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No, you're missing an important point. When they get sick they're not allowed to "recover or die", they're culled. Even if they were to recover they'd still be genetically predisposed to the particular disease. Obviously other birds in the flock would also have been exposed to the particular pathogen. The ones that don't get sick are the ones you keep to breed from.
BINGO....If a bird show any sign of the disease/worm/parasite/infection it is culled. Other birds that exsist it the same enviroment may be dealing with the disease/worm/parasite/infection but they are fighting it "in their own way" but show no apparent symptoms of the "inner battle". These are the birds that you would want to use as your breeding foundation. Potenetially they may have some "genetic sequence" or natural immunity which, you as the breeder want to propogate. There may be nothing special about any particular bird but then again There May Be...Unfortunately this pratice isn't followed by the majority of breeders, all species included. The breeder doesn't want to absorb the cost of losing too many birds so they "over madicate" to hide the symptoms, and selling them or breeding them. Thus inheritantly weakening future birds. Building a foundation stock that is prone towards disease resistence doesn't happen overnight. It requires years of breeding and raising healthy birds and heavy culling....You could almost compare the culling method to culling for a show quality bird....Again foundation stock is important, start with junk end with junk....Start with birds from an SQ program cull, to meet the standards, and you have an SQ line....Start with birds from a Line that is prone to be disease resistant, cull birds that don't seem to be AS resistant , and you have a line that is prone to disease resistance...If you look at other species you will soon see that Purebreed/Fullblood Show Quality animals are not, in most cases, the Most Disease Resistant Animals...Breeders consentrate on SQ animals and then MEDICATE to compensate.....
Just to add...everyone would like to have every one of their birds genetically profiled...BUT due to cost reason, Responsible Breeders breeding for a certain trait must rely on the APPARENT absence or presence of the trait we WANT....So we genetically profile by common sense not scientific proof....IMO