The Genome and Development-Dependent Transcriptomes of Pyronema confluens: A Window into Fungal Evolution
The species tree was built using PhyML  based on 426 single-copy, widespread genes (see Materials and Methods for details). A bootstrap of 100 repetitions was also reconstructed, bootstrap values for all branches were 100%. A species tree constructed with the super-tree reconstruction program DupTree  based on all 6,949 trees reconstructed in the phylome had the same topology. The divergence time of the Pyronema and Tuber lineages was estimated at 260 or 413 Mya using r8s  calibrated with divergence times of 723.86 Mya and 1147.78 Mya, respectively, for Schizosaccharomyces pombe and the remaining ascomycetes (see Materials and Methods).