I have a question concerning the time scale (x-axis) of Bayesian Skyline Plot (BSP) analysis as implemented in BEAST. I am not very familiar with the model underlying this analysis.
I run BSP analyses on three different dataset (one each population) for the mitochondrial COI (537bp). The first population included 97 sequences, the second population 167 sequences, and the third population 48 sequences. The programs (Beauti + BEAST + Tracer) produced 3 BSPs with different time scales: the first population, 0 to 450 Kya; second population, 0 to 1800 Kya; and third population 0 to 350 Kya. My question is “how the more ancient value of x-axis is obtained? It seems related to the number of sequences in the original dataset, does it? If so, which is the relation between the number of sequences and the length of x-axis (time) of the BSP?
Any suggestion will be greatly appreciated.
Ciao
Ferruccio
Hi Ferruccio,
The Bayesian Skyline plots show the relationship between the population size (y-axis) and the amount of change (x-axis) inferred from the number of analyzed sequences. Therefore, the units on the axes of the plot (for each group of analyzed populations) will depend mainly on the form of the calibrating information wich could be obtained using a known rate or nodal ages.
Good luck!
The paper by Atkinson et al (Proc Roy Soc B, 276:367-373, 2009) shed light on the problem addressed in my question. The answer is that Bayesian Skyline Plots are truncated to the median estimate of each population's TMRCA. Problem fixed! Thanks!
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