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

[Vojtěch Zeisek]

Hi,
I'm not sure if it is the point, but there are two common workarounds for 
polyploids and microsatellites. First is if one has more ploidy levels, e.g. 
tetraploids and hexaploids and used software requires only one ploidy level, 
one can add zeroes (or NAs) to „mimic“ the highest ploidy level. In the 
mentioned case, the tetraploids would get extra data to look like hexaploids. 
I have doubts about that approach.
Second possibility is to recode microsatellites as presence/absence data. This 
is particularly useful if the ploidy level is high and one cann't be sure 
about the pattern (Do I have 88/88/88/90 or 88/88/90/90? And so on.), PCR can 
be sometimes hard to read. Then one has similar problem with too much zeroes 
and/or NAs, especially when mixing ploidy levels.
So that the problem can be „How to code my data to keep as much information as 
possible for the software.“.
Sincerely,
Vojtěch

Dne Út 26. srpna 2014 11:23:22, Jombart, Thibaut napsal(a):
> 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

-- 
Vojtěch Zeisek
http://trapa.cz/en/

Department of Botany, Faculty of Science
Charles University in Prague
Benátská 2, Prague, 12801, CZ
http://botany.natur.cuni.cz/en/

Institute of Botany, Academy of Science
Zámek 1, Průhonice, 25243, CZ
http://www.ibot.cas.cz/en/

Czech Republic
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