Hi Nora,

I'm not familiar with using dominant markers in STRUCTURE. Perhaps the papers below will give you some useful instruction.

https://onlinelibrary.wiley.com/doi/full/10.1111/j.1471-8286.2007.01758.x

Culley. Population Genetic Analysis of ISSR Data.pdf

https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-294X.2002.01512.x

Gristinaa etc al., 2014, Hybridization in Capparis spinosa L.: molecular and morphological evidence from a Mediterranean island complex..

Regarding parameters, are you letting the program run long enough e.g. a burnin ~ 50,000 and MCMC ~ 500,000..?

Good luck.

Dear Nora,

In my experience, most researchers failed to conduct Structure analysis with dominant marker due to incorrect input format/setting.

First you should create new project in Structure and set the ploidy of your data as "1" because your ISSR data is dominant (not codominant as SSR).

Second, you should define code of recessive (0 in your case) in first line of your input data and carefully check whether you click the right option during constructing project in Structure.

Thank you so much for your answers. I did put the ploisy on 1 and I got the correct input data, but what I'm struggling with, is which parameter set to go with..which ancestry model and whether the allel frequency is correlated or not..

The attached picture shows my file structure, if anyone finds that helpful to answer

Hi Nora, just have a play around with parameters. You could try running with different ancestry models etc. Best to refer to the early STRUCTURE papers and of course to other literature. The parameters you choice should best suit your organism.

Good luck.

Dear Nora,

I will recommend you both admixture and non-admixture model and confirm that you get consist results.

For the allele frequency dependent / non-dependent model, it depends on your sampling. Therefore, I am afraid that I cannot give you more suggestion except you could provide more detail on your sampling strategies.

Thank you Bing-Hong Huang !

No I got one more question. I got some results, always mentioning Q. But what ist Q?

Using 98 individuals, with 100 loci, I run the programm with burning length 50000 and MCMC 500000, K=10, no admixture modell, locprior model and independent allel frequency.

I got following plots (attached). But I' not quite sure, what to do with these results, is there somewhere a legend, od what is what?

I also attached the Result file. Hope somenone can help me again!

Dear Nora

You can take a glance of you "2_run_1_f" (using notepad or wordpad)

You will find these

Inferred ancestry of individuals:

Label (%Miss) : Inferred clusters

1 E3 (0) : 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000

2 E5 (0) : 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000

3 6 (0) : 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000

4 8 (0) : 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000

.....

This matrix is individual Q-matrix.

Furthermore, I will recommend you to use Evanno's method to evaluate best K.

There are instructions in the website.

http://taylor0.biology.ucla.edu/structureHarvester/