[R-sig-genetics] Simulated hybridization from same locus but different alleles with hybridize function in adegenet
Hugo Harrison
hugo.harrison at my.jcu.edu.au
Mon Feb 23 13:38:59 CET 2015
Dear Benjamin,
I can’t offer a solution to your problems in Adegenet, but I can offer a work-around in the mean time.
The software HYBRIDLAB by Nielsen et al 2006 can simulate purebred and hybrid genotypes and has been used to distinguish hybrid genotypes in fishes and trees (see references below). I think what you’re attempting is exactly what we did for the nemo story. I don’t think HYBRIDLAB is still supported but I can send you a copy.
Adegenet would of course, be a much more elegant and flexible solution, though HYBRIDLAB certainly does the job. I would be keen to hear of the solution to your problems.
Regards,
Hugo
Simpson SD, Harrison HB, Claereboudt MR, Planes S (2014) Long-Distance Dispersal via Ocean Currents Connects Omani Clownfish Populations throughout Entire Species Range (JA Craft, Ed,). PLoS ONE, 9, e107610.
Harrison HB, Feldheim KA, Jones GP et al. (2014) Validation of microsatellite multiplexes for parentage analysis and species discrimination in two hybridizing species of coral reef fish (Plectropomus spp., Serranidae). Ecology and Evolution, 4, 2046–2057.
Burgarella C, Lorenzo Z, Jabbour-Zahab R et al. (2009) Detection of hybrids in nature: application to oaks (Quercus suber and Q. ilex). HEREDITY, 102, 442–452.
Guichoux E, Lagache L, Wagner S, Léger P, Petit RJ (2011) Two highly validated multiplexes (12-plex and 8-plex) for species delimitation and parentage analysis in oaks (Quercus spp.). MOLECULAR ECOLOGY RESOURCES, 11, 578–585.
NIELSEN EE, BACH LA, KOTLICKI P (2006) hybridlab (version 1.0): a program for generating simulated hybrids from population samples. MOLECULAR ECOLOGY NOTES, 6, 971–973.
Hugo B. Harrison, PhD
Research Fellow
ARC Centre of Excellence for Coral Reef Studies
James Cook University
Townsville, QLD 4811
Australia
Ph: +61 (0) 747816358
Mob: +61 (0) 499523939
hugo.harrison at my.jcu.edu.au <mailto:hugo.harrison at my.jcu.edu.au>
ResearcherID: F-6830-2012 <http://www.researcherid.com/rid/F-6830-2012>
www.coralcoe.org.au <http://www.coralcoe.org.au/researchers/dr-hugo-b-harrison-postdoctoral-research-fellow>
> On 23 Feb 2015, at 8:52 pm, Benjamin Alric <benjamin.alric at imbe.fr> wrote:
>
> 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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