One question that comes to mind immediately for me is the difference between breeds that are, essentially, offshoots of some basic stock vs. breeds that are amalgams of multiple breeds. One could say that to some extent both are true of all breeds, but I think that would be wrong. For instance, the mountain dogs such as the Bernese and the Pyrenees are probably bred from Tibetan mastiffs more or less directly, thus involving a reduction in genetic variation within the breed. In contract, the Newfoundland is also bred from a mastiff stock but possibly with another very distantly related breed added in for special effect (thus offsetting the variation). The doberman is one of the most complex breeds of recent times, with several different breeds used to achieve a true breeding highly specialized form. Breeds that derive mainly from divergence should have different patterns (genetically) than breeds derived from combinatorial breeding.
<a href="http://scienceblogs.com/g...">(I've blogged about this paper here)</a>
