Influence of sampling scheme on the growth rate parameter estimation.

<p>For setting (), we modified the birth-death tree simulations to include periods of higher () and lower sampling (either , subfigures A and B, or , subfigures C and D). We simulated 100 birth-death trees (A and C) and corresponding coalescent trees (B and D) under various sampling schemes (see x-axis annotation). We display a summary in form of the median values of the start and the end of the 95% HPD intervals, and the median of the medians of the posterior estimates for all 100 trees per setting. For the settings where the constant rate birth-death method produced very severe biases, we also analysed the trees with the birth-death skyline model with 10 intervals for the sampling probability (BDSKY, light-blue lines). The summary for trees simulated under constant sampling throughout, is represented on the very left of each figure ( on the x-axis). Next, we varied the sampling as to e.g. sample no tips () in the early phases ( until ) when going forward in time and then sampling all the tips that die () from onward (corresponding to the setting denoted as “p = 0 from t = 0 to t = 9”).