Ant backbone phylogeny resolved by modelling compositional heterogeneity among sites in genomic data

Area of Science:

• * Entomology
• * Evolutionary Biology
• * Systematics

Background:

• * Ants (Formicidae) are ecologically dominant arthropods, making their phylogeny critical for understanding evolution, diversification, and biogeography.
• * Previous phylogenetic studies using molecular data have yielded conflicting results, necessitating re-examination with improved methods.
• * Understanding ant evolutionary relationships is key to deciphering their global ecological impact and diversification patterns.

Purpose of the Study:

• * To investigate sources of conflict in ant phylogenetic studies using comprehensive genomic and Sanger-sequencing datasets.
• * To re-evaluate the phylogenetic position of Martialis heureka using advanced model comparison methods.
• * To resolve contentious nodes in ant phylogeny by adequately modeling among-site compositional heterogeneity.

Main Methods:

• * Re-analysis of published Sanger-sequencing and genome-scale ant datasets.
• * Application of model comparison methods, including Bayesian cross-validation and posterior predictive model checking.
• * Utilizing the Bayesian infinite mixture CAT model (CAT-GTR+G4) to account for among-site compositional heterogeneity.

Main Results:

• * The CAT-GTR+G4 model, identified as the best-fitting model, resolved contentious nodes in ant phylogeny.
• * Martialis heureka is resolved as sister to all ants except Leptanillinae, contradicting previous hypotheses.
• * Model comparison revealed that the resolution of certain phylogenetic relationships is dependent on the statistical model used.

Conclusions:

• * Adequate modeling of among-site compositional heterogeneity is crucial for reconstructing deep insect phylogeny.
• * The study resolves a lasting controversy regarding the phylogenetic position of Martialis heureka.
• * Phylogenetic model selection significantly impacts the inferred evolutionary history of ants.