Origins Of Honey Bees

DNA double helix
Photo by Braňo on Unsplash

Genetic science has come on in leaps and bounds in the last few decades. It turns out that appearances can be deceptive as far as genes go. Even with their large population and worldwide distribution, humans have a remarkable lack of genetic diversity. Despite what we look like and where we live, we are all very close. With honey bees, it’s different. Of course, honey bees have been around for approximately 60 million years (give or take a few million). In contrast, modern humans appeared about 200,000 years ago. So bees have had a lot more time.

Subspecies of Apis mellifera

When biologists classified the various honey bee subspecies, they focused on appearance, behaviour and geography – not DNA. I believe there are now 33 different subspecies, which seems like a lot. Lots of clever research has been done using modern genetic science, including testing material from old honey bees preserved in museums. There is constant gene flow between most subspecies nowadays due to the lack of natural isolation mechanisms (the ice age is long gone). Some isolated populations have remained on mountains and islands, but there is massive ongoing hybridisation. 

Based on morphological similarities and separation of regions, five main ‘lineages’ of honey bees were established. These are five genetically distinct evolutionary lineages where genetic differences between subspecies within lineages are relatively small and genetic differences between lineages are large. Arguments continue regarding the species’ ancestral origin and subsequent expansion into Europe (C and M lineage), Africa (A lineage), and Asia (O and Y lineage). 


Some funky genetic science, which I don’t properly understand, in this article was done analysing different subspecies. It turns out that the main lineage groups (M, C, O, A) work out pretty well. Carnica and ligustica are close genetically and geographically. So, apparently are mellifera and iberiensis.

Honey bee lineage clusters
Clusters of genetic similarity correspond to lineage


Recent advances in population and quantitative genomics of honey bees (Kathleen A Dogantzis and Amro Zayed): The availability of bee genomes and SNP resources has significantly facilitated our ability to study admixture and estimate ancestry proportions in honey bee populations. The geographic proximity of Apis mellifera’s ancestral lineages, combined with human-mediated dispersal of bee populations, has resulted in a considerable degree of genetic admixture between natural and managed honey bee colonies. For example, recent studies of M lineages subspecies from Western Europe have found signs of introgression from C lineage bees. In the new world and Australia, honey bee importations for apiculture – primarily subspecies from the M and C lineages – has resulted in heavily admixed commercial colonies. Furthermore, the introduction of A. m. scutellata (A lineage) from South Africa to South America in 1956 has led to genetically introgressed populations of invasive Africanized bees comprised of approximately 75% A and 25% M lineage ancestry.

So, a combination of the ending of the last ice age plus explosive growth in trade and movement of livestock by humans has led to increased mixing up of honey bee genes. I don’t know if that’s good or bad, but if humans were involved, it’s probably bad. 

Colony Level

Suppose we zoom in a bit down to the individual colony scale. In that case, we can see the mating of queens is designed to lower inbreeding and increase the mixing up of genetics. The queen mates with lots of drones and mixes up their sperm which she retains in her spermatheca. This leads to multiple patrilines in the colony, where many workers are half-sisters. Perhaps this ‘covering of all bases’ strategy gives the colony the best chance of adapting to environmental changes. For anybody trying to breed bees and create a pedigree, nature is not helping. The only way to do this successfully is to use isolated mating stations or instrumental insemination. 


In my country (England), it’s safe to say that most honey bees are hybrids. Lots of people blame all manner of ills on this fact. If your bees are evil or swarmy or rubbish, it must be because foreign genetics have been brought in from ‘outside’. Some people even think that moving bees 50 miles or so is messing up their local gene pool. When I look at the map of the main lineages, I find that odd. The M lineage covers a large swathe of northern and western Europe. 

Map of honey bee lineages
Lineage map (source: Recent advances in population and quantitative genomics of honey bees Kathleen A Dogantzis and Amro Zayed)

I’m not too bothered about the genetics of my bees because (a) I can’t do much about it, and (b) I think it’s the traits of individual queens that matter, not a whole subspecies. I can raise queens from my best and get rid of the daughter queens that turn out to be horrible. Over time, one hopes, the overall quality of my bees improves. It’s a theory. The best argument against the importation of bees (apart from cost and hassle) is the disease angle. Surely there are different variants of bee viruses in other regions and maybe different gut microbiomes determined by alternative diets. Plus, of course, bees quickly revert to whatever the locals are anyway. Unless you want to continually pay for ‘outsider bees’, you will end up with locals. 

Amm Dominates much of UK

The best argument for bringing them in is that the local bees are terrible. Still, you really are climbing the escalator the wrong way in such a situation. I don’t know how successful individual beekeepers would be at changing the local bee gene pool. More likely, you’d be committed to continuing to buy in queens every year. Murray McGregor has thousands of colonies in Scotland and conducts queen rearing on a large (for the UK) scale. He said on a forum post recently:

For more years than I care to remember, I have had a running disagreement with some of the ‘local black bee’ people about us breeding for our desired criteria, using the occasional bought in breeder queen…who stated vehemently that we were ruining the local gene pool. They could not keep their bees free of our genetics. I always pointed out that it is not us undoing their work but the reverse. We find that the local black bee genetics dominate…if we put a nice well-bred line into the field colonies and leave it as a free-standing unit, raising a new queen from it when required, in 3 to 4 generations, you see the colony has largely reverted back to local normals. 

The bees are darker, runnier, swarmier, sometimes nippier; production becomes more uneven. Eventually, they become just local bees. Typically pretty mediocre and harder work. It is a constant battle to keep our genetics fresh and up to scratch.

Ingress of the local bee into ours is the main direction of travel…not so much from ours to theirs. Even when we have more bees than all the locals combined, there are still abundant black drones in the air at mating time, and field colonies quickly revert. We have to saturate the areas around our mating units, or the queens raised there have progeny that are a harder job to manage.

A thesis by Catherine Thompson in 2012 on the background populations of honey bees in the UK showed that although hybridisation is widespread, the black bee tends to be dominant. The higher the density of hives, the lower the proportion of black bee genetics, down to a base level of about 40%. The amount of Amm is often above 50%. Areas of Scotland and possibly Wales tended to have more black bee genetics than England. Overall there wasn’t a significant difference between feral and managed colonies, so they are probably the same population.

Quality queens

Genetics isn’t the whole story if your goal is high-quality queens. The conditions in which queens are raised is critical. They need to have a constant diet of the right type at the right time throughout their development. They need to be kept at the right temperature at all times. Conditions for mating need to be good so that she does not hang around for three or four weeks before her mating flight. A queen with great genetics that did not develop in ideal conditions will probably never be great. The thing is, most of us will struggle to control genetics – so why not make an extra effort to ensure that our queens are raised in perfect conditions? Also, if genetically speaking, whatever we bring to our apiary will quickly revert to local bees, why not buy local or raise your own? This does raise the question, “what is local?” but that’s a tricky one too.

2 thoughts on “Origins Of Honey Bees

  1. ex-wbkachairmam ex-mbkachairman member bfa

    Hi Steve

    I’ll be honest, the mention of honeybee genetics usually makes my eyes glaze over. Being far more interested in the practicalities of beekeeping, I’ve always found the biology and morphology of bees a scary reminder of my Biology exams.

    However I found the article interesting but must take issue with your view that ‘if human influence is involved , it’s probably bad’…..

    I know you’ve interviewed some exceptional bee breeders – they are humans influencing bee genetics – and for the good of beekeeping in my opinion.

    In the wider area of agriculture, human influence has improved crop yields through selective breeding, ditto animal agriculture.

    I know where I’d prefer to be in an age of guaranteed food supplies vs scratching around in the dust to eke a minor food intake.

    I also think your view on the hybrids and importation doesn’t reflect the demand from hobbyists and commercial beekeepers alike, and our limited season doesn’t allow for enough early build up for queen mating or nuc/package production does it ?

    If we suddenly saw an ice age return and all of the UK blanketed in ice, bees would come from the warmer climes of Europe as the Ice retreated… in effect the ‘black bee’ would be no more and is only a relative newcomer vs the bees in the warmer climes…

    Anyway, I hope you’re well and have a good Christmas. With a few days off I’ll probably comment on a few other threads.

    Best Wishes

    Stephen Auty

    • Hi Stephen, glad you found it interesting. At least I said “probably”! I agree that humans do good too – including many farmers. Regarding importation did you look at the link to the article ‘what is local?’ – I think my view of local is wider than many. Anyway, thanks so much for reading and commenting, and I hope you & yours have a lovely Christmas.

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