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popgenmethods / momi2

Infer demographic history with the Moran model
GNU General Public License v3.0
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Questions about the N_e values in momi2 #72

Open Github-Yilei opened 7 months ago

Github-Yilei commented 7 months ago

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 commented 7 months ago

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.