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

[Stefano Montanari]

Hi Thibaut,

thank you for your prompt reply, it was very clear. Just a quick question
about optim.a.score: I had used it before, and this morning I tried again
just to make sure I remembered the results correctly. For one dataset
(N=109, 12 loci) it finds that 17 PCs is the best; for the other (N=83, 20
loci), retaining only 1 PC (not possible since PC=>2) gives the highest a
score. This worries me. Do you think these data should not be used for
DAPC?

Cheers

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


On 13 February 2013 01:12, Jombart, Thibaut <t.jombart at imperial.ac.uk>wrote:

> Hi Stefano,
>
> thanks for reposting on the forum. It gives me the chance to clarify an
> important point.
>
> For the first point, there is not a linear relationship between
> 'stability' of DAPC results and the number of PCs retained in the PCA step.
> 'xxx' PCs can represent 2% of the variance in one analysis and 60% in
> another. If the two data table have fairly comparable dimensions, it would
> be best to retain roughly the same proportion of variance. If their
> dimensions are very different, then the same number of PCs makes sense.
>
> STRUCTURE or similar approaches have a model which partitions genotypes
> into groups. It is basically a mixture distribution problem with a
> multinomial distribution for each locus and group. So the 'admixture'
> coefficient has a a straightforward biological interpretation.
>
> In DAPC, assignment of individuals to groups using the discriminant
> functions are based on a geometric criteria. In other words, "tell me where
> you are in the discriminant space, I will tell you the probability that you
> belong to groups xxx, yyy and zzz". This is of course dependent on the
> discriminant space. The more dimensions retained in the PCA step, the
> easier it is the find a space providing perfect discrimination. The
> obtained group membership probabilities can reflect admixture, but they do
> not represent the proportion of the genome assigned to a given group. In
> your case, use a smaller space, you may start seeing less clear-cut group
> definition. optim.a.score may help selecting the number of PCs.
>
> Cheers
>
> Thibaut.
>
>
> ________________________________________
> From: adegenet-forum-bounces at lists.r-forge.r-project.org [
> adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Stefano
> Montanari [stefanomontanari at gmail.com]
> Sent: 11 February 2013 21:58
> To: adegenet-forum at lists.r-forge.r-project.org
> Subject: [adegenet-forum] compoplot, STRUCTURE, and the analysis of a
> hybrid zone
>
> 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<mailto:stefanomontanari at gmail.com>
> Work: +61 7 4781 5441
> Mob: +61 404 736 509
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20130213/090cb43b/attachment.html>