Put the Pen to the Paper

:The Poodle and the Chocolate Cake by Dr. John Armstrong
August 2, 2008, 2:52 pm
Filed under: :Genetics

The Nature of Diversity

Think of genes as recipes. They carry the instructions for the various components that go into making up an organism. Each recipe specifies a particular component, and different individuals may carry different versions of the same recipe. (In the jargon of genetics, we say that they carry different alleles of a particular gene.) Individuals within a population often carry similar or identical recipes, for example, chocolate cake for a Poodle, lemon cake for a Beagle, and white cake for a Samoyed. A different canine species might be represented by a fruit cake. When you consider animals that are quite different, such as frogs and chickens, you will generally find “homologous” recipes, say for pies or puddings. Thus, there is more diversity among mammals than among carnivores, more among the carnivores than among the Canidae, and more among the Canidae than among the wolf group.


An organism carries a collection of recipes, and the collection defines the organism. The great diversity in the possible collections of recipes is the reason for the great diversity in the animal and plant kingdoms. The more closely related two individuals are, the greater the similarity in their collections. The number of combinations is huge, and during evolution, the recipe collection was undoubtedly reshuffled many times. The combinations that worked well survived and multiplied. Those that did not work quickly died out. In theory, one may make a meal of Champagne with tacos and Yorkshire pudding, but they don’t really belong together. As time passed, exchange of recipes became difficult between animals that differed substantially in their physical and behavioural characteristics. Different groups, therefore, became constrained to work with only a subset of the total possible collection of recipes.

One definition of a species is that members of two different species bred to each other cannot produce a fertile hybrid. However, a more modern definition is that two species are geographically, physiologically, or behaviourally isolated such that they do not normally produce hybrids. Additionally, they should have features that differ sufficiently to allow them to be distinguished from each other. The domestic dog, wolf, coyote, and jackal can all mate with each others (barring size constraints) to produce viable and fertile hybrids. Yet, they have been considered different species (within the genus Canis) because they normally live in different places, behave differently, and can usually be told apart. (Though there has been a recent move to change Canis familiaris to a subspecies of Canis lupus.) However, a jackal will not mate with a dog unless they have been raised together from pups (presumably due to a learned behavioural difference). Furthermore, no Canis species can produce a hybrid with a fox. This is not because the kinds of genetic recipes are greatly different, but because foxes do not share the same number of chromosomes. (In other words, their recipes are filed under a different, incompatible system — somewhat akin to filing one under DOS and the other on a Mac.)

Genetic recipes may get modified when they are passed on. Many of the modifications will make no noticeable difference, or only a very subtle one. Some may improve the recipe and others will not. If we are making a chocolate cake and a critical ingredient is forgotten, or the cake is baked too long or at the wrong temperature, we end up with a disaster. (If we don’t understand what has gone wrong, we will likely throw out the recipe and look for a new one.) We may even make deliberate modifications in an attempt to get a more memorable cake. Among the “chocolate cake” population, there will be a variety — or diversity — of recipes and, therefore, of cakes.

This, I would say, is a “good” thing. Do we always want the same chocolate cake? Surely we will tire of it, and even if we don’t, we lose the pleasure of anticipation. If, for some unforseen reason, everyone suddenly loses their taste for THE chocolate cake, it will surely go extinct. To have the potential for evolution and adaptation, we must risk the possibility of the bad. That is the “cost.”

In a large, naturally breeding population, we will end up with a number of versions (alleles), some so slightly different that we will never notice, some perceptibly different (but still functional), and some that just don’t work at all. However, if we remove the diversity we lose the potential for evolution and for surviving unexpected change. To have the potential for evolution and adaptation, we must risk the possibility of the bad. Geneticists call that cost genetic load. This “bad” group persists because every individual carries two copies of every recipe, and often having just one “good” copy is enough for normal function. In most populations, every individual carries a portion of the load — three to five bad recipes out of several thousand. The load is so well distributed that if two individuals compare their recipe collections they will generally not have two copies of the same bad recipe.

Loss of Diversity

Suppose we start a new population with only six or eight founders. (A number of breeds have started with that few.) We will get rid of hundreds of bad recipes, but the remaining dozen or two will be encountered much more frequently. Furthermore, if there are several good or excellent recipes, the chance of dropping one of these from the collection grows greater as the number of founders diminishes, and the risk of losing one remains high as long as the effective population size remains low. Working with small numbers will inevitably decrease the diversity, simply because individuals do not pass on their recipes equally to the next generation and some recipes are accidentally lost. This has the superficially desirable result of giving a more reproducible phenotype, but at the expense of an overall reduction in quality, health, and longevity.


If breeders had the ability to recognize each individual recipe and choose only those that were excellent, breeds could be produced with a small number of individuals that lacked genetic problems. However, what we see (the phenotype) is the product of all the recipes and, for the most part, we cannot distinguish the individual recipes. Moreover, we do not have the option of selecting recipes individually. When we select an animal for breeding, we are forced to accept a complete set. Even in those few cases where we now have a DNA test for a bad recipe (allele), we do not possess the ability to correct or selectively discarded it. We are therefore forced to work around it, or to discard the whole collection, with the attendant risk of discarding something excellent along with it.

The common practice of almost everyone rushing to breed to the currently-popular male show champion is probably the most significant factor reducing whatever diversity remains. Consider your own breed (the situation for most breeds is similar). Can you find one or more males that appear in most pedigrees? Almost everyone decides they like the recipes of (insert name) — or at least the ones they can see readily — and abandons other recipes with little thought to the eventual consequences. In a few generations, almost everyone has a substantial number of his recipes, though not necessarily his exceptional ones, and many excellent alternatives are very hard to find.

How precious is the individual that comes along with some of the missing recipes and relatively few of the “popular” collection? Do we hesitate because there are also a few bad recipes in this alternate collection? Are we now so accustomed to dealing with the more-popular collection that we have lost the vision of the “memorable” chocolate cake?

Population Genetics and the Breeder

What is often called Mendelian genetics deals with the outcome of specific crosses. Population genetics deals with the distribution of alleles in a population and the effects of mutation, selection, inbreeding, etc., on this distribution. As a breeder, you are a practicing geneticist. A knowledge of both Mendelian genetics and population genetics is critical, not only to your own success, but also to the survival of your breed.

:Dog genome project
July 29, 2008, 12:15 pm
Filed under: :Genetics

:DNA from the beginning
July 29, 2008, 12:12 pm
Filed under: :Genetics

:Incest in nature
May 25, 2008, 12:37 pm
Filed under: :Genetics
Incest in Nature
Six years ago, I wrote about the science and ethics of incest (“The Love That Dare Not Speak Its Surname“). At the time, a study showed that having a child with your first cousin raised the risk of a significant birth defect from about 3-to-4 percent to about 4-to-7 percent. The authors concluded that this difference wasn’t enough to justify genetic testing of cousin couples, much less bans on cousin marriage.
Now the incest taboo has taken another hit. Ecologists Kelly Zamudio and Chris Chandler have published a study in Molecular Ecology on sexual selection among spotted salamanders. From this and other research, Science News reporter Ewen Callaway has teased out a fascinating theme: Incest, apparently for sound Darwinian reasons, is surprisingly common in nature.
Through interviews with biologists and ecologists, Callaway looks at several cases. Among spotted salamanders, DNA analysis shows inbreeding “at the level of first cousins, on average. Despite having hundreds of possible mates to choose from, females tended to fertilize their eggs with sperm from related males.” Another study found that “Japanese quail prefer first cousins over brothers and sisters and over less-related birds.” Among ambrosia beetles: “Brothers and sisters tend to mate.” A comparison over two generations of mating found that “inbred beetles fared no worse than outbred insects, and the eggs produced by brother-sister pairs were likelier to hatch than the eggs of unrelated pairs.”
At least one fish species similarly prefers brother-sister mating. Scientists “found that fathers from brother-sister couples spent more time, on average, defending their caves and that both parents tended to pay more attention to their kids than unrelated couples.” This makes obvious sense. The ecologist who supervised the study reports, “Couples which are full siblings are more cooperative in brood care. … [T]he males and females stay with the offspring for several weeks and guard them—they defend them—and there’s less aggression between full siblings.”
These aren’t the only rationales for inbreeding. Paraphrasing a Cambridge biologist, Callaway notes, “Many organisms might have slight genetic tweaks or adaptations tuned to their local habitats, and too much genetic mixing with outsiders can dilute these adaptations.” Among ambrosia beetles, the practice “may cement the slight genetic differences between the insects,” thereby helping to “create new species.”
Nor is inbreeding universally taboo among humans. A study in Pakistan found that “three out of five marriages were between first cousins.” Another in India that found “one-fifth of marriages occurred between uncles and nieces and a third between first cousins.” And before you dismiss this as Eastern barbarism, read up on Charles Darwin and Rudy Giuliani.
The incest taboo does have a firm biological basis. As Callaway explains, “Inbreeding ups the chances that a child will inherit two versions of a disease-causing gene.” Data show higher mortality among infants born from first-cousin pairs. But beyond that range, there’s evidence that breeding within the family has advantages. Two months ago, a study in Science reported “a significant positive association between kinship and fertility,” with a likely “biological basis.” The study found “the greatest reproductive success” among “couples related at the level of third and fourth cousins.” On average, these cousins produced more kids than less related—and more related—pairs did.
The upshot seems to be that there are advantages and disadvantages to breeding with a relative, and as far as nature is concerned, the ideal course is to strike a balance. You’re free to argue that incest is wrong, of course. But be careful what you call unnatural.