Electrophoresis of products and fluorescence trace data generation were conducted by The Genome Analysis Centre TGACC), Norwich.
Item generation was conducted through 24 interviews of RTR.
Sequencing and consensus sequence generation were conducted as described (9 ).
For Bayesian inferences, for each data set, two runs of 2 million generations were conducted with 0.25 burn-in frequency and resulting posterior probabilities were taken as indicators of phylogenetic reliability.
Two separate runs of five million generations (sampled every 250 generations) were conducted simultaneously.
A total of 1,000,000 generations were conducted, and the sampling frequency was assigned as every 100 generations.
Two simultaneous runs of 10 generations were conducted, each with 4 Markov chains, and trees were sampled every 100 generations.
For each Bayesian analysis, two concurrent runs of 20 million generations were conducted with trees sampled every 1000 generations.
Three replicate runs of 500 million generations were conducted, sampling trees and parameter estimates every 50,000 generations.
