Fwd: Problem with tracer statistics and skyline plots

[Rou-Ya Bai]

Dear all,

I am an undergraduate researcher in the field of genomic epidemiology and have been using BEAST2 v2.6 for analyzing the changes of effective population size (Ne) of tuberculosis through the years. Recently, I've encountered an issue regarding the inconsistency between Tracer statistics and Bayesian skyline plots.

Here are the Tracer statistics and the skyline plots.

As you can see, the bPopSizes.1 is 82533.389, which is consistent with the skyline plot of "mean" of Ne in recent time. Besides, bPopSizes.2, bPopSizes.3, bPopSizes.4 are much lower than bPopSizes.4 looking considerably lower in magnitude. However, four of them in the skyline plot are equal to about 82533.389 in the mean of Ne through the years. Theoretically, it should be a ladder-like line, instead of a straight line.

Even if I exported the data table and used R to draw the plot, the results were the same. I have attached the PPT file to this email if you couldn't see the figures clearly.

Your assistance in understanding my problems would be valuable. Thanks for any comments.

Best regards,
Noah