Inbreeding leads to:

Increased homozygosity.

Increased expression of recessive traits.

Decreased expression of dominant traits.

Increased heterozygosity.

An allele:

Is one of possibly many variations of a gene.

Can be recessive.

Can be dominant.

Is a synonym of “gene.”

A gene:

Is a unit of heredity that is transferred from parent to offspring.

Controls the transmission and expression of one or more traits.

Can code for multiple and otherwise unrelated phenotypic effects.

Codes only for a single discernible phenotypic effect.

Can be dominant or recessive.

If an individual has inherited the same allele for a gene from both parents, they are said to be:

Homozygous.

Hemizygous, Nullizygous, Allozygous, Heterozygous.

Phenotype refers to:

The set of observable characteristics of an individual.

The morphology, behavior, and development of an individual.

The genetic makeup of an individual.

Both expressed and unexpressed genetic variation.

Which of the following trait types can “breed true?” To “breed true” means that two organisms with a particular heritable phenotype produce only offspring with that same phenotype.

Recessive traits. (e.g. brown coloring, rough coats, tri-color, etc.)

Dominant traits. (e.g. black coloring, smooth coats, etc.)

Heterozygous Semi-Dominant traits. (e.g. Merle, Bobtail, Chinese Crested Hairless, German Shepherd Panda, etc.)

Heterozygous Co-Dominant traits. (e.g. AB blood type, red-white Roan in horses, etc.)

What mode of inheritance do the following traits have in common: Merle, Bobtail, Harlequin, Panda (German Shepherds), Hairlessness (Xolo, Chinese Crested, etc.) ?

They are Lethal.  Lethal genes are capable of causing death.

They are all semi-dominant. When the heterozygote has a different, intermediate phenotype compared to the homozygous dominant or homozygous recessive individuals, it is said to be “semi-dominant.”

They are all recessive.

They are all dominant.

They are sex-linked.

They are all co-dominant.

Inspired by the Genetics Survey on Gene Expression and an inquiry from the CanineGenetics-L yahoo group, I figure it might be fun to post an occasional genetics quiz to reinforce some of the concepts covered on this blog and provoke discussion of the sorts of genetics knowledge that is most helpful to dog enthusiasts.

The results are not tracked, it’s completely anonymous, and the correct answers will be revealed tomorrow. I tried several automated quiz plugins but they are a pain, so we’ll just go old school.  If you run across an answer that you want to discuss, do leave a comment.

February is the month of sweethearts, so there’s no better time to bone up on what happens when love is in the air and dogs are swapping genes. For the inaugural monthly quiz, here are some questions long time readers of the blog should be able to answer.

Multiple Correct Answers are accepted and often required.

Inbreeding leads to:

Increased homozygosity.

Increased expression of recessive traits.

Decreased expression of dominant traits.

Increased heterozygosity.

An allele:

Is one of possibly many variations of a gene.

Can be recessive.

Can be dominant.

Is a synonym of “gene.”

A gene:

Is a unit of heredity that is transferred from parent to offspring.

Controls the transmission and expression of one or more traits.

Can code for multiple and otherwise unrelated phenotypic effects.

Codes only for a single discernible phenotypic effect.

Can be dominant or recessive.

If an individual has inherited the same allele for a gene from both parents, they are said to be:

Heterozygous.

Homozygous.

Hemizygous.

Nullizygous.

Allozygous.

Heterozygous.

Phenotype refers to:

The set of observable characteristics of an individual.

The morphology, behavior, and development of an individual.

The genetic makeup of an individual.

Both expressed and unexpressed genetic variation.

Which of the following trait types can “breed true?” To “breed true” means that two organisms with a particular heritable phenotype produce only offspring with that same phenotype.

Recessive traits. (e.g. brown coloring, rough coats, tri-color, etc.)

Dominant traits. (e.g. black coloring, smooth coats, etc.)

Heterozygous Semi-Dominant traits. (e.g. Merle, Bobtail, Chinese Crested Hairless, German Shepherd Panda, etc.)

Heterozygous Co-Dominant traits. (e.g. AB blood type, red-white Roan in horses, etc.)

What mode of inheritance do the following traits have in common: Merle, Bobtail, Harlequin, Panda (German Shepherds), Hairlessness (Xolo, Chinese Crested, etc.) ?

They are Lethal.  Lethal genes are capable of causing death.

They are all semi-dominant. When the heterozygote has a different, intermediate phenotype compared to the homozygous dominant or homozygous recessive individuals, it is said to be “semi-dominant.”

They are all recessive.

They are all dominant.

They are sex-linked.

They are all co-dominant.

Answers Here

The retina of a Briard with an inherited blindness disease that was later cured with gene therapy.

Back in 2001, scientists first treated inherited blindness in dogs using gene therapy. In that instance it was Congenital Stationary Night Blindness which manifests in Briards and is analogous to Leber congenital amaurosis in humans, both defects in the RPE65 gene.

Dogs blinded by an inherited retinal degenerative disease had their vision restored after treatment with genes from healthy dogs, marking the first successful gene therapy for blindness in a large animal. The treatment offers hope for humans with a similar condition.
…
“We have shown that gene therapy can restore vision in dogs with one of the most clinically severe retinal degenerations,” says Acland, a research veterinarian at Cornell’s James A. Baker Institute for Animal Health.
…
The RPE cell layer in the eyes of humans, dogs and other mammals supports the retina by providing nourishment and removing waste products while supplying vitamin A to the photoreceptors. Puppies and human infants with defective RPE65 genes produce a mutant form of the RPE65 protein, resulting in early vision loss, degeneration of the retinas and near-total blindness later in life.

The canine form of this retinal degenerative disease has been found only in the briard dog breed. In the gene therapy experiments, researchers used RPE65 genes that were cloned from dogs without the disease, together with a viral vector (recombinant adeno-associated virus, or AAV) to carry the normal dogs’ DNA. They injected the combination into the subretinal space of the eyes of 3-month-old briard-beagle mix dogs that were known to have the defective RPE65 gene and had been blind since birth. Within six weeks, the treated eyes were producing the correct form of RPE65 protein. By three months, a series of tests (electroretinography, pupillometry and obstacle-avoidance tests in a dimly lit room) demonstrated that vision was restored to the treated eyes.

In 2010, the same team successfully returned function to the cones of previously blind dogs affected by a form of blindness called Achromatopsia.

Now, scientists have again used gene therapy to prevent and reverse another form of blindness in dogs and humans called X-linked Retinitis Pigmentosa associated with a mutation in the RPGR gene.

The disease in humans and dogs is caused by defects in the RPGR gene and results in early, severe and progressive vision loss. It is one of the most common inherited forms of retinal degeneration in man.

“Every single abnormal feature that defines the disease in the dogs was corrected following treatment,” said lead author William Beltran, assistant professor of ophthalmology at Penn’s School of Veterinary Medicine.

“We were thrilled,” said senior author Gustavo Aguirre, professor of medical genetics and ophthalmology at Penn Vet. “The treated cells were completely normal, and this effect resulted from introducing the normal version of the human gene into the diseased photoreceptor cells.”

This is exciting for dog owners because there are numerous breeds that have epidemic levels of eye disease and the proliferation of these advancements could lead to routine treatments that would treat or cure the disease in individuals.

There’s still a barrier to a permanent cure for breeds that would extend to the offspring of treated individuals.  Treated dogs only receive the working DNA in the somatic cells at the location of the viral vector.  Somatic cells are all the cells in the body besides those directly involved in producing offspring.  If there’s a mutation in a somatic “body” cell, it will not be passed on to future generations.

The cells that produce the sperm and egg are called germline cells and they are not necessarily amenable to the same gene therapy techniques that work on individual somatic cells.  You can effectively cure the blindness by providing a working copy of the genes within the eye, but other cells in the body will not have the new gene and the germline cells will not produce sperm or eggs that benefit from the disease-free allele either.

This effect is called the Weismann barrier, which is the theory that genetic information moves only in one direction, from germline cells to somatic cells.  This is why when you get an x-ray the tech is more concerned with lead shielding your private parts than the rest of your body because germline mutations have serious consequences for your offspring and germline cells are theoretically immortal (they can replicate for the entire life of the organism) whereas somatic cells only divide 30-50 times.

If the Weismann barrier can be broken, it’s theoretically possible for the treatment of eye cells to result in genetic change in somatic cells and thus in the offspring.

There’s also the potential to apply gene therapy techniques to germline cells (such as the sperm or egg) directly and this would enable genetic engineering that would last over generations.  Scientists have already created lasting changes in organisms that do not differentiate somatic-germline cells (like plants: thus we have GMOs), but I’m not aware of any ongoing progress on germline gene therapy and there are currently institutional barriers against work in that area given the potential ethical implications of genetic engineering.  Scientists have successfully inserted synthetic chromosomes into mice that were heritable but the current focus in treatment of human offspring disease is to perform IVF and genetically profile the blastocysts before implantation.

So this is good news for dogs, and possibly the beginning of an amazing new world of animal husbandry when genetic engineering will allow for some truly incredible health advancements and possibly some radical experimentation.

The breed is believed to be the creation of one man, Heinrich Essig, who was a dog dealer and traveling salesman; his claimed formula was Landseer Newfoundland x Saint Bernard, followed by more Saint Bernards and a Pyrenean Mountain Dog with the goal being a large white dog that was fashionable at the time.  After Essig’s death in 1889 his nephew had the inspiration to promote the breed as a lion-like mascot for the town of Leonberg and established the final conformation of the dogs as having a lion-like rough coat with reddish-brown coloration, a black mask and black sable accents.  Like most breeds, the origin mythology is poorly documented and stud books were not kept in earnest on the breed for several decades after its establishment.

As a German breed, the Leonberger was severely affected by both World Wars: only 5 known breeding dogs survived the first war and only 8 pedigreed dogs emerged from the second.  Two severe bottlenecks like this are not conducive to preserve genetic diversity within a closed population.

That is why I was surprised to find that the 5 Leonbergers which were DNA tested as part of a study analyzing the genetic composition of Alaskan Sled Dogs showed that they had excess heterozyosity compared to Hardy-Weinberg equilibrium. Of 141 breeds tested over 96 genetic marker sites, there were only 9 purebred breeds found to be surplus heterozygous and most of those are only marginally so.

Note, this is not a measure of gross diversity in the breed, it’s a measure of which way the breed is being pushed genetically, either toward more conformity and homozygosity or toward more diversity and heterozygosity.

Genetic rescue requires a push toward heterozygosity before reaching a new equilibrium with the new alleles.

Inbred or Outcrossed? Bars that extend to the left indicate excess heterozygosity compared to the Hardy-Weinberg equilibrium (red line), suggesting active selection for allele diversity (i.e. outcrossing). The Leonberger is one of the most heterozygous breeds tested.

Here is the actual data represented in the chart.  The purposely out-crossed hybrid sled dogs were found to be 20% more diverse than equilibrium and the Leonberger was second only to the Puli with over 10% excess heterozyosity.

I’ve only found one documented outcross on the Leonberger books: In 1954 a Leonberger stud Arko von Leonberg with a COI of 20% was bred to a Newfoundland dam Grisette von Bruckberg and one female from that litter, Alma von Rossbach, would cement herself into the Leonberger gene pool.

More recently European kennel clubs have registered Leonbergers with full breeding rights certificates “titre initial” (as opposed to a 3 generation provisional appendix registration “registre initial”) which are given after a number of criteria are met; typically an evaluation against the breed standard or significant show success, health testing, and perhaps even temperament evaluations.  These dogs are believed to be pure-blooded Leonbergers instead of hybrid dogs which would normally take 3 generations to be admitted into the gene pool with full breeding rights and purebred status in registries that allow new blood.  Sometimes they come with full pedigree and while the kennel club would void the known pedigree and perhaps calculate the COI of offspring as 0%, it’s not clear that either the registre initial or titre initial schemes are a source of new Leonberger blood.

Another possible source of Leonberger diversity lies in the history of Germany and the East after the wars.  The Leonberger isn’t just a dog of the West and so it existed on both sides of the Iron Curtain.  It is unknown and undocumented what sorts of possible crosses came into the breed during the Cold War before the reunification of Germany and the resumption of normal trade across Europe.

The last and least verifiable source of unexpected diversity would be intentional and unintentional pedigree fraud or error.  It’s possible that some breeders when faced with a line that was not producing what they wanted or suffering from inbred disease or infertility decided to outcross, or an accidental litter proved sufficiently virtuous to register and the breeder either could not or did not choose to disclose this.

There’s also the possibility that I simply haven’t accounted for some factors which would have preserved heterozygosity in Leonbergers and that the bottlenecks did not have the expected effects on the gene pool.  Certainly more questions than answers, but what an intriguing mystery it is.

The wolves of Isle Royale Michigan

Sweeping comparisons between wild animals and domesticated pets are dangerous given the unique and often mutually exclusive conditions in which those two groups often find themselves.  Wild animals must hunt for their food, compete for resources, suffer predation, lack medical intervention, self-select their mates, and exist in numbers based upon a complex interaction between their own merits and the conditions in their environment. Pet dogs are fed from a bowl daily, compete only for our affection and attention, are largely free of predation, have ready access to modern veterinary techniques and treatments, have their mates chosen for them–sometimes from dogs long dead or on other continents, and exist in numbers based upon human concerns and rarely on their own merits or the environmental carrying capacity.  Their selection is very much unnatural. But there are very few scientific studies of domesticated pets versus numerous investigations into wild populations, so dog lovers would be remiss in not learning lessons from our pets’ wild cousins.  One particularly interesting ongoing scientific inquiry is the study of the wolf and moose populations on Isle Royale Michigan.

Wolves colonized Isle Royale, a wilderness island in Lake Superior, North America, in 1949 or 1950. The population is isolated from mainland wolves by a channel of frigid water, 24 km wide. In many, but not all years, this channel freezes for several days or weeks. Although an occasional ice bridge makes immigration possible, the analysis of mitochondrial DNA and the Y chromosome suggests that the population was originally founded by only one female and two males.

This makes Isle Royale analogous to a small dog breed based on a few founders or even a single kennel that rarely brings in any new blood.  Nova Scotia Duck Tolling Retrievers, Leonbergers, Cavalier King Charles Spaniels, Vallhunds, and many other breeds were founded by only a few sires and dams and have had very little influx of blood since and there are quite a few old time breeders who would only occasionally bring in a sire from outside their own moderately sized kennels. As with the above breeds, the mostly-closed gene pool on Isle Royale became steadily inbred over time.

By the late 1990s, the population’s estimated inbreeding coefficient had risen to 81%. Fifty-eight per cent of Isle Royale wolves showed congenital bone deformities compared with only 1 per cent in two outbred wolf populations. Some of these deformities could reduce individual fitness, particularly components of fitness associated with predation and reproduction.

So the first lesson to be learned from the Isle Royale Wolves is that isolation leads to inbreeding and inbreeding is detrimental.  In dogs, closed registries and kennel blindness are a form of isolation and in both cases we see rising inbreeding followed by increased expression of otherwise rare diseases.

Some of the most studied wolf packs in the world are in serious jeopardy. Researchers report that the occurrence of debilitating bone deformities in wolves marooned on Isle Royale, an isolated island in Lake Superior north of Michigan, has risen sharply over the past five decades due to inbreeding.

Diseased wolf vertebra due to inbreeding of Isle Royale wolves.

A genetic defect now common in the Isle’s wolves causes bones in the spine, the vertebrae, to grow gnarled and crooked. Also found in domestic dogs – close wolf relatives – the bone malformations  can pinch nerves in the spinal cord, causing pain that makes it tough to walk and can lead to paralysis of the back legs and tail in severe cases, according to research published in February’s issue of Biological Conservation. Back in the 1960s, about a quarter of Isle Royale’s wolves appeared to have the anatomical abnormality, but now the percentage of afflicted wolves has risen to nearly 60 percent of the population. “In normal, healthy wolf populations without inbreeding, you are only supposed to see this kind of defect in about one out of a hundred animals,” says paper coauthor John Vucetich, an assistant professor of wildlife biology at Michigan Technological University (MTU) in Houghton. The deformity, discovered during autopsies of recovered, dead wolves, has grown so rampant, Vucetich says, “we haven’t found a normal wolf in the past decade.”

- Scientific American

The second lesson to learn from the Isle Royale Wolves is that hybrid vigor is real and powerful and that inbreeding depression is real and powerful.

We used molecular techniques to document the consequences of a male wolf (Canis lupus) that immigrated, on its own, across Lake Superior ice to the small, inbred wolf population in Isle Royale National Park. The immigrant’s fitness so exceeded that of native wolves that within 2.5 generations, he was related to every individual in the population and his ancestry constituted 56 per cent of the population, resulting in a selective sweep of the total genome. In other words, all the male ancestry (50% of the total ancestry) descended from this immigrant, plus 6 per cent owing to the success of some of his inbred offspring. The immigration event occurred in an environment where space was limiting (i.e. packs occupied all available territories) and during a time when environmental conditions had deteriorated (i.e. wolves’ prey declined).

This event is an excellent example of what one outcross might do for a small breed and especially a single kennel. The immigrant wolf’s offspring were true hybrids, a mix of the formerly isolated pool and fresh blood; versus having an outside pack supplant the locals in toto, as one might expect in a contiguous geography that was not isolated like the Isle.

We have here an analogous situation that fits existing human patterns of behavior regarding dog breeds and strains that have virtual barriers instead of physical ones.

The astounding aspect of this immigrant on Isle Royale is just how potent his genetics were to effect change on the island.  None of the existing males could even compete with him and he became the sole sire.  His initial success is likely caused by the inbreeding depression in the inbred Isle wolves.

The high fitness of this immigrant wolf was also associated with distinctive behaviour and physical appearance. First, he was physically larger than most Isle Royale wolves. As alpha male of the Middle Pack, his high fitness was also reflected by his dominance over other ISRO packs. Specifically, he exhibited strong territorial behaviour that completely displaced West Pack, driving that pack to extinction by 1999.

This immigrant wasn’t necessarily a super-wolf, he was in all probability a young male that was driven out of his birth pack’s territory for being non-competitive with that pack’s alpha male. His success on Isle Royale shows just how compromised the inbred population had become.

The inbred Wolves of Isle Royale, genetically refreshed by the genes of a new sire.

It’s an open question if and how much the influx of new genes has changed the bone deformities which had come to define Isle wolves.  Surprisingly, before the results of the bone study were published, Isle Royale was used as an example of a wild population that was thriving and unharmed by inbreeding and isolation.  This is why I’m cautious of anyone who argues from ignorance regarding their ability to inbreed and avoid disease.  This is the third lesson: don’t assume that inbreeding can exist in high levels without detriment and don’t cite wild populations if no one has ever done a detailed health study to document the true health of the population.

The new results offer the first evidence of the wolves’ closed population leading to a decline in natural fitness. This is important, Vucetich says, because for years some policy makers and conservationists have pointed to the apparent health of the Isle Royale wolf packs as an indication that small animal populations can maintain proper genetic diversity. “Isle Royale is not this robust place that some people thought it was,” says Vucetich.

Now, not all the lessons are positive ones.  Given the isolation of the island, the complete genetic sweep of the immigrant male, and the small population size the rates of inbreeding swiftly ticked back up.  The smaller the population size and the greater degree of inbreeding done following new blood, the shorter time you’re going to reap the benefits of that new genetic material.  Outcrossing can forgive a myriad of sins, but it needs to be used in measure to the problem.  On Isle Royale, this new wolf didn’t simply add to the sires on the island, he supplanted them and then bred with his children, creating more inbreeding instead of extending the benefits of outcrossing.

This isn’t an advisable strategy for refreshing a dog breed, essentially going from one popular sire to another.  Diversity in breeding males should be maintained over each generation and proceeding to breed father to daughter–and similar–after a single outcross will swiftly return the gene pool to inbred status. The other issue that researchers have is that to complete a “genetic rescue” one must be able to document the benefit on a population level, an this is often done with the most crude methods, namely demography (head counting).  An increase in population size was not observed here, although there was a precipitous drop in the wolves’ main food source, Moose, during this time and the wolf numbers did not suffer either.

Genetic rescue, in which the introduction of one or more unrelated individuals into an inbred population results in the reduction of detrimental genetic effects and an increase in one or more vital rates, is a potentially important management tool for mitigating adverse effects of inbreeding. … The immigration event occurred in an environment where space was limiting (i.e. packs occupied all available territories) and during a time when environmental conditions had deteriorated (i.e. wolves’ prey declined). These conditions probably explain why the immigration event did not obviously improve the population’s demography (e.g. increased population numbers or growth rate). Our results show that the beneficial effects of gene flow may be substantial and quickly manifest, short-lived under some circumstances, and how the demographic benefits of genetic rescue might be masked by environmental conditions.

This is not a problem with outcrossing at all, rather it’s a problem of the limitations of the crude science of demography. Head counting might speak to quantity, but it is wholly lacking in useful information about quality.

Demography is likewise a poor tool to employ when analyzing domesticated dog health.  The numbers of dogs within breeds has little to do with their vitality and much more to do with fashion and the whims of a handful of breeders.  No one would claim that a Pug is popular due to competitive natural gifts of robust health and fitness, rather they are much like the inbred wolves on Isle Royale, they are artificially supported by beneficial conditions, easy access to food, and a blunting of natural pressures against their survival; in the wolves’ case it’s the benefits of living on an island, in the case of the Pug it’s being coddled by owners and breeders willing to spend a pretty penny on their upkeep.

In open and competitive environments, population numbers can serve to estimate vitality when better data has not been taken, but it seems that on Isle Royale, the wolves have a sheltered niche as the apex predators with ample food supply.  The Moose can’t migrate away and there is little in the way of competition for the wolves.  In such conditions, even sickly inbred wolves can reach a carrying capacity at about the same numbers as more robust wolves can.  It’s possible that more wolves could have thrived had the main food source not plummeted, or it could be that even at the lowest levels the moose populations were not small enough to be a significant factor in the head count of the wolves.

Without a marked improvement in population size on the island and without documentation of the rates of disease and bone deformities improving with the influx of the immigrant wolf, the technical definition of a “genetic rescue” has not been met with the current state of knowledge about the Isle Royale wolves.

Biologist Claire Wade and her Toller "Burn" during an NSDTRC-USA Field Test.

The 2011 study A Genealogical Survey of Australian Registered Dog Breeds is a shoddy piece of work and a disgrace to the scientific method.

The world-wide population of Cavalier King Charles Spaniels descends from only 6 dogs.  This bogus study manufactured 836 observed CKCS “founders.”

GIMME AN F!

The authors Mohammad Shariflou, John Hames, Frank Nicholas, and Claire Wade did themselves and the canine community no service in writing it and I contend that Claire Wade allowed her own bias for and attachment to Nova Scotia Duck Tolling Retrievers to taint her judgment. Combined with her failure to disclose her extant conflicts of interest as a Toller owner, breeder (stud service), trainer, and breed club member, this bias and its resultant corruption of the methods and characterization of the results by the authors are de facto academic fraud.

The authors begin by suggesting that their analysis is circumspect and all encompassing when it’s anything but:

To better understand the actual nature of pedigree dog population structure on a whole-population basis, we examined data records for a representative sample of recognised pedigree breed populations in Australia.

This is a lie.  This paper did NOT look at a whole-population basis at all, in fact the researchers went out of their way to limit the information they were looking at and purposely excluded data that is both informative and readily available.

The world-wide population of Pekingese Lion Dogs descends from only 5 dogs.  This bogus study manufactured 1053 observed Peke “founders.”

GIMME AN R!

They looked at only a fraction of the data available in one registry in Australia, going out of their way to remove all known dogs before import which were certainly contained on their import pedigrees but not included in the analysis.  This means that they failed to look at the whole-population of any dog breeds  despite claiming otherwise.  They didn’t even come close.

Only one breed, the Australian Terrier, passed the 10 generations of data mark. The other native Oz breed, the Australian Cattle Dog, fell short at only 9.7 generations but this low mark still greatly surpassed the imported breeds.

Generation Equivalents (EqG): 3.0, 2.1, 3.5, 5.4, 4.4, 3.1, 3.4, 3.3, 4.8, 4.1, 4.1, 1.7, 7.6, 2.6, 10.1, 9.4, 7.7, 8.3, 8.1, 7.6, 9.7, 7.6, 6, 7.5, 7.3, 8.7, 6.6, 4.8, 6.7, 6.6, 4.9, 8
mean: 3.9

These scientists threw away so much prior-to-import data and the documented history within Australia is so limited for almost all these breeds that their results are based upon an average of only 3.9 generations! This is less information than would appear on one single import pedigree and we know that most of these breeds have many more generations of documented history.

The world-wide population of Nova Scotia Duck Tolling Retrievers descends from only 9 dogs.  This bogus study manufactured 84 observed NSDTR “founders.”

GIMME AN A!

As I’ve shown before, Nova Scotia Duck Tolling Retrievers should have between 11 and 22+ generations of documented pedigrees.  I’ve traced my own Border Collies back (including significant history in Australia) between 20 and 70 generations.

It’s really laughable then that they claim their results are “comparable with other species of domesticated animals.”  How can you compare genetic analysis of an entire species to a circumcised look at a niche registry in a remote island country?

Why would you make such a comparison when your data doesn’t support it and your methodology precludes making such comparisons in the first place? These sorts of throw away comments suggest an author with an agenda to create sound-bites for breed apologists instead of a scientist with ethics and objectivity.

Claire Wade's Toller "Burn" a.k.a. Am, NSDTRC-US CH Edlyn Seastar Dodge N Burn WC CGC CCD JD, is a conformation show champion.

Using complete national pedigree data supplied by the Australian National Kennel Council (ANKC), this study examined the levels of inbreeding and popular sire use in 32 Australian dog breeding populations with different registry sizes.

This statement is misleading.  It says “using complete national pedigree data” but as you’ll soon find out the researchers discarded much of that data, so the use of “complete” is highly inappropriate.  If you want to use the word ‘complete,’ you should include all known pedigree data, worldwide, period.

The world-wide population of Samoyeds descends from fewer than 20 dogs.  This bogus study manufactured 149 observed Sammy “founders.”

GIMME A U!

For Nova Scotia Duck Tolling Retrievers, this analysis was already completed and published before the Wade paper in 2009 by Katariina Mäkii: Population Structure and Genetic Diversity of Worldwide Nova Scotia Duck Tolling Retriever and Lancashire Heeler Dog Populations. For the Australian subpopulation, the study found an inbreeding level of 28% and looked at 13.2 complete generation equivalents worth of pedigree data.

It’s not that this data contradicts the ANKC data, it’s that the Mäki data was not artificially manipulated to exclude known relationships and create bogus founders out of thin air.

The Wade study looks at but the tip of the iceberg and pretends that everything below water doesn’t exist.

Claire Wade's Toller "Burn" is an import to Australia and a stud dog for hire. He's sired at least two litters to date.

The evaluation of data over the entire registration histories of breeds shows inbreeding trends over time.

The world-wide population of Leonbergers descends from only 5 dogs.  This bogus study manufactured 149 observed Leonberger “founders.”

GIMME A D!

This statement is misleading and if it was intended to suggest to the reader that these researchers were looking at “the entire registration histories” then it is a bold lie.

Even for the few breeds which were developed in Australia, I’d like to see some evidence that they were founded within the ANKC and that their breed is represented well within just that registry.  I have my doubts as the study claims to only have data from 1954 from the Australian Cattle Dog and 1955 for the Australian Terrier.  It’s likely that the ANKC is not the parent/founding registry for these breeds and thus their formation is not contained in their registry database (or that data has been excluded in this study).

In the genealogical analysis, animals with known parents born from 2000 to 2009 inclusive were used as the reference population. The completeness of pedigree information was determined by complete equivalent generations (EqG) in the reference population. Founders (f) were defined as animals with unknown parents (typically imported dogs with known parentage but outside of the Australian registry) contributing to the gene pool in the reference population.

This little gimmick is what completely invalidates this entire study.  They are creating “founders” out of thin air, throwing away the information which documents inbreeding and then declaring that there is no inbreeding!

This is Australia we’re talking about so almost every single breed was developed elsewhere and there’s a good chance that the two Australian breeds were not developed within the AKNC, so this one step not only obliterates evidence of the true founder effects on the breeds, it also white washes the very real import bottleneck that Australia has.

Import bottlenecks are no small matter.  Think of the rising inbreeding documented in culturally or geographically isolated human communities: Muslims in Europe & Australia; Polygamist Mormons; Ashkenazi Jews; Bedouins; Martha’s Vinyard, Pitcairn Island, Faroe Islands, Easter Island, Iceland; Hirado, Japan.

As far as dogs are concerned, Australia is no different.  Not only are they geographically isolated from the countries of origin and the largest dog markets in the world, there are also historical import barriers that prevented the easy flow of dogs into the country.  Many of these barriers still exist: it’s very expensive and laborious to sort through all the red tape, bureaucracy, and quarantine to import a dog into Australia.  This greatly limits the gene pool versus the global population of a breed.

If you read this study as presented, you’d be given the mistaken impression that Australian dog breeds are miraculously well off genetically.  This is true only if you blind yourself to reality. But that’s exactly what Wade has done:

Observed values for breed mean inbreeding coefficients are considerably lower than those reported by Maki (2010), who analysed international pedigrees of rare breeds, but are in line with those reported by others based on national data (Calboli et al., 2008; Leroy et al., 2006). For example, it is likely that the observed disagreement with the Maki analysis for the Nova Scotia duck tolling retriever breed (Australian F = 0.03 vs. International F = 0.26) is related to the treatment of imported individuals in our data and, as part of this, the lack of pedigree information from ancestors of the imported dogs. The correspondence of our breed mean results with other national data collections suggests that the majority of the inbreeding identified by Maki (2010) for this breed is probably derived from distant rather than recent co-ancestry. Recent inbreeding is expected to be more deleterious to population health (Hinrichs et al., 2007) and so inbreeding coefficients calculated over more recent population history (such as are presented in this analysis) may have more relevance to breed health than total inbreeding.

The first bit of intentional distortion here is that Mäki didn’t just look at all International data, she also published subdata which included Australia.  Wade clearly doesn’t want to point out that the Australian subpopulation of Tollers is actually more inbred than the International average at 28% inbred versus the 26% Wade quoted.

Wade is trying to claim that the post-import Australian breeders are doing such a bang-up job of avoiding inbreeding that they’ve dropped their COI numbers, this isn’t the case, obviously, as the Australian dogs are more inbred on average, not less.

The second distortion is that Toller inbreeding is “distant” versus “recent.”  Tollers are not an old enough breed to distinguish between distant and recent inbreeding.  As you saw from my recent COI post, Toller inbreeding skyrockets after only 4 generations: 9.57% at 7 generations, 19.35% at 8 generations, and 25.9% at 9 generations.  This is NOT distant inbreeding.

Wade quotes the 2007 paper by Hinrichs et al to suggest that Toller inbreeding is somehow so distant that they are protected from the effects of inbreeding.  The Hinrichs paper defined “new” inbreeding as at least 25 generations of pedigree information! Tollers don’t even have that many generations in their entire history, so the notion that the Hinrichs paper is applicable to Tollers is a joke.  The fact that Wade would try and apply the Hinrichs paper but redefine “new” inbreeding as under 4 generations and “old” inbreeding as anything over that is a horrible distortion of the truth and of another researcher’s work.

When you look at less and say it’s more, you are a liar.

When you look at more and say it’s less, you are a liar.

Claire Wade and the other authors of this paper looked at less information and claimed that it was more.  Knowing that COI levels were more, they manipulated their data to tell you it was less.  

This is fraud. 

At the end of many research papers you’ll find a signed statement that reads something like this:

The Conflict of Interest statement signed by Claire Wade

This represents a commitment to the integrity of the scientific process, the credibility of the presented findings, and a reaffirmation of public trust that is central to peer review and publication.  Conflicts of Interests arise when an author or researcher has any relationship or interest which can influence their judgement and the potential for bias can exist and should be disclosed even if the author believes that such a relationship will not affect their scientific judgment.

While financial conflicts are the most obvious (Researcher X is currently employed by Pharmaceutical Company Z whose drug Amazicure is being investigated in this study), conflicts can arise from personal relationships or rivalries, academic competition, and even a passion for the subject being studied.

Claire Wade is a Toller owner, breeder, trainer, and conformation show exhibitor.  She imported her Toller “Burn” into Australia and it’s possible that his offspring are included as data in this study.  She has a vested interest in the promotion and breeding of Tollers and that is a conflict of interest that should have been disclosed in this study and it was not.

What does that spell?  F-R-A-U-D!   F-R-A-U-D!   F-R-A-U-D! 

This is a chart of what I found as I looked at Burn’s COI from 1 Generation all the way up to 12 generations.

Claire Wade's NSDTR "Burn" has a COI of nearly 30%. If you're a fool you might pretend it's lower than that by looking at only a few generations.

COI is a measure of inbreeding in an individual and it’s almost always denoted with the number of generations that are being looked at in the calculation.  For example, a COI5 or COI(5) is looking at 5 ancestor generations and only calculating the inbreeding that is seen within those dogs.  It ignores consanguinity of any dogs further back in the pedigree for the sake of calculation simplicity.  A COI of rank N is intentionally blinded to all dogs in generations N+1 and beyond.  Some pedigree software packages treat generation 1 differently, so it’s wise to confirm just how many dogs are being looked at if you’d like to compare COIs calculated by different software packages (some count the individual as generation 1, others count the parents as generation 1).

Why would someone want to intentionally blind themselves to more information?  First, the COI calculation is not trivial and doing it by hand is time consuming and arduous for most people.  Second, the calculation requires extensive pedigree information that is not always available for many generations.  Third, looking at lower N COIs will measure recent inbreeding versus deeper inbreeding.

Am, NSDTRC-US CH Edlyn Seastar Dodge N Burn WC CGC CCD JD "Burn" A Nova Scotia Duck Trolling Retriever owned by biologist Claire Wade.

But let’s not fool ourselves that lower N COIs are better or more accurate or that higher N COIs are trivial.  COI calculations are meant to predict the level of homozygosity (doubled up alleles) in an individual due to the same ancestors showing up multiple places in the pedigree.  No matter how many generations you look at, the dog’s pedigree and ancestry doesn’t change.  Consanguinity has created a certain level of doubling up on alleles in the dog and that will not change if you blind yourself to more distant generations.  The more generations you look at, the closer your calculation will approximate the real level of inbreeding present in your dog.  That’s why a COI calculation of N+1 is in general always superior to COI(N).  More information is always equal to or better than less information.

In practice though, we run across both pedigree collapse and a limit to how far back our knowledge extends.  Once we start hitting founder dogs, going back any further generations on those dogs won’t actually give us more information because that information is lost or unknown.  If the oldest known ancestor is at most 10 generations back from our current dog, taking a COI(15) won’t really tell us anything that a COI(11) will.  But how do we know when our COIs are giving us diminishing returns?  Well, we can keep taking higher N COIs until they stop changing much.  They might stop changing because we’ve taken into account all known inbreeding or they might stop changing because we’ve run out of useful information, or both.

To illustrate this, I’ve graphed Claire Wade’s pet Toller Burn’s COI over N generations from N=1 to N=12.  You can see this chart at the top of the post.  Notice how as we look at more generations the COI quickly rises and it doesn’t start to stall until the 10th generation and we don’t see significant change only two generations after that.  If you asked me what this dog’s COI was, I’d say at least 28%.  There’s really no reason to look at fewer generations as none of those numbers would tell you anything of value.

A pedigree chart of Claire Wade's Toller "Burn" showing pedigree collapse

Now if we look at Burn’s graphic pedigree again, we can see why the COI peters out at 12ish generations: there’s really no more information after that point which can move the COI significantly.  Every dog on Burn’s complete pedigree can be traced back to Burn in 11 generations or less.  In the following chart, the “Min Gen” column shows the first generation a given ancestor shows up in and the Max Gen shows the last generation they show up in.  Count records how many times they show up in the pedigree total.  As you can see, all the ancestors show up in 11 generations or less as 11 is the largest number in the Min Gen column.

While there’s certainly information after the 12th generation, we aren’t adding any new names to the pedigree after that point, just connections between them. Each generation after we’d need to see twice the level of inbreeding just to begin to make a difference on the COI given that there are theoretically twice as many possible breedings each level. Seeing as most paths going back are already dead ends, there’s no way we can keep that up. The few lines that go to 20 generations or more are likely to have already contributed to for/against the COI in a significant way already.

In her published paper, Claire Wade would have you believe that looking at 4.1 generations of Toller data is enough. What do you think now that you’ve seen the whole truth?

“The greatest shortcoming of the human race is our inability to understand the exponential function.”

- Professor Albert Bartlett, CU Boulder

This is called exponential growth, and very few natural systems which exhibit this growth model can sustain it for very long given just how explosive the resource requirements are to maintain it.  Overpopulation alarmists use this model to project human populations looking forward in time, and it is often referred to as “The Malthusian Law” after Reverend Thomas Malthus who wrote an early and very influential doom tract on human population growth.

In pedigree analysis we use this model to look backward in time to analyze past generations instead of future ones.  As each older ancestor generation is double the size of their children’s generation, there is one more ancestor in that next oldest generation than all the previous younger generations combined.  When our knowledge of the pedigree runs out we call that last generation the foundation, and much like a real pyramid, it’s theoretically a large base upon which all further generations are built.

The 10 generation pedigree chart for my Border Collie Mercury

Although this tree grows backwards in time, we live life going forward so we can not manufacture twice the ancestors every new generation to accommodate our theoretical tree.  We quickly discover that as we go back in time the number of theoretical ancestors keeps growing as the number of actual new ancestors falls.  At 32 generations we’ve accounted for 8.5 Trillion ancestors, and this is more ancestors than total people alive today.  While it might be hard for you to think of your 32nd Great Grandfather, this actually isn’t such a great genealogical distance for dogs.

The distance between my Mercury and Old Hemp who was born in 1893 varies between 15 and 71 generations.  The dogs that show up between 25 and 35 generations ago are almost all clustered in the mid 1950s.  So one human lifetime is enough to witness a great many generations of dogs.  An equivalent number of human generations might take you back to the mid 14th century when the Black Death wiped out huge swaths of Europe’s population.

There weren’t even 4.3 trillion people on the planet in the 1350s, the number was much closer to 430 million, only one tenth the number of people we’d need to fill spaces in our 32nd generation of our pedigree.  So even if the entire population of the world at that time was one “generation” and an equal ancestor, they’d each have to appear 10 times.  This is a pedigree collapse of 90%.

80 generation pedigree chart of my Border Collie Mercury showing the diamond shaped pedigree collapse

If we choose to not repeat ancestors and give each unique ancestor only one space in our tree, but still draw branches connecting them to all their offspring and their parents, we could visualize how our actual ancestor tree differs from the theoretical.  You’ll notice in the above pedigree of my Border Collie Mercury that after expanding out in the predicted pyramid shape the pedigree eventually starts to shrink.  The resulting diamond shape is a visual representation of pedigree collapse.

Pedigree collapse is caused by inbreeding; both recent close breeding and more distant founder effects.  When a breeder inbreeds they are cutting the pedigree pyramid of their stock down dramatically.  When two cousins mate, creating a COI of only 6.25%, they have actually permanently cut out 25% of the possible ancestors for their offspring.

A normal person has 8 great grand parents, the product of a first cousin mating has only 6, a 25% pedigree collapse.

Normal Norma is not inbred and she has the expected 4 grand parents and 8 great grandparents.  Inbred Ted’s parents are first cousins, meaning that one of their parents are siblings.  This means that Ted has only 6 great-grandparents because two of them are doing double duty in his pedigree.  This represents a pedigree collapse of 25% and that continues back forever into his history.

Pedigree collapse and the resulting loss of genetic diversity doesn’t require recent inbreeding to have a devastating effect.  When breeds are formed from a small founding generation and/or go through population bottlenecks, there simply aren’t enough ancestors to go around and there aren’t enough mating combinations to sustain genetic diversity.  This causes inbreeding to rise even though breeders avoid close pairings.

A complete pedigree chart of Claire Wade's Toller "Burn" showing pedigree collapse. Burn is on the far left and the founding Tollers on the far right, sires on top, dams on the bottom.

For example, let’s look at Claire Wade’s Nova Scotia Duck Tolling Retriever: Am, NSDTRC-US CH Edlyn Seastar Dodge N Burn WC CGC CCD JD  3/8/2007 a.k.a. ”Burn.”  I’ve rotated his pedigree pyramid so that it fits nicely on a computer screen and matches the standard presentation on written pedigrees: sires over dams, older generations to the right.

Burn's 5 generation pedigree showing few repeated ancestors.

Burn’s breeding is not very close in recent generations;  his first repeated ancestors are three great grandparents.  Two of them show up again once in the next generation and one shows up twice.  But you can see from his complete pedigree chart above that Burn’s pedigree quickly collapses into only a handful of dogs.  You can even see the popular sires and dams as they have a fan of connections coming into them; each one of those lines represents ancestor loss as that connection could have been made with a unique dog, but the Toller’s foundation is so small that swift pedigree collapse was guaranteed from the founding of the studbooks combined with early and often popular sires and an aversion to outcross to new blood.

Burn's 7 generation pedigree showing many repeated ancestors.

When we look at only two more generations of Burn’s pedigree you can see that the vast majority of ancestors in those later generations is highlighted in a variety of colors indicating repeat ancestors that show up elsewhere on the pedigree.  This is inevitable in all Tollers as there are only so many ancestors they have to work with and many of those ancestors were not widely bred.

Remember that in my earlier post I showed how a founder would have to have over 10 children that each survived to pass along their genes for the gene pool as a whole to retain over 99.9% of that founder’s genome.  As you can see in the fish shaped pedigree chart above, several of those “founder” dogs on the far right had only one recorded child in the Toller studbook. At most 50% of their genes would be conserved in that child and we can see that often their children had very few children as well.  This indicates that Tollers had a very small founding population and that a big chunk of the extant genetic diversity in that small founder pool was lost almost immediately.

In my next Toller post, I’ll examine how looking at a limited number of generations for a Toller COI can attempt to hide the real situation that breed is in.

The staff here at BorderWars diligently monitoring the airwaves.

There’s nothing more rewarding as a blogger than to have a reader use your blog as a resource to add intelligently to a discussion elsewhere on the Internet.  BorderWars reader JackieD recently posted a link back here that started a good discussion on the UK’s Dog Rescue Pages.

Here are some of the comments and my thoughts on each:

misty11 - 3rd Oct 2011, 7:37 pm

The problem is there are so many people doing research into the breed that everyone picks up on it! Toller breeders are very open about everything and all info is shared worldwide. Tollers are very healthy compared to other breeds, but it’s easy to find out about any health problems because we are so open it is all easily available.
The ‘only’ health problem in tollers is auto-immune disease. How many health problems do, for example, golden retrievers, border collies, GSD’s have?
and tollers are long lived, many live to over 14.

Here misty11 is parroting Claire Wade in a knee jerk response to any Toller analysis: we’re just being picked on because we’re so open!  This is nonsense. Tollers are being looked at because all breeds are being looked at and in Tollers we have a few studies and not a lot of consensus on what’s going on in the breed and what the best path forward is, most notably the scientist vs. scientist war of letters regarding out-crossing.

This issue is being hashed out on several dog blogs right now, most notably on Jemima Harrison’s Pedigree Dogs Exposed blog in three posts so far:

• Will this Toller x litter save the breed?
• Tollers Take Two…
• Toller x pups 6-8 weeks old

More on this from me soon.

jackied - 4th Oct 2011, 8:26 am

He’s done articles on how astonishingly inbred Border Collies are

Yes, two of the articles worth checking out are:

• Only 8 Border Collies
• Impending Doom

Boo’smum - 4th Oct 2011, 1:02 pm

Surprised to hear BCs are so inbred! Guess I just assumed that, with there being so many of them (and so variable), therefore, I’d thought, they’d have a pretty wide gene pool? Clearly not! (Goes to show what I know… which isn’t much, admittedly!)

One small quibble though: “inbred” is a term I’d use for an individual and not for a breed per se, unless like Tollers, nearly every member of the breed is highly inbred.  Being inbred, as one might measure with a COI calculation, really only looks at the genetic diversity of an individual, which for most genes can carry only 2 possible copies (alleles).  But in populations, we might have dozens and dozens of variations of any gene or certain loci might be fixed with just one allele.  This sort of mechanism can work independently of any individual’s level of inbreeding.

So, for Border Collies, the problem is not just that some individuals are highly inbred, it’s more that the overall levels of diversity in the gene pool are dropping like almost every other breed.  Inbreeding is like broiling one piece of meat… cooking it quickly, but loss of genetic diversity is like turning up the temperature in every oven just a few degrees.  Inbreeding is fast and localized as to how it throws away genetic diversity.  Genetic drift and patterns of selection are slower and more spread out, but they also remove genetic diversity (intentionally and unintentionally) from an essentially closed population.

Inbreeding can be undone with one outcross. Loss of genetic diversity would require many individual insertions of new DNA (or restoration of lost DNA) over time and all over the breed’s gene pool.

The two processes ARE related.  You can’t turn up all the ovens and not expect to burn some steak, nor can you broil a lot of beef without shifting the average meal from medium rare to well done.  A breed like Border Collies is mostly a slow burn save for a few popular sires who more than make up for their small number by their significant impact on the breed.  In Tollers or Cavaliers, you also have the issue of extreme population effects trumping recent breeding patterns: too few founders make inbreeding unavoidable even though breeders on the whole aren’t trying to close breed individual litters.

jackied - 4th Oct 2011, 8:26 am

The problem with Border Collies is that just a few champion sires were used so extensively for breeding that their genes came to dominate the entire breed, even though there are so many Border Collies registered. Detailed analysis of the ISDS studbook reveals that genetically the foundation stock of Border Collies is equivalent to just 8 dogs, worse than many ‘rare’ breeds.

Probably the only redeeming feature is that in the past the emphasis on performance over appearance in BCs has been stronger than in some other breeds.

Yes!  But it’s important to note that the 8 genomes is not the original founding population, rather the breed has been pared down from the original founders and their theoretical genomes down to just 8 today.  Many rare breeds (and some quite popular breeds) have the problem of having a founding population that is quite small.

Border Collies have around 1000 nominal “founders,” and in the ISDS there are just under 650 that still have any influence on the current population. As you can see from the following chart, there are several means of looking at genetic variability in a breed and like-sounding terms are not always directly comparable.

The effective number of unique Border Collie genomes across the entire extant ISDS population is only 8.3 individuals worth of information.

So I don’t know how BCs compare to rare breeds without being able to look directly at the same information, but the message I think this data is telling is that BCs are not special in regards to the general trend in all closed populations to lose genetic information over time, often quickly.

mum24dog - 4th Oct 2011, 8:26 am

But then most BCs/WSDs won’t be ISDS registered so who knows what has gone into their genetic make up?
And just because a dog is ISDS registered doesn’t mean that it only has BC genes – google Turnbull’s Blue – a Beardie whose line still throws up hairy faced dogs today. (I assume we’re ignoring the KC version and discussing the real thing.)

It would be a major error to draw conclusions about a breed as whole from only registered dogs of a working type breed – a clear case of selection bias. There must be 1000s of dogs that warrant the description of BC out there going about their daily job that pass right under the ISDS radar.

And of course we can’t ignore the culling factor. Many dogs don’t reach an age to test their genetics for one reason or another.

But at least the ISDS stud book isn’t closed like that of any breed unfortunate enough to have caught the eye of the KC. Dogs still can obtain registration on merit.

The ISDS population is special and significant in all Border Collies.  This is the founding population and every single border collie on the planet can be traced back  to ISDS registered dogs and I’d venture to say that the vast majority of BC genetics worldwide are from ISDS registered stock originally.  One cannot claim to understand the genetics of the breed without knowing the ISDS studbook.

Remember that the BC is NOT foremost a working breed, it is a breed formed around the SPORT of sheep trials.  This is the reason for the stud books, the name, the society, and the requirements for registration on merit.  The working sheep dog, while related in both purpose and genetics, is a more nebulous concept that we have much less solid genetic information on.  There are, of course, WSDs that are from pure registered BC stock, but there are also mixes and dogs that have been off the books for decades or centuries.

My own Border Collie stock has been breed to an unpapered “Border Collie,” both working on a cattle ranch, and their offspring have gone on to work on that ranch and others, all without papers, all joining the greater WSD landrace, but all off the books and not easily studied by pedigree research.

In general this is a one way trip, as very few WSDs make their way back into the papered registries and even fewer go on to have a significant genetic impact there.

If you have an unpapered WSD, you probably don’t have a lot to worry about since you can always breed it to whatever you want, you obviously don’t care a lot about pedigree papers.  But if you have a Border Collie, don’t pretend that you get all the benefits of the collie landrace when your dog probably hasn’t had the benefits of that model for more than 100 years and 30 generations.

This isn’t selection bias at all!  It’s looking at known quantities with specific names and definitions.

Despite claims by BC elitists like Eileen Stein, BCs are NOT being bred like sled dogs (as in, a richly diverse landrace with new blood entering all the time and all over the gene pool).

mum24dog - 5th Oct 2011, 10:45 am

And yet with the BC we have a breed that is used worldwide to perform a multitude of tasks, most requiring great physical fitness. Clearly any loss of genetic diversity is not a huge problem for the success of the breed.

Popularity and genetic variability are really two different issues!  Trying to downplay one because the other is thriving is not really good analysis.

Bananas are incredibly popular worldwide, but that doesn’t change the fact that the superior Gros Michel banana is now all but extinct and we are left to eat the smaller, less tasty, and more fragile Cavendish banana today.

• Yes! We Have No Bananas

Similarily, the great personality, intelligence and dexterity of the Border Collie have made it an incredibly popular dog worldwide.  This does not mean, however, that they are healthier today than they were 50 years ago or a century ago.  This does not mean that we are taking the right steps to preserve them for another 50 or 100 years.

Genetic diversity isn’t a “huge” problem… until it is.  TNS wasn’t a problem in Border Collies until BOOM, suddenly it was a problem, mostly because it didn’t have a name, a clear diagnosis, and any breed wide awareness.  It was always there, but no one put the pieces together.

Uric acid problems in Dalmatians were always there, it just wasn’t until there was a DNA test and people found out that there wasn’t a single genetically normal dog in the entire breed.

Epilepsy is a problem in Border Collies.  But we have no solutions, so it doesn’t get a lot of air time.  When we get a test, a firm diagnosis, a means of inheritance, and eventually a study that shows just how prevalent it is within the breed, we’ll get more openness and admission.

mum24dog - 5th Oct 2011, 3:31 pm

In any breed a list of potential defects needs to include the level of incidence so far as it can be measured, along with a breakdown of sub groups within the breed where there are distinct populations such as the BC so the likely risk can be assessed.

This! This! A million times this!  Why is it so hard for dog people to understand that the NUMBER of diseases seen in a breed is not nearly as important as the INCIDENCE of disease across all diseases.

If Dalmatians only had 1 disease, high uric acid levels, they’d still be worse off than a breed that had 100 listed diseases but where only 10% of those dogs had one or more of those diseases, because ALL Dalmatians have high uric acid levels.

If we wanted to think like an engineer, we could actually perform a calculation like this to really compare breeds in a relevant and fair manner:

For every dog and every disease add up [% dogs with the disease] * [severity of that disease].

Wouldn’t you agree that having more sick dogs is worse than fewer dogs? And wouldn’t you agree that a painful and untreatable disease is worse than a mostly benign condition that doesn’t cause much pain or other problems?

Also, the entire tactic of comparing your breed against other breeds is suspect in the manner many breed apologists are doing it.  NO ONE WANTS COMPARATIVE HEALTH!  We want actual health.  It’s not any comfort that your breed has 2% less cancer than another breed when you’re both above 50% cancer rates.

No one should care that some online website lists 5 diseases for your breed and 9 for another and so you think you can ignore what you’re doing and sit on a high perch.  In the land of the blind, the one eyed man might be king, but that sucker still doesn’t have depth perception!  Come on people, don’t accept early deaths, smaller litter sizes, poor quality of life and many other problems simply because you can find one breed that’s worse off.

That’s settling for mediocrity simply because something else is atrocious.  Mediocrity is WORSE when it allows you to be complacent instead of taking action to solve the problems when they’re minor or before they are a crisis.  We’ve spend the better part of the last decade dealing with bursting bubbles: the dot com crisis, the housing crisis, the banking crisis; do we REALLY need to keep suffering the damage of explosive bubbles when long standing problems come to a head or will we finally realize that the time to act and to change our ways is BEFORE permanent and extensive harm is done?  An ounce of prevention and all….  or were you too busy getting foreclosed and watching your 401k languish to worry about the problems that might blow up in our faces next year or the year after that?

NUNC LENTO SONITU DICUNT, MORIERIS.

Now, this Bell tolling softly for another, says to me, Thou must die.

PERCHANCE he for whom this bell tolls may be so ill, as that he knows not it tolls for him; and perchance I may think myself so much better than I am, as that they who are about me, and see my state, may have caused it to toll for me, and I know not that.

- John Donne, Devotions Upon Emergent Occasions

Nova Scotia Duck Tolling Retrievers don’t know they’re genetic wrecks, they are blissfully unaware that in the transition from regional purpose-bred sporting dog into a studbook governed purebred show dog, their gene pool was severely bottlenecked and harmful diseases came to the surface.

They know not that the bell is tolling for them.  But those who are about them, breeders and scientists alike, have no excuse to deny the precarious and unsustainable genetic position the breed is in today.

This Toller probably isn't the product of a father x daughter mating, but the gene pool is so small, it has the same level of inbreeding.

Two recent genetic studies have brought this issue to light but with very different conclusions.  One study was done by Katariina Mäki (PhD Animal Science) a Finn who does not own, show, or breed Tollers and the other study was done by Claire Wade (BSc PhD) who is a breeder and exhibitor of Tollers in Australia.

One of the studies is comprehensive and looks at a near exhaustive global studbook for the breed and the other study looks at only those pedigrees that are in one country only (and not even a very important country for the breed at that) and intentionally throws away the pedigree information from the country of origin and all other countries too.

One of the studies found nearly 13 generations of Toller ancestors for their COI calculations (about 16,000 ancestors) while the other one found just over 4 generations of ancestors (about 30 ancestors).  That’s more than 500 times the information.

One study traced every dog it could back to the true founding population, the other study pretended that the second a dog landed in Australia, its pedigree was erased and it was a amazingly unrelated to all the other import dogs and was thus a “founder” of the breed.

One study looked at 28,668 Tollers and found 9.8 effective founders while the other study looked at only 589 Tollers but declared there to be 84 founders with 26 founder equivalents.

One study found that the average inbreeding coefficient in Tollers was 26%, while the other study declared it to be less than 3%.

One study found that the effective population size was only 18 individuals while the other found that the value was 47.

Which study would you trust more?  The one with 50 times as many dogs, a comprehensive pedigree analysis, done by an unbiased researcher OR the one done by a show breeder who has a vested interest in making her breed look good who intentionally limited the scope of her analysis to the dogs that were imported into her own country?

Guess which researcher claims that the Tollers are a robust and healthy breed and that any thoughts of out-crossing are scandalous and should be ignored?

Professor Claire Wade, of course, who is a biased hack that should clearly know better.  In a future post, I’ll walk you through her paper and explain her deliberate attempt to whitewash the state of her breed and how her own bias and unchecked conflict of interest drove her to commit academic fraud.