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Four chains were used for each run, and convergence was confirmed via visual inspection of trace plots and Brooks Gelman Rubin convergence statistics near one (Brooks and Gelman 1998).
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The tracefiles and treelists of all four chains were used to check for convergence.
Four chains were used with a random initial tree.
Four Monte Carlo Markov chains and a temperature of 0.2 were used for each analysis.
Four Markov chains were used and the dataset was run for 10,000,000 generations to allow adequate time for convergence.
Four MCMC chains were used with initial random starting trees.
One cold and eleven heated chains were used in both analyses, sampling for every 10,000 generations.
For each analysis, four incrementally heated chains were used per run, with samples taken from the cold chain every 100 generations.
Three independent MCMC chains were used with randomised starting values.
For Bayesian reconstruction, the dataset was partitioned into codon positions and four Markov Chain Monte Carlo (MCMC) chains were used with the default temperature of 0.1.
One hundred and forty random primers were used for RAPD-PCR (polymerase chain reaction).
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