First, we created a dated phylogeny for the species tree. We included the node separating the species S. fugax from the other Solenopsis species. The directory species_tree_dating includes all scripts used for this, including:
- De novo assembly of the genomes of different fire ants
- The use of BUSCO to identify single-copy orthologs between these species
- Multiple-sequence alignment between these single-copy orthologs
- Dated phylogeny with IQ-Tree
We then created dated tree with all samples in our analysis (for the supergene and the rest of the genome), calibrated with nodes retrieved from the tree above. The scripts used in this analysis are in the directory supergene_dating.