Can anyone help me with interpreting Bayesian Skyline Plot

[Surya P Sharma]

I have run BSP for C. palustris using concatenated (cytb,cox1 and dloop). The model was selected using jmodeltest in CIPRES. The substitution rate was used was 5.72E-4 and chain length was 100000000.

Thanks 

[Carlo Pacioni]

Hi Surya,

I think your BSP is simply saying that there's no demographic chages over time.

I would consider to partition your seq by genes as it is unlikely that the dloop has the same mutation rates of cyt b and cox1 genes and apply your mutation rate for whatever gene it is relevant  (btw, what the time units?) If you want to go by the book,  you may want to further partition by codon position the cyt b and cox1 seqs. I don't think that any of this would change much your demographic results but it would be formally more correct.

Cheers

Carlo 

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From: beast...@googlegroups.com <beast...@googlegroups.com> on behalf of Surya P Sharma <suryap...@gmail.com>
Sent: Saturday, July 20, 2019 3:54:35 PM
To: beast-users <beast...@googlegroups.com>
Subject: Can anyone help me with interpreting Bayesian Skyline Plot

 

I have run BSP for C. palustris using concatenated (cytb,cox1 and dloop). The model was selected using jmodeltest in CIPRES. The substitution rate was used was 5.72E-4 and chain length was 100000000.

Thanks 

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[Surya P Sharma]

Dear Carlo,

Thank you very much for your suggestion. 

Yes the plot shows a stable population. However, I am not sure about the effective population size. It should not be near "0". The time unit I have unit is million year i.e (500 yrs, 1000 yrs, 1500 yrs, 2000 yrs in my case). For substitution rate I kept an average of all from  literature. 

And I don't know if it is possible to select different substitution model in BEAUti.

Please suggest.

Regards,

Surya     

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Surya P. Sharma
DST-INSPIRE Fellow

suryap...@wii.gov.in
+91-7895248369

[Supriya Bhatt]

Hi Surya,

Yes different model for different sequences can be taken  in  BEAUti . Also, if for some sequences substitution rates are not there then it can be estimated in the program itself. 

Supriya Bhatt,
Animal Ecology and Conservation Biology Department,
Wildlife Institute of India,
Chandrabani, Dehradun 248001.
Email: supr...@wii.gov.in, supriy...@gmail.com

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