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The optimal k was determined based on the likelihood plot of models and stability of grouping patterns across 20 runs.
Trees were sampled every 1000 generations, while the first 200 trees were discarded as burn-in (according to the likelihood plot).
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Visual examination of parameter and likelihood plots in TRACER v.1.4 [22] confirmed that this burnin was sufficient.
The likelihood plots for both datasets also showed that MCMC reached the stationary phase by this time (PSRF = 1.000 for both data sets).
The three reconstructions and likelihood plots obtained using different matrices were compared.
Convergence was assessed by examining likelihood plots through time using TRACER v. 1.4.1 [ 35].
According to the log likelihood plots 200 trees were discarded as burnin.
The proportional hazards assumption was tested by examining the log-log survival plots-2 * log likelihood plots.
QTL were robustly detected for both traits as shown in the QTL likelihood plots in Figure 3.
2 M generations were discarded as "burn-in" (trees sampled before the likelihood plots reached a plateau) and consensus trees constructed from the returning sample.
To identify the most probable number of ancestral populations, we investigated the mean and variance of the likelihood plots of the data for different K-values (i.e., plot of ln Pr(X/K) vs. K).
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com