I used the correspondence analysis on GENETIX to analyze multilocus microsatellite data on an individual level. When I used the AFC 2D or AFC 3D options I obtain overlap of my two groups (putative populations). When I use AFC 3D 'sur populations' as my analysis option my two groups separate out nicely. Also, my inertia for the first 2 factors goes way up - totalling 100%.
Is what I'm doing appropriate? When I look in the literature some authors use the 'sur populations' analysis but most don't. Any suggestions will be greatly appreciated.
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