adegenet (version 1.0-0)

nancycats: Microsatellites genotypes of 237 cats from 17 colonies of Nancy (France)

Description

This data set gives the genotypes of 237 cats (Felis catus L.) for 9 microsatellites markers. The individuals are divided into 17 colonies whose spatial coordinates are also provided.

Usage

data(nancycats)

format

nancycats is a genind object with spatial coordinates of the colonies as a supplementary components ($xy). Beware: these coordinates are given for the true names (stored in $pop.names) and not for the generic names (used in $pop).

source

Dominique Pontier (UMR CNRS 5558, University Lyon1, France)

References

Devillard, S.; Jombart, T. & Pontier, D. Disentangling spatial and genetic structure of stray cat (Felis catus L.) colonies in urban habitat using: not all colonies are equal submitted to Molecular Ecology

Jombart, T.; Devillard, S.; Dufour, A. & Pontier, D. A multivariate method to investigate spatial patterns of genetic variability submitted to Molecular Ecology

Lalo"e D., Jombart T., Dufour A.-B. and Moazami-Goudarzi K. (2007) Consensus genetic structuring and typological value of markers using Multiple Co-Inertia Analysis. accepted in Genetics Selection Evolution.

Examples

data(nancycats)
nancycats

# summary's results are stored in x
x <- summary(nancycats)

# some useful graphics
barplot(x$loc.nall,ylab="Alleles numbers",main="Alleles numbers
per locus")

plot(x$pop.eff,x$pop.nall,type="n",xlab="Sample size",ylab="Number of alleles")
text(x$pop.eff,y=x$pop.nall,lab=names(x$pop.nall))

par(las=3)
barplot(table(nancycats$pop),ylab="Number of genotypes",main="Number of genotypes per colony")

# are cats structured among colonies ?
if(require(hierfstat)){

if(require(ade4)){
gtest <- gstat.randtest(nancycats,nsim=99)
gtest
plot(gtest)
}

dat <- genind2hierfstat(nancycats)

Fstat <- varcomp.glob(dat$pop,dat[,-1])
Fstat
}