Estimating population growth rate after a founder event with N(t)=N(o)ert

[guill...@gmail.com]

Hello,

Thanks in advance for your help!

In a 3 populations system, I'm estimating the growth rate of a population (POP0) arisen from a founder event 40 generations ago from MSFS. I created the est file using the current population size (NPOP0 parameter in tpl and est files) as N(t), a number of N(0) founders (COLON parameter in est file) ranging from 2 to 50 diploid individuals and solving growth rate (GROWTH0 in the est file) as GROWTH0 = ln(NPOP0/COLON)/40. However, I'm unsure if I should change the sign of GROWTH0 in the est file, so the result is a negative number indicating positive population increase after the founder event, or if being based in other parameters, the search is already performed in reversed. Command line and input files:

fsc26 -t M1.tpl -e M1.est -n 200000 -M -u -m -L 100 -c 12 -B 24

M1.tpl:

//Parameters for the coalescence simulation program : fsimcoal2.exe

3 samples to simulate :

//Population effective sizes (number of genes)

NPOP0

NPOP1

NPOP2

//Samples sizes and samples age

28

24

56

//Growth rates  : negative growth implies population expansion

GROWTH0

0

0

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

1

//Migration matrix 0

0 0 0

0 0 0

0 0 0

//historical event: time, source, sink, migrants, new deme size, new growth rate, migration matrix index

2 historical event

40 0 1 1 RESIZE0 0 0

TDIV 2 1 1 RESIZE1 0 0

//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 generation recombination and mutation rates and optional parameters

FREQ 1 0 2.21e-9 OUTEXP

M1.est:

// Search ranges and rules file

// ****************************

[PARAMETERS]

//#isInt? #name   #dist.#min  #max

//all Ns are in number of haploid individuals

1  NPOP0       unif  100    1e4     output

1  NPOP1       unif  1000   1e6     output

1  NPOP2       unif  1000   1e6     output

1  NANC0       unif  1000   1e6     output

1  NANC1       unif  1000   1e6     output

1  TDIV        unif  100    1.8e4   output bounded

1  COLON       unif  4      100     output

[RULES]

[COMPLEX PARAMETERS]

0  RESIZE0  = NANC0/NPOP0  hide

0  RESIZE1  = NANC1/NANC0  hide

0  PNRR0    = NPOP0/COLON  hide

0  LBR0     = log(PNRR0)   hide

0  GROWTH0  = LBR0/40      output

[guill...@gmail.com]

Hello, I have corrected some problems in my input files from the previous post but my question remains the same, should I change the sign of my growth rate estimation resolved as GROWTH0=log(NPOP0/COLON)/40 for estimating the growth rate after a founder event by a number of individuals = COLON that happened 40 generations ago? The plot of the par interpreter seems to say so.

TPL file:

//Parameters for the coalescence simulation program : fsimcoal2.exe

3 samples to simulate :

//Population effective sizes (number of genes)

NPOP0

NPOP1

NPOP2

//Samples sizes and samples age

22

20

28

//Growth rates  : negative growth implies population expansion

GROWTH0

0

0

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

1

//Migration matrix 0

0 0 0

0 0 0

0 0 0

//historical event: time, source, sink, migrants, new deme size, new growth rate, migration matrix index

2 historical event

40 1 0 1 RESIZE0 0 0

TDIV 2 0 1 RESIZE1 0 0

//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 generation recombination and mutation rates and optional parameters

FREQ 1 0 2.21e-9 OUTEXP

EST file:

// Search ranges and rules file

// ****************************

[PARAMETERS]

//#isInt? #name   #dist.#min  #max

//all Ns are in number of haploid individuals

1  NPOP0       unif  100    1e4     output

1  NPOP1       unif  1000   1e6     output

1  NPOP2       unif  1000   1e6     output

1  NANC0       unif  1000   1e6     output

1  NANC1       unif  1000   1e6     output

1  TDIV        unif  100    1.8e4   output bounded

1  COLON       unif  4      20      output bounded

[RULES]

[COMPLEX PARAMETERS]

0  RESIZE0  = NANC0/COLON  hide

0  RESIZE1  = NANC1/NANC0  hide

0  PNRR0    = NPOP0/COLON  hide

0  LBR0     = log(PNRR0)   hide

0  GROWTH0  = LBR0/40      output      (Or 0  GROWTH0  = LBR0/-40?)