[R-sig-genetics] Simulated hybridization from same locus but different alleles with hybridize function in adegenet

[Jombart, Thibaut]

Hello, 
this email belongs to the adegenet forum (I'll reply there), where you posted the same question already. 
Please avoid double-posting.. 
Thanks and all the best
Thibaut

________________________________________
From: R-sig-genetics [r-sig-genetics-bounces at r-project.org] on behalf of Benjamin Alric [benjamin.alric at imbe.fr]
Sent: 23 February 2015 10:52
To: r-sig-genetics at r-project.org
Subject: [R-sig-genetics] Simulated hybridization from same locus but different alleles with hybridize function in adegenet

Dear all,

I would like simulated hybridization between two population to assess
the power of admixture analysis (STRUCTURE).
I built two subsamples consisting of 30 indivudals showing the highest q
values for the cluster1 or cluster2 of previously STRUCTURE analysis.
 From these two subsamples I would like simulated hybridization (using
hybridize function of the adegenet R package) to assess the power of
admixture analysis.
For each population, genotype were determined through 8 microsatellite
loci for wichi one allele is code by a character string of 3 numbers.
Here you are the command:

Dg<-import2genind("B_Dg.gtx",package="adegenet")
Dl<-import2genind("B_Dl.gtx",package="adegenet")
Dg<- #####################
    ### Genind object ###
    #####################
- genotypes of individuals -

S4 class:  genind
@call: read.genetix(file = file, missing = missing, quiet = quiet)

@tab:  30 x 33 matrix of genotypes

@ind.names: vector of  30 individual names
@loc.names: vector of  8 locus names
@loc.nall: number of alleles per locus
@loc.fac: locus factor for the  33 columns of @tab
@all.names: list of  8 components yielding allele names for each locus
@ploidy:  2
@type:  codom

Optional contents:
@pop:  factor giving the population of each individual
@pop.names:  factor giving the population of each individual

@other: - empty -

Dl<-#####################
    ### Genind object ###
    #####################
- genotypes of individuals -

S4 class:  genind
@call: read.genetix(file = file, missing = missing, quiet = quiet)

@tab:  30 x 33 matrix of genotypes

@ind.names: vector of  30 individual names
@loc.names: vector of  8 locus names
@loc.nall: number of alleles per locus
@loc.fac: locus factor for the  33 columns of @tab
@all.names: list of  8 components yielding allele names for each locus
@ploidy:  2
@type:  codom

Optional contents:
@pop:  factor giving the population of each individual
@pop.names:  factor giving the population of each individual

@other: - empty -

hybrdis<-hybridize(Dg,Dl,n=100,pop="Hybrids")
g1<-genind2df(hybrids)
g1<-
          pop       10_14      Dp512     SwiD1            SwiD10
SwiD12    SwiD14    SwiD15    SwiD5
h001 Hybrids 226226    129         131143          194201 112119
181185   093098    161161165
h002 Hybrids 220226    129         126138          200201    112 175
181181   089098    151153165
h003 Hybrids 220226    129         126134143    200 123123    185185
093098    153163165
h004 Hybrids 220226    129         126131          200201 119123
185185   093098    153153165
h005 Hybrids 220226    129         126136136    199 123123    181185
089098    153161165
h006 Hybrids 226226    129129   136136          194 112112    181181
089098    153161165
h007 Hybrids 220226    129133   134143          194          119 175
181185   093          151153163165
....

We would expect to see two allele for each locus but it is not the case
for all microsatellite loci.
Somebody know why and where does the problem?

I checked the example dataset "microbov" for hybridize function, and I
see that temp$Salers and temp$Zebu (used to perform simulated
hybridization with hybridize function) presented the same count of
alleles at each locus.
When I check now my two datasets, I see that there are not the same
number of allele between the two populations. such a difference in the
number of allele between the two population could be the origne of the
problem...

Dg at all.names
$L1
     1     2     3
"220" "226" "231"

$L2
     1     2     3
"125" "129" "133"

$L3
     1     2     3     4     5     6
"126" "131" "134" "136" "138" "143"

Dl at all.names
$L1
     1     2     3
"223" "226" "229"

$L2
     1     2     3     4     5     6
"129" "133" "136" "137" "138" "139"

$L3
     1     2     3     4     5     6     7
"118" "134" "136" "138" "145" "150" "152"

Thank in advence for your help.

Sincerely yours,

Benjamin ALRIC



--

--
Benjamin Alric,PhD
UMR 7263-CNRS / 237-IRD - Institut Méditerranéen de Biodiversité et d'Ecologie (IMBE)
Equipe "Ecologie des Eaux Continentales"
Aix-Marseille Université, Faculté des Sciences, site de St Jérôme
52 Avenue Escadrille Normandie Niémen
13397 Marseille cedex 20 - France
Tél: +33 (0)4 13 59 46 46

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