About the clock mean value

[Abhishek Gupta]

Hii Everyone 

I am working on invertebrate phylogeny particularly in mosquitoes and little bit confuse about how to analyse clock mean value to estimate TMRCA for a particular population. I have searched a lot in literature but could not find anything. I am really forward to answer my question.

Thanks

Abhishek 

[Omar Mejía]

You can use  the substitution rate used in other studies. aAe you working with a phylogeographic or a phylogenetic approach? Which molecular  marker(s)?

If you provide additional info would  be better 

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[Abhishek Gupta]

Thankyou for the reply.

Actually, I am using the full mitochondrial genome for phylogeography. I have set the clock mean time as 0.00000002 with struct clock. its general substitution rate of mitochondria invertebrate then i am getting the 32000 years time for my population in tracer file in tree height value. so this is the correct way though i am getting results or should do any kind of change in this analysis. Thanks in advance, I am really looking forward to an appropriate answer for my question.  

[Omar Mejía]

Hi Abshinek,

I don`think that your substitution rate be correct. For example, assume that the reported substitution rate of mitochondrial D-loop in mammals is 2% per million years. You need to estimate the quotient, that is 2/100= 0,02, but due that you are working with an haploid genome you need to divide the aforementioned value by 2, that is 0,02/2= 0,01

So, if you want to assess a 2% substitution rate for a molecular marker in Beast you need to put 0,01 as substitution rate

For example, in fishes substitution rate in cytb is near 0,8% per my, if you make the math will be 0,8/100= 0,008 and then 0,008/2= 0,004

In summary, the substitution rate that you are using of 0.00000002 is wrong, this imply a 0,00004% substitution rate per my

Best regards

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Omar Mejía G

Laboratorio de Variación Biológica y Evolución

Departamento de Zoología

Escuela Nacional de Ciencias Biológicas-IPN

[HS]

Hi,

The mutation rate of 2E-08 make sense. It is in per year basis, and ages (heights, etc.) will be in years. I am not sure I can suggest a known rate for mosquitos, but the value used is close to mean rates for humans (1.68E-08 -  2.67E-08) for whole mitochondrial DNA.

Best,

Hovhannes

[Omar Idris]

I do not think you need to account for haploid mitochondria it is calculated given that.

Sent from my iPhone

On Jun 4, 2025, at 3:57 PM, Omar Mejía <posgradobio...@gmail.com> wrote:



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[Abhishek Gupta]

Thanks for fruitful replies. i have one more doubt as i am running beast to know TMRCA for 5 population of same species. so which model i need to select like Yule Model or Calescent constant or exponential model. 

Thanks in advance.