[adegenet-forum] compoplot, STRUCTURE, and the analysis of a hybrid zone

Stefano Montanari stefanomontanari at gmail.com
Mon Feb 11 22:58:08 CET 2013

Dear Dr. Jombart,

I hope this email finds you well. We have exchanged thoughts before, and I
wish to thank you for having gotten back to me in the past.

I have been going through your latest vignette about dapc in adegenet (Nov
2012). I have used dapc on a butterflyfish hybrid zone in the past
(Montanari et al 2012, Ecology and Evolution), and now I am going through a
second dataset, and would like to compare the 2. Hence, I have a couple of
questions for you:

- am I correct in thinking that I want the same level of stability between
the 2 analyses if I am to compare the results? (eg, in both have retained
PCs = N/3)

- in your tutorial you mention that dapc$posterior used to construct
compoplot are not the same as structure admixture coefficients. Could you
point me in a direction that would allow me to understand how they are not?
I have run the results through structure and the hybrids show up nicely as
50/50 clustred with parent 1 and 2 (k=2). adegenet also reckons that k=2
should be the best, but the compoplot shows no membership misassignment
(even if the # of PCs is conservative). Do you have any suggestions as to

Hoping to have been clear enough and not to have bored you senseless, I
look forward to hearing back from you.

Best regards,


Stefano R. Montanari
PhD Candidate
James Cook University
School of Marine and Tropical Biology
ATSIP (Building 145 James Cook Drive)
4811 Townsville QLD
stefanomontanari at gmail.com
Work: +61 7 4781 5441
Mob: +61 404 736 509
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