[adegenet-forum] confusing p value in mantel test

[Kelly Bennett]

Hello,

I have run a mantel test with the following code

dna <- read.dna(file = "dna_manteltest.fasta", format = "fasta")
dna.dists <- dist(dna, method = "euclidean")
as.matrix(dna.dists)[1:5, 1:5]
geo <- read.csv(file = "geo_matrix.csv")
geo[1:2, 1:2]
geo.dists <- dist(geo, method = "euclidean")
as.matrix(geo.dists)[1:5, 1:5]
mantelresult<-mantel.rtest(dna.dists, geo.dists, nrepet = 9999)
cor.test(geo.dists, dna.dists)
plot(mantelresult <- mantel.rtest(dna.dists, geo.dists), main = "Mantel's test")
mantelresult

>From my plot it looks like there should be isolation by distance and a correlation test shows a significant association but my p value for the Monte Carlo test = 1

Does anyone have any ideas about this contradiction? I have attached the plot to this email

Thank you very much,

Kelly


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