Tracer/Demographic Reconstruction

[rotariu...@yahoo.co.uk]

Hello group,

I did run a model in BEAST using SNPs from E.coli O157 strains ( I did use the following settings - HKY, Gamma+invariant sites, Log Normal relaxed clock, and Exponential growth) . I repeated the model 5 times and converged. However I have a problem in interpreting the Demographic reconstruction (from Tracer) and I will really appreciate any help with this.

I'm did a demographic reconstruction in Tracer for the ExponentialGrowth model (with Population Size parameter: exponential.popSize). The exponential growth I obtain is attached.

It is not clear for me what is plotted on the vertical axis. Is it population size N? If that's the case, what does it represent (Is it the number of unique strains of O157  existent at a particular time?).

How would I get the Effective population size (is it Ne= N/Tc? If that's true how is the generation (in calendar units), Tc, determined?)

Many thanks in advance for any suggestions on this.

Kind regards,

Ovidiu

[Alexei Drummond]

Hi Ovidiu,

You need to know the generation time in years in order to convert the y-axis to effective population size.

The generation time is something like the average time between subsequent infections (if R is close to 1). This is something you need to know from a separate source as it can’t be estimated from genetic data alone under a coalescent model.

Cheers

Alexei

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<ExpGrowth.pdf>

[Remco Bouckaert]

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