>Temper shifts in colonies can simply be related to season itself, food availability, pest presence etc.
Temper. Yes. Color. No.
I am hearing exactly what you say, but this has not been published. It has been said to me by a few beekeepers over the years. I'm not saying it doesn't happen either.
In most cases their queens are not marked or wings clipped and they cannot guarentee 100% that it was the original queen.
I've worked 300 colonies for the last 15 years and can't say I've seen this happen. It doesn't mean it doesn't, but it would be a hard one to research and publish without many replicates.
What you see visually and what you see with genetics can be deceiving from both directions. As I said, we have genotyped 1000,s of colonies with 200 bee samples and all subfamilies are always represented.
It is 100% verified by removing the queens spermatheca and genotyping the sperm within it.
There is still a lot we don't know about things like sperm competition and mate choice (wether they can naturally avoid in-breeding or not) however it's not yet published but we a working on it.
We have just completed a large experiment individually watching more than 300 queens going on mating flights, how many flights, duration, mating sign,s etc. We have then genotyped the brood to look at the amount of sub-families present, over several seasons and in multiple countries.
We are also looking at mate choice in remote location by providing queens with related drones, unrelated drones, and mixed populations to investigate the issue of mate choice.
Hopefully we will have some useful answers shortly.