Bee Genetics

A primer in honeybee genetics for better management

So we’ve talked about the fact that honeybees are not native, to, well, basically anywhere people who are reading this are from. And we all know bees die pretty easily, at least the domesticated bees. But why, and what can we do about it? Well, we’ve gotta go way back in time to the last ice age.

Honeybees migrated south, and the pressures of climactic change created intense selection pressure on the bees that survived. And for European honey bees, which is what most of our honeybee stock comes from, generally settled in 1 of 4 different regions; Iberia, the Balkans, Greece & Italy. Now, the regions aren’t particularly important, but what is important is to know that as breeding took place in these isolated conditions, mutations occurred, and these mutations led to different subspecies of honeybees. We’re talking millions of years.

While many mutations did not survive, the ones that did ultimately led to the traits we see today in these different honeybee subspecies.

Iberia is comparatively flat, which meant as the ice age receded, those bees were able to quickly work their way up into northern Europe far before the others could. These bees crossbred with other various bees in the region, creating the dark European honeybee. Further, honeybees from northern Africa were able to cross the strait of Gibraltar and cross with the bees which were already there, which led to what is now known as the Spanish honeybee. New climate and geographical factors steered them towards these new areas with new genetic variances.

So that’s a bit of the backdrop here. Now, let’s look at the environment these bees lived within. Much like most of the prole models series, we know most landscapes across Europe were wooded or lightly wooded 8,000 or so years ago. Human impact was framed within their subsistence, and for the most part, beekeeping wasn’t a thing. Bees lived in tree cavities, not skeps, not hives, and they were self-organized throughout the landscape. Only the best colonies survived to swarm and continue to reproduce.

Hives, even healthy ones, only live for a few years, say three or so.  They’ll swarm, and if you’ve been reading this series, we’ve talked about why this is the case, from the wax in the hives to pests and everything in between. The reason I’m bringing this up is that for these hives to continue to exist, this meant an annual swarm caused populations to grow, but obviously, that’s not continuously sustainable, meaning probably a third of these swarms did not make it.

Queens are diploids, meaning they carry chromosomes from both their mother, a queen bee, as well as their father, a drone. Queens are basically egg factories, laying a mix of diploids— the worker bees with 2 sets of chromosomes, and haploids—, eggs with only 1 set of chromosomes for drones. Mixing the genetic code down for 1 set of chromosomes is done through a process called meiosis, which is where genetic material is exchanged between both sets of chromosomes randomly, and more importantly, the two pairs of chromosomes are reduced to 1. But, most importantly here, is that the chromosomes in the egg for drones aren’t from the DNA of the drone the queen mated with, but the drone who is her father, and, not her own DNA, but that of her mother.

ATheefforts that genetics go through itoshare and reorganize these sections of chromosomes are qnique to bees.  And it makes sense, right? We know that worker bees don’t impact the genetic pool, and drones are all basically clones, so where would genetic diversity otherwise come from? Now, let’s talk about those drones real quick. They come from unfertilized eggs, meaning they only have 1 set of chromosomes, and that means that there’s no genetic variation, there’s no way for recessive traits to be carried; if there’s a congenital weakness, it will be exposed fairly quickly. This process helps quickly filter out genetic weaknesses.

The mating process is called competitive polyandry. Mating takes place in the air in a drone congregation area, with up to 20,000 drones from over 200 colonies, mating every 15 seconds. Out of those 20,000, the queen will mate with 15 or so drones, and that sperm will be used by the queen for the rest of her life. So out of a ton of drones, only a few mate, meaning only the strongest survive, but also it’s based on the random chance of which drones happen to be there, because 20,000 drones isn’t a lot out of 200 colonies. So there’s a weird mix of survival of the fittest and random change.

That randomness is known as genetic drift. Having multiple fathers from this mating process does create subfamilies within the hive, each genetically distinct, with the potential to behave and even look differently to the other subfamilies. And this all boils down to an entire colony-level gene expression.

I want to talk about how this happens, and that’s through what’s called quantitative trait loci, or what exact genes are causing this. One thing we’ve done is try to make bees more gentle. But gentleness isn’t a concrete thing like when you’re breeding pumpkins; is the pumpkin sweeter— yes or no? The point is that there are several genes involved in these generally understood interests people have when it comes to breeding their bees. Hygiene in particular is an interest worth exploring further, for obvious mite-related reasons. Other genes studied are around cleanliness, gentleness, foraging capability, and so on. We can look at these traits and see that they break down into several pieces. Cleanliness doesn’t just mean the bees themselves, but the hive, brood-rearing, and so on. 

It’s not just one gene that controls all of these specific traits, right? Researchers smarter than me cconcluded that in targeting these specific expressions, 68% of colonies were okay, 14% were good or bad, and 2% were excellent or awful.¹ Now, could we breed for that 1%? Sure. But to breed for a selective trait, you’re going to whittle down the gene pool hard. So, being good at mite resistance doesn’t mean they’ll have other traits we want. When you’re shrinking that genetic diversity, you’re at higher risk of causing those other desirable traits to be less likely.

If you’ve looked in a hive before, you might notice some bees look a little different; brighter stripes and that sort of thing. But that’s not all, it can impact honey bee behaviors, including things like hygiene and even things like the waggle dance, and how it’s understood. Based on their genetic lineage, the interpretation can be very different. And since that’s how bees tell their siblings where to find honey, getting the wrong directions isn’t great. The point is here, that this genetic variability is important to colony health.²

In practice, the diversity from how queens are mated allows for enough diversity that someone is good at something at any given time. We talked in the other recent bee articles about the life cycle of bees, that they don’t just have 1 job in their lives, and that rotation is fantastic because one of those jobs is something they’re going to be good at. And that specialization is important for efficiency. In unique situations, when more of the colony needs to focus on one particular thing, having those specialists step in instead of every worker allows the colony to provide a proportionate response to that new circumstance.³

The point is that this diversity allows the bees to have these specializations because of the genetics of the fathers. There’s been evidence showing that greater diversity significantly improves resistance to all sorts of parasites and viruses.⁴ This diversity, skills division, and resistance are all tied to polyandry.⁵ And the bees have evolved to make sure this diversity of genetics happens by basically forcing inbred colonies to nuke themselves.

And this has major implications for how we breed bees.

So we know that fertilized eggs create worker female bees and unfertilized eggs are drones, right? But this isn’t *always* the case. If you look in a healthy beehive and look at all the capped comb, in the mix of the bee larvae you’ll always see some random empty cells. Well, they weren’t empty, the larvae had been eaten by the other bees. For a while, researchers thought this was just some weird phenomenon, but we now know that the larvae were diploid drones, which, if males are typically haploid, seems like it might be a problem, right? Well, this is a byproduct of inbred genetics. The funnel of genetic diversity that natural selection takes in keeping only the survival of the fittest when paired with a small genetic diversity– say, an isolated cluster of different colonies that can only breed with one another, will increase the likelihood of these diploid drones, which are basically when queens breed with their brothers, and it has an amplifying effect, meaning in a few generations a few diploids can turn into a what’s called a ‘shotgun effect’ in honeycomb, where up to 60% of cells have these cannibalized diploid drone larvae.

Natural selection will eventually wipe these isolated bees out. But what happens when a well-intentioned beekeeper keeps weak, isolated beehives alive longer than they should be? Well, I mentioned earlier that bee genetics are not as simple as, say, traditional genetics where we can see recessive traits and so on.

Now let’s focus on how this plays out in an apiary. The first and most obvious thing is that inbred bees that are kept alive are bad, right? The second fact is that a study in the 60s highlighted that bees not only respond to their environmental conditions but quickly develop ecotypes that try to predict things like big nectar flows, including bees that have population peaks before major flows. 

The idea of ecotypes isn’t unique to bees. When we lose this ecotype variety that has very specifically survived because of its adaptation to a climate, the term used is outbreeding depression, and it’s exactly what it sounds like. Bringing in new genetics is often good, but not when species become highly specialized. This can be proven using isozyme studies which show that different geographic latitudes favor different enzyme variants. Genomic studies are showing different favored alleles on different continents.⁶

So if we can show it exists biologically, can we breed for it? In a sense, yeah. But we don’t. Not only do we not allow our bees to survive based on their strengths, but we order our bees from a handful of places, most often not locally, so the idea of an ecotype bee for our region is impossible without starting a small apiary and expecting to lose like 90% of your hives in the first 5 years.

For example, in Sweden in the early 2000s, 150 hives were left to fend for themselves and 8 still survived 5 years later, but then those bees and their genetics continued to survive, creating the early stages of a varroa-resistant ecotype for the climate.⁷

But does this create a genetic bottleneck? Even though it does bottleneck, in a sense, because of the way the genetics express themselves because of the unique conditions that they’re living in, there is a fair amount of diversity, although I’m not sure about how long those genetics can stay isolated before there are issues.

So if we want honey in the future, we have to accept that 95% of our beehives have to die first. Sort of. And that’s hard to accept as a beekeeper, not just because you care about them, but also because bees are expensive. And it’s also not entirely true, either. Nature doesn’t wanna die, despite our best efforts. Genetic sequencing has shown that many of the ‘landrace’, as we’ll call them, honeybees in places like the UK have not only been able to mostly survive, but they’re impacting the foreign genetics brought in.

And this makes sense; they’ve developed for the climate so they’re likely to survive and ultimately breed with the non-natives, introducing their genetics into lines that end up more likely to survive because they have those unique traits. In some cases, in the UK, for example, native bees overtook 99% of the genetics of imported bees.⁸

With this, we have a general understanding of beekeeping genetics and how our decisions as beekeepers impact the future viability of beekeeping as a whole. Our decision-making must be framed in science-based evidence, and not by simply attempting to address symptoms that arise because of our poor practices in the name of scalability, profitability, and ease.

If you’ve enjoyed this piece, which is equal to a 9-page chapter, of (so far) a 745 page book with 375 sources, you can support our work in a number of ways. The first is by sharing this article with folks you think would find it interesting. Second, you can listen to the audio version of this episode, #141, of the Poor Proles Almanac wherever you get your podcasts. If you’d like to financially support the project, and get exclusive access to our limited paywalled content, you can become a paid subscriber on Substack or Patreon, which will both give you access to the paywalled content and in the case of Patreon, early access to the audio episodes as well.

1. Chambers, John. “Basic Honey Beekeeping Genetics for Beekeepers”, 2019 National Honey Show. https://www.you tube.com/watch?v=w-pAQt6pFhM&t=

2. Espregueira Themudo, G., Rey-Iglesia, A., Robles Tascón, L., Bruun Jensen, A., da Fonseca, R. R., & Campos, P. F. (2020). Declining genetic diversity of European honeybees along the Twentieth Century. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-67370-2

3. Collison, Clarence. “A Closer look at the Factors Affecting Queen Quality”, 2019 National Honey Show. https://www.youtu be.com/watch?v=PQ9OxDsTu6M

4. Tarpy, D. R. (2003). Genetic diversity within honeybee colonies prevents severe infections and promotes colony growth. Proceedings of the Royal Society of London. Series B: Biological Sciences, 270(1510), 99–103. https://doi.org/10.1098/rspb.2002.2199

5. Slater, Garett “Honey Bee Case Systems: Part 2 - How Genetics and the Environment shape Honey Bee workers and Queens” June 5, 2019. https://beeinformed.org/2019/06/05/honey-bee-caste-systems-part-2-how-genetics-and-the-environment-shape-honey-bee-workers-and-queens/

6. Kükrer, M., Kence, M., & Kence, A. (2017). Honey Bee Diversity Is Swayed by Migratory Beekeeping and Trade despite Conservation Practices: Genetic Evidences for the Impact of Anthropogenic Factors on Population Structure. https://doi.org/10.1101/154195

7. Thaduri, S., Locke, B., Granberg, F., & de Miranda, J. R. (2018). Temporal changes in the viromes of Swedish varroa-resistant and Varroa-susceptible honeybee populations. PLOS ONE, 13(12). https://doi.org/10.1371/journal.pone.0206938

8. See above-cited John Chambers video.