I have to say that I was a little surprised by your interpretations.

>> The identification of evolutionary lineages of honey bees based on forewing venations proved to be highly reliable, which confirms earlier studies. The accuracy of honey bee subspecies identification was less consistent and ranged from 100 to 50% ... 

PB: If the differences between subspecies are nearly impossible to detect..

The study did not say "nearly impossible"

>> In order to keep those breeding lines as pure stocks, breeders need to eliminate colonies representing other subspecies.

PB: These breeders are interesting in marketing "breeds." That can hardly be justification for the prohibition of other "breeds."

If you are trying to keep pure sub-species then surely you must try eliminate other sub-species from your breeding programme.  Is that not logical?

>> The current analysis clearly pointed out difficulties with the discrimination of some subspecies.

PB: Or, it may mean that they aren't different subspecies at all, just differently colored. 

This may or may not be true, but it seems to me to underline the fact that relying on one character (in this wing venation) is not a good idea.

>> The IdentiFly computer software presented here was shown to be highly effective in the discrimination of the evolutionary lineages of honey bees. It was also satisfactorily effective in discriminating most honey bee subspecies, though it failed in some, particularly within the African A lineage.

PB: Again, if you can't tell them apart they shouldn't be split into subspecies at all

A little disingenuous?  That one particular piece of software - despite being "satisfactorily effective in discriminating most honey bee subspecies" - is unreliable for some within the African A lineage, does not lead to the conclusion that "you can't tell them apart".  Other software or other methods might work perfectly well.

PB: Here's an example of two types that are very different externally, but not genetically:
> A.m. capensis and A.m. scutellata have distinctive physiological and behavioral differences ... even if currently no genetic diagnostic markers have been identified for either subspecies.

Perhaps the operative word here is "currently"?

Those of us who have spent a considerable amount of time on forewing morphometry are well aware that the results must be used in conjunction with other characters, e.g. A.m.m. is generally dark brown, overhair length, tomenta width, it produces pure white cappings due to the airspace underneath them, is frugal with winter stores and does not turn feed into more bees regardless of conditions.
But there are some very clear indications from wing morphometry, e.g. A.m.m. is the only sub-species with a negative Discoidal Shift Angle and A.m.c. has a very high Cubital Index (CI) - so high in fact that my software had to be modified to accommodate it (3 is a maximum for other sub-species but A.m.c. can go to 6).  True there is a small overlap between A.m.l. and A.m.c. for CI, but surely colour would then separate them?

Best wishes

Peter 
52°14'44.44"N, 1°50'35"W

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