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metazoan-mixtures

A single tree is insufficient to describe evolutionary relationships between early animals

Caitlin Cherryh

March 2024

Summary

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.

Contents

  • 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

Instructions to reproduce the analyses:

  1. Download and install the software programs necessary to repeat these analyses:
  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

Datasets

Original Publication Repository Matrix
Dunn et al. (2008) Li et al. (2020) Dunn2008
Philippe et al. (2009) Philippe et al. (2009) Philippe_etal_superalignment
Pick et al. (2010) Li et al. (2020) Pick2010
Philippe et al. (2011) Philippe et al. (2011) UPDUNN_MB
Nosenko et al. (2013a) Nosenko et al. (2013b) nonribosomal_9187_smatrix
Nosenko et al. (2013a) Nosenko et al. (2013b) ribosomal_14615_smatrix
Ryan et al. (2013) Redmond and McLysaght (2021) REA_alignment_includingXenoturbella
Moroz et al. (2014) Li et al. (2020) ED3d
Borowiec et al. (2015) Borowiec et al. (2016) Best108
Chang et al. (2015) Feuda et al. (2017) Chang_AA
Whelan et al. (2015) Whelan et al. (2016) Dataset10
Whelan et al. (2017ba Whelan et al. (2017b) Metazoa_Choano_RCFV_strict
Laumer et al. (2018a) Laumer et al. (2018b) Tplx_phylo_d1
Laumer et al. (2019a) Laumer et al. (2019b) nonbilateria_MARE_BMGE

Citations

  • Borowiec, M.L., Lee, E.K., Chiu, J.C., Plachetzki, D.C., 2016. Data from: Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa. https://doi.org/10.5061/DRYAD.K6TQ2

  • 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

  • Moroz, L.L., Kocot, K.M., Citarella, M.R., Dosung, S., Norekian, T.P., Povolotskaya, I.S., Grigorenko, A.P., Dailey, C., Berezikov, E., Buckley, K.M., Ptitsyn, A., Reshetov, D., Mukherjee, K., Moroz, T.P., Bobkova, Y., Yu, F., Kapitonov, V.V., Jurka, J., Bobkov, Y.V., Swore, J.J., Girardo, D.O., Fodor, A., Gusev, F., Sanford, R., Bruders, R., Kittler, E., Mills, C.E., Rast, J.P., Derelle, R., Solovyev, V.V., Kondrashov, F.A., Swalla, B.J., Sweedler, J.V., Rogaev, E.I., Halanych, K.M., Kohn, A.B., 2014. The ctenophore genome and the evolutionary origins of neural systems. Nature 510, 109–114. https://doi.org/10.1038/nature13400

  • 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