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many thanks again Thibaut :-)
<div class="">all the best</div>
<div class="">M.</div>
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__________________________________</div>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; " class="">
<font class="Apple-style-span" color="#004D95"> Massimiliano Virgilio, PhD <br class="">
<br class="">
Royal Museum for Central Africa <br class="">
Leuvensesteenweg 13, B-3080 Tervuren, Belgium, +32 (0) 27695366 <br class="">
<br class="">
<a href="mailto:massimiliano.virgilio@africamuseum.be" class="">massimiliano.virgilio@africamuseum.be</a> <br class="">
<br class="">
<a href="http://www.africamuseum.be/home/contact/staff/VIRGILIO_Massimiliano/" class="">http://www.africamuseum.be/home/contact/staff/VIRGILIO_Massimiliano/</a></font></div>
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<blockquote type="cite" class="">
<div class="">On 07 Jan 2015, at 12:00, <a href="mailto:adegenet-forum-request@lists.r-forge.r-project.org" class="">
adegenet-forum-request@lists.r-forge.r-project.org</a> wrote:</div>
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When replying, please edit your Subject line so it is more specific<br class="">
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Today's Topics:<br class="">
<br class="">
1. Re: still on Mantel's test (Jombart, Thibaut)<br class="">
2. Re: still on Mantel's test (Virgilio Massimiliano)<br class="">
<br class="">
<br class="">
----------------------------------------------------------------------<br class="">
<br class="">
Message: 1<br class="">
Date: Tue, 6 Jan 2015 15:54:06 +0000<br class="">
From: "Jombart, Thibaut" <t.jombart@imperial.ac.uk><br class="">
To: Virgilio Massimiliano <massimiliano.virgilio@africamuseum.be>,<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>"adegenet-forum@lists.r-forge.r-project.org"<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span><adegenet-forum@lists.r-forge.r-project.org><br class="">
Subject: Re: [adegenet-forum] still on Mantel's test<br class="">
Message-ID:<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span><2CB2DA8E426F3541AB1907F98ABA6570ABEB6C48@icexch-m1.ic.ac.uk><br class="">
Content-Type: text/plain; charset="windows-1252"<br class="">
<br class="">
Hi,<br class="">
<br class="">
and yes, happy new year.<br class="">
<br class="">
Please do not post attachments that large - saved a png your figure would be a lot smaller, with the same quality.<br class="">
<br class="">
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.<br class="">
<br class="">
Cheers<br class="">
Thibaut<br class="">
<br class="">
<br class="">
________________________________<br class="">
From: adegenet-forum-bounces@lists.r-forge.r-project.org [adegenet-forum-bounces@lists.r-forge.r-project.org] on behalf of Virgilio Massimiliano [massimiliano.virgilio@africamuseum.be]<br class="">
Sent: 06 January 2015 15:29<br class="">
To: adegenet-forum@lists.r-forge.r-project.org<br class="">
Subject: [adegenet-forum] still on Mantel's test<br class="">
<br class="">
Hi again,<br class="">
and happy new year again :-)<br class="">
<br class="">
The second question I have for today is the following:<br class="">
I got this beautiful kernel density of individual geographic vs genetic distances (still playing around with Mantel?s test).<br class="">
It looks like there are a couple of red areas possibly indicating discontinuities between two groups of individuals.<br class="">
<br class="">
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?<br class="">
<br class="">
Cheers<br class="">
<br class="">
Massi<br class="">
<br class="">
<br class="">
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------------------------------<br class="">
<br class="">
Message: 2<br class="">
Date: Tue, 6 Jan 2015 15:58:29 +0000<br class="">
From: Virgilio Massimiliano <massimiliano.virgilio@africamuseum.be><br class="">
To: "Jombart, Thibaut" <t.jombart@imperial.ac.uk>,<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>"adegenet-forum@lists.r-forge.r-project.org"<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span><adegenet-forum@lists.r-forge.r-project.org><br class="">
Subject: Re: [adegenet-forum] still on Mantel's test<br class="">
Message-ID: <D0D1C48F.116E%massimiliano.virgilio@africamuseum.be><br class="">
Content-Type: text/plain; charset="windows-1252"<br class="">
<br class="">
Many thanks for the quick reply,<br class="">
it?s done now<br class="">
All the best<br class="">
M.<br class="">
<br class="">
From: <Jombart>, Thibaut <t.jombart@imperial.ac.uk<mailto:t.jombart@imperial.ac.uk>><br class="">
Date: Tuesday 6 January 2015 16:54<br class="">
To: Massimiliano Virgilio <massimiliano.virgilio@africamuseum.be<mailto:massimiliano.virgilio@africamuseum.be>>, "adegenet-forum@lists.r-forge.r-project.org<mailto:adegenet-forum@lists.r-forge.r-project.org>" <adegenet-forum@lists.r-forge.r-project.org<mailto:adegenet-forum@lists.r-forge.r-project.org>><br class="">
Subject: RE: still on Mantel's test<br class="">
<br class="">
Hi,<br class="">
<br class="">
and yes, happy new year.<br class="">
<br class="">
Please do not post attachments that large - saved a png your figure would be a lot smaller, with the same quality.<br class="">
<br class="">
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.<br class="">
<br class="">
Cheers<br class="">
Thibaut<br class="">
<br class="">
<br class="">
________________________________<br class="">
From: adegenet-forum-bounces@lists.r-forge.r-project.org<mailto:adegenet-forum-bounces@lists.r-forge.r-project.org> [adegenet-forum-bounces@lists.r-forge.r-project.org<mailto:adegenet-forum-bounces@lists.r-forge.r-project.org>] on behalf of Virgilio Massimiliano
[massimiliano.virgilio@africamuseum.be<mailto:massimiliano.virgilio@africamuseum.be>]<br class="">
Sent: 06 January 2015 15:29<br class="">
To: adegenet-forum@lists.r-forge.r-project.org<mailto:adegenet-forum@lists.r-forge.r-project.org><br class="">
Subject: [adegenet-forum] still on Mantel's test<br class="">
<br class="">
Hi again,<br class="">
and happy new year again :-)<br class="">
<br class="">
The second question I have for today is the following:<br class="">
I got this beautiful kernel density of individual geographic vs genetic distances (still playing around with Mantel?s test).<br class="">
It looks like there are a couple of red areas possibly indicating discontinuities between two groups of individuals.<br class="">
<br class="">
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?<br class="">
<br class="">
Cheers<br class="">
<br class="">
Massi<br class="">
<br class="">
<br class="">
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