Genetics and Breeding  -  The Importance of Genetic Diversity

What is genetic diversity?  Every animal has a given number of chromosomes which are paired. A "gene locus" refers to a site on a chromosome where the gene for a particular trait is located. Any one of a number of variations of that gene may be found at that site. These variations of the gene are called "alleles".  When the alleles at a given locus are identical on both chromosomes of the pair, the animal is said to be homozygous for that gene. If the two genes are different, the animal is said to be heterozygous for that gene. In a normal population, a number of different genes (alleles) are represented, in the population as a whole,  for each locus, some of these will be more frequent, some rare. There will also be a low level of homozygosity found in the individual members of that normal population. Such a population is said to be genetically diverse.

Why is this important?  In Nature, the presence of a diverse complement of DNA within a population enables that population to respond to changes in the environment.  Individuals whose genetic makeup favors their survival through changed circumstances, will be able to propagate and renew the species, even though the less well equipped animals don’t make it.  Whereas if all the members of a population had the same genetic makeup, a serious environmental change could wipe out the entire population.  Many species have been wiped out this way in our lifetimes.  Shrinking numbers, isolation and inbreeding have caused the loss of the genetic diversity needed to adapt to changes in habitat.  This need for sufficient numbers and diversity in a population has only recently been recognized.

Selective breeding is nothing new.  Animal breeders were employing selective breeding before Father Gregor Mendel  ever published his work on wrinkled and smooth peas which marked the beginning of the study of genetics.  Probably as long as men have been keeping animals, they have noticed that some characteristics were inherited more strongly than others.  We read in Genesis that Laban made a deal with his son-in-law, Jacob, that if Jacob would tend his flocks, Jacob could keep all the spotted cattle for himself.  Crafty Jacob evidently knew something about genetics because he manipulated the breeding of his father-in-law’s cattle so that nearly ALL the calves were spotted. (And don’t believe that story about the white stakes at the well!)

Selection is the key.  Natural selection brings about changes in living organisms as mutations in their DNA occur.  Most of these mutations are either deleterious, or neutral.  The deleterious ones, exert a negative influence on the organism’s fitness to survive and reproduce, and these tend to gradually be eliminated.  The neutral ones are just that.  But every now and then a mutation occurs that confers a slight advantage.  The animals that possess it are better able to compete for resources, and more of their children, who possess the advantageous gene survive to reproduce themselves.  The genetic composition of the population shifts very slowly under natural selection.

But natural selection is not the only mechanism for genetic change.  There is another, and perhaps more important mechanism of evolution called genetic drift. Most people have a reasonable understanding of natural selection but they don't realize that drift is also important. The anti-evolutionists, in particular, concentrate their attack on natural selection not realizing that there is much more to evolution. Darwin didn't know about genetic drift, this is one of the reasons why modern evolutionary biologists are no longer "Darwinists". (When anti-evolutionists   equate evolution with Darwinism you know that they are behind the curve with their reading!)

One aspect of  genetic drift is the random process of transmitting alleles from one  generation to the next,  such that only a fraction of all possible genetic combinations ever become mature adults. The easiest case to visualize is the one in which parents (such as dogs) have only a small number of offspring, thus not all of the two parent's alleles will ever be passed on to their accumulated progeny due to chance assortment of chromosomes at meiosis (reductive gamete cell division). As you can see, the tendency of genetic drift is toward the loss of alleles, making the population more and more homozygous. And in fact this random process has the same tendency as does inbreeding.

In a large population this will not have much effect in each generation because the random nature of the process will tend to average out. But in a small population the effect could be rapid and significant.  Imagine if you will a small isolated group of 10 dogs.  One of these dogs dies accidentally.  Suddenly 10% of the genes in that population have been eradicated, some of them perhaps crucial to the long term survival of the population.  Now imagine that the same 10 dogs have multiplied for several generations, and their numbers are now 500.  The original complement of genetic material is now dispersed among 500 instead of 10.  The loss of a single individual now represents a loss of many fewer genes (0.2% rather than 10%) and the likelihood that a critical gene is among those lost is similarly reduced.

Drastic reduction of population numbers often make it difficult for a species to recover.   Such a reduction is called a genetic “bottleneck”. This inability to recover is due to a loss of diversity and perhaps loss of important alleles from the population.  The native American Passenger Pigeon was so reduced in numbers from over hunting in the 19th century, that even though small flocks still existed, the species became extinct.

“Disasters such as earthquakes, floods, or fires may reduce the size of a population drastically, killing victims unselectively. The result is that the small surviving population is unlikely to be representative of the original population in its genetic makeup – a  situation known as the bottleneck effect.... Genetic drift caused by bottlenecking may have been important in the early evolution of human populations when calamities decimated tribes. The gene pool of each surviving population may have been, just by chance, quite different from that of the larger population that predated the catastrophe." (Campbell, N.A. in Biology 2nd ed. Benjamin /Cummings 1990 p.443)

Another example of the bottleneck effect is the northern elephant seal which was hunted  almost to extinction. By 1890 there were fewer than 20 animals but the population now numbers more than 30,000. As predicted, there is very little genetic variation in the elephant seal population but the survival of the twenty animals that made it through the slaughter was more likely due to luck than to fitness.  The Cheetah underwent a bottleneck about 10,000 years ago such that all cheetahs today are extremely inbred.  Though protected, their numbers continue to fall as they encounter the pressures from human populations and competition for resources from better equipped predatory competitors.

One more example of genetic drift is known as the founder effect. In this case,  a small group breaks off from a larger population and forms a new population. This effect, which is the basis of the Lhasa Apso breed today, is well known in human populations:  

"The founder effect is probably responsible for the virtually complete lack of blood group B in American Indians, whose ancestors arrived in very small numbers across the Bering Strait during the end of the last Ice Age, about 10,000 years ago.”   (Suzuki, D.T., Griffiths, A.J.F., Miller, J.H.  and Lewontin, R.C. in An Introduction to Genetic Analysis 4th ed.  W.H. Freeman 1989 p.704).)

When humans step into the picture, environmental resources and hazards are usually eliminated as selective pressures, since the humans provide the resources.  Now selection is at the command of the breeder, who can, like Jacob, put the spots where he wants them.  When Mendel published his landmark work on dominant and recessive inheritance, animal breeders finally had a clear mathematical model to work with, and modern selective breeding was born.

As practiced by breeders today, there are several selection methods employed.  All of them seek to alter the random processes of population growth, and introduce dramatic changes in the genetic makeup of the selected populations.  All tend to restrict or eliminate the genetic diversity of populations.

Phenotypic Selection.  Phenotype refers to the qualities we can see or know about an animal, such as health, appearance, longevity, size, color etc.  When we select for phenotype we are simply pairing up two unrelated animals with the same or similar physical characteristics.  Many breeds of dogs were developed this way, ditto for pigs, cattle chickens, etc.  Breeding like to like without inbreeding tends to accumulate the genes for the characteristics we want, without necessarily concentrating genes for the invisible things we may or may not want.  It is a somewhat slow but fairly safe type of selection, since it does not tend to introduce a high level of homozygosity.

Geneological Selection. (Linebreeding and Inbreeding)  This breeding model selects animals on the basis of their pedigrees.  The thesis is that we can identify the carriers of traits we wish to keep and those we wish to eliminate. Then by breeding close relatives who presumably have similar if not identical sets of alleles, we can make the desired loci homozygous.  It certainly CAN be done, but it carries with it two major unintended effects:

1. In order for two formerly different genes at one locus to become identical, one of them has to be eliminated.  Now this would probably be just fine if all the genes could be manipulated individually, like a bag of marbles poured out on a table.  However, genes exist like strings of beads.  In order to get rid of one bead, you have to throw away the whole string.  Unfortunately, though we may not miss the unwelcome gene that we could see, there are a whole lot of other genes in the “string of beads” that we cannot see.  In the process of acquiring that homozygous straight leg, we may have tossed out the immune system, fertility, or some other much more subtle function that escapes notice for a while.

2. Some gene complexes are required to be heterozygous for proper functioning of the organism. The MHC or major histocompatability complex, an important component of the immune system, has to be heterozygous for proper immune function.  Studies of AIDS patients have shown that those with a high degree of heterozygosity of the MHC can often live with the HIV virus while those whose MHC is homozygous quickly succumb despite treatment.

The popular sire effect is closely related to inbreeding in it’s effects – that is to increase homozygosity, but it does it on a grand scale rather than an individual basis.  In a small population, let us say 10 bitches and 10 dogs, if all the bitches are bred to one dog and the other 9 dogs castrated, 45% of the genes in the population would be instantly discarded.  In addition the resulting generation would all be half siblings, causing an 25% homozygosity in the group.

Selection for preservation of diversity This third form of selection is now practiced by biologists working to save endangered populations by minimizing the effects of genetic drift, population loss, bottlenecking and resultant inbreeding.  The idea here is to plan breedings in such a way that all the individuals in a population have an equal chance to reproduce and pass their genes back into the general genepool  in the same proportions as these genes were found in the founder population.  In other words it is selection to combat selection.  Returning to our example of the 10 dogs with one killed, and the loss of 10% of the population’s alleles, the object is to build up the population as rapidly as possible, making sure that ALL the individuals contribute to the pool equally.  Now we have a group of 500 animals with a much more dispersed distribution of the more rare alleles and therefore much smaller chance of losing important alleles due to some mishap.

Right now in Lhasa Apsos just such a project is underway, to rescue the genetic legacy of a small genetically isolated group of dogs originating in the Himalayas.  Some people have had various misconceptions of the reasons for doing this allelic conservation breeding with this group of dogs.  Some have asked why these dogs could not have been simply dispersed to individual breeders to augment the existing breed's genepool.  This would be a poor use of the animals’ DNA, because each animal has only it’s own two alleles for each trait, and with so few animals, the entire array of genes would not be available to anyone, and the genes of one individual would be available to only a handful of people.  These ten drops of DNA would be swallowed up in a proverbial ocean!

Secondly, there would be no opportunity to evenly distribute the genes of the founders into a larger population.  This can only be accomplished by a rigorous breeding program designed to preserve the diversity of the founders, and is necessary as was mentioned earlier to combat the effects of genetic drift within the population.

I hope this little introduction to the study of genetics of populations will be of some use to our ALAC breeders.  It is a topic that will be of increasing importance as more and more research comes to light every day.