Does the rate of evolution is the rate of nucleottide substitution

[Wansadaj Jaroenram]

Dear all,  I am analysing whole genome sequences of PstDV virus (30 strains) using the BEAST2.1.3. I tested the path sampling to get the best-fit model. I got it. The problem is after viewing the BEAST output (performed under the best-fit model) file by Tracer, I got the mean rate of substitution of 1.95 × 10^-4 substitutions/site/year (95% highest posterior density, HPD: 5.38 × 10^-7 10-9 – 4.27 × 10^-4). ESS of all parameters >200 

The simple question is Is the rate of substitution (1.95 × 10-4) the rate of evolution? If not, how to compute please?

Really confused,

Please help me.

Thank you so much for your kindness

Best regards, 

[Andrew Rambaut]

The mean rate is the rate of evolution. However, your intervals span 3 orders of magnitude so I am would consider the mean to be a reliable estimate.

What is the sampling time span of your sequences? 

Andrew

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[Wansadaj Jaroenram]

Dear Andrew,

Thank you so much for your quick response.

the MCMC is 50,000,000 and sampling every 1000. 
The best-fit model is Relaxed log model

1) In conclusion, the mean rate of substitution is the rate of evolution, is it correct?

2) where can I get the rate of mutation please? (rete.varience=1.37x10-7, ucld mean = 2.87x10-4) 

Thank you so much for your kindness.

Best regards, 

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Wansadaj Jaroenram

PhD student

School of Veterinary and Biomedical Sciences

Faculty of Medicine, Health and Molecular Sciences

James Cook University, Townsville QLD 4811 Australia

Tel: +61747816875 E-mail: kung...@gmail.com, wansadaj....@my.jcu.edu.au 

[Andrew Rambaut]

The estimated rate of evolution is the quantity called ‘Mean Rate’ which you say has a mean value of 1.95x10^-4. This is different from the

ucln.mean because it is scaled by the length of the branches. However, what I was warning you about is that your HPDs for this go from

10^-7 to 10^-4 which is a thousand-fold range.  This suggests that you really don’t have much information about what the rate is.

My question to you was what was the range of dates of collection for your samples (i.e., the date of the earliest sample to the most recent)?

Andrew

Andrew Rambaut 

Institute for Evolutionary Biology | Centre for Infection, Immunity & Evolution 

Ashworth Laboratories, University of Edinburgh, Edinburgh, EH3 9JT, UK

contact – a.ra...@ed.ac.uk | http://tree.bio.ed.ac.uk | tel +44 131 6508624

[Wansadaj Jaroenram]

Oh sorry I got confused. The sampling period is 19 years starting from 1993 till 2012. Do I have to increase the sample site please?

Thank you so much for your kindness.

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

[Wansadaj Jaroenram]

Oh sorry I got confused. The sampling period is 19 years starting from 1993 till 2012.

The rate of 1.95x10-4 is the mean of the clock rate value I got from Tracer. I am not sure that whether or not it the same as the 'Mean Rate' you mentioned. Could you please tell me?

Thank you so much for your kindness.