Questions about the N_e values in momi2

[Github-Yilei]

Hi,

I am using momi2 to estimate possible demographic scenarios with 3 populations. I find that N_e value seems have significance influence on the likelihood and divergence times.

My question is that:
What is the proper way to set this parameter?

Thanks in advance.

[jackkamm]

N_e is simply the default size when a population's size has not been otherwise specified. If you explicitly specify the population size with add_size_param() and add_leaf() or set_size(), then N_e should have no effect, and the model can infer the maximum likelihood for the population size parameters.

If not inferring population sizes, then a reasonable default for N_e is organism specific, and should be the number of generations for two samples to coalesce to a common ancestor. For humans 10,000 is a reasonable number.

[Shaileshdesai76]

Hii, Thank you for continue helping others.

My question was related to this, so, currently i am working with non-modal organism and dont know Ne here, so should i select the default one or i should try to estimate through other methods, and just to know that i want to estimate population size, divergence and migration among my 7-8 populations.
I have mutation rate, but i think momi2 does not use it ?

Thank you.