DOI: 10.5061/dryad.pk0p2ngsj
title: Data sets for phylogenomic analyses in: Ant backbone phylogeny resolved by modelling compositional heterogeneity among sites in genomic data

description: Ants are the most ubiquitous and ecologically dominant arthropods on
 Earth, and understanding their phylogeny is crucial for deciphering their
 character evolution, species diversification, and biogeography. Although
 recent genomic data have shown promise in clarifying intrafamilial
 relationships across the tree of ants, inconsistencies between molecular
 datasets have also emerged. Here I re-examine the most comprehensive
 published Sanger-sequencing and genome-scale datasets of ants using model
 comparison methods that model among-site compositional heterogeneity to
 understand the sources of conflict in phylogenetic studies. My results
 under the best-fitting model, selected on the basis of Bayesian
 cross-validation and posterior predictive model checking, identify
 contentious nodes in ant phylogeny whose resolution is
 modelling-dependent. I show that the Bayesian infinite mixture CAT model
 outperforms empirical finite mixture models (C20, C40 and C60) and that,
 under the best-fitting CAT-GTR+G4 model, the enigmatic Martialis heureka
 is sister to all ants except Leptanillinae, rejecting the more popular
 hypothesis supported under worse-fitting models, that place it as sister
 to Leptanillinae. These analyses resolve a lasting controversy in ant
 phylogeny and highlight the significance of model comparison and adequate
 modelling of among-site compositional heterogeneity in reconstructing the
 deep phylogeny of insects.
description: This Readme file summarizes the resultant files of my phylogenetic
 analyses deposited in the DRYAD repository of the paper: Cai, C., 2024.
 Ant backbone phylogeny resolved by modelling compositional heterogeneity
 among sites in genomic data. Communications Biology. The results of my
 phylogenetic analyses are listed in two root folders, corresponding to the
 two previously published studies: Borowiec et al. (2019) and Romiguier et
 al. (2022). 1-Borowiec et al. 2019: This folder includes four folders,
 showing results based on four datasets of Borowiec et al. (2019) under the
 site-heterogeneous CAT-GTR+G4 model in PhyloBayes.
 1-Full_data_set_unconstrained-7451 NT sites: Full 11-gene matrix (123
 taxa, 7,451 nucleotide [NT] sites). * D1-bpcomp.bpdiff: bpdiff result
 using the bpcomp tool in PhyloBayes * D1-bpcomp.con.tre: consensus tree of
 the PhyloBayes analysis 2-AT-rich_outgr_removed-7451 NT sites: Full matrix
 with the most AT-rich outgroups excluded (117 taxa, 7,451 NT sites).、 *
 D2-bpcomp.bpdiff: bpdiff result using the bpcomp tool in PhyloBayes *
 D2-bpcomp.con.tre: consensus tree of the PhyloBayes analysis
 3-GC-rich_outgr_removed-7451 NT sites: Full matrix with the most GC-rich
 outgroups excluded (117 taxa, 7,451 NT sites) * D3-bpcomp.bpdiff: bpdiff
 result using the bpcomp tool in PhyloBayes * D3-bpcomp.con.tre: consensus
 tree of the PhyloBayes analysis 4-Homogeneous-3995 NT sites: Homogeneous
 matrix with heterogeneous partitions removed (123 taxa, 3,995 NT sites). *
 D4-bpcomp.bpdiff: bpdiff result using the bpcomp tool in PhyloBayes *
 D4-bpcomp.con.tre: consensus tree of the PhyloBayes analysis 2-Romiguier
 et al. 2022: This folder includes five folders, showing results based on
 four filtered supermatrices of Romiguier et al. (2022) under the
 site-heterogeneous CAT-GTR+G4 model in PhyloBayes, as well as the simpler
 LG4X+R, LG+C20, C40 and C60 models in IQ-TREE. Results of the model
 comparison and posterior predictive model checking analyses using
 PhyloBayes are also listed. 1-Matrix 1: it includes phylogenomic results
 based on Matrix 1 (in phy. format) under three evolutionary models. Models
 used in the analyses are incorprated in the folder names. * Matrix 1.phy:
 with 38 taxa and 647114 amino acid sites * 1-iqtree-LG4X+R: resultant
 files under the LG4X+R model * antc1.phy.contree: consensus tree generated
 by the IQ-TREE analysis * antc1.phy.log: log file for the IQ-TREE analysis
 2-iqtree-LG+C20: resultant files under the LG+C20 model *
 c20-antc1.phy.contree: consensus tree generated by the IQ-TREE analysis *
 c20-antc1.phy.log: log file for the IQ-TREE analysis *
 3-phylobayes-CAT+GTR: resultant files under the CAT-GTR+G model *
 m1-bpcomp.bpdiff: bpdiff result using the bpcomp tool in PhyloBayes *
 m1-bpcomp.con.tre: consensus tree of the PhyloBayes analysis 2-Matrix 2:
 it includes phylogenomic results based on Matrix 2 under three
 evolutionary models. Models used in the analyses are incorprated in the
 folder names. * Matrix 2.phy: with 47 taxa and 623908 amino acid sites
 1-iqtree-ant-wasp-LG4X+R: resultant files under the LG4X+R model *
 antw6205.phy.contree: consensus tree generated by the IQ-TREE analysis *
 antw6205.phy.log: log file for the IQ-TREE analysis
 2-iqtree-ant-wasp-LG+C20: resultant files under the LG+C20 model *
 antw6205.phy.contree: consensus tree generated by the IQ-TREE analysis *
 antw6205.phy.log: log file for the IQ-TREE analysis
 3-phylobayes-ant-wasp-CAT+GTR: resultant files under the CAT-GTR+G model *
 m2-bpcomp.bpdiff: bpdiff result using the bpcomp tool in PhyloBayes *
 m2-bpcomp.con.tre: consensus tree of the PhyloBayes analysis 3-Matrix 3:
 it includes phylogenomic results based on Matrix 3 under five evolutionary
 models. Models used in the analyses are incorprated in the folder names. *
 Matrix 3.phy: with 47 taxa and 983951 amino acid sites 1-iqtree-LG+F+G4:
 resultant files under the LG+F+G4 model * antw15.phy.contree: consensus
 tree generated by the IQ-TREE analysis * antw15.phy.log: log file for the
 IQ-TREE analysis 2-iqtree-LG+C20: resultant files under the LG+C20 model *
 antw15.phy.contree: consensus tree generated by the IQ-TREE analysis *
 antw15.phy.log: log file for the IQ-TREE analysis 3-iqtree-LG+C40:
 resultant files under the LG+C40 model * antw15.phy.contree: consensus
 tree generated by the IQ-TREE analysis * antw15.phy.log: log file for the
 IQ-TREE analysis 4-iqtree-LG+C60: resultant files under the LG+C60 model *
 antw15.phy.contree: consensus tree generated by the IQ-TREE analysis *
 antw15.phy.log: log file for the IQ-TREE analysis 5-phylobayes-CAT-GTR:
 resultant files under the CAT-GTR+G model * m3-bpcomp.bpdiff: bpdiff
 result using the bpcomp tool in PhyloBayes * m3-bpcomp.con.tre: consensus
 tree of the PhyloBayes analysis 4-Matrix 4: it includes phylogenomic
 results based on Matrix 4 under three evolutionary models. Models used in
 the analyses are incorprated in the folder names. * Matrix 4.phy: with 17
 taxa and 1692050 amino acid sites 1-iqtree-LG4X+R: resultant files under
 the LG4X+R model * ant2.phy.contree: consensus tree generated by the
 IQ-TREE analysis * ant2.phy.log: log file for the IQ-TREE
 analysis 2-iqtree-LG+C20: resultant files under the LG+C20 model *
 ant2.phy.contree: consensus tree generated by the IQ-TREE analysis
 * ant2.phy.log: log file for the IQ-TREE analysis
 3-phylobayes-CAT+GTR: resultant files under the CAT-GTR+G model *
 m4-bpcomp.bpdiff: bpdiff result using the bpcomp tool in PhyloBayes *
 m4-bpcomp.con.tre: consensus tree of the PhyloBayes analysis 5-Matrix 5:
 it includes phylogenomic results based on Matrix 5 under three
 evolutionary models. Models used in the analyses are incorprated in the
 folder names. * Matrix 5.phy: with 82 taxa and 21902 amino acid sites
 1-iqtree-LG4X+R: resultant files under the LG4X+R model *
 ant0203.phy.contree: consensus tree generated by the IQ-TREE analysis *
 ant0203.phy.log: log file for the IQ-TREE analysis 2-iqtree-LG+C20:
 resultant files under the LG+C20 model * ant0203.phy.contree: consensus
 tree generated by the IQ-TREE analysis * ant0203.phy.log: log file for the
 IQ-TREE analysis 3-iqtree-GHOST: resultant files under the GHOST model *
 ant0203.phy.contree: consensus tree generated by the IQ-TREE analysis *
 ant0203.phy.log: log file for the IQ-TREE analysis 4-phylobayes-CAT+GTR:
 resultant files under the CAT-GTR+G model * m5-bpcomp.bpdiff: bpdiff
 result using the bpcomp tool in PhyloBayes * m5-bpcomp.con.tre: consensus
 tree of the PhyloBayes analysis 6-model comparison and posterior
 predictive model checking: It contains two folders detailed as follows;
 all analyses were based on the comparative small Matrix 3. * 1-model test:
 Two efficient and reliable approaches, the leave-one-out cross-validation
 (LOO-CV) and the widely applicable information criterion (wAIC), were
 used. This folder contains the input and outfiles of the model test
 analyses: data.phy: the tested dataset, Matrix 3; this file was also used
 for the Posterior predictive model checking analysis below tree.tre: the
 contree file of the Phylobayes analyses; this file was also used for the
 Posterior predictive model checking analysis below result of model
 test.txt: the debiased scores under five tested models: LG+F+G,
 LG+C20+F+G, LG+C40+F+G, LG+C60+F+G, and CAT-GTR+G * 2-Posterior predictive
 model checking: this folder contains one file resulted from the analyses
 of Matrix 3 Posterior predictive analyses.xlsx: results for the tested
 models, including LG+F+G, LG+C20+F+G, LG+C40+F+G, LG+C60+F+G, and
 CAT-GTR+G