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-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.