Inconsistency in Tracer Statistics and Bayesian Skyline Plots

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Feb 7, 2024, 1:22:59 AMFeb 7

Dear all,

I am an undergraduate researcher in the field of genomic epidemiology and have been using BEAST2 for analyzing the changes of effective population size (Ne) 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 years. Besides, bPopSizes.2, bPopSizes.3, bPopSizes.4 are much lower than bPopSizes.4. However, four of them are equal to about 82533.389 in the mean of Ne through the years.

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. Thank you for your time and consideration.

Best regards,
Inconsistency in Tracer Statistics and Bayesian Skyline Plots.pptx
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