For a long time, genetics has been the answer to our agricultural problems. I don’t mean modern gene-splicing where you combine genes from different species, but the old-fashioned kind of breeding where you cross hand-selected individuals in order to amplify their best traits. This traditional method has yielded bigger, fatter, disease-resistant, and high-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 a cajillion breeds of dog.
Inadvertently, we’ve done the same thing with undesirable organisms. 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. It’s the same selection principle operating in the opposite direction. Closer to home, we’ve bred Varroa mites that are resistant to nearly everything we throw at them.
Why don’t we breed better bees?
So why don’t we just breed better bees? What’s taking so long?
The answer here is simple: we already have. Breeders have managed all kinds of marvels with honey bees. They can build 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. Why does this keep happening?
The problem has many causes, but four come to mind.
- Honey bees in North American 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.
- The honey bee genome is limited in the number of genes that allow for detoxification. Instead of evolving quickly to protect itself from environmental threats, the honey bee uses other mechanisms such as hygienic behavior, propolis, and sacrifice of the individual for the good of the colony. While mosquitoes, cockroaches, and even Varroa mites become resistant seemingly overnight, the honey bee is more genetically stable, less changeable.
- The honey bee, like all Hymenoptera, is haplodiploid. Haplodiploidy means that some individuals have two sets of chromosomes (diploid) and some have only one set (haploid). If your knowledge of genetics is limited, suffice it to say that haplodiploidy is weird and doesn’t operate like the simple Mendelian genetics you learned in high school. This complexity makes breeding more difficult. In honey bees, males are produced from unfertilized eggs, which means each drone has only one set  of chromosomes. Female bees, both workers and queens, have two sets. In most animals, all individuals have two sets of chromosomes.
- Honey bee are 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 of any single sub-family have the same mother and father and are called “super sisters” because they share about 75% of their genes. 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 the answer: they represent different sub-families in the same nest.
Successful bee breeders cross queens and drones that exhibit the characteristics they are looking for. Those most successful use instrumental insemination and have a way to control the drone mothers. It is really helpful to have a remote island or vast tracts of land free of other colonies. Successful breeders inundate their area with acceptable drones, and thereby shift the gene pool in their favor. This is especially important in breeding for Varroa resistance and hygienic behavior because all the genes are recessive.
Beekeeping in the real world
But let’s go back to the trouble. In the real world, a carefully bred and inseminated queen will work as advertised. Say for example, 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 the 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 from the local stock of drones. Perhaps some of those fathers 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.
It’s a numbers game
Imagine that the local bee club in 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 1000 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. And all of them are eager to mate with the offspring of your 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.
Altering the local gene pool takes time
Those beekeepers who are successful at raising treatment-free bees have generally been working in the same area for many years and are at least somewhat protected from outside shipments. These two factors mean they have had a lot of influence on the wild 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. It is not unusual to hear of treatment-free beekeepers who willingly give away resistant stock to new beekeepers in their area to keep them from importing package bees.
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 hive 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, which is exactly why we see pockets of Varroa resistance where a lot of breeding has been done. Moving that resistance to another part of the country is not an easy task.
In summary, a persistent beekeeper with a lot of hives can significantly shift the gene pool in his favor. But if the area is constantly bombarded with random bees, it is extremely difficult to get a resistant line of bees going. It will require time, effort, and significant planning.
I’m not saying that you shouldn’t try to breed better bees. But you need to understand why it’s a long row to hoe and why it is so hard to imitate the success of others. It takes a long time to make a difference.
 Drones also arise from fertilized eggs that have identical alleles of the sex gene, a common result of inbreeding. Known as diploid drones, these bees are discovered early by the worker bees and consumed by them, leaving obvious holes in the brood pattern.
Honey Bee Suite