I would second what Peter said about phenotypical differences being quite observable while genetic differences may be minute.  Let me give an example.  Holstein cattle historically were black and white.  There was even a definition of how much white and where that white had to be in order to register a critter as pure bred, even if that critter was produced by two registered parents.  Then some red mutations snuck into the bred via bulls that passed on great milk production, but happened to be heterozygous for red.  The ultimate result is today there are registered red Holsteins.  Does that red make them genetically different?  Only at one tiny locus which would likely never even show in a study such as the one on Australian ferals and domestics.  Likewise in Dads herd we had one behavior problem cow.  She was mean.  Looking at the transmission of this to her daughters it was an autosomal dominant.  Would this have shown in a genetic study such as was done on bees?  Not at all likely, but I can tell you if you were the one milking this gal you would figure it out real quick.

My point is there is a big difference between looking at a couple of phenotypes and looking at overall genetic structure.  The two can give very conflicting answers.

Dick
" Any discovery made by the human mind can be explained in its essentials to the curious learner."  Professor Benjamin Schumacher talking about teaching quantum mechanics to non scientists.   "For every complex problem there is a solution which is simple, neat and wrong."  H. L. Mencken

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