> Has anyone come across references about genetic analysis suggesting the presence of capensis in the New World?


Technically, by way of Kerr, capensis genes are in Brazil and the lower US because they are basically indistinguishable from scuts at the mitogenomic level.  But, as Pete points out, the discussion about subspecies differentiation is ongoing in Africa and elsewhere.    In this case, though, I think it's safe to argue that capensis and scuts are different subspecies based on morphometrics and behavior and that they only interact parasitically with beekeeper intervention. (See the Capensis Calamity literature for details)  Why capensis evolved with the capability for thelytokous parthenogenesis (the ability of workers to lay diploid, female-destined eggs without mating) is interesting but perplexing because they don't act as parasites when they have a capensis queen.   



> A stable hybrid zone separates the populations of A.m. capensis and A.m. scutellata in the RSA [Republic of South Africa], with A.m. scutellata to the north and A.m. capensis to the south. Neither subspecies has naturally expanded into the other subspecies’ geographic region despite their parasitic (A.m. capensis) or invasive (A.m. scutellata) capabilities. In addition to the wide variety of behavioral and reproductive differences between the two subspecies, morphometric comparisons demonstrate that the subspecies have undergone sufficient morphological differentiation to be recognized as distinct subspecies. 

> Mitochondrial genome diversity and population structure of two western honey bee subspecies in the Republic of South Africa
Amin Eimanifar, Rebecca T. Kimball, Edward L. Braun, and James D. Ellis

>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5778041/

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