Inbreeding Levels in Different Breeds

Let’s take a look at the inbreeding in the various breeds.

As we have gotten more and more data on various breeds at BetterBred.com, we can see the same results found by Dr. Niels C. Pedersen and his team at UC Davis from a variety of angles. In the tables below, we color code the breeds by numbers of dogs in our database (not UC Davis’) so that we also know if there are enough results to come to conclusions about the breeds. Over 100 dogs is generally reliable, between 50 and 100 is conditional and under 50 dogs is not yet conclusive. (If you have results from your test and your breed has under 100 dogs in the database, we’d love to include your results!)

Overall inbreeding in a breed is an indication of loss of genetic diversity. In natural populations, this occasionally happens due to isolation or some event like a plague that wipes out a huge portion of a species. Out of the huge number of species on earth, only very seldomly do entire species survive with low genetic diversity. Cheetahs, famously, are one, Channel Island Foxes are another. Channel Foxes seem to have survived due to a delicate balance in their environment. Their isolation seems to have isolated them also from bigger predators. One bad virus could potentially wipe them out. Cheetahs in captivity are very susceptible to disease for this reason. Both of these species have nevertheless adapted well to their natural environments because they have the phenotype and genotype to do so. Another famous isolated population, the Isle Royale Wolves were studied for nearly 60 years. All wolves descended from a single bitch, and went from a high of 50 in 1979 to a low of 2 in 2016. Interestingly, the inadvertent introduction of canine parvovirus wreaked havoc with the wolf population and in two years the population fell from 50 to 12, indicating that only 25% were capable of surviving the virus. The Isle Royale wolves are expected to be extinct soon as there are doubts about the viability of the remaining two.

These are a small number of examples and nearly all the research on heterozygosity and fitness has shown that more diversity – meaning more genes in the population and individuals – is better. In purebred dogs, each breed has a different level of homozygosity. Breeds with small numbers of dogs tend to get more homozygous faster, simply because they have fewer breedings and fewer potential mates – meaning fewer opportunities to pass along all the existing genes. Larger populations tend to retain diversity more easily, unless they are subject to man-made bottlenecks, sustained generational inbreeding, or selection for extreme traits.

There’s been a lot of recent attention paid to the plight of the English Bulldog, based on Dr. Pedersen’s latest paper, though that breed is not the only one at risk due to loss of genetic diversity. The bulldog’s complicating issue is that many of their known problems are due to extreme traits that are considered desirable, like the size and shape of their heads, wrinkly skin and their body shape, while less extreme traits seem to have largely been bred out of the breed. These extreme traits affect basic functions like breathing and whelping. Ideally, breeders would simply select for healthy head shapes and easier whelping, but research suggests this will be very difficult to accomplish.  Why?

Most breeders will understand a  simplified scenario. For instance, if 100% of Labradors were chocolate, would it be possible to breed toward black Labradors? Of course not, because if all the genes for black coats were bred out, you cannot manufacture a new black gene. You’d have to breed to any black dog, and breed back into the brown Labradors. In a few generations, you’d have Labrador type back and black dogs, but this of course is not necessary in Labradors, because they aren’t all brown.

For English bulldogs, the genes for moderate phenotype may no longer exist in enough dogs to be able to change things without causing yet more inbreeding, since a few remaining moderate dogs could easily become overly popular as well. This is why all breeders should care about the genetic health of their breed as a whole. Bulldog breeders would never have done this knowingly. Luckily, they now have various tools that can help them improve life for their dogs without losing the essence of the breed.

Now let’s look at the inbreeding table. The numbers with a red background mean we don’t have enough of these results yet in the BetterBred database (different from the UC Davis database)  to be able to come to  any conclusions. But the yellow ones have more information and the green ones have enough. And what do we see? First look at the average alleles per locus. Diversity means there are lots of different genes in a population and this is where you can see which breed has more possible diversity. The Standard Poodle has the highest average number of alleles per locus, but this is largely due to the numbers of dogs tested.  The Alaskan Klee Kai has the fewest – and we know why. They have only 9 founders and are a relatively new breed. One good way to compare breed diversity and look for evidence of depletion is to compare the average alleles per locus to the “effective” alleles per locus. At each locus there are alleles that are more common than others. In breeds with reduced diversity there are sometimes a few that are much more common due to selective breeding. When that selection is too severe, or there’s been a bottleneck, a few alleles at each locus become very common. The effective alleles are the ones that are common enough to make an impact on the population. When that number gets very low, the breed is like cheetahs or  Channel Island foxes – vulnerable. In the case of the English Bulldog, which has extreme traits, there is probably not enough diversity to modify those traits. Dr Pedersen, along with Hongwei Liu and Ashley Pooch, looked at other indicators of loss of diversity to confirm this. Other measures of homozygosity we can use like homozygosity by locus (HL) also show the differences clearly. The Japanese Akitas are likely quite vulnerable too, though they have more functional type than Bulldogs do

On the positive side, the Havanese look like they are doing well, as do Miniature Poodles. Standard Poodles have the diversity but the big gap between their average alleles and effective alleles shows evidence of their known bottleneck.