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

[Mark Coulson]

Hi Nikki,

Your interpretation of the plot seems correct, however I'd ask if you ran the xvalDAPC cross validation? It may be that you have kept too many PCs so are overfitting the data. The xvalDAPC will find the optimal number of PCs to retain for your two groups. Then use this number of PCs to run a new DAPC. It will likely result in more overlap between the two groups, which would then be more consistent with the low differentiation you are seeing based on FST.

Hope this helps.

Mark

From: adegenet-forum-bounces at lists.r-forge.r-project.org [mailto:adegenet-forum-bounces at lists.r-forge.r-project.org] On Behalf Of Nikki Vollmer
Sent: 30 January 2018 18:08
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] How to interpret Density Plot for K=2


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



Inverness College UHI, a partner in the University of the Highlands and Islands www.inverness.uhi.ac.uk Board of Management of Inverness College (known as Inverness College UHI), Scottish Charity No SC021197.
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