bee biology

Why is it so difficult to breed better bees?

Breeders can and do produce excellent queens with helpful traits. The real problem is in the field where the traits quickly disappear within the massive number of honey bees.

Those new to beekeeping fre­quently ask why we don’t just breed better bees. This is a logical question because breeding has long been the answer to many agricultural problems. When I say “breeding,” I don’t mean modern gene-insertion techniques that allow us to raise glow-in-the-dark cats, but the old-fashioned kind of breeding where you cross hand-selected indi­viduals in order to amplify their best traits.

This article first appeared in American Bee Journal, Volume 158 No 8, August 2018 and was reprinted in An Beachaire, The Irish Beekeeper. Vol. 73 No. 11, November 2018. It was first published on Honey Bee Suite November 16, 2018.

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 roadblocks to maintaining better bee stocks

There are three main roadblocks 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 better bees 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 bee 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 for bee breeders

Other genetic problems affect our ability to develop and maintain improved beekeeping stock. The first, restricted gene flow from outside North America, is due in part to the Honey Bee Act of 1922. The second is inherent in the way social insects respond to danger.

Restricted gene flow from outside North America

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.

Limited genes for detoxification

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 bee 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, you see 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.
A key to fixing a recessive trait in a local environment is drone saturation.

At 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 disappears into 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 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: one good queen is easily overwhelmed

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


  • 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.


  • 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…

  • 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.


  • 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.

  • 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?

    • Andrew,

      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.

      • There was a recent paper discussing results of testing the selection of larvae of emergency queens that is relevent to this topic:
        The paper:

        From what I have read of research on bee sex, the drone sperm gets mixed very thoroughly in the spermatheca. I don’t think the queen reserves specific sperm cells to select the DNA lineage for her daughter queens. The biological and/or biochemical mechanism for this is hard to conceive of, and I would think that it would have been discovered or at least postulated by bee scientists.

        I think that it is more likely that the decision of which eggs / larvae will become fully-emerged queens is also made by the worker bees. The workers can choose which “promoted” larvae continue to be fed royal jelly; they can choose whether to continue to build the queen cell around the larva or break it down; they can choose whether to cap the cell. I have also been told by a mentor who grafts many queens that he has seen the workers “hold back” some queens that would otherwise emerge simultaneously with their sisters, preventing a “fair fight” between emerged queens.

        It is all fascinating stuff. “I am but an egg.”

        • Rob,

          I totally agree that it’s the workers do larvae selection, not the queen. The queen only decides whether to lay male or female.

  • 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

    • 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.

    • Hello,
      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.

      • 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.


      • 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.


  • 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)?

    • Kelsey,

      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?”

  • Regarding:
    “… you have (250 x 1000 x 90) x 15% or 3,375,000 drones in your area during that three-month period..”.

    While we understand the idea of this demonstration, this is not really admissible and overly inflated.

    * I am chemical-free keeper running 10-20 colonies using three yards, geographically organized in roughly a triangle with a side of about a mile so to ensure drone flight overlapping
    * I use natural comb and the bees can build whatever cell size and type they want at any time
    * I let my bees to raise as many drones as they wish (which they do)
    * also, I do not cull older queens, but rather maintain them in drone-generating colonies (the older queen, the more drone she lays); old, desirable queens are an important asset (hardly understood and not promoted by conventional “best practices”).
    * there are other colonies in the vicinity, but no large scale commercials (it is safe to state there are under 50 colonies in my area)
    * all other colonies in my area are conventionally maintained (package sources/foundation used/drone generation is prevented or mitigated because they are considered “wasteful”/older queens are culled per the conventional “best practices”).

    I can continue..
    But one can see it is possible to create high enough and persistent enough density of the drones that come out of your own apiary and contribute enough into the local population so NOT to be diluted away.

    • Greg,

      Your argument makes no sense because you left off the first part of the premise. It says, “But imagine for a moment that the local bee club in your town just pur­chased 250 packages from a producer in the south.” You didn’t imagine that, you imagined something else. In fact, you say 50 colonies, which is way different than the 250 I suggested. Please read.

  • Thanks so much for your clarity and scholarly writing. My son and brother are beekeepers far away from my New York City apartment. There are many parks with flowers and flowering trees in the neighborhood and I wonder if feral local bees could be lured into a window sill hive.

  • Genial. Simplemente genial. Soy criador de reinas en Galicia (Spain) y la forma de mostrar tus argumentos es fácilmente entendible. Me encantaría que me dejases explicarlo en los cursos de formación que doy de esta manera. Citándote, por supuesto.

    (Cool. Just great. I am a queen breeder in Galicia (Spain) and the way to show your arguments is easily understandable. I would love for you to let me explain it in the training courses that I give in this way. Quoting you, of course.)

  • This is a really interesting article, thanks for explaining bee genetics in some detail. I had no idea it was this complicated.

    So from what I can deduce, normal beekeepers do not have control over mate selection like most farmers do, hence the difficulty in maintaining traits over multiple generations. Wild stock (or more probably, other beekeeper’s stock) are going to be mating with your next generation of queens, messing up any selective breeding that has been done before.

    Surely it would be possible to build a complicated hive system that only allowed new queens through to a special chamber which your chosen drones could be introduced to? Thus allowing beekeepers without the aid of a high-tech lab to maintain selected traits.

    Or not?

    • Lycanthea,

      All kinds of structures have been tried for controlled matings of honey bees, including gymnasium-sized enclosures, netted fields, and huge greenhouses. But honey bees are having none of it. It’s a fascinating problem.

  • Rusty – you are correct that, short of instrumental insemination, controlled mating is difficult. However, their is one technique that may be fairly workable for most of us, and has been described for plus or minus 100 years. This is the concept of the inducing the mating flight at abnormal hours.

    It is described by Wedmore in 1932 (you can read about it here on pages 68-69)

    Also by John Hogg in the May 1991 edition of the American Bee Journal:

    It also appears to be used in Europe under the term “Moonlight Mating”:

    I have not tried this technique myself, but would like to. It seems doable, and likely to work. Perhaps it is the key to establishing “heirloom varieties” of bees.

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