adegenet (version 1.4-2)

sim2pop: Simulated genotypes of two georeferenced populations

Description

This simple data set was obtained by sampling two populations evolving in a island model, simulated using Easypop (2.0.1). See source for simulation details. Sample sizes were respectively 100 and 30 genotypes. The genotypes were given spatial coordinates so that both populations were spatially differentiated.

Usage

data(sim2pop)

encoding

UTF-8

format

sim2pop is a genind object with a matrix of xy coordinates as supplementary component.

source

Easypop version 2.0.1 was run with the following parameters: - two diploid populations, one sex, random mating - 1000 individuals per population - proportion of migration: 0.002 - 20 loci - mutation rate: 0.0001 (KAM model) - maximum of 50 allelic states - 1000 generations (last one taken)

References

Balloux F (2001) Easypop (version 1.7): a computer program for oppulation genetics simulations Journal of Heredity, 92: 301-302

Examples

data(sim2pop)

if(require(hierfstat)){
## try and find the Fst
temp <- genind2hierfstat(sim2pop)
varcomp.glob(temp[,1],temp[,-1])
# Fst = 0.038
}

## run monmonier algorithm

# build connection network
gab <- chooseCN(sim2pop@other$xy,ask=FALSE,type=2)

# filter random noise 
pca1 <- dudi.pca(sim2pop@tab,scale=FALSE, scannf=FALSE, nf=1)

# run the algorithm
mon1 <- monmonier(sim2pop@other$xy,dist(pca1$l1[,1]),gab,scanthres=FALSE)

# graphical display
temp <- sim2pop@pop
levels(temp) <- c(17,19)
temp <- as.numeric(as.character(temp))
plot(mon1)
points(sim2pop@other$xy,pch=temp,cex=2)
legend("topright",leg=c("Pop A", "Pop B"),pch=c(17,19))