Dismantling the Mantel tests
  The simple and partial Mantel tests are routinely used in many areas of evolutionary biology to assess the significance of the association between two or more matrices of distances relative to the same pairs of individuals or demes. Partial Mantel tests rather than simple Mantel tests are widely used to assess the relationship between two variables displaying some form of structure.   We show that contrarily to a widely shared belief, partial Mantel tests are not valid in this case, and their bias remains close to that of the simple Mantel test.   We confirm that strong biases are expected under a sampling design and spatial correlation parameter drawn from an actual study.   The Mantel tests should not be used in case auto-correlation is suspected in both variables compared under the null hypothesis. We outline alternative strategies. The R code used for our computer simulations is distributed as supporting material. 
Gilles Guillot and Fran\c{c}ois Rousset
q-bio.PE