Rescaling factor and large parameter estimates

[emilye...@gmail.com]

Dear Dr. Excoffier and fsc users,

My question is in regard to the rescaling factor.  The model output I see from fsc often has a large rescaling factor, such that when I multiple it to the estimated divergence times then multiple by the generation time, the estimates are unreasonably large given what is known about species age.  I understand that the rescaling factor is the observed polymorphism divided by mutation rate * tree length (ie- estimated polymorphism), thus it seems that my model is underestmating the polymorphism.  The things that should effect that are mutation rate and Ne, and I'm estimating Ne in the model.  When I run one population models, the rescaling factor is 1; therefore,  this occurs as the model complexity increases.  

Does anyone have thoughts on why this may occur or how to assess specific model parameters that influence the rescaling parameter? 

My .tpl and .est files are below, and am running the following command:

fsc26 -t ./Uamer.tpl -e ./Uamer.est -n 100000 -M -m -l 30 -L 60 -x -c8

Also, if it's helpful, I mapped WGS reads to the reference genome, called variants, filtered for biallelic SNPs, masked genes, then used bcftools +prune to thin linked sites.  I used PGDspider to convert the VCF to .arp, then used Arlequin to make pairwise SFS for the four populations.

With sincere thanks,

Emily

.tpl

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

4

//Population effective sizes (number of genes=2*NumIndividuals):

Eak

Eeast

Ewest

Egye

//Samples sizes and samples age 

8

8

6

6

//Growth rates : negative growth implies population expansion

0

0

0

0

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

3

//

0 0 0 0

0 0 0 0

0 0 0 0

0 0 0 0

//

0 0 MIG02 0

0 0 0 0

MIG20 0 0 0

0 0 0 0

//Uarct-Uamer migration

0 0 0 0

0 0 0 0

0 0 0 MIG23

0 0 MIG32 0

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

8 historical event

TAD    3 2 AD$ 1     0 0

Teast  1 1 0  Beast 0 0 instbot

Teast  1 0 1  1     0 1   

Tak    0 0  Bak   0 0 instbot

Tak    0 2 1  S2west 0 0    

15300  2 2 0  Samer  0 0   

15300  3 3 0  S2gye  0 0

461500   2 3 1  Rurs  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 2.5e-8 OUTEXP

.est

// Priors and rules file

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

[PARAMETERS]

//#isInt? #name   #dist.#min  #max 

//all Ns are in number of haploid individuals

1 TAD   unif 1000  12000 output 

1 AA    unif 1  10000 output

1 BB    unif 1  10000 output

1 Ewest      unif 500  10000  output

1 Eak        unif 100  10000  output

1 Eeast      unif 100  10000  output

1 Egye       unif 100  1000   output 

1 Nwest      unif 500  10000  output

1 Nak        unif 100  10000  output

1 Neast      unif 100  10000  output

1 Ngye       unif 100  1000   output

1 Nanc       unif 1000 60000  output REFERENCE

0 Bwest   logunif 0.0001 1 output

0 Bak     logunif 0.0001 1 output

0 Beast   logunif 0.0001 1 output

0 Bgye    logunif 0.0001 1 output

0 AD$    unif 0.01 0.1 output

0 MIG02  unif 1e-6 1e-3 output

0 MIG20  unif 1e-6 1e-3 output

0 MIG23  unif 1e-6 1e-3 output

0 MIG32  unif 1e-6 1e-3 output

[RULES]

[COMPLEX PARAMETERS]

0 S2west = Nwest/Ewest output 

0 S2gye  = Ngye/Egye output 

0 Samer =  Nanc/Nwest  output

1 Teast = TAD + AA output

1 Tak = Teast + BB output