To address these questions, you must know what the coefficient of inbreeding (COI) is and what it tells you. (Here and elsewhere, I always mean the actual level of inbreeding, as you would get from genomic DNA or a pedigree database that is complete back to founders.)
The inbreeding coefficient was originally devised to give animal breeders a way of estimating the degree inbreeding in their stock. But what is inbreeding? Animal breeders figured out long ago that if you repeatedly bred related animals together, the quality of the offspring began to decline, something they termed "loss of vigor". They knew that a cross with an unrelated animal restored normal vigor to the animals. What they needed was a way to determine the level of inbreeding in their animals so they could determine the "tipping" point,
in the tradeoff between benefits and costs of inbreeding. In populations of animals with complicated pedigrees, it could be difficult to do this. What was needed was a way to derive inbreeding quantitatively based on the relationships of the animals in the pedigree.
The coefficient of inbreeding was devised specifically for this purpose. If an animal inherits two copies of an allele that is passed on down both sides of a pedigree from a common ancestor, this produces homozygosity at this locus. This specific form of homozygosity, where two copies of the same allele are "identical by descent", is the definition of inbreeding.
The inbreeding coefficient reflects the fraction of loci that are homozygous because of two copies of the same allele were inherited from a single ancestor. (It is also the probability that a specific locus will have two copies of the same allele inherited from a common ancestor.)
So here's the burning question: Why do we need to worry about inbreeding? What exactly is the problem caused by homozygosity of alleles that are identical by descent?
But what if there is lots of inbreeding in the population? Many individuals might have the same allele, and for some that allele could even be homozygous. If it happens to be an allele that confers resistance, the population will be fine. But otherwise, the population will take a hit, with reduced reproduction or even death of animals with the other alleles.
This is a simple example, but you can image a similar situation for many genes in the genome of a animal, which will be reflected in the allelic diversity of the population. Individuals in healthy populations of wild animals usually have an inbreeding coefficient in the very low single digits, even 0%.
These two charts (below) depict the individuals chromosomes of a wolf (left) and a German Shepherd dog (right) (Wang et al. 2012). The regions on each chromosome that are "low diversity regions" (LDR; i.e., homozygosity) are in dark blue. It is easy to see that the German Shepherd has much more dark blue, indicating regions of homozygosity. A population of wolves like this one with low inbreeding is more likely to have the allelic variation that will allow it to adjust to variations in the environment than a population of inbred Germans Shepherds that has much less allelic variation. This effect is so strong that it tends to keep inbreeding levels of wild populations extremely low as long as the population is relatively large and there is some exchange of individuals from other packs.
This is the question often voiced by breeders: What level of inbreeding is "safe"?
To address this question, we can look at data for effects of inbreeding on "fitness", i.e., traits that reflect the ability of the animal to grow, reproduce, and survive.
Thanks to the tendency of royalty to marry their relatives, we have interesting data for humans on the effects of inbreeding for various traits. One such dynasty was the Spanish Habsburgs, for which we have data for various parameters of interest (Alvarez et al. 2011). These are data for survival of children to at least 10 years of age as a function of the degree of inbreeding estimated from pedigrees. Children with the longest lifespans had inbreeding levels less than about 6%. Above this, survival to 10 years dropped sharply, with less than 50% achieving this age.
There are similarly dramatic effects of inreeding on lifespan in dogs. In Standard Poodles, dogs with inbreeding less than 6% live longer than those with higher COI. The penalty paid for an increase in inbreeding from 6.25% (first cousins) to 12.5% (half sib mating) was about 4 years! At 8 years old, more than 80% of dogs with low inbreeding are alive, while only 60% of dogs with inbreeding > 6.25% survived to this age. In dogs with low inbreeding (< 6%), 80% survived at least to 12 years old; only 30% of inbred dogs survived to that age.
There is a similarly dramatic effect of inbreeding on lifespan in Bernese Mountain Dogs, many of which fail to live beyond 6-9 years old (Klopfenstein et al 2016). This chart (Long & Klei, Bernergarde) shows that each 10% increase in COI reduces lifespan by 200 days. That is, lifespan is reduced by 20.6 days for each 1% increase in inbreeding (Long & Klei, 2009). For a dog with a COI of 30%, that's a reduction in lifespan of almost two years.
The effects of inbreeding on longevity have been compiled (Leroy et al 2014) for a group of breeds that include Bernese Mount Dog, Basset Hound, Cairn Terrier, Epagneul Breton, German Shepherd Dog, Leonberger, and West Highland White terrier. This chart shows longevity of each breed at three levels of inbreeding, with signifiant effects indicated by asterisks.
Consequences of inbreeding can be manifested at a very early age. These data for Beagles show that there is more than 20% mortality of puppies at 10 days of age at COIs up to 25%. (The data from 0% to 25% are pooled, so we can't determine how mortality was affected by inbreeding levels less than 25%). As inbreeding increases above 25%, the mortality increases significantly, to about 30% for dogs with COI between 25-50%, and about 50% for inbreeding of 50-67%.
Reproduction
Inbreeding reduces reduces fertility and effective length of reproductive period in humans (Alvarez et al 2015).
Inbreeding affects various aspects of reproduction in dogs as well. These are data for litter size as a function of inbreeding coefficient for six breeds of dog from the Swedish Kennel Club database. The top graph is litter size in number of puppies, the graph below is the decline in litter size from the value at the lowest level of inbreeding (litter size as a 5 of maximum), so all breeds start at 100% and decline from there.
The slopes of these lines tell us about the "cost-benefit" ratio on inbreeding. For these breeds, the slopes are about 0.1, which means that an increase in inbreeding of 10% reduces litter size by about 1.
If normal litter size is about 6, a COI of 30% - which is not uncommon in many breeds would reduce the litter size by HALF. That is half as many offspring from which to choose your "pick", and on top of this realize that these puppies will have reduced fitness in the ways noted by Wright - they are likely to be smaller, less vigorous, have more birth defects and higher mortality, grow more slowly, have shorter lifespan, and of course increased incidence of genetic disorders caused by recessive mutations.
These are data from the same study of longevity by Leroy et al. mentioned above. The data show that higher levels of inbreeding in both the dam and the litter negatively affect litter size. (Leroy et al 2014).
A recent study (Chu et al 2019) has taken advantage of the data from the Golden Retriever Lifestudy sponsored by Morris to show that inbeeding reduces litter size in Goldens. The average level of inbreeding in 93 dogs used in the study averaged 31.6%, and ranged from 18.7% yo 49.9%. A quick look at the levels of inbreeding in the various studies mentioned above makes clear that the inbreeding in these Goldens is extremely high, with all individuals higher than the 12.5% COI that would result from a cross of half siblings. While they did find a negative effect of inbreeding on litter size, note that we would expect to see a substantial reduction in litter size over the range from 0% to 20%, for which they have no data.
Diseases
The detrimental effects of inbreeding can be manifested as increased incidence or risk of disease.
In humans, inbreeding increases the prevalence of multiple disorders including cancer, Schizophrenia, and epilepsy Alvarez et al 2011). In the chart below, asterisks indicate significant difference from the prevalence at the lowest level of inbreeding (0.6%). Note that the highest level of inbreeding in these data is only 3.6^%, far less than we would be worrying about in a dataset for purebred dogs. It's also clear that the relationship between prevalence and inbreeding appears to be roughly linear, potentially allowing prediction of disease incidence at much higher levels of inbreeding.
You know that there is a long list of genetic disorders in dogs that can be linked to recessive mutations. For these, animals with only a single copy of the mutation are considered to be "carriers" without detrimental effects. However, crossing two carriers runs a risk of approximately 25% of offspring inheriting two copies of the mutation, resulting in expression of the disorder. We could reduce the risk of producing puppies that are homozogous for a particular mutation by avoiding pairings that are closely related. The problem, of course, is that the loss of genetic diversity and high levels of inbreeding have resulted in populations of dogs that are extremely similar genetically. Trying to reduce the incidence of disease by selective breeding in such populations might be possible if considering only one or two mutations, but for breeds with multiple known mutations that need to be avoided, avoiding known risks might be impossible. Of course, we don't know all of the mutations hiding in the gene pool of a breed, so testing for and avoiding the documented mutations does not mean a dog is clear of deleterious mutations - only the ones we know about. Doing DNA testing to prevent a 25% risk of genetic disease from a known mutation, then doing a cross with a 25% risk of producing homozygosity for some other yet-to-be-identified mutation, demonstrates a failure to understand the notion of inbreeding and its consequences.
I have pulled out data above for humans and dogs because I could find examples of data for both and the particular traits are familiar to breeders.
But don't think that the scanty data presented here is flimsy justification for arguing that we do need to worry about the negative effects of inbreeding, even at very low levels. In fact, there are mountains of data for the consequences of inbreeding in livestock and other domestic animals, because the profitability of commercial breeding hangs on getting the best level of inbreeding to balance benefit with detriment.
This takes us back to the livestock breeders we mentioned above. They recognized that there were some benefits produced by inbreeding, including more predictable, consistent traits in the offspring. But they also realized that more of a good thing didn't make things even better. Breeders needed a quantitative estimate of inbreeding so they could know the level of inbreeding at which the costs began to outweigh the benefits. Hence, the development of the coefficient of inbreeding. They explicitly embraced the realization that there were negative consequences to inbreeding, but in some instances the risk might outweigh the particular negatives. With a way to estimate COI for any animal and any potential cross, and data for how the traits they were interested in were affected by increeding, they could fine tune their mate selection to have the greatest likelihood of maximizing benefit relative to detriment.
To be able to do this, they have carefully collected the trait data to use in an analysis like this from thousands or even millions of animals over many generations. Dog breeders are not likely to do this, but the point is that we are entirely casual about inbreeding, and we should assume that just because we don't have the data to show that there are deleterious effects doesn't mean there aren't any. Notice also that this paper considers both pedigree and genomic estimates of inbreeding, and advocates that breeders should use both to get the best information to use in breeding. Notice that with data like this, they can estimate the effects of very small differences in levels of inbreeding on a trait, even as little as a 1% increase in inbreeding coefficient.
From the information presented here, it is clear that inbreeding at any level has consequences, and that even very small changes can be relevant. In a litter of puppies, no two puppies will be genetically identical, so even if they have the same level of inbreeding, the homozygosity will likely be at different loci on the chromosomes. So you can have a puppy with 5% COI that is robust and healthy, and another also with 5% inbreeding that happened to be homozygous for loci that produced a negative effect. For this reason, COI is not an index of "health". It is a prediction or estimate of homozygosity, and that homozygosity might be either good or bad. But we know that in general, homozygosity has deleterious effects and should be avoided when possible for that reason. The bottom line is that NO level of inbreeding is "safe" or without consequences.
Find the data for your breed on the charts below. If your breed is not on the first set of graphs, download the file just below labeled "Bannasch et al 2021", which contains some additional breeds.
If your first response on finding the data for your breed is to assume that the data must be from some non-representative population, because "inbreeding in my breed is nowhere near that high", I can assure you that these data are indeed representative of your breed. These are averages of a sample of dogs, so some individual dogs will have lower than average inbreeding, but at the same time some individuals will be higher. The point is that the livestock breeders try to keep inbreeding lower than about 5%, because at levels higher than this the detrimental consequences of inbreeding outweigh the benefits. These breeders demonstrate that you can have levels of uniformity and consistency in a group of animals at very low levels of inbreeding, so it is simply not the case that (as often claimed by dog breeders), high inbreeding is necessary to "fix type" produce consistency. This is nonsense. We CAN have both health and breed quality, but not at the levels of inbreeding typical of most purebred breeds.
Breeders that are serious about preservation of their breeds will recognize the fix we're in right now and take steps to remedy a really bad situation. It is possible to accomplish genetic "rehabilitation" of a breed, to restore it to health and preserve the traits that make each breed unique.
But this will require these breeders to step out of the bubble of ideology and misinformation that has justified ridiculous and completely unnecessary levels of inbreeding, and use the tools and information of science to return to breeding strategies that maintain type without compromising health.
There are additional data in the paper by Bannasch et al that I have displayed in this graph (below).
bannasch_et_al_2021_cavaiers_fadj.png |
Alvarez et al, 2009. The role of inbreeding in the extinction of a European royal dynasty. PLoS ONE 4:e5174. doi:10.1371/ journal.pone.0005174.
Alvarez et al, 2011. Inbreeding and genetics. Advances in the study of genetic disorders.
Alvarez et al 2015. Darwin was right: inbreeding depression on male fertility in the Darwin family. Biol. J. Linnean Soc 114: 474-483.
Armstrong JB, 2000. Longevity in the Standard Poodle. The Canine Diversity Project.
Bannasch et al, 2021. The effect of inbreeding, body size and morphology on health in dog breeds. Canine Medicine and Genetics 8: 12. doi.org/10.1186/s40575-021-00111-4.
Charlesworth & Willis. 2009. The genetics of inbreeding depression. Nature Reviews: Genetics 10:783-796. doi:10.1038/nrg2664
Chu et al 2019. Inbreeding depression causes reduced fecundity in Golden Retrievers. Mammalian Genome 30: 166-172. https://doi.org/10.1007/s00335-019-09805-4.
Klopfenstein et al 2016. Life expectancy and causes of death in Bernese mountain dogs in Switzerland. BMC Veterinary Research 12: 153. DOI 10.1186/s12917-016-0782-9.
Leroy et al 2014. Inbreeding impact of litter size and survival in selected canine breeds Vet. J. 203: 74-78.
Long P & B Klei, 2009. Inbreeding and longevity in Bernese Mountain Dogs.
Rehfeld 1970. Definition of relationships in a closed Beagle colony. J. Am. Vet. Res. 31:723-732.
Wang et al 2012. The genomics of selection in dogs and the parallel evolution between dogs and humans. Natre Communications 4:1860. DOI: 10.1038/ncomms2814.
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