resolving difficult phylogenetic questions: why more sequences are not enough. PLoS Biol 9, e1000602–e1000602. https://doi.org/10.1371/journal.pbio.1000602

• Philippe, H., Derelle, R., Lopez, P., Pick, K., Borchiellini, C., Boury-Esnault, N., Vacelet, J., Renard, E., Houliston, E., Quéinnec, E., Da Silva, C., Wincker, P., Le Guyader, H., Leys, S., Jackson, D.J., Schreiber, F., Erpenbeck, D., Morgenstern, B., Wörheide, G., Manuel, M., 2009. Phylogenomics revives traditional views on deep animal relationships. Current Biology 19, 706–712. https://doi.org/10.1016/j.cub.2009.02.052

• Pick, K.S., Philippe, H., Schreiber, F., Erpenbeck, D., Jackson, D.J., Wrede, P., Wiens, M., Alié, A., Morgenstern, B., Manuel, M., Wörheide, G., 2010. Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships. Molecular Biology and Evolution 27, 1983–1987. https://doi.org/10.1093/molbev/msq089

• Redmond, A.K., McLysaght, A., 2021. FROM: Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding. https://doi.org/10.6084/m9.figshare.12746972.v2

• Ryan, J.F., Pang, K., Schnitzler, C.E., Nguyen, A.-D., Moreland, R.T., Simmons, D.K., Koch, B.J., Francis, W.R., Havlak, P., Smith, S.A., Putnam, N.H., Haddock, S.H.D., Dunn, C.W., Wolfsberg, T.G., Mullikin, J.C., Martindale, M.Q., Baxevanis, A.D., 2013. The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science 342, 1242592. https://doi.org/10.1126/science.1242592

• Whelan, N.V., Kocot, K.M., Moroz, L.L., Halanych, K.M., 2016. Error, signal, and the placement of Ctenophora sister to all other animals. v3. https://doi.org/10.6084/m9.figshare.1334306.v3

• Whelan, N.V., Kocot, K.M., Moroz, L.L., Halanych, K.M., 2015. Error, signal, and the placement of Ctenophora sister to all other animals. Proceedings of the National Academy of Sciences of the United States of America 112, 5773–5778. https://doi.org/10.1073/pnas.1503453112

• Whelan, N.V., Kocot, K.M., Moroz, T.P., Mukherjee, K., Williams, P., Paulay, G., Moroz, L.L., Halanych, K.M., 2017a. Ctenophore relationships and their placement as the sister group to all other animals. Nature Ecology & Evolution 1, 1737–1746. https://doi.org/10.1038/s41559-017-0331-3

• Whelan, N.V., Kocot, K.M., Moroz, T.P., Mukherjee, K., Williams, P., Paulay, G., Moroz, L.L., Halanych, K.M., 2017b. Ctenophora Phylogeny Datasets and Core Orthologs. Dataset. https://doi.org/10.6084/m9.figshare.4484138.v1