I think it is worthwhile to recap what Mike Allsopp actually says regarding bee breeding:

> Researchers (e.g. Danka et al 1997; Rinderer et al 2001) have argued that there would be no natural resistance to varroa, and that all unmanaged colonies would be eliminated with only especially bred commercial stock being able to survive. Chemical or biotechnical treatment of colonies (Van Dung et al 1997; Goodwin & Van Eaton 2001), and the breeding of selected stock to develop resistance (Rinderer et al 2001), are held as the only way to maintain colonies faced with the varroa mite. There have also been suggestions that this resistance needs to be maintained through controlled mating and/or gene based selection made possible by the Honeybee Genome project (Evans 2005), much as happens in many varieties of livestock and plant crops. 

> The existence of naturally occurring varroa tolerant honeybee populations around the world makes a mockery of these claims, and I would argue that this methodology, albeit seductive, would be ineffective, as has been the case with bee breeding in general. Captive breeding programmes and especially gene selection programmes can never adequately keep up with the changing environment, certainly not to the extent that a “live-and-let-die” approach can. Allowing natural selection to determine who the winners are, will always be the most sensible strategy. This may not sit well with generations of bee-masters and bee scientists, but the dominance of unmanaged bees takes some explaining away. The success of A.m.scutellata in the Americas and the failure of bee diseases in Africa, are two examples that support this approach. 

source: Allsopp Thesis

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