I'm using Lositan with 734 SNP's for 72 individuals across a latitudinal cline, maybe structured in 2 main clusters and possibly in IBD.
If I use few iterations the envelope looks good (50K) (Fig1), but with more (>500K) looks terrible (Fig2), too ragged, and too many outliers. I've played with all parameters (#pops, force Fst, FDR,etc.) and keep getting the same,
There is something that is not clear to me at this stage:
What value is lositan reporting for the sample size (is that 10?). This is different from the total number of simulated populations (which would start as 2 in your case). If I understand well, you have 76 samples. Are these approximately equally divided by both populations? Lositan should be reporting back a much bigger number for sample size (surely not 10 if you have 76 samples)
The effect could be explained by low sample size and possibly low number of populations.
So, are you splitting this in two populations? or more? What is the sample size reported when you load the data?
Thanks for your quick reply. Yes my file has two populations, the sample size reported is 2 populations. I'm basing this in a preliminar structure and DACP analyses. However, I have played with the expected total pops quite a bit (2, 10, 20, 50, 100), and getting the same behaviour. Should I split the file in more "artificial" populations? I see how that might help, but then I guess the question is if the result will depend on how populations are assigned?
Just to be sure: on the bottom middle panel you have:
Expected total pops
Are you reporting the "Expected total pops" or the "sample size"?
Mean Fst= 0.05
Expected total of pops, I have used different values and get same results= 2, 10, 40 and 100
Mutation model= Infinite sites
Sample size = 69 individual, 734 loci
Some improvement when the original file is divided in 9 populations, see fig. However still some spikes in low He and Fst. This was using expected pop=20 and subsamplesize= 50, assumed Fst 0.06.
However, if I use default parameters --> expected pops = 9 and sub sample size = 10, I get many more "spikes"
Greetings. I am trying to use LOGISTAN for my SNP dataset. I have tried several times but it seems does not run for my data. I have SNP data with VCF extension and I converted to Genpop format and run by program but it did not run!
I assume something wrong happened during file conversion or something else. Could you help me how can I proceed with this issue?
Thanks for your attention,