How to estimate migration rates with microsatellite genotyping data similar to those obtained from output files with .bestlhoods extension obtained from SFS of SNPs?

[Rodrigo Francisco Justino]

How to estimate migration rates with microsatellite genotyping data similar to those obtained from output files with .bestlhoods extension obtained from SFS of SNPs?

Hello everyone.

I am estimating the ancestral migration rate (long-term) of genotyped markers SNPs through the ESTIMATING PARAMETERS FROM THE SITE FREQUENCY SPECTRUM method explained in the fsc 26 manual: HIERARCHICAL ISLAND MODEL: .tpl file, .est file and the _jointDAF ... obs files (generated in arlequin from VCF converted in pgdspider to .arp). I obtain the migration rates from the .bestlhoods output file.

 I would like to know: Is it possible to generate SFS files from microsatellite data (if such an approach exists) or is it possible to make this estimate in another way in fsc26? I am attaching the input (.obs is just an example among all my files) and output files for SNPs ( in a microsatellite genotyping file (diploid, genepop). In my model, there is an ancestral population that splits into two populations. Each of the two populations gives rise to the others 2 groups, which can only migrate within groups (pops 0 to 4 and pops 5 to 10). If you need any extra information, don't hesitate to ask me.

 

Any help is appreciated!

Thank you very much!