Both authors state the problems with mitotyping (based upon mitochondrial
DNA), but neither makes it clear to me that they are comparing SNPs only
from nuclear DNA (which would be the genes associated with behavioral
traits). Could you please clarify this for the benefit of the List?

I think mitochondrial dna was chosen for analysis back in the 1980s because the mitochondrial genome is relatively small. For example, if you count the base pairs as letters (GATC), the length of the mitochondrial genome is like a 4000 or so word article. You could read it in 15 minutes. The honey bee genome has an estimated 270 million bases, which would be roughly the same number of letters in the Encyclopedia Britannica (about 55 million words).  By focusing on one area of the mtDNA, one can easily differentiate between African, European and Asian bees, for instance, but not between Italians and Carniolans.

> Moritz et al. investigated mtDNA restriction fragment polymorphisms in nine honeybee hives representing three European subspecies, A.m. carnica, A. m. ligustica and A. m. caucasica. They observed little variation among the three subspecies; ... they found no differences between A. m. ligustica and A. m. carnica, and estimated 0.76 % sequence divergence between these two subspecies and A. m. caucasica.  -- Smith, D. R., & Brown, W. M. (1988). Polymorphisms in mitochondrial DNA of European and Africanized honeybees (Apis mellifera). Experientia, 44(3), 257-260.

The initial problems with whole genome sequencing were excessive cost, technical difficulty and the problem of processing and analyzing so much data. These problems have been significantly reduced. Given the ability to analyze whole genome information, a much more fine grained picture emerges of the difference between various honey bee genotypes. 

When reading through these papers, one sees reference to SNPs (single nucleotide polymorphisms). A SNP is an instance where one letter in a sequence has changed. Usually this is due to spontaneous mutation or copy error, and usually these SNPs do not change function, especially if they occur in non-coding regions. Sometimes a single letter mutation is lethal, but then that mutation would not get passed on. Sometimes mutations lead to changes which contribute to evolution of the species, and even new species. 

Anyway, the most recent work by Harpur & Zayed describes 3,606,720 SNPs. Obviously this did not come from mtDNA because there aren't that many base pairs, let alone potential sites for single point mutations. Oldroyd lists only 95 needed to identify African bees, however this still represents a lot of DNA that would need to be analyzed. Yet this is minuscule compared to 3.6 million variants. Also, they have identified mutations occurring in known gene regions, which may help to identify functional changes:

> With 3,606,720 SNPs and 155,336 SNPs within 11,365 genes, this data set is the largest genomic resource available for AHBs and will enable high-resolution studies of the population dynamics, evolution, and genetics of this successful biological invader, in addition to facilitating the development of SNP-based tools for identifying AHBs.

See:
A variant reference data set for the Africanized honeybee, Apis mellifera.
Samir M. Kadri, Brock A. Harpur, Ricardo O. Orsi & Amro Zayed
Published: 8 November 2016     www.nature.com/scientificdata

PLB

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