########################################################
#### Perform Mantel tests for both species. ####
########################################################
########################################################
##### Genetic distances included Gst (Nei 1973) #####
##### and G''st (Hedrick 2005) #####
########################################################
##### Geographic distances were evaluated with #####
##### and without log transformation #####
##### (i.e., Rousset 1997, 2000) #####
########################################################
##### Load required packages #####
library(vegan)
library(geosphere)
library(mmod)
library(VPLandscapeGenetics)
data(VPLandscapeGenetics)
##### Calculate genetic and geographic distances #####
## Genetic distances
hedrick.SS <- as.matrix(pairwise_Gst_Hedrick(genind.SS))
nei.SS <- as.matrix(pairwise_Gst_Nei(genind.SS))
hedrick.WF <- as.matrix(pairwise_Gst_Hedrick(genind.WF))
nei.WF <- as.matrix(pairwise_Gst_Nei(genind.WF))
## Linearized genetic distances
hedrick.SS.lin <- hedrick.SS / (1-hedrick.SS)
nei.SS.lin <- nei.SS / (1-nei.SS)
hedrick.WF.lin <- hedrick.WF / (1-hedrick.WF)
nei.WF.lin <- nei.WF / (1-nei.WF)
## Geographic distances
geoDist.SS <- as.numeric(distm(latLong.SS, fun=distGeo))
dim(geoDist.SS) <- c(90, 90)
dimnames(geoDist.SS) <- list(1:90, 1:90)
geoDist.WF <- as.numeric(distm(latLong.WF, fun=distGeo))
dim(geoDist.WF) <- c(87, 87)
dimnames(geoDist.WF) <- list(1:87, 1:87)
## Log transform geographic distance
geoDist.SS.log <- log(geoDist.SS)
geoDist.WF.log <- log(geoDist.WF)
##### Perform Mantel tests #####
mantel.hedrick.SS <- mantel(as.dist(hedrick.SS.lin), as.dist(geoDist.SS), permutations = 9999)
mantel.hedrick.log.SS <- mantel(as.dist(hedrick.SS.lin), as.dist(geoDist.SS.log), permutations = 9999)
mantel.nei.SS <- mantel(as.dist(nei.SS.lin), as.dist(geoDist.SS), permutations = 9999)
mantel.nei.log.SS <- mantel(as.dist(nei.SS.lin), as.dist(geoDist.SS.log), permutations = 9999)
mantel.hedrick.WF <- mantel(as.dist(hedrick.WF.lin), as.dist(geoDist.WF), permutations = 9999)
mantel.hedrick.log.WF <- mantel(as.dist(hedrick.WF.lin), as.dist(geoDist.WF.log), permutations = 9999)
mantel.nei.WF <- mantel(as.dist(nei.WF.lin), as.dist(geoDist.WF), permutations = 9999)
mantel.nei.log.WF <- mantel(as.dist(nei.WF.lin), as.dist(geoDist.WF.log), permutations = 9999)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.