The reslice was repeated a second time with default settings to obtain sagittally oriented images.
Scanning was performed using an Amersham Typhoon Trio+ with default settings.
For each gene phylogeny, we used ClustalW2 to generate a neighbor-joining tree with default settings.
The identified bHLH domains were aligned using a ClustalX 2.0 program with default settings [ 40].
GSEA was run with default settings (1000 gene set permutations).
MaxQuant version 1.3.0.5 with default setting was also used for database search with default settings.
The PE reads were merged in a pairwise fashion using CLC Genomics Workbench v. 6.5 with default settings.
To this end we used Partek software with default settings, including a covariance dispersion matrix (Methods).
Specters were grouped with default settings by a ProGroup algorithm build-in to ProteinPilot.
These analyses employed an approximately maximum likelihood approach (ML) using FastTree 2 [114] with default settings.
Trees were built from each replicate using FastTree with default settings and then a consensus tree was constructed with Consense from Phylip using default settings.
