[adegenet-forum] How to interpret Density Plot for K=2

[Nikki Vollmer]

Hi,


I am trying to analyze ~200 RADseq loci for ~200 individuals.  STRUCTURE results suggest the best number of populations given the data is 2.  Pairwise Fst values are quite low for my taxa (<0.003) with pvalue 0.01802.  I was trying to do a DAPC on this same data to compare results. DAPC similarly suggested the best # of clusters is 2 and I was able to plot a 1-dimensional density plot for the one DF I kept (attached).  However, I am not sure how to interpret the plot.  Is it correct to say that because the two peaks do not overlap that suggests the 2 clusters are quite differentiated from one another (similar to two clusters on a scatter plot being in opposite quadrants)?  (...or is that logic flawed?)


I am trying to figure out if these 2 groups are very genetically differentiated or not, and I am not clear what the density plot is supporting/suggesting.


I very much appreciate any guidance on this matter!


Thank you,

Nikki

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