Description Usage Arguments Details Value Author(s) References See Also Examples
Simulate admixture dynamics with or without selection on a few loci. Although space matters for local density-dependent competition, mating and dispersal are random (uniform) with respect to space.
1 2 3 4 5 |
minX, minY, maxX, maxY |
Limits of the model space in x and y dimensions. |
XY |
Matrix of initial x,y coordinates of individual organinisms. |
Genotypes |
Matrix of genotypes of initial organisms. Each genotype should be coded as 0, 0.5, or 1 for the frequency of alleles derived from one parental population. Rows are organisms, columns are unlinked loci. The first four loci can cause fitness variation. |
beta |
Steepness of an environmental gradient affecting the first locus. |
sel |
Strength of environmental selection affecting the first locus. |
mid |
Midpoint of the environmental gradient affecting the first locus. |
h |
Selection on heterozygotes at the second locus. |
DM |
Matrix of 2-locus fitness values for the 3rd and 4th loci (see |
sigmac |
Local competition parameter: Standard deviation of Gaussian competition function. |
R |
Instantaneous growth rate of the Beverton-Holt model. |
M |
Determines the local carrying capacity of the Beverton-Holt (K = (R-1)*M). |
gens |
Number of generations to simulate. |
immigrants |
If FALSE, the model space is closed to immigration and all boundaries are reflecting. If TRUE, the model is open to immigrants from pure parental populations at each edge of the x-dimension. If TRUE, |
plotgrowth |
If TRUE, the population size at each generation will be plotted. |
m |
Immigration parameter. If |
For the DM incompatibility, the matrix of fitnesses is 3x3, with rows corresponding to the first DM locus and columns correspinding to the second DM locus. Entries are W[i,j], where i and j index genotypes 0, 1, and 2 at the first and second locus, respectively. See example.
A list with
XY |
The x,y coordinates of the diploid individuals in the final generation. |
Genotypes |
The genotypes of the diploid individuals (rows) in the final generation. |
mothers |
The genotypes of the successful mothers in the next-to-last generation (roughly, an "after selection" sample from that generation). |
Benjamin M. Fitzpatrick
Fitzpatrick, B. M. Alternative forms for genomic clines. In review
See spatial.HZ
for a version with limited dispersal and mating distances. The simulated data can be analyzed with Cline.fit
, but the genotypes must be multiplied by 2.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 | ## Not run:
# define space:
minX <- minY <- -3
maxX <- maxY <- 3
# 100 individuals randomly placed:
XY <- cbind(runif(100,minX,maxX),runif(100,minY,maxY))
# simulate secondary contact by sorting aling the x dimension and assigning parental genotypes on each side of the centerline:
XY <- XY[order(XY[,1]),]
Genotypes <- rbind(matrix(0,nrow=sum(XY[,1]<=0),ncol=10),matrix(1,nrow=sum(XY[,1]>0),ncol=10))
# competition parameters:
sigmac <- 0.2; R <- 1.75; M <- 5
# selection, inlcuding heterozygote disadvantage at locus 2 and a DM incompatibility between 3 and 4:
beta <- 0
sel <- 0
mid <- 0
h <- 0.4
DM <- rbind(
c(0,0.2,0.4),
c(0,0.0,0.2),
c(0,0.0,0.0))
# simulate 10 generations, open to immigration:
G10 <- spatial.AD(minX,minY,maxX,maxY,XY,Genotypes,beta,sel,mid,h,DM,sigmac,R,M,gens=10,immigrants=TRUE)
## End(Not run)
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