Conflict in ant phylogeny results from complex interaction between multiple evolutionary signals and tree reconstruction artifacts.

Ants, Formicidae, are a group of small social insects that inhabit nearly all terrestrial environments. Three competing hypotheses of ant relationships have been proposed, differing in the placement of Martialinae, a subfamily of cryptic, endogean ants. We used BUSCO genes to investigate the signals in individual and concatenated gene datasets. We found that gene trees support all three hypotheses. After concatenation, the three signals persist but their relative strength is model-dependent. The CAT-posterior mean site frequencies approach (which our model adequacy tests show best explains the across-site compositional heterogeneity of the data) finds Martialinae as the sister of all ants but Leptanillinae. We tested the effect of across-lineage compositional heterogeneity using data-recoding and excluding highly heterogeneous taxa. These tests did not lead to the emergence of significant support for alternative tree topologies. However, we identified strong gene- and site-discordance in the data and evidence that signals representing incongruent evolutionary processes exist in ant genomes supporting all three hypotheses. Incomplete lineage sorting and/or introgression seem to have significantly affected early ant evolution, which might make it impossible to establish whether Leptanillinae, Leptanillinae plus Martialinae, or Martialinae represents the sister of all the other ants.