Hi Anna!

A post-doc in my lab used GenAlEx (http://biology-assets.anu.edu.au/GenAlEx/Welcome.html) to evaluate pairwise relatedness.

If you're feeling adventurous, there are several R packages that you can use: https://cran.r-project.org/web/packages/Demerelate/Demerelate.pdf ; https://www.bioconductor.org/packages/release/bioc/html/GeneticsPed.html and many more of course. 

Good luck!

It is unclear to me if you are looking for relatedness/differentiation at the population level or individual level (or both?).. For the former, you have already shown a clustering/assignment method (Structure), and can also do a PCA or DAPC in Adegenet depending on your familiarity with R (?).. And can calculate some simple pop-gen things in GenAlEx (e.g. proportion shared alleles) or in various R packages... Or Genepop, Arlequin (personally I don't really like either of these, although they are popular), etc... All of these give some information on delimitations between populations (such that they 1) exist and 2) are apparent in your data)...For the latter- and what I generally think of as "relatedness"- there are many options for individual-level kinship assessment, probably the most popular programs are Cervus and COLONY2.. Or at least I see them both cited often... If this is indeed the route you are going I've linked to a review which may be helpful (or not). Good luck

https://web.natur.cuni.cz/~muncling/Jones%202010%20paternity.pdf

Hi Anna

I think the best software for genetic relatedness is Spagedi (http://ebe.ulb.ac.be/ebe/SPAGeDi.html)

Cheers

Pablo

Yes, SPAGEDI

Hi, Anna,

I strongly recommend you GenAlex and COANCESTRY, althoug in your case STRUCTURE could be helpful. I attached you a paper in which we used. Regards!

Thank you all for your input! I am looking at relatedness at the individual level, and I think I am going to use a combo of STRUCTURE, GenAlEx (PCoA, Pairwise Relatedness, private and fixed alleles) and I think I will look into COANCESTRY, COLONY2 and SPAGEDI. Any and all suggestions are greatly appreciated :)

You may use also populations software which provides a wide diversity of genetic distance at an individual level (http://bioinformatics.org/populations/#ancre_telechargement)

COLONY is by far the most powerful Programme when you also Need to account for Genotying Errors or low sampling rate of parents. I use mostly CERVUS and COLONY side by side. COLONY also allows to generate Genotypes for unknown parents.

I suggest GenAlex, it's a complete and useful software with many options.

Bye