When comparing the heterogeneity of the BSD to that observed within the AKC breeds some caveats should be addressed. One may initially expect long established, well-defined dog breeds to be much less heterogeneous than reported here. While some breeds do have a low HE, such as the Boxer with a HE of 0.320, breeds like the Jack Russell Terrier have a high HE of 0.713 and overall their HE is higher than that of the dingo.So, a breed that's got more genetic diversity than a wild canid with a large population and distribution? I leave for others to decide how that might have happened, but consider that the collie-descended dogs appear similarly situated; the Australian Shepherd is fourth (HE=.696) and the Border Collie is seventh (HE=.669) on this list, and both are in the top third (Table 1). It speaks to the surprising diversity of the breeds, and while it does raise my hopes for the English Shepherd, only an actual study will tell us about genetic diversity there. It certainly makes me wonder what the JRT people do to arrive at that result. Genetic diversity, of course, isn't a panacea for genetic disease (coff hip dysplasia coff collie eye anomaly coff), but it is vastly better than a dozen or more breeds I could name.
Update 4/11/2015: Patrick Burns has more to say about this.