Data sets for phylogenomic analyses in: Ant backbone phylogeny resolved by modelling compositional heterogeneity among sites in genomic data

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-..., , , 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).、

* ...