PSMC parameter choosing (-t, -p)
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4 months ago
clinnaeus ▴ 10

Hi all -

I'm running a series of PSMC on several different bird species, and I haven't really seen a lot of clear guidance on choosing appropriate -t and -p parameters. I'm interested in Ne data as far back as possible, but I also don't know how accurate the method is beyond 1 MYA, so I hesitate to overinflate the -t value. I've posted about this in the GitHub, where I uploaded some example plots.

You can see a huge difference between the graphs, but as I wrote, I suspect it is because of one graph being "truncated" relative to the other one. I don't know that I like the idea of just "picking" the one that goes furthest back in time, doesn't seem very objective. So how do I know when I've reached an appropriate set of values? The manual warns about overfitting, but doesn't have much to say about what that looks like. I've tried to use existing literature to guide my choices, but the parameters are never really explained or rationalised so I have a hard time understanding why those values were chosen. Any thoughts are welcome :)

Cheers!

parameters history size psmc demographic population Ne • 191 views
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