Saturday, August 19, 2023

DNA breed testing and kennel club breeds

Perhaps the first consideration when understanding DNA "breed" identification is just what a "breed" is.
Most breeds have only existed for the last couple of hundred years. They have come about by selecting dogs for a specific look, use, colour or nature etc. By definition this eliminates unwanted genetic features. It does not result in new genes being created. There are no single DNA markers that identify a particular breed. Kennel club breeds, with few exceptions, are closed groups of related dogs and dogs outside of that cannot be added. Embark can use the length of genetic segments a dog shares with their reference dogs to see how many generations it has been since they last shared an ancestor. Long segments of DNA that are identical to known purebred dogs tell Embark's scientists that the dog being tested has a relative from that breed. By testing over 200,000 genetic markers, they build up the dog being tested genes one DNA segment at a time, to learn the ancestry. Other dog DNA tests look at many fewer genetic markers and have to take a guess at breed ancestry based on that. Just what DNA is in a breed can differ in different countries since not every dog in a breed has been used for breeding in geographically separated countries and some DNA may have been lost in one country but not another. It is therefore reasonable for the testing company to know what country a pedigree dog is from. The DNA test in such cases will confirm that the dog does or does not have any other mix in it. Likewise, a dog of unknown origin will reasonably give information of the mix, or otherwise.  It is kennel clubs that decide and control what a breed makeup is and not DNA test companies. Likewise in a breed where an outside dog may be added, when that happens the DNA testing company will of course add that information to their DNA profile for that breed. 

When it comes to our ancient origin dogs much the same applies. It would be impossible to test every such dog in every country and dogs probably do not move between these countries as often as in the past when dog were first introduced to these countries. 

A recent comparison of some DNA test companies showed just how poorly some perform as linked below. The dog from Kuwait shows how many expats still fail to understand that free born dogs in the region are simply not mixes of the "breeds" they are familiar with. Embark remains the only company able to identify our village/desert/wadi/baladi dogs. 

Thursday, February 2, 2023

Time for pedigree Canaan dog breeders to get serious about genetic health.

As one of the few kennel club breeds still open to new dogs being added it is vital to check such new additions for all known possible genetic health issues before breeding them. If breeders do not do that then they could be adding to the overall problems in the future which could then be difficult to remove. Some of these potential problems increase the chances of a dog developing problems but may not cause a problem in every dog even if it has both copies of the gene. Surely prevention is better than a cure but why take a chance? 

 Intervertebral Disc Disease (Type I)

This has rarely been found in Canaan dogs, but it is present. This is not yet recognized as a problem, and it may be that when it got into the breed testing was not available. Now we do know about it and is still not too late to track it down and eliminate it.  Type I Intervertebral Disc Disease (IVDD) is a back/spine issue that refers to a health condition affecting the discs that act as cushions between vertebrae. With Type I IVDD, affected dogs can have a disc event where it ruptures or herniates towards the spinal cord. This pressure on the spinal cord causes neurologic signs which can range from a wobbly gait to impairment of movement. Embark uses linkage testing for this so positive result should be checked using specific tests. If confirmed, then having a dog checked by a vet who finds no sign of this problem does not mean the DNA test is wrong. The issue mainly shows up in dogs with a long body and short legs, such as Dachshunds so again may not show up in dogs of other morphotypes.

Looking back at pedigree records this could have come from any of a number of dogs including, Ben Yarden Me Dlbaan Jimi, Pereh Me Nachal Yealem, Mocha Givat Har Adar, Keliv El Kashhar, Zahava El Kashar, V'Makole de Solemel, Lilo Me Shaar Hagai, Bayud Bedoui Me Tel Arad, U'nes Ha Bedouim de Solemel, Tihelah de Solemel, or Tofee Me Shaar Hagai. That is eleven dogs that could be the origin of this, some of which are probably no longer alive but could have passed this gene on to any number of offspring. So where to start? 

For the dog we know has both copies both parents, Noked Me Shaar Hagai and Angie od Dvou cedru,  must have carried at least one copy, so if breeders want to nip this in the bud they should ideally not be used for any further breeding and all their offspring, if intended to be used for breeding, tested with the aim of not breeding any positive dogs from these. Where did these 2 get it from? Potentially Or Ve-Tel Me Shaar Hagar and Toot Bar (at least one of which must carry it) and Chakede de Solemel and Chanyah de Solomel (at least one of which must carry it. Depending on results of testing these dogs breeders could then go further back to trace the potential presence of this gene in other ancestors and any of their pups intended for breeding. Complicated? Yes. A lot of work? Yes, but do breeders really want to ensure the Canaan breed does not end up with avoidable problems. 

This gene has not shown up yet in any of the "Arabian village dogs" (a small number of which were used to establish the Canaan breed) I have seen, but of course it and others are probably there in small numbers. It is essential that any new dogs brough into the Canaan breed, be fully tested before even being considered as additions. Breeders have the tools available today that Menzel did not have. Why not use them?


Sunday, January 15, 2023

Notes on potential genetic health issues and Reference ranges.

 

Most of these are autosomal recessive so dogs need 2 copies of the variant to develop disease, one from each parent.

 

While figures are small, based on a total of 78 village dogs with publicly available health information.

Degenerative Myelopathy (DM) 15 carry 1 copy (19%) It is probably fair to assume there are desert dogs out there that are born with 2 copies even though none showed up in this group. Data of many “village dogs” tested do not show health figures in public profiles, either because only breed was tested or because that is the default set by Embark and has not been changed by owners. It is no surprise that with inbreeding of pedigree Canaan dogs that are derived from a small number of “village dogs” that DM has become a major issue in the breed. When the breed was established, no genetic testing was available.

Von Willebrand type 1 – 2 dogs (2.56%)

Factor VII – 1 dog (1.28%)

Collie Eye Anomaly, so called because it was first found in Collies but more accurately called Choroidal hypoplasia (75% of Collies, 80% of Stabyhoun and 71% of German spitz have this) – 2 related dogs (2.56%)

Bald thigh syndrome – 2 dogs (2.56%)

Lunderhund Syndrome (affects neuroendocrine cells in the intestinal tract causing stomach and intestinal problems) – 1 dog (1.28%)

 

 

ALT potential low normal 39 (50%) have 1 copy, 17 (21.8%) have 2 copies. This is not a health issue as such but may mean that a dog with this gene may have a reference range lower that test books state so could give results that seem to be in range but are somewhat raised for that dog.

Reference ranges for laboratory tests are often incorrectly called “normal ranges”.  These are typically defined as the range of values of the median 95% of the healthy population. It is possible that a given sample even from a healthy individual will show values slightly outside of the range for some tests. Other factors such as race (breed in the case of dogs), altitude, age, and sex etc. can also result in variation. People living at high altitudes will have higher levels of haemaglobin than those at sea level. Few laboratories establish reference ranges for the local healthy population. In one laboratory I worked in where the altitude was around 3500 meters up to a maximum 4000 we went to great lengths to establish local reference ranges. Sadly, some years later with staff changes, no one was aware of this and when doctors raised questions as to why the laboratory reference ranges in the computer were not those to be found in textbooks pathology staff at the time had no answer.

Among a small number of Canaan breed dogs at least 3 have the genes that increase the risk for Chondrodystrophy and Invertebrate disc disease developing, 1 has the gene predisposing it to having Urate crystals forming in the kidney and bladder stones. This does does mean they will have a problem but are at increased risk so need to be watched as time goes on.

Most village dogs that have homes are neutered but Canaan breeders need to be aware of the potential for genetic issues other than DM also being present in the breed, as well as the potential for adding some not yet present when new freeborn dogs are added. Better to test and eliminate all mutations before they become an issue later.

Monday, June 21, 2021

A look at the genetic relations in groups of dogs

What do we really know about free living groups of dogs? Published work by the Swiss animal behaviourist, Rudolph Schenkel, of his wolf studies in the 1930s and 1940s gave rise to the idea of pack leaders and this idea is still referred to all too often today. His work was based on captive wolves in a zoo and has since been recognized, including by Schenkel, as not giving a picture of free-living wolves or dogs. More recently claims have been made that a “pack” consists of the mother and her pups and that only the “alpha female and alpha male breed”. This is then also picked up and claimed to be the same with free living dogs. Free living dogs do not have rules they follow and there has not been any long-term study of many dog groups, individuals or their movements done over several generations to give a clear picture and it is unlikely that one size fits all. From genetic studies we do know, however, that in general freeborn dogs have a lower coefficient of inbreeding (COI) than do human controlled breeds suggesting movement between groups is common. There is of course an occasional exception when a parent and sibling or 2 siblings have mated but his seems to be rare and may be a result of movements having been restricted when dogs find themselves caught in a built-up city area. One of the dogs in the group initially tested, Aswad, was later shown by Embark to have a close relative, Ramy. On checking it was confirmed that they had both came into the same shelter together and that the size difference suggested they might be a father and son. From the genetics they share 28% similarity, so it seems they were half siblings from separate litters, with their haplotypes suggesting they probably had the same father but different mothers. Genetic results of other dogs living in a group or close by groups show interesting connections as follows. Of the dogs tested none of the dogs in the same group as Pack leader, so named because of the role the people feeding these dogs observed him to be, showed as his pups. He was related to Figa, Hannah and Finn at a level of half siblings, aunts/uncles or grandparents, and to Jimmy and Jenny as first cousins and yet Hannah and Figa were living together in a separate area to Pack leader. Hannah and Figa shared their genetics (40%) at a level where they were probably half siblings or possibly aunts/uncles or grandparents. They have the same maternal haplotype so likely had the same mother. Hannah and Finn could also be half siblings of Pack leader but did not have the same mother as Pack leader since Pack leaders maternal haplotype was different. Jimmy and Jenny could be as related to Pack leader as first cousins and share 43% of their genetic makeup and have the same maternal haplotype that none of the other dogs had, so probably had the same mother. They were in a separate group. Most closely related were Jenny and Jimmy at 43% and with the same mother as they both have the same maternal haplotype. Hannah and Figa at 40% and again with shared maternal haplotype so same mother but different to Jenny and Jimmy. Dasha and Dave with 31% and again the same mother as they have the same maternal haplotypes but different to the other siblings. Lara and Luna at 22% and again share the same maternal haplotypes so had the same mother that none of the others had. Figures shown are the percentage of DNA shared between connected dogs.
Hannah and Figa share 40% of their genes so are probably half siblings and share the same maternal haplotype A437 so probably the same mother.
Jenny and Jimmy share 43% of their genetic make up so are probably full siblings and share the same maternal haplotype C34 so probably the same mother. They were from a different group to Hannah Figa and Pack leader.
Lara and Luna share 22% of their genes as well as the same maternal haplotype so probably have the same mother but different fathers and were not family relatives of other dogs tested. Savvy and Sandy from Dhahran were thought to be siblings or half siblings but only share 17% DNA, a level equivalent to first cousins. They do share the same maternal haplotype suggesting their mothers may have been siblings.

Complicating this in dogs is that in one litter it is possible that more than one male dog may have mated. On average, siblings who share the same parents are approximately 50% genetically related. But if more than one male fathers a litter, the half-siblings puppies are only ~25% genetically similar. This is known as superfecundation and while extremely rare in humans it can occur in twins.

Wednesday, July 1, 2020

Where did all the German Shepherd genes come from?


Almost every “village dog” shows a trace of German Shepherd in its DNA. A range of other “breeds” also show up infrequently including Saluki, Basenji, Doberman Pinscher, Pomeranian, Boxer, Collie, Harrier, Labrador Retriever, Dalmatian,  and others. Considering that all of todays human established breeds originally come from the early natural dogs or by mixing other breeds to get a type wanted it is not surprising to find some shared DNA and the more pariahs that are tested the more are likely to be found. Some also have the same haplogroups and haplotypes  that are found in some “pedigree Canaan dogs”. It would be surprising if that was not the case since the Canaan breed is simply a small group, or family, established by taking in some 30 of these pariahs and breeding them for sale then excluding the rest. “The “breed” can be distinguished in much the same way as a human family that has bred in a closed community could be identified from other humans in the same geographic area. Most dogs in todays breeds are as closely related as second cousins. It is rare to find a dog with no genetic structure linking it to other breeds.

When “pedigree” dogs or unknown dogs that turn out to fit the genetic profile of the “pure” breed are tested then any trace breed found does not get reported. When a new “pariah” is added to the “Canaan breed” kennel clubs only require that the offspring breed true for 3 generations with existing registered dogs. That is equivalent to going back as far as great grandparents, each of  which would show up as 12.5% of the dogs genetic makeup. Once a new pariah is introduced to the breeding program and its offspring “breed true” to and is registered and its DNA added to the breed profile then all the related dogs will of course also test as being “pure Canaan”. If the relative finder on Embark tested 100% pure Canaan dogs is used GSD’s do show up as here:
So how do we explain the presence of this connection.
From Grace Gartel: “Since we first started testing dogs at Embark (and even before then, during our village dog research), the Embark team noticed that most village dogs across the globe share some German Shepherd Dog DNA (when it is less than 5% of their DNA, they are a "trace breed"). To be honest, we're not yet sure exactly why this is, but it definitely is a real biological phenomenon and has been noted by other labs (see for example https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5492993/).
The average amount of relatedness varies across the globe, and the exact amount varies between village dogs from the same region. This could relate to German Shepherd Dogs traveling around the world in the World Wars and other times, but we are not certain of that at this time. As we work to understand village dog genetics and history better, we hope to unravel this mystery!”
The suggestion that GSD’s were introduced by military into the area seems unlikely to explain this. Many other dog breeds have also been introduced and there is no reason to believe GSD’s could have bred so widely with pariahs worldwide that close to all pariahs even in remote areas now have some GSD in them. A more likely explanation would be that it is simply a continuation of genetic strains dating back to ancient times and has remained as a stable pattern. 


4 of 67 village dogs from this region had a trace of Gray wolf in their genetic makeup, 2 from Israel, 1 from Jordan and 1 from Kuwait. No doubt there are others not tested and again this is further evidence of the ancient origin of our desert dogs.
Some potential genetic health issues have been found in pariahs. Apart from the more common degenerative myelopathy (DM), which has become a major issue in the pedigree breed due to inbreeding, others already spotted in lower numbers in the pariahs include von Willebrands type II , factor VII deficiency (a blood clotting deficiency) and “Collie eye” Without fully testing any new pariah intended to be added to the breed BEFORE using them breeders could well be creating future problems. Thousands of desert dog pariahs still survive but, sadly, efforts to eliminate them by “rescuing” them or by Trap Neuter and Release (TNR) or worse,  to shoot or poison them if “successful” could lead to the end of these natural dogs while we still have much to learn from them.




Sunday, January 26, 2020

Dogs of ancient Egypt




Dogs have lived in Egypt for thousands of years and there are many artistic depictions of them. These include both carvings and paintings. Thousands of mummified dogs were placed in one tomb that has been known for some time but only recently properly studied. Many of these dogs may have been killed as part of a ritual but some had received better and more careful treatment and were likely to have been loved pets.

A number of distinctly different breeds were recognised. Rosellini attempted to put together a collection of the various dog types found and produced the following 2 plates. Most modern popular breeds have existed for a mere few hundred years but many people try to link them to Egyptian dogs for prestigious reasons but without factual proof. Today’s Pharaoh hound for example has been proven to be a modern mix designed to resemble the original. Africa’s Basenji is more likely to have descended from Egyptian types. Sighthounds were reserved for the elite people and their descendants have continued until today. Today’s Baladi dog in Egypt is another likely survivor from ancient times and is probably related to the desert pariah found throughout the middle-east and which has probably followed Bedouin and earlier hunter gatherers where ever they moved, throughout the Arabian peninsula and perhaps the ancient fertile crescent where man settled and grew crops. These desert dogs have survived in harsh conditions often without help from man and are the natural stock of today’s Canaan breed selected from these pariahs. The popular and intelligent (one has been shown to know over a thousand words) border collie, with known origins in the English/Scottish border area has also been claimed by some to have desert pariah connections.
















Monday, January 6, 2020

Genetics of registered Canaan dogs versus pariahs.


Here is an interesting illustration of just what the difference is between the pure free living pariah dogs and the pure Canaan “breed” established by simply capturing pariahs and breeding them for sale.  Kiva is a dog I saw as a puppy in 2013 in Israel. Her parents were Janey, a freeborn bitch from Jordan, and Tsuk, a freeborn from Israel. She now lives in America. Based on that information only her gDNA results could be expected to show her as a “village dog”. However she comes out as a Canaan. Looking deeper gives the explanation. Unlike most established breeds that have long been totally closed, the Canaan breed still adds new dogs after they have gone through a kennel club process. In simple terms this is based on the new dog coming from the area i.e. not from other continents where similar looking pariahs exist, then by breeding through 3 generations with the offspring breeding true to the look. The 3rd generation can then be registered as a Canaan with the kennel club. When it comes to DNA identification of any breed this is of course based on what kennel clubs deem to be the breed.  At least two maybe three dogs related to Kiva have been incorporated into the breed and have had their DNA checked by Embark so are therefore now part of the Canaan breed profile. At least one of these was descended from a brother of Janey.  Therefore Kiva now fits the updated Canaan profile.  Sadly many of Janey’s pups from her 3 litters were considered “aggressive” and were killed rather than spend the time needed to work on this. This is NOT the way to go if breeders honestly want to preserve this type of dog.  Starting at bringing in more new dogs they should be fully tested with state of the art methods (Embark being the only available one with pariahs in their database). This would firstly ensure that the dog is not a mixture. It would also ensure that no potential genetically associated health issue is added and could become a problem in future.  There is no simple “marker” that says a dog is a Canaan. The only “Canaan” that may be found living free is one related to the few that have been used to create the “breed” or have been added to them.   There is no reason why a pariah or village dog that tests as a pure Arabian or Middle Eastern village dog should not be added to the Canaan breed if it also has no genetic health issue. Ideally it would be preferable to concentrate on allowing these free living dogs to live where they are and as they have done for thousands of years without human interference, provided they are not in unsafe areas where they are at risk of being killed.

Of the pariahs I tested the close relatives were all from the same pack of dogs living together.