Interesting paper, but I think it misses a fundamental point: the genetic diversity of the apple is very well represented by the zillions of wild seedling trees all over the world. These wild apple trees contain much more diversity than all the heirloom varieties that have (or may) disappeared.
Just today, one man invited me to visit his piece of land. We found there dozens of thriving apple trees plus many very young trees that will insure next generation. The variety of flavors was simply awsome, some acidic, some sweet, more or less sugar, more or less juicy, some nice and big others small and ugly, some with bitterness or astringency, no scab... There were also dozens of apple tree skelettons - trees that have died 10 or 20 years ago. In other words there is in this mixed forest a population of apple trees that have adapted and survived for maybe 150 or 200 years. And this place is just one of thousands of similar sites in North America. That is where the genetic diversity lies.
Also let's remember a variety is actually an individual that has been cloned into millions of identical trees. It is in the nature of things that individuals die, and new individuals are born, live, reproduce themselfs and die... There is no reason to regret the dozens of apple tree skelettons we saw today - but each was a unique individual and could have been named to become a cultivar. Just that no one was there to assess their qualities - only bears, deers, racoons and porcupines.
Jolicoeur OrchardZone 4 in Quebec
Author,
The New Cider Maker's Handbook