search

dipetkov / eems

Estimating Effective Migration Surfaces
GNU General Public License v2.0
102 stars 28 forks source link

RAD distance matrix: choosing number of demes #16

Closed z0on closed 6 years ago

z0on commented 7 years ago

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)

isopods_pops_polygon

z0on commented 6 years ago

Turns out, I switched lats and lons in my sample coordinates! Silly mistake. Now everything looks reasonable, with 75 and 100 demes.