DOI: 10.5061/dryad.t1g1jwtbd
title: Supplementary data from: New perspectives in phylogenetic support assessment: Using the new relative contradiction index to investigate the phylogenetic controversies in Crocodylia

description: Numerous tools have been developed since the advent of phylogenetic
 methods to assess tree robustness. Identifying the degree of contradiction
 in a phylogenetic matrix, as well as the specific contribution of each
 taxon and character, is essential for estimating its reliability. In
 parsimony-based phylogenetic inferences, classically used by
 paleontologists, a phylogeny results from the interaction of all the
 characters used in the analysis. Consequently, the support initially
 provided by the characters in the matrix may differ from that after
 optimization in the final tree, severing the link between the phylogenetic
 content of the matrix and that of the final tree. Thus, all methods aimed
 at measuring support only do so indirectly, and the impact of individual
 characters or taxa can only be assessed after the analysis. Three-taxon
 analysis (3ta) is a phylogenetic method that can circumvent these issues
 by precisely measuring the support of targeted characters and/or taxa
 directly from the phylogenetic matrix. In 3ta, characters are coded as
 trees and decomposed into three-taxon state- ments (3ts). The analysis
 searches for the largest set of non-contradicting 3ts to compute the
 optimal phylogeny. Because the analysis is a compatibility procedure, not
 an optimization procedure, character supports on the tree are independent
 from one another. This enables direct assessment of support from the
 matrix, providing meaningful insights into the topology of the optimal
 trees. Moreover, the decomposition of characters into 3ts allows for
 precise quantification of the impact of the characters/taxa in the
 results. In this study, focusing on Crocodylia (a subject of ongoing
 debate over recent decades), we use 3ta to measure the support of specific
 characters and/or taxa in the recently published matrix of Rio and Mannion
 (Rio J.P., Mannion P.D. 2021. Phylogenetic analysis of a new morphological
 dataset elucidates the evolutionary history of Crocodylia and resolves the
 long-standing gharial problem. PeerJ 9:e12094). This conflict revolves
 around two competing hypotheses—Longirostres and Brevirostres—supporting a
 different placement of the Gavialoidea clade. We also introduce here the
 Relative Contradiction Index (RCI) to evaluate node support, a metric that
 reflects the degree of contradiction in a matrix between competing
 cladistic hypotheses, ranging from 0.5 (maximum contradiction) to 1 (no
 contradiction). We show that although the Longirostres hypothesis is the
 best-supported, it is strongly challenged by the Brevirostres hypothesis
 (RCI = 0.62). Furthermore, we find that Tomistominae provides 61% of the
 supporting evidence for the Longirostres hypothesis, such that, when
 removed, the matrix supports the Brevirostres hypothesis. Individual
 tomistomines’ contributions vary only from 2% to 7% of the total support
 to the Longirostres hypothesis. Finally, we show that characters
 correlated to longirostry only provide a fraction (22%) of the total
 support to the Longirostres hypothesis. Thus, our method can quantify the
 impact of specific characters or taxa on a phylogenetic result. This
 should prove very useful to phylogeneticists, especially when dealing with
 incomplete material such as fossils.
description: # New perspectives in phylogenetic support assessment: the case of
 crocodylia
 [https://doi.org/10.5061/dryad.t1g1jwtbd](https://doi.org/10.5061/dryad.t1g1jwtbd) ## Description of the data and file structure ### **Supplementary File S1a** **General information** Title: Modifications performed on the matrix from Rio & Mannion (2021) Principal investigator: Paul Aubier **Data and file overview** Description: This file specifies the modifications we performed on the original data matrix from Rio & Mannion (2021) Date of creation of the file : 2023-07-10 ### **Supplementary File S1b** **General information** Title: Polarization arguments **Data and file overview** Description: This specifies which type of argument we used to polarize each character. The first column specifies the character number in our study, the second provides the corresponding number as in Rio & Mannion (2021) study. The third column specifies the type of argument(s) that were used for the polarization of the character: Outgroup, Generality, Progressive (i.e. progressive complexification, see main text), Presence/Absence, Ontogeny and/or Following (i.e. argument n°6, see main text). The fourth column provides additional comments specifying relevant information from Rio & Mannion (2021) second Appendix. Date of creation of the file : 2025-01-28 ### **Supplementary File S1c** **General information** Title: Polarization Criteria **Data and file overview** Description: This doc file presents the different arguments that were used to polarize each character. Date of creation of the file : 2025-01-30 ### **Supplementary File S1d & S1e** **General information** Title: Phylogenetic matrices **Data and file overview** Description: This file includes the phylogenetic matrix we used. S1b includes the parsimony in a nexus format. S1c includes the three-taxon analysis matrix in a hmatrix format. Date of creation of the file : 2023-02-23 ### **Supplementary File S2** **General information** Title: R script **Data and file overview** Description: This file include the whole R script used to perform the quantification presented in the study. Date of creation of the files : 2023-10-22 ### **Supplementary File S3a** **General information** Title: Support provided by character Principal investigator: Paul Aubier **Data and file overview** Description: This file includes the support provided by each character from the matrix we used to both the Longirostres and Brevirostres hypotheses. The first column specifies the character number in our dataset, the second the corresponding character number from Rio & Mannion (2021). The last column correspond to the contradictory index. Date of creation of the files : 2023-10-21 ### **Supplementary File S3b** **General information** Title: Anatomical categories Principal investigator: Paul Aubier **Data and file overview** Description: This file specifies which characters are included in each anatomical category. The first column specifies the character number in our dataset, the second the corresponding character number from Rio & Mannion (2021). The third, fourth and fifth columns representing different degree of anatomical categorizations. The one used in the study is the last one, the broadest (Class_n+2). Date of creation of the files : 2023-06-19 ### **Supplementary File S4a** **General information** Title: Triplet matrix Principal investigator: Paul Aubier **Data and file overview** Description: This file provides the 3ts matrix, originating from the decomposition of the characters. BEWARE, the file is very large so using a .csv viewer may cause crashes. The best way I found to visualize it is to use R. Date of creation of the files : 2023-04-17 ### **Supplementary File S4b** **General information** Title: Retention Index **Data and file overview** Description: This file corresponds to the output provided by Agatta. It specifies the amount of fractional weights provided by each character as well as the fraction of it that was retained in the optimal tree (Retention Index). Date of creation of the files : 2023-02-22 ### **Supplementary File S5a-c** **General information** Title: Three-taxon analyses trees. **Data and file overview** Description: These files includes the 3ta strict consensus tree (S5a), optimal trees (S5b) and optimal tree excluding the ‘Tomistominae’ (S5c) in newick format. ### **Supplementary File S5d-g** **General information** Title: Parsimony analyses trees **Data and file overview** Description: These files includes the parsimony strict consensus tree (S5d), optimal trees (S5e), strict consensus excluding ‘Tomistominae’ (S5f) and optimal trees excluding the ‘Tomistominae’ (S5g) in newick format. ### **Supplementary File S5h** **General information**\ Title: Complete consensuses in pdf. **Data and file overview** Description: This file displays the complete consensuses in .pdf format of the parsimony including ‘Tomistominae’ as well as both 3ta and parsimony analyses strict consensuses excluding ‘Tomistominae’. Date of creation of the files : 2023-09-04 ### **Supplementary File S6** **General information** Title: Individual ‘Tomistominae’ effect **Data and file overview** Description: This file provides the support to Longirostres and Brevirostres as well as the Contradictory Index for the whole matrix after having excluding each ‘Tomistominae’ member (first three columns). This resulted contributions of each member of the group to all three of these metrics are thus also displayed (last three columns). Date of creation of the files : 2023-11-02 ### **Supplementary File S7** **General information** Title: Support provided by each anatomical category **Data and file overview** Description: This file provided the precise quantification for the support to Longirostres and Brevirostres provided by each anatomical category. It also provides the same quantifications when discarding the ‘Tomistominae’ as well as their consequent contribution. Date of creation of the files : 2023-10-22