#####   To generate Mantel correlations between genetic distance and geographic distance, first install the ecodist package into R:

require(ecodist)

#####  Next, you will need to enter geographic distances into R.
#####  We have distance matrices in the files drain.csv and linear.csv.
#####  Import each of these into data frames called drain and linear (What do these look like?):

  drainage<-read.csv("drainage.csv")
  linear<-read.csv("linear.csv")

###### Convert the data frames into matrices, dropping the first row and column:

  drainage.mat<-as.matrix(drainage[2:13,2:13])
  linear.mat<-as.matrix(linear[2:13,2:13])

######  The following command will extract the lower triangle below the diagonal of the matrix,
######  you will need this for the mantel test below:

  drainage.mat[lower.tri(drainage.mat)]

#####   Genetic distance matrix from STRUCTURE (brought into Excel, converted to CSV, diagonal made NA.
  genetic<-read.csv("genetic.csv")
  genetic.mat<-as.matrix(genetic[2:13,2:13])

#####   Use the function mantel to calculate your Mantel correlations:

mantel(genetic.mat[lower.tri(genetic.mat)]~linear.mat[lower.tri(linear.mat)],nperm=100)
mantel(genetic.mat[lower.tri(genetic.mat)]~drain.mat[lower.tri(drain.mat)],nperm=100)

#####  Why did we go through all this trouble rather than just running a Pearson's correlation?

cor(genetic.mat[lower.tri(genetic.mat)],linear.mat[lower.tri(linear.mat)])
cor(genetic.mat[lower.tri(genetic.mat)],drainage.mat[lower.tri(drainage.mat)])