Village dog groups

 Kennel club registered breeds are mostly closed groups, so the genetic profile of a breed is fixed. In rare cases such as Canaan dogs when "new blood" is added and that dog or its relatives DNA tested, that is then added to the overall breed genetic profile. It is kennel clubs that fix what any breed is and not DNA test companies. 

With village dogs there is no such limitation. These dogs know nothing of human imposed country borders and have long moved freely throughout various areas. Therefore, separating them into areas becomes much more complex and is likely to be fluid. It is impossible to test every dog in a region or country, so the DNA profile is dependent on what dogs have been tested and we simply do not know what may have been missed.

For example, is a "West Asian" dog, or its parent, that is found in Dubai or North Africa a recent arrival or has its DNA profile simply not have been previously included. It is interesting to speculate but we cannot be sure.

Recently Embark, as the acknowledged best village dog DNA experts have altered their list of what village dogs they test for. They no longer list "Arabian village dogs", "Northeast African village dogs" and others. Instead, they now have groups based on countries such as UAE, Bahrein, Egypt, Israel. Notably a number of other countries in the region, that still have large numbers of village dogs, such as Saudi Arabia, Gaza and others are not mentioned. 

A couple of weeks ago I asked Embark to explain this and if they will now be updating dogs previously tested from the now no longer existing groups to the current ones. At the time of writing, I have received a "ticket number" and a note that they are currently very busy so may be slow to respond. I will update this blog when I get more information.

WHAT IS A DOG?

 "What is a dog" is the title of a book written by Raymond and Lorna Coppinger that I would highly recommend to all. 

What Is a Dog?, Coppinger, Coppinger, Beck (uchicago.edu)

When published in 2016 their best guestimate was that there could be a billion dogs in the world. Just as the human population grows it is likely that so too has the dog population since then. Most dogs in the world remain the free living "village" dogs, or what WHO refers to as "unrestrained" dogs. It is estimated that 85% of dogs are not the inbred pets most people know but these free-living dogs. Few people of the "western" or "developed" countries understand this simply because the only dogs they have experience of are these human controlled artificial "breeds" or mixed "mongrels" that have come from breeds. Of Canis species in the world some 95% are dogs. At the time of writing this I have seen people commenting on the village or Baladi dogs of Egypt saying that they must come from dogs originally dumped. No, they do not! The complete opposite is true. Humans did not create dogs. To state that reinforces a total lack of factual knowledge of these dogs. Most of the Baladi dog groups on FB, however well meaning, also fail to get the full story correct, and that includes a thesis I have seen about "Baladi" dogs that earned the writer a university degree. People like that simply cannot get their heads around the fact that dogs have never needed to be told by people how to produce puppies. It really does not matter what local names people use for these dogs, there are many, Baladi, wadi, desert, to mention a few. As with any language there are also different words used in some countries but not others, "Baladi" is such an example and is not found in many Arabic dictionaries outside of Egypt. Dogs are a domestic animal, as are pigeons, chickens house sparrows and many others. This is different to "domesticated" that refers to a wild animal that has been selectively bred to live in a domestic situation. Here is an interesting link to worldwide dog populations although not all countries are shown. 

Dog Population by Country 2024 - Worldostats

Coefficient of Inbreeding (COI)

 COI as measured genetically by Embark shows that while pedigree Canaan dogs overall are still somewhat better than that for all breeds, village dogs left to choose their own partners have much less in breeding. In pedigree dogs there may well be measurably more inbreeding in dogs from particular breeders who like to create their own "line" of dogs. An inbreeding coefficient of 0 indicates a dog that comes from two unrelated parents; 6.25 is equivalent to mating of first cousins; 12.5 equates to the genetic equivalent of a dog produced from a grandfather to granddaughter mating; 25 would equate to the genetic equivalent of a dog produced from a father to daughter mating. Data and graphs from Embark.

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. 

How accurate are dog DNA tests? We unleash the truth | CBC News

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?

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.

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.