DOI: 10.5061/dryad.9p8cz8wr8
title: Coping with ineffective overlap in multilocus phylogenetics

description: Missing data is a long-standing issue in phylogenetic inference, which
 often results in high levels of taxonomic instability, obscuring otherwise
 well-supported relationships. Multiple approaches have been developed to
 deal with the negative effects of ineffective overlap on tree resolution,
 often by identifying taxa for removal. Here we repurpose a heuristic
 method developed to identify unstable taxa in morphological data matrices,
 concatabominations, and combine it with a novel gene-tree jackknifing on
 matrix representation of trees to identify candidates for targeted
 sequencing. Using a multilocus caecilian dataset, we illustrate the
 method's capacity to identify candidate taxa and loci for additional
 sequencing, compare the results to those of the mathematics-based gene
 sampling sufficiency approach, and explore the terrace space associated
 with the multilocus dataset. We show that our approach yields tractable
 numbers of loci/taxa for targeted sequencing that successfully mitigate
 topological instability due to ineffective overlap, even when modest
 amounts of data are added.
description: # Coping with ineffective overlap in multilocus phylogenetics
 Supplementary data for: Serra Silva, A. et al. (2025). Coping with
 Ineffective Overlap in Multilocus Phylogenetics. *In press.* Detailed
 descriptions of analyses and parameters can be found in the main document
 and its supplemental information, but all folders below include the
 scripts necessary to repeat the analyses. File extensions and naming
 conventions are shared between zipped folders and are explained below
 using the Dobrin_etal2018_CC0compliant.zip as an example. If the geneTrees
 subfolder includes subfolders named after phylogenetic inference software
 and no additional listing of files is given, then ALL file extensions
 correspond to the software's default output. ### Contents of each
 folder * Dobrin_etal2018_CC0compliant.zip: contains the analyses based on
 the datasets used in [Dobrin et
 al.](https://link.springer.com/article/10.1186/s12862-018-1162-9) (2018) *
 Each dataset subfolder has the following organisation: * Astral: has the
 input and outputs of the Astral analyses * *_localPP* - Astral output with
 branch local posterior probability * *_quartet* - Astral output with
 branch quartet scores (QS) * *_noQMs* - any branches with branch support
 QS = '?' edited to QS = '0' * *_collapsed* - branches
 with QS &lt; 0.51 collapsed * concatabominations: has the scripts to
 generate the MRs and the input to the [Concatabominations
 pipeline](https://github.com/agalychnica/Concatabominations_v5) *
 Subfolders named allLoci include all loci alignments, subfolders starting
 with 'no' do not contain the named locus (e.g., if a subfolder
 is named no16S, then that is the removed/jackknifed alignment) *
 MRP_test.py - [p4](https://github.com/pgfoster/p4-phylogenetics) script to
 generate matrix representation (MR) of splits * mrp.nex - output of
 MRP_test.py * mrpCleanUp.sh - script to convert mrp.nex into the
 Concatabominations-compatible mrp_concat.nex * mrp_concat.nex -
 concatabomination pipeline input * mrp_concat.nex.* - files output by
 concatabominations * mrp_concat.nex.html - [Safe Taxonomic
 Reduction](https://academic.oup.com/sysbio/article-abstract/44/4/501/1680423) results * mrp_concat.nex.taxonomicEqiv.sim.txt - concatabominations network (required input for [Cytoscape](https://cytoscape.org/)) * geneTrees: contains the scripts to run the [RAxML](https://academic.oup.com/bioinformatics/article/30/9/1312/238053) searches and their outputs * *RAxML.sh - script to run the RAxML tree searches * output_RAxML.zip - includes ALL intermediate output files for all loci * RAxML_bestTree.* - inferred best likelihood tree for each locus * MRP: has the input, script, and output of the MRP searches * Paup_morphoblock.nex - script to run [PAUP](https://paup.phylosolutions.com/) using mrp_concat.nex as input. All other files in this subfolder will be generated by running the PAUP script and are named therein. * seqs: contains the modified phylip data matrices; all alignments have a minimum of four taxa * For the Mammals and Primates subfolders, please email us for the ***modified*** alignment files. We cannot provide them here due to licensing constraints; any re-use of these files requires citing their original publications. * Terraphy: contains the output of the [terraphy](https://github.com/zwickl/terraphy) analyses * Astral: input, script, and output of terraphy run on the [Astral](https://github.com/smirarab/ASTRAL) tree * input - contains the rooted tree and datamatrix * preprocessing - intermediate files generated by the terraphy analyses * run_all_analyses.sh - script to run the terraphy analyses * build.tre - [BUILD](ttps://doi.org/10.1137/0210030) consensus of the [terrace](https://www.science.org/doi/10.1126/science.1206357) * parentCount - text file with the number of trees in the terrace * strict.tre - strict consensus of terrace * MRP: input, script, and output of terraphy run on the Astral tree * same subfolder and file organisation as the Terraphy/Astral folder * Gordon1986.zip: contains the terraphy analyses on [Gordon](https://link.springer.com/article/10.1007/BF01894195)'s (1986) trees * GymnoTree_2022-03-15.zip: contains the data, scripts, and outputs of the caecilian trees * Alignments: contains the unprocessed and masked gene alignments * Raw - [Mafft](https://mafft.cbrc.jp/alignment/server/index.html) alignments * GBlocks - [GBlocks](https://www.biologiaevolutiva.org/jcastresana/Gblocks.html)-masked alignments * Astral_supertrees: input and output of Astral analyses with the following organisation (used throughout all subfolders) * [MrBayes](https://academic.oup.com/bioinformatics/article/17/8/754/235132) * 16SnoHmont: *Hypogeophis montanus* present in BDNF alignment but not 16S rRNA * 16SwHmont: *Hypogeophis montanus* present in BDNF and 16S rRNA alignments * noHmont: *Hypogeophis montanus* not present in any alignment * remaining folders follow the naming convention described in the Dobrin*.zip folder listing * RAxML * 16SnoHmont: *Hypogeophis montanus* present in BDNF alignement but not 16S rRNA * 16SwHmont: *Hypogeophis montanus* present in BDNF and 16S rRNA alignments * noHmont: *Hypogeophis montanus* not present in any alignment * concatabominations: contains script to generate matrix representations (MR), processed MRs, and output of the concatabominations pipeline split into * MrBayes_geneTrees * RAxML_geneTrees * concatenatedMatrices: input, scripts, and output of analyses on concatenated matrices, split into * MrBayes_concat * RAxML_concat * geneTrees: input, scripts, and output of analyses on individual gene alignments, split into * MrBayes * RAxML * MRP_supertrees: input, scripts, and output of MRP searches * MrBayes_geneTrees * RAxML_geneTrees * pseudoData: concatabominations and terraphy results for the pseudoData analyses, organisation follows the same as main concatabominations and terraphy folders * terraphy: input, scripts, and output of terraphy analyses * Astral_supertrees * concatenatedMatrices * MRP_supertrees ### Citations If you use the datamatrices in the Dobrin_etal2018_CC0compliant.zip, we encourage you to cite the original publications. They can be found in Table 4 of the main text or in [Dobrin et al.](https://link.springer.com/article/10.1186/s12862-018-1162-9) (2018) Table 1.