[adegenet-forum] possibility to use adegenet on seeds data

[valeria montano]

Dear Thibaut and Diane,

I was thinking... considering that leaves' genotypes are parental
generation and seeds are progeny 1 and so they are different individuals
(despite the fact that the seeds are physically all together on the same
plant), maybe you could just put any genotype as a single ind, instead of
creating a super-gen.ind-pop-object which in this case would be rather a
"gen.fam" (family, each pop is mother plant and children). If you put them
separately, you would have a lot of individuals in a pop with a
high inbreeding coefficient and overlapping generations (light years far
from HW equilibrium), but as long as you are interested in pop structure,
maybe this is better than a pop composed by multi-related-genotyped
individuals. Or do you think it doesn't make that much difference?

(sorry for the nerdy explicit content of this post)
Cheers

Valeria

On 22 November 2011 11:26, Jombart, Thibaut <t.jombart at imperial.ac.uk>wrote:

> Hello,
>
> yes; what you need to do is have a factor defining "plants" and use it
> when constructing your genpop object, so that leaves and seeds of a given
> plant will give allele frequencies in the plant, considered as a
> "population" (i.e. a group of genotypes).
>
> Then you can run multivariate analyses on the obtained genpop.
>
> Cheers
>
> Thibaut
> ________________________________________
> From: Diane Bailleul [diane.bailleul at u-psud.fr]
> Sent: 22 November 2011 10:14
> To: Jombart, Thibaut
> Cc: adegenet-forum at r-forge.wu-wien.ac.at
> Subject: Re: [adegenet-forum] possibility to use adegenet on seeds data
>
> Hi and thanks for your answer.
> I've got proper genotypes for seeds and leaves. The only difference is
> that I've got one leaf for each plant and several seeds for the same
> plant. And the genotypes of the seeds that belong to the same plant can
> be similar, or not.
> I'd like to perform a PCA on my data to see if there's a genetic
> structuration of my big populations.
> If I transform each bunch of seeds per plant in a genpop object (if I
> understand correctly what you suggest), will I be able to mix these
> genpop objects with the leaves informations in a genind object ?
>
> Le 11/21/2011 12:44 PM, Jombart, Thibaut a écrit :
> > Hello,
> >
> > I know some users have used adegenet to analyse plant data... anyone
> care to share his/her experience?
> >
> > I am not sure about what your seed data look like. Is it a mixture of
> alleles? Or do you have proper genotypes? In the second case, then I would
> consider genotypes as 'individuals' (genind object), and seeds as
> 'populations'. You would probably carry out most of your analyses at a
> 'population' (seed level) using a genpop object. Having a look at the
> vignette "adegenet-basics" (type vignette("adegenet-basics")) may help for
> genind/genpop conversions.
> >
> > Cheers
> >
> > Thibaut
> >
> > ________________________________________
> > From: adegenet-forum-bounces at r-forge.wu-wien.ac.at [
> adegenet-forum-bounces at r-forge.wu-wien.ac.at] on behalf of Bailleul [
> diane.bailleul at u-psud.fr]
> > Sent: 19 November 2011 21:45
> > To: adegenet-forum at r-forge.wu-wien.ac.at
> > Subject: [adegenet-forum] possibility to use adegenet on seeds data
> >
> > Good afternoon,
> >
> > I'm sorry to bother you but I've read the adegenet documentation and I
> can't find the answer to my question.
> >
> > I've got a data set of genotypes of plant samples of leaves and seeds
> divided between different populations.
> >
> > For leaves, each genotype is an plant. But for seeds, I've got 2 or 8
> differents genotypes of 2 or 8 seeds for the same individual.
> >
> > The data set is divided as followed : populationX/plantX/seedX for seeds
> or populationX/plantX for leaves.
> >
> > Can I use the adegenet package to analyse my data ? Is there is any risk
> that each seed will be considered as one plant ?
> >
> > Thanks for your answer,
> >
> > Diane
> >
>
>
> --
> Diane Bailleul
> Doctorante
> Université Paris-Sud 11 - Faculté des Sciences d'Orsay
> Unité Ecologie, Systématique et Evolution
> Département Biodiversité, Systématique et Evolution
> UMR 8079 - UPS CNRS AgroParisTech
> Porte 320, premier étage, Bâtiment 360
> 91405 ORSAY CEDEX FRANCE
> (0033) 01.69.15.56.64
>
>
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