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

[Stefano Montanari]

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
why?

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

Best regards,

Stef

--------------------------
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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