You appear to ignore the following statement in the paper cited:

"While SNP analyses can differentiate other honey bee subspecies belonging to different evolutionary groups 29,57,58, mitogenome sequences are not able to differentiate A.m. capensis and A.m. scutellata. "

This does not mean the same type of nuclear SNP analysis would fail with capensis compared to scutellata.  To the contrary the implication is it would work.  It is just a lot more work than doing mitochondria due to the much larger amount of sequencing required.  These authors simply appear to have been looking for an easy way to do the analysis and unfortunately it failed as easy ways do so often.

It comes as no surprise at all to me that phenotype observations show zero correlation with mitochondria.  Take Africanized bees as a good example.  There are really mean bees produced by crossing Africanized drones with non Africanized queens.  The resulting progeny from such a cross will have 100% of their mitochondria from non Africanized sources and if all you look at is mitochondria you will say those mean bees are not Africanized.  It is possible this is epigentic.  Nuclear epigenetics is still genetics.  We just are pretty primitive today in our epigenetic sequencing capabilities.

Dick

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