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Why is it so hard to breed better bees?


This article first appeared in American Bee Journal, Volume 158 No 8, August 2018, pp. 915-918.

This traditional method has yield­ed bigger, fatter, disease-resistant, and higher-yielding plants and ani­mals that are the backbone of modern agriculture. Over the years, it gave us more milk, bigger cherries, sweeter apples, blight-resistant tomatoes, pink daffodils, and hairless dogs.

Of course, what you do on pur­pose, you can also do by accident. Inadvertently, we’ve created a host of undesirable organisms using simi­lar techniques. Methicillin-resistant Staphylococcus aureus (MRSA) and similar pathogens arose because we killed off most, but not all, of the in­dividuals. Those that survived were the strongest, best adapted, and most able to persist in spite of antibiotics. We selected for the strongest ones by eliminating the weaker ones—the same selection principle operating in reverse. Closer to home, we’ve bred varroa mites that are resistant to near­ly everything.

Why don’t we breed better bees?

So why don’t we just breed better bees? The answer is simple: we al­ready have. Breeders have managed all kinds of marvels with honey bees. They have built bees that are gentle, bees that overwinter well, bees with increased honey production, and even bees that cope with varroa mites. Breeding isn’t the problem.

The problem with honey bees occurs after the queens leave the breeder. The traits bred into honey bee queens in carefully-controlled breeding programs soon disappear when the daughters of these queens are allowed to mate with open stock. Within a generation or two, the de­scendants of these super bees are right back to square one. The question is, “Why does this keep happening?”

The road blocks to maintaining better stocks

There are three main road blocks to maintaining well-bred populations—haplodiploidy, polyandry, and pan­mixia—plus a few other minor com­plications. And while those words may sound intimidating, don’t worry. Just fasten your seat belt, and you’ll be an ex­pert on all three in no time. Get ready to impress your friends at the next dinner party.


Like all other members of the or­der Hymenoptera—including ants, wasps, and sawflies—honey bees are haplodiploid. Haplodiploidy means that some individuals are diploid, having two sets of chromosomes, while others are haploid, having only one set of chromosomes. If your knowledge of genetics is limited, suffice it to say that haplodiploidy doesn’t operate like the simple Men­delian genetics you learned in high school. I, for one, thought I was a ge­netic genius after I had the dominant/recessive pea grid worked out, but things in real life are not that simple.

Haplodiploidy makes breeding more challenging, and it has some surprising consequences. In honey bees, drones are produced from un­fertilized eggs, which means each drone has only one set of chromo­somes, while females—both workers and queens—have two sets. In most animals other than Hymenopterans, all individuals have two complete sets of chromosomes. Also, haplodip­loidy results in inexplicable axioms, such as a drone has a grandfather but no father and can have grandsons but no sons.

But it gets even weirder. What they don’t teach you in Beekeeping 101 is that some fertilized eggs become diploid drones—that is, drones with two sets of chromosomes. This hap­pens because the thing that actually determines sex is not the presence or absence of fertilization but the pres­ence or absence of heterozygous al­leles at the sex locus. Don’t click away yet—you can do this.

A piece of chocolate cake

Many recipes lead to chocolate cake. Photo of cake and coffee.
Many recipes lead to chocolate cake. Like recipes, alleles are alternative sets of instructions.

You see, instead of having an entire chromo­some that determines sex, like the X and Y chromosomes in humans, bees have one gene on one chromosome that determines sex. Specific places on chromosomes are called loci (the singular is locus), so the “sex locus” is just the place (think address) on the chromosome where the sex gene is found.

The European honey bee has about 18 different alleles of the sex gene. An allele is just a variation of a gene. All sex alleles do basically the same thing, but the genetic coding is a little different in each one. You can com­pare it to having 18 different recipes for chocolate cake—the end products are similar but the instructions for getting there vary.

So different bees are running around with different alleles (or in­structions) for the sex gene. If an egg is not fertilized, there is only one set of instructions and the bee becomes a drone. If an egg is fertilized and has two different sets of instructions, the bee becomes a female. But—and here’s the kicker—if the egg is fertil­ized but receives two identical sets of instructions (two identical sex alleles) the bee becomes not a female but a diploid drone. Think of it like this: one set of instructions printed twice is not the same as two different sets of instructions.

The fate of diploid drones

These diploid drones do not survive. In col­onies of social insects such as honey bees, the workers eat or destroy the diploid drones soon after the eggs hatch. Because they are destroyed early, having many diploid drones in a colony results in “shot brood” or “scattered brood”—brood combs that have lots of empties or brood of many different ages interspersed. In some solitary bees, the diploid male may die in the cell, or may emerge and mature but be sterile.

The table below shows what would happen when a honey bee queen (with two different alleles of the same gene) mates with five dif­ferent drones, each with one allele. In this case, two of the drones have the B allele and the rest have differ­ent alleles.

Wherever you have homozy­gous alleles for the sex gene (two of the same alleles), you get a diploid drone. This table shows an extreme example because it has a small num­ber of alleles and a small number of matings, but it illustrates how homozygous alleles happen. In this example, one queen with two dif­ferent alleles for the sex gene mates with a series of five drones, resulting in only 70% viability of the fertilized offspring.

For the average beekeeper, this property doesn’t make much differ­ence. Since honey bees have about 18 alleles for the sex gene, and a queen may mate twelve or more times, there is little likelihood of diploid males. But for breeders who are trying to control the gene pool of both the queens and the drones, diploid drones can become a real concern. Inbreeding decreases the number of alleles in a population and thereby increases the occurrence of diploid drones. Large numbers of diploid drones weaken a colony be­cause the nurse bees waste resourc­es trying to raise these bees only to kill them later.

Drones Queen #1 Allele A Queen #2 Allele B
Drone #1 Allele A AA BA
Drone #2 Allele B AB BB
Drone #3 Allele C AC BC
Drone #4 Allele B AB BB
Drone #5 Allele D AD BD


Honey bees are also polyandrous. Polyandry means “many men” and refers to the fact that a queen bee mates many times. Having many mates is not unusual by itself, but a queen bee stores all the sperm in her body for the rest of her egg-laying life. So when she lays her eggs, the eggs are fertilized by an assortment of males. Each of these different cou­plings represents a different sub-fam­ily in the brood nest.

Workers within any single sub-family have the same mother and father and are called “super sisters” because they share about 75% of their genes.1 Workers belonging to different sub-families have the same mother but different fathers. They are known as half-sisters, and share about 25% of their genes. When peo­ple ask, “Why are my bees all differ­ent colors?” that’s often the answer: they represent different sub-families in the same nest. It’s most apparent if a queen mates with both Italian (yel­low) and Carniolan (black) drones.

But color is not the only differ­ence. Because subfamilies are the offspring of different drones, they will vary in many ways such as overwintering ability, disease re­sistance, temperament, or foraging strength. Even more important, sub­families tend to stabilize a colony. If the queen had a bad mating—or even two—the offspring of the bad mating are only a small proportion of the entire colony, meaning the col­ony can survive even though some individuals do not.


In addition to haplodiploidy and polyandry, honey bees are famous for a trait called panmixia. Pan­mixia refers to totally random mat­ing, resulting in a thorough mixing of genes throughout a population.2 Drone congregation areas—loca­tions where, just as the name implies, large numbers of drones collect and hang out until a virgin queen flies by—were designed with panmixia in mind. They assure excellent mixing of genes, because drones from large geographical areas meet and com­pete for the right to mate.

While polyandry by itself assures multiple matings, panmixia assures the mates are not all boys from the local ’hood. Instead, the bees in a drone congregation area represent a diverse population. Panmixia has a stabilizing influence on a population, providing a check against genetic drift and inbreeding depression, a fancy term that indicates a reduction in fitness due to sharing too many of the same genes. It provides a buf­fer against genetic tragedy unless, of course, you are a breeder trying to se­lect for certain traits—then it’s more like an albatross.

Additional Genetic Problems

Honey bees in North America have had a restricted gene pool for a long time. This is partly due to the Honey Bee Act of 1922 which prohibited the importation of honey bees into the United States. The idea was to pre­vent honey bee disease organisms, specifically tracheal mites, from en­tering the country. But the unintend­ed consequence was to cut off the flow of genes from the honey bee’s native lands.

Although I hear this argument from time to time, I personally don’t give it much credence. After all, there were no restrictions during the 300 years from the early 1600s to 1922. In addi­tion, honey bees proliferated across the continent in those years, having plenty of opportunity for natural ge­netic variation that occurs in any large population. Even so, in recent years genetic materials via drone sperm have been imported into the US in or­der to supplement the gene pool.

On a different front, recent research has shown us that the honey bee genome is extremely limited in the number of genes that allow for de­toxification, a trait common among social insects.3 Scientists speculate that instead of evolving quickly to protect itself from environmental contaminants, the honey bee tradi­tionally used other mechanisms of defense. Traits such as hygienic be­havior, propolis collection, and sacri­fice of the individual for the good of the colony are tools used to protect a colony from such danger.

However well this worked in the natural world, it is problematic in an environment filled with man-made hazards including insecticides. While other invertebrates including mos­quitoes, cockroaches, and even varroa mites can develop resistance during the evening news, the honey bee is more genetically stable and less able to respond quickly to environmental toxins. This characteristic has been called “ecological naïveté.”2 It ap­pears that nature prepared the honey bee for a world that was simpler and more innocent than the complex one in which it now resides. As a conse­quence, it takes longer—perhaps too long—to develop natural resistance.

A lesson from conservation biology

Island biogeography is the study of how species form and why they go extinct. Both speciation and extinc­tion happen faster on islands because there is a restricted flow of genes into a protected area. The mantra of is­land biogeography is simple, “Isola­tion plus time equals divergence.”2 In other words, to change a population you must isolate it and keep it sepa­rate over time.

Breeding for a specific trait is not the same as speciation, but it works in much the same way. In order to breed for a specific trait, you must restrict the flow of genes into your breeding population over a number of genera­tions. This increases the probability of the desired gene showing up in any single individual. Unfortunately, it also increases the incidence of un­wanted genes—something breeders must prepare for.

Although it would be helpful to own an island or remote tract of land for breeding purposes, an “island” can be formed from other types of isolation. A freeway, a mountain range, a lake, a city, or a dearth of floral resources are all things that can restrict the flow of genes into an area. A famous exam­ple is Central Park in New York City. From the sky it is a huge green park surrounded by immense buildings and endless pavement. Central Park would not be an island to honey bees because they can fly great distances, but it is an island to certain native bees with foraging ranges of several hun­dred yards at most.

Those beekeepers who are success­ful at raising varroa-resistant bees have generally spent many years in an area that is somewhat protected from genetic contamination. These two factors, time and separation, mean they’ve had a lot of influence on the bee populations in their local area. In other words, they have been able to flood their area with “good” genes, so there is a higher probability that their queens will mate with drones who also have varroa-resistant traits. In es­sence, they shift the gene pool within their “island.”

Beekeeping in the real world

A key to fixing a recessive trait in a local environment is drone saturation.

In the beginning of this article, I said that breeding wasn’t the problem. Now, thinking about the traits I just mentioned, let’s go back and look at the trouble. In the real world, a carefully bred and inseminat­ed queen will work as advertised. Say you buy a queen bred and mated for hygienic behavior. Her offspring will most likely show the desired trait and the varroa mites will be dispatched. But at some point, the colony swarms and your queen is lost to the wilds.

If you do not intervene, one of her daughters will become the new queen. She carries the desired trait from both her mother and father, but when she mates, she mates with the local stock of drones. Perhaps some of those drones have the hygienic gene, especially if some other local beekeepers bought bees from the same breeder. But most of the drones have no such trait. So whether your colony shows resistance or not is a numbers game.

Nearly all varroa-resistant genes are recessive,4 so if your new queen mates 16 times, and only one or two of those matings are with a drone with varroa-resistant genes, you will have, at most, just two subfamilies in your colony exhibiting the trait. Assuming all subfamilies are repre­sented equally, that would be about 1/8 of the bees or 12.5%—perhaps too low to do much good. The more varroa-resistant drones in the area, the better chance you have of seeing some resistance.

Bees by the numbers

But imagine for a moment that the local bee club in your town just pur­chased 250 packages from a producer in the south. Assume for a moment that they all survived. You would then have, theoretically at least, 250 queens each laying 1,000 eggs per day for the months of April, May, and June. If you assume 15% of those bees are drones, then you have (250 x 1000 x 90) x 15% or 3,375,000 drones in your area during that three-month period. And those are just the drones from the new packages, not those from established and feral colonies. Worse, each and every one of them is eager to mate with the offspring of your expensive hygienic queen.

Sure these are ballpark numbers, but the message is clear. If you bring a varroa-resistant queen into an area where there are lots of bees, but little varroa resistance, the trait will soon disappear.

In summary, a persistent beekeeper with a lot of colonies can significantly shift the gene pool in his favor. But if an area is constantly bombarded with random bees from other places, it is extremely difficult to develop a resis­tant line. It will require time, effort, and significant planning.

I’m not saying we shouldn’t try to breed better bees. But we need to un­derstand why it’s a long row to hoe, why it may be difficult to imitate the success of others, and why the resis­tant traits are hard to maintain. Be­cause of the unique biology of honey bees, it can take a long time to see substantial change.

Honey Bee Suite


  1. Breed MD, Moore J. 2015. Animal Behav­ior. Elsevier Inc. Academic Press 71-107
  2. Quammen D. 2004. The Song of the Dodo: Island Biogeography in an Age of Extinctions. New York. Scribner.
  3. Evans JD, Aronstein K, Chen YP, Hetru C, Imler JL, Jiang H, Kanost M, Thomp­son GJ, Zou Z, Hultmark D. 2006. Im­mune pathways and defence mechanisms in honey bees Apis mellifera. Insect Mol Biol. 15(5):645-56.
  4. Kefuss J, Vanpoucke J, Bolt M, Ke­fuss C. 2016. Selection for resistance to Varroa destructor under commercial beekeeping conditions, Journal of Api­cultural Research: 54(5) 563-576, DOI: 10.1080/00218839.2016.1160709


This artcile was reprinted in An Beachaire, The Irish Beekeeper. Vol. 73 No. 11, November 2018.


Peter Borst

Hi Rusty

A terrific overview of the various factors and issues. One thing I would add is that the breeding system is a product of many millions of years of evolution and it has served the honey bee well in a variety of geographic locations.

We could be way off based thinking that we can “improve” upon it. For example, even selecting for so-called desirable traits, other traits may be lost in the process. Also, the mixing of multiple patrilines seems to be very important to the long term survival of the honey bee colony.


ET Ash

Another outstanding article. We (my well known neighbor and myself) rear some no treatment bees here in Central Texas… and many of your points are right on target in regards to the rearing of no treatment stock.

Gene in Central Texas…

William F Abell Jr

Wow! Pass the aspirin please.



Aspirin? Really? I tried to dish it out slowly.

Ken Armes

Whew Rusty, you’ve made my head hurt, had to read the article three times to get an idea of what was being said. That said enjoyed the article, gave me an inkling of some of the problems we face. But I’m a great believer in “The Great Architect Of The Universe“ eventually the ship will right itself.


Granny Roberta in nw CT

This wasn’t completely new to me but you’ve taken a complex and confusing subject and made it both understandable and entertaining. Just so you know, I’m not just here for the beekeeping, but also for the great writing.



Thank you! You need to talk to Ken and William.

Andrew Hogg

So some beekeepers do mite control by, in part, removing drone comb. Does this potentially lead to “inbreeding” if they are the dominant source of bees in a large area?



I doubt it. There are so many drones out there, and they can travel so far, I don’t think it’s an issue.


Great article Rusty!! I recently attended a conference talk on genetic diversity. It was said that with DNA testing of worker bees and swarm cell queen bees they found that the queen used a different drone’s sperm for the swarm cell queens that was not found anywhere else in the hive. Somehow she reserves that particular sperm for this purpose. I’ve wondered since then how much difference it makes to the outcomes of our breeding programs when we use worker cell eggs to graft into queen cells. That’s probably a question we’ll never be able to answer.



It does pose a very interesting question. I wish I knew more about the research.

Glen Buschmann

Thank you Rusty for diving deep into this topic. In the years I’ve spent working with Mason bees (Osmia lignaria) there are times where I expect I have done more harm than good, especially regarding emergence time. Early emerging bees get the best pick of housing, late emerging bees — a desirable variation — are out of luck and have to go elsewhere. In the wild this is not a problem, as a late emerger has almost as good a chance at finding random favorable crevices and cavities as does an early emerger. But with the artificial system, early emergers have a bonanza of holes, clean (hopefully) and uniform, while late emergers have to keep patrolling for random cracks and crevices.

I don’t know if this has been studied. I do know that with each year I try to increase randomness and reduce uniformity with my offered housing.

Thanks again, Glen



I have to admit, I never gave this any thought, even when I had zillions of O. lignaria. But you’re right, it’s an interesting question and it would, in a way, seem to favor early-emerging bees. But perhaps late-emerging bees nest further from the crowd, and further away means less chance of being attacked by the host of predators and pathogens that congregate in dense populations of hosts. I will have to think about this.


Hope you don’t mind commenting on your comment!
I was wondering if time of emergence is genetically coded or if it depends on specific conditions for each bee – richness of food, sun exposure, etc. – that might influence speed of development. If so, than you wouldn’t be positively selecting time of emergence.
Just guessing.

Glen Buschmann

Hi Pedro and Rusty –

When I started working with mason bees, 20 plus years ago, I kept expanding and expanding with identical sized holes. It looked very honey bee orderly but for the thousands of solitary bees competing for identical holes it was socially very chaotic. Their breeding efficiency dropped while pest problems increased. At some point my spouse questioned both my sanity and my science — and she was correct. Over the years since I have disperse my bees and reduced the number of holes available at any one site. And I’ve introduced more and more randomness that more naturally mimics natural systems of solitary bees, varying hole size and nesting materials while improving my ability to track the age of the nests.

This past spring health issues caused me to abandon management of most all my nests. This coming year will be an experiment, as I am going to place empty nests (and no bees) at some locations I had previously maintained, “trap-nesting” for feral populations that established themselves independent of my nests.

One of the big challenges is that most Osmia research is carried out by commercial growers who use techniques that are simple and mass-scale but not necessarily healthy for the bees.


glen Buschmann

I meant to also say that diameter of nests up to a point does seem to influence the size of the mason bee. This is not a total surprise. Some bees, such as bumble bees, grow larger with each generation during a season – the more food the bigger the bumble. It could be that simply running out of food kicks out a response that it is time to morph.

It raises a point of whether beeks who raise foundationless bees notice any size variation. I’ve heard discussions about queen size variations. GB


Thank you very much for your input, Glen.

My comment was a mere theoretical supposition, while you have years of experience with solitary bees!

It was enriching to read about your experience, thank you.


David Maloney

Your article seems to support the argument that new beekeepers should not even attempt to go treatment free, given the challenges of maintaining the desired trait of mite-resistance. Yet, there are those going TF. There are Facebook pages devoted to TF beekeeping. Are all these TF’ers located in remote areas where they can maintain a level of mite-resistance sufficient to get away without treating for mites (IPM not withstanding)?



Becoming a successful treatment-free beekeeper requires more than joining a Facebook page.


Thanks for the post. I’m confused about the number of allele in Apis mellifera. I read somewhere it was 150+.



Each gene has a set of alleles. In this case, we are talking about only one gene (the sex gene) and it has about 18 alleles. If you added up all the alleles of all the different genes, it would be a great number.


So many questions, so little time! Great item as always Rusty. Maybe the question should really be “Should we be trying to genetically modify an insect which as been around for so long and actually, without our interference, will probably be around at least as long again?”

David Isenhour

Excellent job of boiling down some difficult scientific aspects into lay terms. Well done.

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