[adegenet-forum] still on Mantel's test

[Virgilio Massimiliano]

Many thanks for the quick reply,
it’s done now
All the best
M.

From: <Jombart>, Thibaut <t.jombart at imperial.ac.uk<mailto:t.jombart at imperial.ac.uk>>
Date: Tuesday 6 January 2015 16:54
To: Massimiliano Virgilio <massimiliano.virgilio at africamuseum.be<mailto:massimiliano.virgilio at africamuseum.be>>, "adegenet-forum at lists.r-forge.r-project.org<mailto:adegenet-forum at lists.r-forge.r-project.org>" <adegenet-forum at lists.r-forge.r-project.org<mailto:adegenet-forum at lists.r-forge.r-project.org>>
Subject: RE: still on Mantel's test

Hi,

and yes, happy new year.

Please do not post attachments that large - saved a png your figure would be a lot smaller, with the same quality.

I can't really see any clear-cut discontinuity here, though there are some hotspots. However, note that these are pairwise distances (each individual corresponds to several points), so there is not clear interpretation of a group of points in the IBD plot in terms of genetic clusters. What you could merely conclude from discontinuity is that the genetic diversity is structured in geographic patches. Methods exist to define these, but not a simple IBD plot.

Cheers
Thibaut


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From: adegenet-forum-bounces at lists.r-forge.r-project.org<mailto:adegenet-forum-bounces at lists.r-forge.r-project.org> [adegenet-forum-bounces at lists.r-forge.r-project.org<mailto:adegenet-forum-bounces at lists.r-forge.r-project.org>] on behalf of Virgilio Massimiliano [massimiliano.virgilio at africamuseum.be<mailto:massimiliano.virgilio at africamuseum.be>]
Sent: 06 January 2015 15:29
To: adegenet-forum at lists.r-forge.r-project.org<mailto:adegenet-forum at lists.r-forge.r-project.org>
Subject: [adegenet-forum] still on Mantel's test

Hi again,
and happy new year again :-)

The second question I have for today is the following:
I got this beautiful kernel density of individual geographic vs genetic distances (still playing around with Mantel’s test).
It looks like there are a couple of red areas possibly indicating discontinuities between two groups of individuals.

Is there a way I can have synthetic information on these two groups or I would just get a list of thousands of inter-individual distances?

Cheers

Massi


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