test of complete panmixia
robertkraus
I am planning to run a model comparison study in migrate-n. From
Beerli & Palczewski, Genetics 185: 313-326 (2010), I understand that I
can run models that differ in allowing/not allowing migration between
some of the predefined pops. Further, one can make up "panmictic" pops
by joining some predefined pops into one for the input file. But how
would I run a model in which all individuals are in one panimctic pop?
Just give only a single population with all genotypes individuals in
the input file?
As an example: Say, I have sampled 4 localities, i.e. 4 pops. The full
model would allow migration between all of them, and a restricted
model would, for instance, mean that migration only happens between 1
and 2, 2 and 3, 3 and 4 (a linear model). If I want to test a model in
which 1 and 2, as well as 3 and 4 are panimctic, I can run migrate-n
with only 2 pops, each comprising pop 1+2 or 3+4, respectively. But
how would I run the model 1+2+3+4, i.e., all individuals belong to one
big panmictic pop?
Cheers,
Robert
shobhit
in the option sampling localities, for one big pop with your normal
infile:
how many sampling sites 4
and then he asks what are the number of pops then enter
1 1 1 1
this means that all your separate populations in your infile are
counted as one panmictic pop
shobhit
7. sampling localities
how many localities are in data set?
4
enter now remappings
1 1 1 1 (one panmictic pop)
1 1 2 2 (for 1 and 2 as one pop and 3 and 4 as the other pop)
Robert Kraus
This sounds straight forward but somehow escaped my attention, sorry.
Cheers,
Robert
-------- Original-Nachricht --------
> Datum: Fri, 27 May 2011 02:38:24 -0700 (PDT)
> Von: shobhit <shobhit...@gmail.com>
> An: migrate-support <migrate...@googlegroups.com>
> Betreff: [migrate-support] Re: test of complete panmixia
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Peter Beerli
be careful when using population-relabel with custom-migration and in particular if you use the geofile option.
Some of these combinations confuse migrate, you will need to adjust the
custom-migration matrix and the geofile to the new situation, this is not a problem when you downsize
4 population to 1 but may occur with 2 for example using
population-relabel={1 1 2 2}
the custom-migration matrix must be of the 2*2 (and not 4*4) for example like this
custom-migration={ *0**}
the geofile also needs to contain a 2*2 matrix and not a 4*4 because currently migrate cannot
recalculate the new location distances.
Peter