[adegenet-forum] adegenet-forum Digest, Vol 77, Issue 2

Wed Jan 7 20:46:16 CET 2015

many thanks again Thibaut :-)
all the best
M.

__________________________________
 Massimiliano Virgilio, PhD

Royal Museum for Central Africa
Leuvensesteenweg 13, B-3080 Tervuren, Belgium, +32 (0) 27695366

massimiliano.virgilio at africamuseum.be<mailto:massimiliano.virgilio at africamuseum.be>

http://www.africamuseum.be/home/contact/staff/VIRGILIO_Massimiliano/

On 07 Jan 2015, at 12:00, adegenet-forum-request at lists.r-forge.r-project.org<mailto:adegenet-forum-request at lists.r-forge.r-project.org> wrote:

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Today's Topics:

  1. Re: still on Mantel's test (Jombart, Thibaut)
  2. Re: still on Mantel's test (Virgilio Massimiliano)

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

Message: 1
Date: Tue, 6 Jan 2015 15:54:06 +0000
From: "Jombart, Thibaut" <t.jombart at imperial.ac.uk>
To: Virgilio Massimiliano <massimiliano.virgilio at africamuseum.be>,
"adegenet-forum at lists.r-forge.r-project.org"
<adegenet-forum at lists.r-forge.r-project.org>
Subject: Re: [adegenet-forum] still on Mantel's test
Message-ID:
<2CB2DA8E426F3541AB1907F98ABA6570ABEB6C48 at icexch-m1.ic.ac.uk>
Content-Type: text/plain; charset="windows-1252"

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

________________________________
From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Virgilio Massimiliano [massimiliano.virgilio at africamuseum.be]
Sent: 06 January 2015 15:29
To: 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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Message: 2
Date: Tue, 6 Jan 2015 15:58:29 +0000
From: Virgilio Massimiliano <massimiliano.virgilio at africamuseum.be>
To: "Jombart, Thibaut" <t.jombart at imperial.ac.uk>,
"adegenet-forum at lists.r-forge.r-project.org"
<adegenet-forum at lists.r-forge.r-project.org>
Subject: Re: [adegenet-forum] still on Mantel's test
Message-ID: <D0D1C48F.116E%massimiliano.virgilio at africamuseum.be>
Content-Type: text/plain; charset="windows-1252"

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

________________________________
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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