Studies & Research
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For those of us who love dogs, using DNA tests to deconstruct our mongrel pooch’s mysterious heritage is appealing because we want to be able to answer the question, “What kind of dog is that?” Companies say that DNA-based diagnostic tests, which sell for about $60, can answer the question by comparing your dog’s DNA to over 100 of the most popular breeds. But are the tests accurate? I decided to find out.
Chance, a 10-year-old mixed-breed dog who has lived with me for six years, was my guinea pig. I tested his DNA using three different tests. In 2008, when I wrote the prequel to this article (read it online at thebark.com/dna ), I had his ancestry tested with the Canine Heritage Breed Test . At that time, the company used 96 markers and tracked them to 38 breeds. A marker is a gene or DNA sequence on a chromosome that indicates “breedness.” The labs claim that the markers they use are 99 percent accurate.
In May 2012, when I began doing research for this follow-up article, I tested his DNA with the amplified Canine Heritage Breed Test again because it had been substantially improved to 400 markers and 120 popular breeds. I could have paid $25 to upgrade the 2008 test. But to be fair in my test-of-the-tests experiment, I submitted his cheek swab under a different name and without a photograph, just in case, as many people believe, the tests are a scam. In addition, I used the MARS Wisdom Panel  Mixed Breed Identification Test. Mars looks at 321 markers and includes 185 breeds in its database.*
To analyze and compare the results fairly, I needed to find out if the tests were processed the same way, and I researched the history of the breeds identified in Chance’s ancestry.
Comparing the Tests
If a primary parent breed can’t be identified in the DNA, the program will look for a secondary grandparent breed, and so on and so forth, until it eventually clusters with a distant breed (if there is one). If there are no purebred ancestors, remnant breeds will be sought.
To identify markers that characterize a breed, labs take samples from multiple thousands of individual dogs representative of more than a hundred breeds. However, those dogs differ from one laboratory to the next. Although their sample sizes are big enough to absorb minor differences, no two dogs are exactly alike. Plus, line-bred dogs can affect results. For example, Labrador Retrievers bred exclusively for hunting may be more like each other than they are like the breed.
Finally, descriptive terminology differs. Canine Heritage uses primary, secondary and in the mix. Wisdom Panel uses parent, grandparent, great-grandparent and next best breed matches that include percentiles.
Because Chance has no purebred parent, his strongest signal would come from a purebred grandparent. One test indicated a Siberian Husky grandparent. However, the other two tests claimed he has no purebred parent, grandparent or great grandparent. In any case, all three tests concur that a combination of spitz breeds provides the strongest signals in Chance’s ancestry — Siberian Husky, Alaskan Malamute and, to a lesser degree, the Pembroke Welsh Corgi, a breed with some spitz lineage. Although it transmits a faint signal, the Pembroke Welsh Corgi is the only breed that showed up in more than one test. The white German Shepherd and blackand-tan German Shepherd, strong and weak signals respectively, are both named as ancestors and are admixtures of one another. Although they are herding dogs, it’s probable that both breeds have some spitz lineage. The Japanese Chin, a miniature Asian breed derived thousands of years ago from larger mastiff and spitz dogs, is also a fairly strong signal.
Large terriers make up the next strongest signals in his DNA. The German Pinscher, Standard Schnauzer and Doberman Pinscher are closely related. German Pinschers were used to develop the relatively new Doberman Pinscher breed. The Standard Schnauzer, originally called the Wire-haired Pinscher, is directly related to the German Pinscher. Sight hounds are mentioned in two tests. In the late 1800s, Borzois were likely mixed with Huskies to increase speed, and terriers were mixed with Italian Greyhounds.
The weakest signals, in some cases less than 2 percent of his makeup, include a ragtag group of breeds, including Border Collie, English Setter, Cocker Spaniel and Leonberger.
Making Sense of the Findings
The ancestral breeds named in the three tests seem absurdly disparate, but they are not contradictory. They all point to one truth: only a few degrees of separation differentiate Chance from all modern breeds. This is because most purebred dogs have a crippling lack of genetic diversity, which is the unintended consequence of modern breeding practices.
Except for 14 ancient breeds — Afghan, Akita, American Eskimo, Basenji, Canaan Dog, Chinese Shar-Pei, Chow Chow, Dingo, Finnish Spitz, New Guinea Singing Dog, Saluki, Samoyed, Shiba Inu, and Siberian Husky — all our modern breeds were developed in the last few hundred years.1 Although each has its own DNA fingerprint, they have so little genetic diversity that if you go back far enough, the DNA of almost every dog, mixed breed or purebred, will cluster with a few common ancestors. This finding raises the question, “How can breeds that look so different be so closely related.”
The complex DNA of stray mutts on the mean streets of, for instance, Lugazi, Uganda, or Zorzor, Liberia, may answer the question. Ubiquitous freeranging dogs living on the fringes of human settlement are not, as previously believed, semi-feral, mongrelized purebred dogs, but rather, are genetically distinct and subject to the pressures of natural selection. Some populations have been isolated for hundreds, if not thousands, of years. Subsequently the village dog genome remains complex and unabridged.
Suspecting that village dogs may be pure genetic remnants of ancient dogs, Adam Boyko, assistant professor in the Biomedical Sciences Department at the Cornell University College of Veterinary Medicine, co-founded the Village Dog Genetic Diversity Project  with his colleague Carlos Bustamante, a genetics professor at Stanford School of Medicine.
The project is a worldwide collaboration of researchers, volunteers and veterinarians who gather canine DNA samples along with photos and information on weight, age, body measurements and coat color. The samples are analyzed at the Canine DNA Bank at the Baker Institute for Animal Health, part of Cornell’s College of Veterinary Medicine, which maintains a growing DNA archive of dogs worldwide.
The scientists believe their work will shed new light on when, where and under what conditions dogs were domesticated, and how dogs have adapted to human settlement, environmental stress and disease.
The first phase of the study included collecting samples from modern breeds, their mixed-breed relatives, breeds reputed to be from remote regions of the world and African village dogs. In 2009, they reported that African village dogs are a mosaic of indigenous dogs descended from more ancient dogs that migrated to Africa.2 Findings also indicated that their genome is being eroded at an alarmingly fast rate as they mate with recently introduced modern dogs. Researchers are now scrambling to find dogs in even more remote locations. In the summer of 2012, workers began collecting DNA samples in Liberia and the Democratic Republic of the Congo.
On a continuum, gray wolves, the progenitor of all dogs, have the most genetic diversity, and purebred dogs have the least. Village dogs’ diversity lies somewhere in between. Because purebred dogs are the result of strong selection for exaggerated traits, they have only a fraction of the genetic diversity displayed by village dogs. The genetic variant that underlies a desirable trait, whether it’s extreme size or intense behavior, has become fixed, wiping away not only competing variants but also variants associated with nearby genes.
Genes located close to each other on a chromosome are said to be linked, and tend to be inherited together or, conversely, wiped away at the same time. Thus, a trait that isn’t selected for can be wiped away simply as a result of being in the wrong place at the wrong time. If that trait happens to affect, for instance, immune response to disease, then that could be a problem.
By comparing the genome of village dogs to that of purebred dogs, scientists hope to be able to identify what’s been lost as a result of intense artificial selection. Dr. Boyko notes that “village dogs offer a chance to understand the mechanisms of certain genetic diseases. Knowing what those genetic variants are might be the first step towards invigorating genetic diversity in some modern breeds.”
The Significance of Canine Origin
Previous studies suggest that dogs originated in places as varied as Eastern Europe, China’s Yangtze River Valley and the Middle East. In a 2002 study, researchers pinpointed East Asia as the place of origin. However, some scientists think these dogs are descendents of an even older population that developed in a different place. Dr. Boyko’s findings confirm this. African village dogs have about the same amount of genetic diversity as those in the East Asian study, suggesting that both groups are the same age. It’s possible that both populations originated together somewhere else and then migrated to East Asia and Africa at about the same time.
To thoroughly complicate matters, the Canidae family does not play by the same rules as most other mammalian families. Unlike, say, horses and donkeys, dogs, wolves, coyotes and golden jackals can interbreed and produce fertile offspring. Consequently, following the genetic trail from domestic dog to wolf leads to a lot of stops and starts and many dead ends as well as plenty of headaches for evolutionary biologists.
A Multi-Disciplinary Approach
As Dr. Larson notes, “There has been so much admixture since dog domestication began, and especially in the last few hundred years, that looking at modern dogs is always going to be problematic. There may be modern populations that are less ‘corrupted’ or admixed, but even they will possess a legacy of several thousand years of crosses with large numbers of populations, and even wolves.” He adds, “The only way forward is to focus on other methods, including, but not limited to, ancient DNA from archaeological dog and wolf remains. And of course, there is the wider interpretation and understanding from lots of other fi elds to put it all in context.”
In the paper, researchers discussed an interesting pattern that emerges when sites with archaeological dog and wolf remains are overlaid onto maps showing the historical distribution of wolves. First, the archaeological remains are not found in the places where ancient breeds are believed to have been developed, intimating that dogs may have been domesticated multiple times from local wolf populations. Second, most of the ancient breeds come from areas where wolves never ranged, suggesting that humans had dogs as they migrated around the globe. Furthermore, dogs only appeared in these locations after agriculture was introduced.
The canine genome’s full story continues to evade scientists, but as DNA technology advances and analysis becomes cheaper and faster, researchers are optimistic that the answers they seek are right around the corner.
Will I continue to test my future shelter rescue mutts to find out who they are, even though I know that the answers will be the same — all modern dogs are so closely related that it’s almost impossible to discriminate ancestry? Probably. Other mysteries lie hidden in our dogs’ DNA. The idea that an animal can be morphed into so many extreme shapes and behaviors yet remain a simple combination of only a few stem parents is one of them.
We like to believe that scientific discovery advances tidily, fact by fact, to prove an irrefutable truth. But science is a messy business. And there is hardly a better example of just how messy than the search to tease out the mysteries hidden in the canine genome.
Photographs by Andrew Pinkham
*See the companies’ breed libraries here: canineheritage.com/breed_list.html wisdompanel.com/ breed_count_matters/breedlisting 
** We learned that in June 2012, Mars Veterinary purchased and discontinued the Canine Heritage Breed Test.
1. Parker, H.G., et al. 2004. Genetic structure of the purebred domestic dog, Science 304 (5674): 1160–1164.
2. Von Holdt, B.M., et al. 2010. Genomewide SNP haplotype analyses reveal a rich history underlying dog domestication. Nature 464 (7290): 898–902.
3. Larson, G., et al. 2012. Rethinking dog domestication by integrating genetics, archeology, and biogeography. PNAS, 2012.