[adegenet-forum] confusing p value in mantel test

[Miguel Navascues]

Hello Kelly,

It looks like there is a NEGATIVE correlation between genetic and 
geographical distance, no isolation by distance...

Best,

Miguel


On 18/06/14 13:45, Kelly Bennett wrote:
>
>
> 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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-- 
Miguel NAVASCUÉS, PhD

Chargé de Recherche (CR2) INRA

UMR CBGP Centre de Biologie pour la Gestion des Populations
Institut National de la Recherche Agronomique
Campus International de Baillarguet, CS 30016
34988 Montferrier-sur-Lez (France)

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