DOI: 10.5061/dryad.fbg79cp3s
title: Data from: PlaceMyFossils: An integrative approach to analyse and visualize the phylogenetic placement of fossils using backbone trees

description: In recent years, there has been a growing interest in using morphology to
 establish the placement of species on phylogenetic trees derived from
 molecular data. This is relevant in the case of recently extinct or fossil
 species, which are usually represented only by fragmentary morphology. In
 the latter case, constrained analyses using backbone trees have also
 proven helpful in evaluating the placement of fragmentary specimens on
 phylogenetic trees derived from morphological data. Consequently, several
 available phylogenetic programs now include functions to run constrained
 searches. However, a comprehensive evaluation of the results obtained is
 not readily available within existing analytical tools. Here, we present
 an integrated approach—PlaceMyFossils—specifically designed to (1)
 thoroughly evaluate the phylogenetic placement of given query species
 (especially fossils) on a reference tree, (2) determine which characters
 and character partitions are most relevant in defining the phylogenetic
 placement, (3) assess the confidence of the results, and (4) define the
 optimal analytical conditions to place the query species. PlaceMyFossils
 combines several analyses implemented as an interactive script for TNT
 (Tree Analysis Using New Technologies software), a popular—and
 free—phylogenetic software that is widely used in paleontological studies.
 Finally, we demonstrate the utility and investigate the performance of
 PlaceMyFossils as compared with other available tools using two disparate
 empirical datasets drawn from conifers and dinosaurs. While primarily
 designed for working with fossils, this tool also holds great potential
 for advancing morphological and molecular systematics. It offers a
 powerful resource for empirical systematists aiming to integrate molecular
 and morphological data. This is particularly relevant given the growing
 interest in morphological evolution as a complementary perspective on
 evolutionary processes and the drivers of diversification.
description: # PlaceMyFossils: An integrative approach to analyse and visualize the
 phylogenetic placement of fossils using backbone trees
 [https://doi.org/10.5061/dryad.rjdfn2zn2](https://doi.org/10.5061/dryad.rjdfn2zn2) ## **Description of the Data and File Structure** The submission includes the datasets (matrices and reference trees) used in the two empirical examples shown in the main text. **Files and Variables** **Description:** This folder contains the datasets required to run the two empirical analyses described in the main text. Phylogenetic matrices and trees are provided in different formats suitable for analyses in **TNT**, **RAxML**, and **MrBayes**. --- **Araucariaceae_example** The folder **"Datasets"** includes three phylogenetic matrices used for the Araucariaceae example presented in the main text. * The file **Araucariaceae_extant_plus_Agathis_immortalis.tnt** contains a matrix in **TNT** format, used in the analyses shown in Figures 3 and 4 of the main text. * The file **Araucariaceae_extant_plus_fossils.tnt** includes a TNT matrix where additional fossil species **were** incorporated. The results of this analysis are presented in the Supplementary Results. * The file **Araucariaceae_extant_plus_Agathis_immortalis-miss.rax**, in **PHYLIP** format, was used to run the **EPA** analysis in **RAxML**. The folder **"ReferenceTrees"** includes the trees used as scaffolds for the **PlaceMyFossils** and **EPA** analyses. * The file **Araucariaceae.tre** contains the reference tree used in the PlaceMyFossils analyses. * The file **Araucariaceae.nex**, in **NEXUS** format, contains the tree used in the EPA analysis with RAxML. The file **RAxML_EPA_commands.txt** contains the command line used to run the EPA analysis in RAxML. --- **Dinosaur_example** The folder **"Datasets"** includes four phylogenetic matrices used in the Dinosaur example described in the main text. * The file **dinosaur_reduced_dataset.tnt** contains a TNT matrix used in the analyses shown in Figure 5. The taxon sampling corresponds to a **maximum agreement subtree** obtained from all most parsimonious trees inferred from the complete dataset (**dinosaur_complete_dataset.tnt**). * The file **dinosaur_reduced_dataset.rax**, in PHYLIP format, was used for the EPA analysis in RAxML. * The file **dinosaur.nex**, in NEXUS format, was used for the **Bayesian/RoguePlots** analysis. The folder **"Reference_Trees"** includes the trees used as scaffolds in the various analyses. * The file **agreement_subtree.tre** contains the tree shown in Figure 5. * The file **agreement_subtree_rax.tre** was used for the EPA analysis in RAxML. * The file **1000mpts.tre** includes 1000 most parsimonious trees obtained from **dinosaur_complete_dataset.tnt**. These trees were used to calculate the agreement subtree included in **agreement_subtree.tre**, and also to run PlaceMyFossils analyses using multiple reference trees. * The folder **"Individual_parsimony_optimal_trees"** contains ten optimal trees used to repeat the PlaceMyFossils analysis, using each tree as a separate reference. The corresponding results are included as Supplementary Material. * The file **Dinos_red.nex.t** includes the trees obtained in MrBayes, that were *a posteriori* used as input data for running the **RoguePlots_commands.r** *R* script.  The file **MrBayes_commands.nex** includes the instructions to run the Dinosaur dataset in MrBayes. The resulting trees were processed using the script **RoguePlots_commands.r** to generate the RoguePlots analysis. The file **RAxML_EPA_commands.txt** also includes the instructions to run the EPA analysis in RAxML. #### File: Supplementary\_Results1.zip **Description:** This file includes all the supplementary results for the Araucariaceae example. The information is organized in subfoulders according to the following order:  ``` 1. Placement of Agathis immortalis 1.1. Extant_species_plus_Agathis_immortalis 1.1.1. Error_analysis 1.1.2. Implied_weighing_Leave_one_out_validation_analysis (Selection of concavity value ) 1.1.3. Maximum Likelihood analysis -excluding continuous characters (RAxML-EPA) 1.1.4. Maximum Likelihood analysis -excluding continuous characters (PlaceMyFossils) 1.2. Analysis_with_more_fossils 2. Error analysis complete character sampling. (This analysis differs from the previous error in placement analysis where the character sampling to calculate the EP, ISE and OSE values was that of Agathis_immortalis (see main text for details). ``` #### File: Supplementary\_Results2.zip This file includes all the supplementary results for the Dinosaur example. The information is organized in subfolders according to the following order:  1.Placement of Nyasasaurus ``` Two different datasets were run in the Dinosaur example to evaluate the placement of Nyasaurus. One dataset included all the species from the original dataset (dinosaur_dataset.tnt). In this case two different set of reference topologies were considered (1) Ten different most parsimonious trees (named as Mpt_N.tre), with Nyasasaurus as the single query species. 2-. An agreement subtree (agreement_dinosaur.tre) as reference, with all the species pruned when calculating the agreement added to the query list. A second dataset with a reduced taxon sampling was also run. In this case the taxon sampling included only the species present in the agreement subtree (dinosaur_reduced_dataset.tnt), the reference tree was the agreement subtree and the Nyasasaurus was the unique query species. All the data to run the analysis is included in the folder “Datasets_and_trees”. The files and folders are ordered as follow: Fig_1SR1: Flowchart_Nyasasaurus_Analyses.docx 1.1. Query_placement: 1.1.1. Maximum Likelihood analysis (PlaceMyFossils) 1.1.2. Maximum Likelihood analysis (RAxML-EPA) 1.1.3. Implied Weighting analysis (PlaceMyFossils) 1.1.3.1. Sensitivity Analysis 1.1.3.1.1 Most Parsimonious trees as reference 1.1.3.1.2 Agreement subtree as reference, Nyasasurus as single query species 1.1.3.2. Concavity value (k) = 6 1.1.3.2.1 Most Parsimonious trees as reference 1.1.3.2.2 Agreement subtree as reference, Nyasasurus as single query species 1.1.4. Maximum Parsimony analysis (PlaceMyFossils) 1.1.4.1. Most Parsimonious trees as reference 1.1.4.2. Agreement subtree as reference, Nyasasurus as single query species 1.1.4.3. Agreement subtree as reference, punned species as query species, Nyasasurus as target species 1.2. Partition_character_analyses: 1.2.1 Maximum Likelihood analysis 1.2.2. Implied Weighting analysis 1.2.3. Maximum Parsimony analysis 1.3-. Multiple_trees_analyses 1.3.1. Modifying_reference_topologies 1.3.1.1. Maximum Parsimony analysis (PlaceMyFossils) 1.3.1.2. Bayesian Analysis + rogue.plot (MrBayes + rogue.plot R package ) 1.3.2. Not_modifying_reference_topologies (MP) 1.4. Error_analyses_sampling_Nyasasaurus 1.4.1 Error_analysis_implied_weighting 1.4.2. Error_analysis_maximum_parsimony 2. Error analysis complete character sampling (This analysis differs from the previous error in placement analyses (1.4) where the character sampling to calculate the EP, ISE and OSE values was that of Nyasasuarus (see main text for details). The reference trees in this case were the 10 most parsimonious trees and the agreement subtree.) 2.1. Implied_weighting 2.2. Maximum_parsimony Fig_2SR1: Regression_Nchars_EP.docx ``` ## Code/software The code of the script described in this contribution (PlaceMyFossils) is included in this submission. It can also be downloaded from [https://github.com/sacatalano/PlaceMyFossils,](https://github.com/sacatalano/PlaceMyFossils) where it will be periodically updated. The script should be run in TNT (Tree Analysis Using New Technologies; Goloboff & Morales 2023). It is important to run the script in the latest version available at [https://www.lillo.org.ar/phylogeny/tnt/](https://www.lillo.org.ar/phylogeny/tnt/). PlaceMyFossils can be run in Windows, Mac and Linux operating systems. In all cases, the TNT dialog version should be used.   ## Access information Other publicly accessible locations of the data: * [https://github.com/sacatalano/PlaceMyFossils](https://github.com/sacatalano/PlaceMyFossils)