I am working on a analytical procedure for 2bRAD for non-model species where I try to avoid calling SNPs altogether and calculate between-individual genetic distances from the fraction of shared unique RAD tags. This seems to work quite well for PCA and hierarchical clustering, and I just made my first poke at EEMS (runeems_snps) and got some results! However I struggle to understand them. I only see color in my plots if I use low number of demes (25), if I go to 50 or 100 I just get zero across my whole seascape. This is of course not implausible - maybe there are really no barriers and no variation in genetic diversity in the Baltic sea for this species - but my 25-deme results seem to be reproducible from run to run.
I also see only three points in my rdist plots, this does not look quite normal...
cheers
Misha Matz, UT Austin
(attaching my polygon and populations - so far analyzed only the named ones)
Dear Desislava -
I am working on a analytical procedure for 2bRAD for non-model species where I try to avoid calling SNPs altogether and calculate between-individual genetic distances from the fraction of shared unique RAD tags. This seems to work quite well for PCA and hierarchical clustering, and I just made my first poke at EEMS (runeems_snps) and got some results! However I struggle to understand them. I only see color in my plots if I use low number of demes (25), if I go to 50 or 100 I just get zero across my whole seascape. This is of course not implausible - maybe there are really no barriers and no variation in genetic diversity in the Baltic sea for this species - but my 25-deme results seem to be reproducible from run to run. I also see only three points in my rdist plots, this does not look quite normal...
cheers
Misha Matz, UT Austin (attaching my polygon and populations - so far analyzed only the named ones)