I am trying to complete pairwise comparisons of 9 forest communities. Communities were significant at p < 0.001 using adonis. However, when I use the same bray curtis matrix with the pairwise.perm.manova funtion I get several insignificant results. Some are understandale, others are not. 4 communities that were insignificant for all pairwise comparisons between each other had the same p value (0.103). looking into the bray curtis matrix, comparison of sites between two of these communities received a bray curtis score of 1.00 in every case and a look into the species assemblage used to make the bray curtis matrix, showed that these 2 communities shared no species with each other. how its it that 2 entirely unique species assemblages prove insignificant? other pairwise comparisons that proved insignificant share very few species and in very dissimilar proportions. also, I did see significance with many other pairwise comparisons that achieved much lower bray curtis scores and much more similar species assemblages.
Can anyone help me with this? it seems so odd that these dissimilar communities all achieved the same insignificant p value (0.103).
SNWR_Over <- read.table("Live_Over_Dom_2019_01_16.csv", sep = ",", header = TRUE, row.names = 1) ####table of sites and the species assemblage
SNWR_Over.t <- (SNWR_Over)^.5
SNWR_ct <- read.table("Plot-Covertype.csv", sep = ",",header = TRUE) ###table of sites and the covertype they represent
SNWR_Over_bray <- vegdist(SNWR_Over.t, method = "bray")
SNWR_disper <- betadisper(d = SNWR_Over_bray, group = SNWR_ct$Covertype)
SNWR_dist_perm <- permutest(SNWR_disper)
SNWR_dist_perm #### p = 0.063
SNWR_adonis <- adonis(formula = SNWR_Over_bray ~ SNWR_ct$Covertype)
SNWR_adonis #### p<0.001