Inferring parameters of an isolation and then migration model

[parul johri]

Dear Dr. Excoffier,

I am using fastsimcoal2 to infer the parameters of a model where (forward-in-time) an ancestral population splits into two populations that remain separated for some generations and then meet at some point in time and start exchanging migrants (i.e., continuous migration). I have written the input files for inference, but I'm not entirely certain if my .tpl file is correct. Would it be possible for you to take a look at what I have done to see if it makes sense? If not, no problem! The contents of the .tpl file are pasted below:

//Parameters for the coalescence simulation program : simcoal.exe

2 samples to simulate :

//Population effective sizes (number of genes)

NCUR1$

NCUR2$

//Samples sizes and samples age

48

22

//Growth rates: negative growth implies population expansion

0

0

//Number of migration matrices : 0 implies no migration between demes

2

//Migration matrix 0

0 m21$

m12$ 0

//Migration matrix 1

0 0

0 0

//historical event: time, source, sink, migrants, new deme size, growth rate, migr mat index

4 historical event

TMIG$ 0 0 0 1 0 1

TCHANGE1$ 0 0 1 RESIZE1$ 0 1

TCHANGE2$ 1 1 1 RESIZE2$ 0 1

TDIV$ 1 0 1 1 0 1

//Number of independent loci [chromosome]

1 0

//Per chromosome: Number of contiguous linkage Block: a block is a set of contiguous loci

1

//per Block:data type, number of loci, per gen recomb and mut rates

FREQ 1 0 8.4e-8

Thank you so much!

Parul