Saturday, September 21, 2019

Some interesting haplotypes found in Arabian village/desert dogs.




Some of the interesting haplotypes found in these dogs with notes from Embark.


H8.1 found in Max from al Khobar and Pavlova from Dubai. H8.1 - Part of the E haplogroup, this haplotype has been spotted in Basenjis, Canaan Dogs, and village dogs spanning from Africa into the Middle East.








H8.4 found in Jimmy from Um al Quwain. H8.4 is found in dogs from the south and east of India.








H9 found in Wiley from Egypt and in Basenjis and African village dogs. Part of the F haplogroup F is the odd duck in the family of domestic dog male lineages. This paternal lineage is genetically closer to wolves, foxes, and jackals than to other dogs. This indicates that it came into the dog population after dogs were originally domesticated, when one particularly attractive male wolf mated with a female dog, over 6,000 years ago. Since then, these dogs found their way into Africa and Mongolia. It hasn't been found outside those areas except in Basenjis.  Basenjis are an iconic African breed, that first made its way to the USA in the early 20th century when a handful of individuals were imported from the Congo. The Basenji is an ancient breed which is distantly related to other dog breeds (most of which are European or Asian), and it has the earliest separation date from all other breed populations. Unsurprisingly, the F lineage has also been found in African village dogs, as well as, surprisingly, some samples from Mongolia. The fact the lineage is found in two very distant places is evidence that it entered the dog population many thousands of years ago.









C1 found in Pack leader, Jenny and Jimmy from um al Quwain. Jenny and Jimmy are siblings and are related to Pack leader.  C1 - Congratulations, C1 is a very exotic female lineage! It is more closely associated with maternal lineages found in wolves, foxes and jackals than with other dog lineages. So it seems dogs in this are group have a common male dog ancestor who, many thousands of years ago, mated with a female wolf!









A158 found in Robin from Dubai. A158 - Part of the large A1e haplogroup, we have detected this haplotype in village dogs in India.











A264 found in Cookie from Jeddah. A264 - Part of the large A1e haplogroup, this haplotype occurs in Irish Wolfhounds and village dogs from Iraq and Lebanon.











B105 found in Honey from Fujairah B105 - Part of the B2 haplogroup, the B105 haplotype occurs most commonly in Middle Eastern Village Dogs. It's a rare find!











B77 found in Tess from Fujairah.  B77 - Part of the B1 haplogroup, this haplotype occurs most frequently in Japanese Chins.



Tuesday, September 17, 2019

Arabian village dogs


ARABIAN VILLAGE DOGS




We now have a separate group listed by Embark as Arabian village dogs, closely related to the earlier single umbrella of Middle-east village dogs.

It is widely accepted at present that domestic dogs originated in south east Asia and that they spread from there in all directions including through the middle east into Europe and Africa. It is only the last couple of hundred years that humans created all the hundreds of breeds we have today by selecting for various traits such as size, temperament etc. In doing so many genetic material was also lost from these so called pure breeds, either deliberately or as a consequence of controlled breeding. Today there are still far more free living dogs in the world than there are these breeds. In much of the western developed world humans have virtually eliminated these real dogs by removing them as undesired vermin. Wherever European colonialist went they considered their breeds as superior to any local dogs and often passed on that idea. Many so called pure breeds are increasingly having genetic health issues and some of these problems are particularly associated with particular breeds. A recent publication looking at genetic health issues in breeds versus mongrels showed that while the mongrels had more of these genes coding for health issues than did breeds they were nonetheless healthier. This is because the mongrels mostly had only one copy of the gene, inherited from one parent while 2 are required to put the dog at risk. Mongrels by definition being dogs born of mixed breed parentage and are not the free living pariahs or village dogs that have never been bred by humans.

The oldest known petroglyphs of dogs working with humans in Saudi Arabia show two morphological types, the well-known Saluki sighthound and the desert pariah as is still to be found throughout the Arabian Peninsula and middle-east. Many of the papers published refer to middle-east dogs but a closer look at them also shows that often the bulk of dogs looked at were from further north.

Following are some facts drawn from studying the DNA of some of the free born dogs in the Arabian Peninsula performed by Embark.

Overall predicted Weight: 12.7 to 25.9 mean 19.1 kilograms, Males mean  20.8 kg, Females mean  18.2kg

Wolfiness is described by Embark as “Most dogs have wolfiness scores of 1% or less. We find populations and breeds with higher scores of 2-4% occasionally, and unique dogs with scores of 5% or above more rarely.” Results for the 47 dogs studied here varied from 0.6 to 25.9 mean 2.86 and only 3 dogs below 1% and 6 dogs above 5%.

Haplogroups and haplotypes: As expected there was considerable diversity and there are probably others since it is impossible to sample every dog .   Notes on their significance copied from Embark.

Paternal haplogroups , A1b=1, D=11, E=3, F=1

The D paternal lineage is very common in well-known populations of dogs. Breeds belonging to the D lineage likely have direct male ancestors that can be traced all the way back to the origin of domestic dogs themselves! One popular breed that commonly sports a D lineage is the Boxer. Boxers were developed in the late 19th century from Mastiff dogs, so it is no surprise that D is well represented among Mastiffs, Bulldogs, as well as Terriers. Intriguingly, D is also found among Lhasa Apsos, an ancient Tibetan breed, and Afghan Hounds. While the presence of this lineage in Polynesia or the New World can be chalked up to interbreeding with European dogs brought during voyages of discovery or later settlement, D is also well represented among village dog populations in the Middle East and Africa. If the fact that we find dogs bearing a D lineage in the Middle East (not to mention the large amount of diversity among Middle Eastern D lineage males) is any indication of ancient residence in that region, then the presence among Oceanian village dogs is peculiar. Rather, it may be that D is part of a broader Eurasian group of ancient paternal lineages which disappeared from the eastern portion of its original range, persisting in the island of New Guinea as well as West Asia and Africa. With the rise of Mastiff breeds, the D lineage received a new life as it became common among many types of working dogs.

The E lineage is sticking around to remind dog lovers of a truly ancient ancestor among all modern domestic dogs. Males with this Y chromosome type are reminiscent of dog-like canids reaching deep into the most recent ice age (the Pleistocene). E is much more common among village dogs than breeds. However, it is found as a minor lineage among the Basenji breed, as well as the ancient dog, which has been present in the Middle East for thousands of years. E is present widely among African village dog populations, as well as among some Mongolian dogs. With its greatest diversity and most frequent occurrences popping up in the Middle East, this lineage extends all the way over into India. Thus, African, South Asian, and Central Asian populations may descend from founders in this region, perhaps somehow tied to the spread of agriculture.

A1b - For most of dog history, this haplogroup was probably quite rare. However, a couple hundred years ago it seems to have found its way into a prized male guard dog in Europe who had many offspring, including the ancestors of many European guard breeds such as Doberman Pinchers, St. Bernards, and Great Danes. Despite being rare, many of the most imposing dogs on Earth have it; strangely, so do many Pomeranians! Perhaps this explains why some Poms are so tough, acting like they're ten times their actual size! This lineage is most commonly found in working dogs, in particular guard dogs. With origins in Europe, it spread widely across other regions as Europeans took their dogs across the world.

F - F is the odd duck in the family of domestic dog male lineages. This paternal lineage is genetically closer to wolves, foxes, and jackals than to other dogs. This indicates that it came into the dog population after dogs were originally domesticated, when one particularly attractive male wolf mated with a female dog, over 6,000 years ago. Since then, these dogs found their way into Africa and Mongolia. It hasn't been found outside those areas except in Basenjis. Basenjis are an iconic African breed, that first made its way to the USA in the early 20th century when a handful of individuals were imported from the Congo. The Basenji is an ancient breed which is distantly related to other dog breeds (most of which are European or Asian), and it has the earliest separation date from all other breed populations. Unsurprisingly, the F lineage has also been found in African village dogs, as well as, surprisingly, some samples from Mongolia. The fact the lineage is found in two very distant places is evidence that it entered the dog population many thousands of years ago.



Paternal haplotype Ha.4/11=1, H7=6, H7.2=5, H8.1=2, H8.4=1, H9=1

 H7 - Part of the D haplogroup, this common haplotype has been found in French Bulldogs, Afghan Hounds, Bull Terriers, and village dogs spanning from South America to Africa and into the South Pacific.

H7.2 - Part of the D haplogroup, the H7.2 haplotype occurs most commonly in Sarplaninacs. We've also spotted it in Middle Eastern Village Dogs and European Village Dogs.

H8.1 - Part of the E haplogroup, this haplotype has been spotted in Basenjis, Canaan Dogs, and village dogs spanning from Africa into the Middle East.

H8.4 - Part of the E haplogroup, we have spotted this rare haplotype in village dogs in southern and eastern India.

Ha.4/11 - Part of the A1b haplogroup, this haplotype occurs most frequently in mixed breed dogs.

H9 - A member of the F haplogroup, this haplotype is found in Basenjis and village dogs throughout Africa.

MATERNAL haplogroups.  A1a = 3, A1d = 5, A1e = 13, B1 = 15, B2 = 3, C1 = 3

A1a is the most common maternal lineage among Western dogs. This lineage traveled from the site of dog domestication in Central Asia to Europe along with an early dog expansion perhaps 10,000 years ago. It hung around in European village dogs for many millennia. Then, about 300 years ago, some of the prized females in the line were chosen as the founding dogs for several dog breeds. That set in motion a huge expansion of this lineage. It's now the maternal lineage of the overwhelming majority of Mastiffs, Labrador Retrievers and Gordon Setters. About half of Boxers and less than half of Shar-Pei dogs descend from the A1a line. It is also common across the world among village dogs, a legacy of European colonialism.

A1d This female lineage can be traced back about 15,000 years to some of the original Central Asian wolves that were domesticated into modern dogs. The early females that represent this lineage were likely taken into Eurasia, where they spread rapidly. As a result, many modern breed and village dogs from the Americas, Africa, through Asia and down into Oceania belong to this group! This widespread lineage is not limited to a select few breeds, but the majority of Rottweilers, Afghan Hounds and Wirehaired Pointing Griffons belong to it. It is also the most common female lineage among Papillons, Samoyeds and Jack Russell Terriers. Considering its occurrence in breeds as diverse as Afghan Hounds and Samoyeds, some of this is likely ancient variation. But because of its presence in many modern European breeds, much of its diversity likely can be attributed to much more recent breeding.

A1e - This female lineage likely stems from some of the original Central Asian wolves that were domesticated into modern dogs starting about 15,000 years ago. It seemed to be a fairly rare dog line for most of dog history until the past 300 years, when the lineage seemed to “explode” out and spread quickly. What really separates this group from the pack is its presence in Alaskan village dogs and Samoyeds. It is possible that this was an indigenous lineage brought to the Americas from Siberia when people were first starting to make that trip themselves! We see this lineage pop up in overwhelming numbers of Irish Wolfhounds, and it also occurs frequently in popular large breeds like Bernese Mountain Dogs, Saint Bernards and Great Danes. Shetland Sheepdogs are also common members of this maternal line, and we see it a lot in Boxers, too. Though it may be all mixed up with European dogs thanks to recent breeding events, its origins in the Americas makes it a very exciting lineage for sure!

B1 - B1 is the second most common maternal lineage in breeds of European or American origin. It is the female line of the majority of Golden Retrievers, Basset Hounds, and Shih Tzus, and about half of Beagles, Pekingese and Toy Poodles. This lineage is also somewhat common among village dogs that carry distinct ancestry from these breeds. We know this is a result of B1 dogs being common amongst the European dogs that their conquering owners brought around the world, because nowhere on earth is it a very common lineage in village dogs. It even enables us to trace the path of (human) colonization: Because most Bichons are B1 and Bichons are popular in Spanish culture, B1 is now fairly common among village dogs in Latin America.

C1 - Congratulations, C1 is a very exotic female lineage! It is more closely associated with maternal lineages found in wolves, foxes and jackals than with other dog lineages. So it seems dogs in this group have a common male dog ancestor who, many thousands of years ago, mated with a female wolf! This is not a common lineage in any breed, though a good number of German Shepherds and Doberman Pinchers are C1. It is also found in breeds as diverse as Peruvian Inca Orchids and Pekingese; it is rarely found amongst Labrador Retrievers, Border Collies, Siberian Huskies, or Cocker Spaniels. Despite its fascinating origins, it is widely distributed around the globe, and even shows up frequently among Peruvian village dogs. It almost certainly survived at low frequency in Europe for millennia and then was dispersed outside of Europe by colonialism, though not as successfully as some other lineages.



Haplotype: A158 = 1, A16/17/99/100 = 1, A233 = 3, A247 = 4, A264 = 2, A228 = 1, A2a = 1, A361/409/611 = 3, A293 = 1, A414/643 = 1, A424 = 1, A435 = 1, A437 = 4, A494 = 1, B105 = 3, B2a=12, B77 = 1, C1/2 = 1, C34 = 2.

A158 - Part of the large A1e haplogroup, we have detected this haplotype in village dogs in India.

A16/17/99/100 - Part of the large A1a haplogroup, this common haplotype is found in village dogs across the globe. Among breed dogs, we find it most frequently in Labrador Retrievers, Newfoundlands, German Shepherd Dogs, and Golden Retrievers.

A233 - Part of the large A1e haplogroup, we see this haplotype in village dogs across Central Africa through the Middle East and into South Asia. As for breeds, we see it in the highest frequency among Irish Wolfhounds, with some detections in Greyhounds, Posavac Hounds, and Beagles as well.

A247 - Part of the large A1d haplogroup, this common haplotype occurs in village dogs all over the world. Among the 32 breeds we have sampled it in, the most common occurrences include Boxers, Labrador Retrievers, and Papillons.

A264 - Part of the large A1e haplogroup, this haplotype occurs in Irish Wolfhounds and village dogs from Iraq and Lebanon.

A228 – Part of the large A1e haplogroup, we have spotted this haplotype in village dogs in the Democratic Republic of the Congo and in the Dominican Republic. Among breeds, we see it frequently in big dogs like Saint Bernards, Leonbergers, and Great Danes. However, we also see it in small breeds including wire Fox Terriers and Rat Terriers. That’s a pretty wide size range!

A2a - Part of the large A1e haplogroup, we see this haplotype in village dogs up and down the Americas as well as French Polynesia. Among the breed dogs we have detected it in, we see it most frequently in English Springer Spaniels, Papillons, and Collies.

A361/409/611 -  Part of the A1b haplogroup, this haplotype occurs most frequently in German Shepherd Dogs, Poodles, and Shiloh Shepherds.

A393 - Part of the large A1a haplogroup, this haplotype occurs most frequently in Yorkshire Terriers, Russel-type Terriers, and Tibetan Terriers.

A414/643 - Part of the A1b haplogroup, this haplotype occurs most frequently in the English Springer Spaniels.

A424 - Part of the A1d haplogroup, this haplotype occurs most frequently in American Pit Bull Terriers, Barbets, and Staffordshire Terriers.

A435 - Part of the A1d haplogroup, this haplotype occurs most frequently in American Pit Bull Terriers, Barbets, and Staffordshire Terriers.

A437 - Part of the A1e haplogroup, the A437 haplotype occurs most commonly in Brussels Griffons, Armenian Gamprs and Russell-type Terriers. We've also spotted it in East Asian Village Dogs, Middle Eastern Village Dogs and American Village Dogs.

B105 - Part of the B2 haplogroup, the B105 haplotype occurs most commonly in Middle Eastern Village Dogs. It's a rare find!

B2a - Part of the large B1 haplogroup, we primarily see this haplotype in Salukis and village dogs in and around the Fertile Crescent (Egypt through the Middle East).

B77 - Part of the B1 haplogroup, this haplotype occurs most frequently in Japanese Chins.

C1/2 - Part of the C1 haplogroup, this haplotype occurs most frequently in Bouvier des Flandres, Collies, and Yorkshire Terriers.

C34 - Part of the C1 haplogroup, the C34 haplotype occurs most commonly in Collies, Anatolian Shepherd Dogs and Teddy Roosevelt Terriers. We've also spotted it in European Village Dogs and American Village Dogs.

Genetic health issues

None of these dogs were at risk for any of the genetic health problems tested by Embark.

Carriers:

9 of 47 (19%) dogs carried one copy of the allele coding for Degenerative Myelopathy (DM) so 81% were normal. The Orthopaedic Foundation for Animals (OFA) in USA figures for 1918 show Canaan dogs, a pedigree breed established in the 1930s from village dogs show an alarming rate of 6.4% abnormal (at risk) for DM with 38.2% carriers with only 55.4% normal. Compared to other breeds Canaan dogs ranked a high 22nd.

2 carried one copy of the allele coding for choroidal hypoplasia, (Collie eye anomaly) . These 2 dogs from Umm al Quwain, UAE were closely related, sharing 40% of their DNA (half siblings).

1 dog from Sohar, Oman carried 1 copy of the allele for von Willebrand type 1 a bleeding disorder.

25 of 47 dogs (53%) had one copy of the allele coding for low normal ALT and 1 had 2 copies. This is important to know since a dog having this when suspected of having liver problems could give an ALT result generally considered normal but could in fact be raised for that dog.

Sadly the European idea of dog breeds and their “purity” is still wide spread in thinking. Right now there is a push in the emirate of Umm al Quwain to remove all of the several hundred free roaming dogs and neuter them. This may be done with the best intention but ultimately will lead to the destruction these ancient types that have survived for thousands of years without human intervention.

The Canaan dog breed is an attempt to preserve this ancient type but sadly fails to recognise, even today with DNA testing available, that there are potential health problems. The breed is based on around 30 dogs selected mainly on looks and already DM has shown up, particularly in some breeders who have been inbreeding, something breeders prefer to call line breeding. While not all the free living dogs have the Canaan look, many do and there is still a golden opportunity for breeders worldwide to throw out the outdated kennel club ideas and concentrate on developing one of the healthiest breeds in the world, which it is not at present. This could be done by selecting the required look from these dogs wherever they are found and testing their DNA first to ensure only dogs that do not carry any known genetic problem are used. It is highly unlikely that any matching the Canaan registered dogs DNA will be found because all the registered breed dogs are by now probably already related closely, in human terms as second cousins or closer. Instead efforts to introduce new blood continue to look for dogs with the “correct” look only without checking their DNA to check that they are not mixed and that they carry no mutant genes.

Since many of todays breeds would have come from the early dogs it is no surprise to see some uncommon or even rare haplotypes associated with other dogs turn up. All of these dogs show a trace of German shepherd in them as well as a smattering of other breeds. This is not an indication of recent mixed breeding but an indication of the presence of ancient ancestral connection of all dogs.


Tuesday, February 12, 2019

Update on the genetic study of Arabian desert dogs



UPDATE ON THE GENETIC STUDY OF ARABIAN DESERT DOGS




Some results of the genetic study under way of our Arabian pariah desert dogs have been shared with me by Dr.Elaine Ostrander and her team at the National Institute of Health. All dogs have now been identified. (See below).




The dogs cluster in 2 groups, one showing a genetic connection to Basenjis. This is not surprising considering that Basenji dogs would have been established from dogs that moved to Africa through the middle-east so some of their genetic material would be expected to still be found among dogs of the middle-east. Basenjis have evolved separately now for some time.

The second cluster is with what is now human controlled “breed” registered as Canaan dogs. These have the same genetic origin with Canaan dogs having been selected from a small number based on appearances without reference to their genetic makeup, since such testing was not available when the breed was established several generations ago. It is to be expected that pedigree Canaan dogs would now have less genetic diversity than our pariahs.

The dogs included in this ongoing work include some born in Jeddah,  Al Qassim, Riyadh, Dammam, Doha, Dubai and other emirates  and Sohar. All of them have an ancient connection and are not mixes of modern dogs. Some had been adopted and living in homes or were in K9 friends, Dubai shelter and some were still living free but were being provided with food and water and had become accustomed to people. 




First is the overall tree as published previously by Elaine Ostrader et. al. It shows where Canaan dogs fit in the world of dog genetics but our dogs had not been included when published. 


The second diagram is an enlarged small section of this tree with our desert dogs added and shown in red. As explained by Dr. Ostrander :-

  1. Small numbers on the lines in black are the bootstrap values.  That indicates how many times out of 100 we ran the same data and got the exact sample architecture of the tree. This tree is amazingly good with most data being at 100%. 
  2. The Canaan dogs are not necessarily closet to the Saluki.  Remember that this is a two dimension graph that can exist in three dimensions.  So the branch with the Saluki can be flipped 180 degrees, putting them closer to anything left of the saluki.  What matters here is the branch position.  Like a real tree--what is relevant is what branch comes from which larger branch, not the twisted position of the single small branch. So focus on the branch structure. "



Photographs of the dogs included in these groups and identified follow. First those clustered with Canaan dogs then those clustered with Basenjis.

THANK YOU FOR ALL WHO PARTICIPATED IN THIS, WITHOUT YOU WE COULD NOT HAVE DONE IT. THESE DOGS ARE IMPORTANT AND DESERVE FULL RECOGNITION AS A PART OF THE NATIONAL HERITAGE OF THIS PART OF THE WORLD AND THE OVERALL WORLD OF DOGS. As more information comes to hand I will update it.




Clustered with Canaan dogs

(In order from left to right on the tree)
Dave and Roxx have rear dew claws.

Hannah

Figa

Pack leader

Jenny

Jimmy

Robin

Genevieve

Melli

Lilly

Hope

Faraji

Dave

Dasha

Coconut

Esra

Lucas

Lara

Luna

Rocky

Bobbi


Roxx

Aswad

Dolly

Pavlova

Tiara









Clustered close to Basenji
(In order from left to right on the tree)

Cookie

Foxy

Savvy

Sandy


Brandy
(no photo)

Shayboo
(No photo)

Nina
(No photo)

McKenzie
(No photo)

Spock
(No photo)
Max

Molly

Bella

Jasmine
(in front)

Jinn
(no photo)

Joann

Leila
(no photo)

Honey

Doodle

Tess

Ben


List of all dogs included 


30606 Pack Leader Carstens, 30609 Hannah Carstens, 30610 Figa Carstens, 30611 Dasha Carstens, 30612 Dave Carstens, 30613 Lara Carstens, 30614 Genevieve Carstens, 30615 Luna Carstens, 30616 Melli Carstens, 30617 Lucas Carstens, 30621 Habibi Groenewald, 30622 Coconut Schroeter, 30624 Bobby K9, 30625 Pavlova K9, 30626 Tiara k9, 30627 Molly Groenwald, 30628, Robin Hart, 30630 Max Beadle, 30631 Savvy Doust, 30632 Cookie Witt, 30633 Sandy Bennett, 30634 Shayboo Androski, 30635 Brandy Androski, 30636 Mckenzie Hassell, 30637 Nina Golez Chang, 30638 Spock Hald, 30639 Roxx Schroeter, 30640 Foxy Velasco, 30852 Jenny Carstens, 30853 Jimmy Carstens, 31081 Honey Carruthers, 31082 Tess Carruthers, 31083 Jinn Crowley, 31084 Joann Groenewald, 31085 Ben Groenwald, 31086 Jasmine Groenwald, 31087 Bella Groenwald, 31088 Doodle K9, 31089 Aswad K9, 31090 Esra K9, 31091 Glitter K9, 31092 Faraji K9, 31093 Dolly K9, 31094 Hope K9, 31095 Leila Kawpevis, 31098 Lilly Koerth, 31099 Rocky Koerth

Geographic areas and group



Al Khobar (Basenji group)


Max


Dharan (Basenji group)


Savvy, Sandy, Brandy, Mckenzie, Nina, Spock, Shayboo, Foxy


Dubai (Canaan group)


Coconut, Trixie, Bobbi, Pavlova, Tiara, Robin, Roxx, Glitter, Aswad, Hope, Feraji, Lilly, Rocky, Esra, Dolly

Dubai (Basenji group)

Doodle

Fujaira (Basenji group)

Honey, Tess, Leila

Jeddah

Cookie

Sohar (Basenji group)

Bella, Ben, Molly, Joann, Jasmine

Umm Al Quwain (Canaan group)

Pack Leader, Neo, Hannah, Figa, Dave, Dasha, Lara, Genevieve, Luna, Melli, Lucas, Jenny, Jimmy