[adegenet-forum] DAPC: shall I keep or exclude repeated genotypes ?

[Thibaut Jombart]

Hello,

changes are to be expected, as repeated genotypes form, by definition,
clusters. So by adding/removing them you are effectively adding or removing
clusters. Mathematically this is reflected by the variance components
(total, between, within), which are all sums over individuals, and
therefore change when adding / removing individuals.

In one case, your clustering solution will likely mostly reflect the
presence of identical genotypes. In the second case, clusters will give an
account of the diversity between unique genotypes.

Best
Thibaut


--
Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology, Imperial College
London
Head of RECON: repidemicsconsortium.org
sites.google.com/site/thibautjombart/
github.com/thibautjombart
Twitter: @TeebzR <http://twitter.com/TeebzR>
+44(0)20 7594 3658

On 24 April 2017 at 13:04, Adrien Rieux <adrien.rieux at cirad.fr> wrote:

> Hi there,
>
> I’ve got a question regarding the assessment of genetic structure from
> microsatellite data using the DAPC method. My dataset contains around 30%
> of repeated genotypes. I observe different and contrasted results (BIC as a
> function of the number of clusters) when I keep or exclude repeated
> genotypes (find.clusters function). Has someone ever experienced this
> situation and how would you explain it ? I would have predicted that
> finding the optimal number of clusters should not be influenced by repeated
> genotypes as the DAPC is only based on the variation between genotypes. Is
> there a general recommendation whether keeping or excluding repeated
> genotypes when performing DAPC ?
>
>
> Cheers,
>
> Adrien
>
> --
>
> Adrien RIEUX
> CIRAD - Dpt BIOS - UMR PVBMT
> Tel: 0262499219
> https://adrienrieux.wordpress.com/home/
>
>
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