[adegenet-forum] number of alleles using microsatellite data for polyploids

[Jombart, Thibaut]

Hi there, 

I'm assuming that for microsat we have access to the genotypes, i.e.88/88 will appear as 88/88 and not just '88'. 

If this is not the case, indeed some estimation is needed, and adegenet does not handle that.

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 Miguel Navascues [m.navascues at gmail.com]
Sent: 26 August 2014 11:07
To: adegenet-forum at lists.r-forge.r-project.org
Subject: Re: [adegenet-forum] number of alleles using microsatellite data for polyploids

Hi Maria,

In order to estimate allele frequencies for polyploids you need specific
methods (see below) that will take into account the type of inheritance
and the probability (given the type of inheritance) of a observed
phenotype of each of the possible genotyopes. With phenotype I mean the
observed size bands (for instance, one individual had bands of size 100,
104, and 108 bp) and with genotype the actual number of copies that the
individual had (for the given example it could be
100,100,100,100,104,108 or 100,100,100,104,104,108, etc., etc., etc.).

To my knowledge adegenet does not implement such methods. You may use
information on presence/absence of one allele though, but I do not
remember how right now...

Best,

Miguel


De Silva et al. (2005) Estimation of allele frequencies in polyploids
under certain patterns of inheritance. doi:10.1038/sj.hdy.6800728


On 25/08/14 23:20, Maria del Carmen David wrote:
> Hello,
> I have a microsatellite data set of an hexaploid organism. I have
> uploaded the data but when I call for the number of alleles per locus I
> get an extra allele (0), it is cause for the zeros I have to put so the
> data can make sense. Now, I'm worried that this allele frequency will
> distortion my results because I want to make a DAPC. In the package
> "poppr" there's a command called "recode.polyploids" to eliminate that
> extra allele but after reading adegenet tutorials I haven't found any
> comment about this issue. Should I eliminate this extra allele or leave
> my data as it is? Thank you for your help.
>
> Maria del Carmen David
>
>
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--
Miguel NAVASCUÉS, PhD

Chargé de Recherche (CR2) INRA

UMR CBGP Centre de Biologie pour la Gestion des Populations
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