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

[Benjamin Alric]

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, Post-Doc
UMR CNRS 5558 - LBBE
"Biométrie et Biologie Evolutive"
UCB Lyon1
Equipe Ecologie Quantitative et Evolutive des Communautés
Bâtiment Grégor Mendel
43 bd du 11 novembre 1918
69622 Villeurbanne Cedex
FRANCE
__________________________________________