A uniform prior was set for topology and the default unconstrained exponential prior was set for branch length parameter.
Four additional models were run with different prior sets for a subset of models, and the demographic estimates were generally consistent regardless of priors (Additional file 1: Table S3).
A normally distributed calibration prior was set for this split, with a mean of 22 Ma and standard deviation of 2 Ma.
A normally distributed calibration prior was set for the age of the N. mogera clade root, with a mean of 1.5 Ma and standard deviation of 0.18 Ma.
The prior was set for the amino acid models to mix, thereby allowing model jumping between fixed-rate amino acid models.
A normally distributed calibration prior was set for the age of the Palmorchestia clade based on the La Palma subaerial formation with a mean of 2,000,000 years [ 25] and standard deviation of 200,000, thus assuming uncertainty associated with the calibration point.
Log-normal uncorrelated relaxed clock and the Yule speciation priors were set for the analyses.
Gamma priors were set for β1, T and β1, E with mean 1 and standard deviation 2, corresponding to a Gamma (1 4, 1 4 ).
Semi-informative priors were set for the rate of decay of spatial correlation, φ, informed by the maximum and minimum distance between schools, and non-informative priors used for other coefficients.
Temperature of 40°C used for prior setting of K40 sample in this study was coincidental with the optimum temperature for endogenous TGase.
No prior criteria were set for sample intake, sequencing, data analysis or clinical interpretation; each laboratory was entirely autonomous in choosing its preferred approach.
