Sam,

Excellent slides. Without hearing your presentation with them (my caveat), there are two items that I thought may help out.

-  While it is true that people use Fst as a measure of differentiation, it is not metric (e.g., there are cases where it fails the triangle inequality) and as pointed out by Wright (1978) that "The fixation index is thus not a measure of the degree of differentiation in the sense implied in the extreme case by the abasence of any common allele.  It measures differentiation within the total array in the sense of the extent to which the process of fixation has gone toward completion."

- While it is true that the Mantel is used due to non-independence, the verbage on the slide suggests that none of the items in the matrices used for the Mante are independent when in actuality, you can get independent samples from a pair-wise matrix (just not too densly).

Rodney

Hi Sam -

The distances would be a good opportunity to link to lecture 3 where these are introduced. 

Fst is heterozygosity based (and pop) and next go on to allele based, individual measures.   It is a little apples and oranges.  Maybe introduce a population based distance measure that is allele similarity/frequency based (Nei's D, genetic chord, etc) before going on to individual based measures.