Dear List members,
I have a question regarding the DAPC scatter.
I have 8 sampled populations (from 8 geographic locations), and the DAPC 
analysis (as well as Structure), found 6 clusters. Now, these clusters 
are not separate geographically, which means that each sampled location 
has a proportion of each cluster. I wanted to see this on a scatter, to 
see how different clusters were, hence I plotted the $ind.coord (I used 
points()), and simply coloured the points by clustering this time (as 
per DAPC analysis) and not by geographic location. I was expecting to 
get same-colour points clustered close together (whereas in the first 
DAPC, where colours were based on geog location, they were all 
overlapping). Instead, colours remained all overlapping. I do not 
understand how this explains the existence of 6 clusters, if they're not 
there on the graph.
Maybe my assumption that re-colouring the points by cluster (and not 
location) would present distinct groups was wrong?
I hope what I say makes sense...
I should say that I re-analysed from the start the same dataset too, 
this time grouping individuals by cluster assignment and not by 
geographical location, and I do get nicely separated clusters on the 
scatter. I thought this was wrong in principle though, as I was basing 
it on a new analysis.
Cheers
Ilaria

-- 
Dr Ilaria Coscia
Institute of Biological, Environmental and Rural Science (IBERS)
Edward Llwyd Building
Aberystwyth University
Aberystwyth
Ceredigion SY23 3DA
UK

tel +44 (0)1970 62 2298


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