Jane Brackman

Jane Brackman, PhD, is an authority on the cultural history of canine domestication and the author of two books on pets in 19th-century America. See her new pup, Barkley, and watch him grow on her blog.

Culture: Science & History
Scientists Searching for Clues to The First Dog
Village dogs’ genetic code may hold clues to canine evolution and health

Like classic twin studies that investigate the interplay of nature and nurture, comparing the genome of village dogs to modern dogs may help disentangle the long-term evolutionary effects of genetic and environmental influences.

Mastiff to Min-Pin, Corgi to street cur: all dogs share the same set of roughly 20,000 genes. What makes one dog different from another—or, in the case of purebreds, almost the same— is how the genes are expressed and restricted from being expressed, and how they communicate with one another. Therefore, it may be safe to say that each of the world’s 800 to 900 million dogs is a distinct combination of different versions of the same genes. Or maybe not. At least, that’s what some scientists suspect, and they think they’ll find answers in the DNA of the ubiquitous, free-ranging canine outcasts that populate developing countries throughout the world.

While village dogs were being socially shunned, modern dogs—a subpopulation that likely split off from village dogs thousands of years ago—were serving society. So tightly woven into the fabric of our lives that we rarely think of them as human-engineered, dogs have been refined for increasingly specialized tasks such as hunting, transportation, protection, warfare, ornament and companionship. As a result of rigorous artificial selection over a long period of time, many of their ancestral gene variants are suppressed. Some have disappeared altogether, creating a fragile homozygous genome that has little diversity.

In contrast, village dogs are barely tolerated by society. Although considered a domestic species, they are the products of thousands of years of natural selection. Consequently, their heterozygous genomes are robust and extremely diverse. In addition, it’s possible that long after modern dogs branched off from the family tree, some village dog populations may have developed new gene variants that protect their immune systems.

Evolutionary biologist Adam Boyko, assistant professor in the Department of Biomedical Sciences at the Cornell University College of Veterinary Medicine, is confident that comparing and contrasting the two branches of the domestic canine family tree will provide answers to some of the mysteries that continue to surround the evolution of the domestic dog: When and where were dogs domesticated? What were the global migration paths of humans and dogs? What genetic changes occurred when wolves became dogs? Which genes are responsible for extreme size, shape and behavior differences? What are the underlying causes of genetic diseases? And how do parasites have an impact on canine well-being?

As a postdoctoral student at Cornell, Boyko worked under the tutelage of Carlos Bustamante, now professor of genetics at the Stanford School of Medicine. Curious about how the underappreciated and even less-studied village dog genome might reframe our current understanding of canine evolution and domestication, Boyko and Bustamante persuaded Ryan and Cori Boyko (Boyko’s brother and sister-in-law, who were then both graduate students in anthropology at the University of California, Davis) to add a few side trips to their otherwise romantic African honeymoon. Their instructions were to catch semi-feral, uncooperative village dogs and draw blood samples, then ship the samples back to the lab for analysis. Information from the preliminary DNA samples indicate that the researchers are on the right track. I asked Dr. Boyko about his research, and if it has future application to invigorating the health of our companion dogs.

Jane Brackman: How will mapping the genome of the village dog help us understand the mechanisms of traits in modern dog breeds?

Adam Boyko: Geneticists have spent a lot of time looking at purebred dogs. When something is selected for, either by natural or artificial selection in a population, geneticists can tell because of the patterns that are left in the genomes of individuals in those populations. In humans, for example, we can clearly see that lactase persistence, the ability to digest milk into adulthood, was selected for in some populations.

When we look for these patterns in purebred dogs, we find that things like ear f loppiness and tail curliness are driving these patterns, or short legs or small/big size. Basically, we find the effects of artificial selection by humans for breed standards. If we did a similar scan for selection in village dogs, perhaps some of those same genes would show patterns of selection, but I think we’d also see a new class of genes showing patterns due to natural selection.

For example, maybe there was a lot of selection in early dogs for genes in certain metabolic pathways because there was such an extreme dietary shift from wolves to dogs. Or maybe new parasites and pathogens caused selection at genes influencing the immune system. Or maybe we’ll see selection around genes that influence behavior and temperament.

Basically, there are all sorts of theories about how dogs became domesticated and what makes a dog a dog. When we look at purebred dogs, the main thing we are able to see is what makes certain dog breeds look and behave one way versus another. Maybe by looking at village dogs, which are much less influenced by the strong and recent artificial selection taking place in breed dogs, we’ll be able to see patterns of selection that occurred earlier in dog history.

JB: Might your findings have application for the future? For example, if you were to come across genes influencing the immune system, would breeders be able to use that information to revitalize the pedigreed-dog immune system?

AB: It is certainly true that my research may find a new MHC-type immunity gene [the major histocompatibility complex mediates the immune system’s white blood cells] that has been lost in many purebred dogs and which could reinvigorate their immune diversity. Or perhaps it will find variants associated with diet, and make us start considering a dog’s genetic makeup when making dietary recommendations. But I’m really not comfortable speculating, since I’m likely to be quite wrong in these predictions.

For example, I would have never guessed that deliberately infecting patients with intestinal parasites [Helminthic therapy] would cure ulcerative colitis, but that seems to be the case, and signatures of selection in the human genome help explain why.

But having said that, I think looking at the genomes of village dogs will be extremely useful. For example, we could get a better picture of the kinds of traits that were selected for in natural dog populations, including disease resistance, which might give us useful insights into diseases we diagnose in our pet dogs.

Conversely, as veterinarians and geneticists find more mutations that cause disease or unique traits in dogs, we can look at the genomes of diverse village dogs to see when and where these mutations arose, and whether they are also found in any other village or purebred dog populations.

It’s a really exciting time to be a canine geneticist, as we have all these new genetic tools at our disposal and many, many purebred and free-ranging populations that have yet to be characterized genetically.

JB: Some populations of village dogs, such as those you’re studying, have been isolated for many thousands of years, evolving under pressures that the stem parents of modern breeds were never exposed to. Is it possible that these dogs have “new” gene variants that don’t exist in the genome of modern breeds?

AB: It’s certainly possible, and it’s something I’m very interested in. For example, my lab is looking at free-ranging dogs in the highlands of Peru to see if they have any genetic adaptations for high altitude. Perhaps more importantly, some village-dog populations might harbor disease-resistant variants for parasites or pathogens that are prevalent in their area, but these variants might not have made it into modern purebred dogs, since those breeds were mostly founded elsewhere.

JB: How urgent is it that we learn more about these ancient dog genomes?

AB: We know how quickly pre-Columbian Native American breeds were lost when Europeans brought dogs with them to the New World, and we see that it will happen like that very soon in other remote parts of the world. So we’re working as fast as we can to get the data before the dogs are gone.

JB: What’s going on in your lab now?

AB: We’re collecting DNA samples and the genetic information we need so we can start piecing together what’s going on in these interesting but largely neglected free-ranging dog populations. We are seeking insights into dog population history to discover patterns of selection around certain genes that can then become the basis of further study. Our work is very hypothesis-driven. We have certain hypotheses about how dogs evolved, and we try to collect the right samples to test these hypotheses.

As geneticists learn more about how genetic variation controls complex traits in purebred dogs, we find it’s quite different than what we see in humans. Why? There are at least two competing hypotheses, and by gathering data from free-ranging dogs, we can start testing them to figure it out. Some of this gets into technical discussion about genetic architecture, recombination, epistasis and pleiotropy and such, so I’ve avoided getting too academic. But I also don’t want to be dismissive of it since those technical, hypothesis-driven aspects of the project are the bread and butter of my lab in terms of student training.

JB: In longitudinal studies such as the Morris Animal Foundation’s Golden Retriever Lifetime Study, researchers gather information from participants’ DNA and then match what they find to traits the test dogs may display over a lifetime. Will you have an opportunity to see how, for example, an immunesystem mutation affects a village dog’s health as it ages?

AB: Our project is a huge undertaking, and there’s a ton of data we’d love to gather on each dog but just simply aren’t able to since, at this point, we’re focused on sampling as many dogs from as many populations as possible to maximize the amount of diversity we can analyze. I really don’t want to overstate what we’re able to do in one visit to check out a dog and draw blood, which is limited to looking for genetic signatures in the genome of these dogs showing signs of selection and/or local adaptation.

But, since we have a fairly good idea of what genes do in modern dogs, at least in a rough sense, if we see a genetic signature in village dogs for positive selection around a gene we know is involved in immune function (for example), that’s a big discovery.

JB: At the risk of oversimplifying, say you’re looking at a region that you know to be linked to a negative trait and you see that the switch is turned off in the village dog DNA and turned on in modern dog DNA—would you feel that you’d found a “smoking gun”?

AB: It’s possible. Then, of course, as you allude, we would want to go back, look at dogs carrying that mutation versus other dogs, and see if there are different health outcomes. Perhaps [dogs with the mutation] are more resistant to intestinal parasites or perhaps they are more prone to autoimmune disease or something. Until we find the mutations, it’s a bit speculative to make predications about what exactly the findings will mean to owners. This is certainly “basic research” in the purest sense.

JB: In people, size is determined by hundreds of genes, each with a small effect. In purebred dogs, body size can be regulated by a single gene. Is this unique to dogs?

AB: It depends. There are other traits in other species controlled by a couple of loci [location of a gene on a chromosome]. I would argue that yes, it’s pretty unique. Whether or not dogs are special in that there is something about their genome that predisposes them to this type of diversity, or perhaps because humans worked so hard at creating them, we don’t know. This debate is still raging in the literature. It is definitely the case that genes have many, many effects. Rather than being a blueprint in which each gene is responsible for just one part of building the whole organism, the genome is more complicated, with each gene taking on different roles at different times or in different tissues.

JB: Do multiple-trait relationships also show up in village dogs?

AB: I think this would also occur in village dogs if the mutations were in those populations. The difference is that selective breeding has actively promoted these large-effect, diversifying mutations in dog breeds, making them relatively more common. Natural selection usually selects against such large-effect mutations in natural populations. You won’t see a short-legged wolf because it couldn’t hunt.

In fact, most of these large-effect mutations probably first arose in village dogs. The difference is that these mutations aren’t usually beneficial to village dogs, but the ones that aren’t too detrimental might persist at low frequency long enough for humans to start trying to promote breeding of that trait. Take achondrodysplasia [a type of dwarfism]. It almost certainly arose in village dogs, but to a free-ranging dog, super-short legs and all that comes with them probably aren’t much of a selective advantage. But once folks started looking for dogs to turn their spits, they found these super-short dogs to be useful, and eventually that genetic variant made its way into a whole host of modern breeds.

For the specific achondrodysplasia mutation, I don’t know if that is the exact story, but I do think this is likely to be the case for many large-effect mutations. Depending on how early in dog evolutionary history the mutation arose, it could be found in most regional village dog populations, or it could be restricted to certain populations that are close to where it first arose. Lots of research still left to be done!

JB: As a lifelong dog lover, you must find it difficult to see the deplorable conditions in which some of these dogs live.

AB: There’s so much disease in these high-density populations. As these communities become more urbanized, dogs are living like rats and pigeons. Getting DNA on these populations is not enough of a reason to allow the animals to exist like this. Life on an urban street is rough existence.

JB: If you adopt a village-dog puppy and raise it in a typical Western environment, what kind of dog will you have?

AB: Adopting the dogs is not part of our project, but we know people who have done this. They can be great dogs. They don’t have some of the aggression issues you might see in some of our dogs, because they are culled for aggression, or for eating a chicken. There are some things that aren’t tolerated. So you might say that people in the villages impose a form of selection. The dogs are smart and resourceful. They seem to adapt.

News: Guest Posts
Behavioral Differences Between Dogs and Wolves

Dogs and wolves share a similar genetic profile. So why are their behaviors so different?

The reasons aren’t clearly understood. In a recent paper in the journal Ethology , evolutionary biologist Kathryn Lord's doctoral research (University of Massachusetts, Amherst) suggests differences in later behaviors might be related to the pups' earliest sensory experiences during the critical period of socialization, the brief period when a puppy's exposure to novel things results in long-term familiarity.

Lord's research demonstrated that dog and wolf pups acquire their senses at the same time:

·     Hearing:  Onset 19 days, reliable by 28 days

·     Seeing: Onset 26 days, reliable by 42 days

·     Smelling: Reliable by 14 days (onset likely earlier)

What's different?

·     Dog pups wait until 28 days to explore their environment when all senses are operational.

·     Wolf pups begin exploring the world at 14 days, relying solely on scent, when they are still blind and deaf.

Although wolves are tolerant of humans and things they were introduced to during the critical period, they don't generalize that familiarity to other people or novel things when they mature. Dogs on the other hand, can generalize, and if properly socialized are not spooked by novel sounds and sights.

Why do mature dogs and wolves behave so differently?  Lord's conclusion is that at the gene level, the difference may be when the gene is switched on, not the gene itself.

What could that mean? Research has shown that the brain is capable or rewiring itself in dramatic ways. Early loss of a sense affects brain development. For instance, even though the developing auditory cortex of a profoundly deaf infant is not exposed to sound stimuli, it doesn't atrophy due to lack of use. Rather it adapts and takes on processing tasks of other senses including sight and touch. Perhaps wolves see the world in smell, and dogs see it a lot more like we do.

Click here to read the paper, A Comparison of the Sensory Development of Wolves (Canis lupus lupus) and Dogs (Canis lupus familiaris), by Kathryn Lord, Ethology, February, 2013.



News: Guest Posts
Latest Genetic Research about Dogs' Diet

“Where goeth the food, so goeth the dog.”  (old proverb)

The earliest archeological evidence dates dogs to about 14,000 years ago. Remains of small dogs in Israel go back 12,000 years. When people settled down in agricultural communities, they began to tinker with the natural environment, bringing about modification, intentionally or accidentally, in plants and animals. Of course dogs joined the party. They always do.

Not everyone agrees about why, where, when or how dogs evolved. But we all believe this:  Whether dog domestication was accidental or intentional, abrupt of slow, happened 10,000 years ago or 80,000, domestic dogs descended from wolves and evolved with people. Perhaps it’s no coincidence then that we ask the same questions about dogs that we do of ourselves: How are we unique? Where do we come from? And when did we get here?  

On Wednesday, January 23, canine geneticists announced they have identified key mutations in three genetic regions that allowed the wolf, a traditional carnivore to thrive on a carbohydrate diet. This adaptation was surely useful for opportunistic animals that were scavenging waste near ancient farming communities.

How they did it

Geneticists Erik Axelsson and his team at Sweden’s Uppsala University looked at DNA from gray wolves and domestic dogs, searching for small differences that might have shown up early in evolution as wolves transitioned to dogs. They zeroed in on specific mutations that dogs have and wolves don’t. In all, researchers found 36 genomic regions that reveal differences. Nineteen of those have to do with brain function, eight are related to the nervous system, and the rest are linked to starch digestion and fat metabolism, three of which carry instructions for making a protein that’s necessary for the digestion of starch. One is an enzyme that turns starch into sugar maltose. Another is an enzyme that turns maltose into glucose.  And the third makes a protein that moves glucose from the gut into the bloodstream.  

What does it mean?

If you think it answers the question as to why, where, and when dogs were domesticated, you’d be misinformed. It’s really more interesting than that.

1. Dogs eat more starch than wolves. The mutation explains why. Keep in mind that just because you have a mutation that lets you digest grain, it doesn’t mean, when given the opportunity, you wouldn’t rather have pork chops than cheerios. Just ask my dog, or my spouse for that matter. Wolves, dogs or proto-dogs (depending on your position) could have had the mutation long before humans planted grains. The study doesn’t suggest a time line.

2. Because all the breeds in the study have the mutation, the mutation occurred before these breeds radiated out from their direct ancestor. However, don’t assume that our modern breeds are representative of any dogs older than 500 years. There is a ginormous gap, at least 8 thousand years, between the ancient agrarian gang of dumpster diver dogs and the not-so-old proto dog that begat our modern breeds. Scientists don’t know if the missing link dog is extinct, and if she isn’t, they don’t know what living dogs would represent her. There’s plenty more work to be done.

3. The birth of agriculture impacted canids. But it did the same to humans, birds, insects, pigs, cows, and goats to name a few.

4. The study is a vindication for all the veterinarians who are treating dogs with kidney ailments as a consequence of the strange trend toward very expensive low-carb, raw meat diets. There’s a reason dog food is only 20- 30 % protein and 40 to 50% carbohydrates.  

What others are saying

“Dogs are not just ‘tame wolves’ but have clearly adapted in a host of different ways to a very novel niche over a relatively short evolutionary timescale," said Adam Boyko, an expert on canine genetics and assistant professor of biomedical science at the Cornell University College of Veterinary Medicine and director of the Village Dog Diversity Project. “I think a lot of focus on dog domestication in the past centered on behavior and tameness. Clearly, they were important for domestication, but this paper also demonstrates genetic changes involved in diet adaptation.”

“The bigger question about the paper, said behavioral ecologist Ray Coppinger, is whether it sheds any light on the evolution of the dog -- whether they were domesticated "purposefully" by humans, or were they a result of humans creating a new niche which several species (including some Canis species) moved in and adapted to.” He added, “The researchers have done a great job showing that dogs and wolves genetically differ in their potential ability to digest starch. But it’s a fallacy to assume that the genes of the modern dogs included in the study are descended from original dogs. Thus the paper, sheds little light on the original dog, and does nothing to answer the question of artificial verses natural selection as the prime cause.”

What’s important about the study is not that it indicates when or where dogs originated. Rather, it’s a new tool that will help us understand how dogs and wolves are different. The research is groundbreaking, but it represents analysis of only 10 of the 36 genomic regions that the team identified. That means more exciting news is just around the corner.

Scholarly study takes on issues that are controversial. The dog origin debate continues to be particularly provocative.  As for me, I just want to know who to thank.


Mark Derr, author of When the Dog Became the Dog has a very interesting post on this subject as well.

The genomic signature of dog domestication reveals adaptation to a starch-rich diet, Journal Nature, published on-line, January 23, 2013.







Good Dog: Studies & Research
Do DNA Tests Reveal Genetic Secrets?
The Beauty of Diversity

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
Each lab analyzes DNA the same way. Upon arrival, samples are logged, tracked and monitored. DNA is extracted from the cheek swab and isolated, and copies are made to ensure a sufficient amount for processing. The genetic material is then chemically enhanced and run through equipment that looks for markers in the dog’s DNA that match breed markers in the database.

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.

Chance’s Results
In total, I tested Chance’s DNA three times. I used the Canine Heritage test twice, in 2008 and 2012, to find out if the expanded breed library would affect the results. (It did.) I also used Mars Veterinary’s Wisdom Panel**. Although results differed, cumulatively the tests indicate that Chance is a mix derived primarily from spitz dogs and large terriers, with a tablespoon of sight hound, teaspoon of herding dog, pinch of guard dog and smidgen of bird dog.

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
Cumulatively, the three tests indicate that Chance is related to 16 different breeds within all AKC breed groups except scent hounds. So the question shouldn’t be, “What kind of dog is that?” A more appropriate query is, “What kind of dog isn’t that?”

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
The closer a village dog population is to the original canine domestication event, the closer it will be to the gray wolf and the more genetic diversity it will have. Will Dr. Boyko’s village dogs turn out to be close relatives of the first dogs? Not likely.

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
Where to now? Some researchers think it’s time to go back to the road not taken. In a paper published in June 2012, Greger Larson, an evolutionary biologist in Durham University’s Department of Archaeology and the paper’s lead author, said that by putting genetic discoveries in the context of archaeology, history and biogeography, the study of the geographical distribution of species might help make better sense of what we already know.3

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.

Culture: Reviews
Rabid: A Cultural History of the World’s Most Diabolical Virus
Book Review
Rabid: A Cultural History of the World's Most Diabolical Virus

Rabies is a relentless killing machine that exploits the very thing we love most about dogs, their sociability with humans. The virus kills 55 thousand people a year; unless bite victims are treated before the onset of symptoms, the pathogen’s mortality rate is nearly 100 percent. According to the World Health Organization, dogs continue to be the source of human death in 99 percent of the cases.

Bill Wasik, senior editor at Wired, and veterinarian Monica Murphy take us into the 4,000-year-old battle against the virus, and humankind’s efforts to cure, treat and prevent it. In addition to reviewing the history of the disease and the legends and myths that surround it, the authors examine an array of folk medicines and dubious cures, from throwing the unsuspecting bite victim into a tank of cold water to making a poultice of the biting dog’s brain.

A word of caution for dog-lovers: the book isn’t for the faint of heart. Suffice it to say that dogs’ lives have not been easy, and they weren’t really our best friends until 1884, when Pasteur and Roux developed the rabies vaccine.

The book includes a case study of how the virus can infect a rabies-free island and kill hundreds of people in only a few years. On Bali in 2009–2010, a botched effort to contain the disease resulted in the brutal butchery of 100,000 dogs. However, one problem with exterminating dogs, infected or otherwise, is that it creates an empty ecological niche and others move into the vacuum, creating even more of a problem. CDC scientists finally convinced authorities to use a trap, test, vaccinate and release program to immunize 70 percent of the canine population, which, statistically, was the reverse “tipping point” required to control the disease.

The book is a terrifyingly entertaining tale of disease, dogs, madness, vampires, werewolves, immunology and hope.

Culture: Science & History
Can DNA Decipher the Mix?
Unraveling the genetic tapestry provides clues to breeds and their mixes

A mongrel dog is like a box of chocolates: You never know what you’re going to get. And therein lies the appeal. What’s more fun than serendipitous unpredictability all bundled up in puppy fur? But when that puppy grows up, we inevitably make assumptions about her ancestry based on how she looks and behaves. Our logic goes like this: “If my pooch is long and low to the ground, and she never barks, she must be a Corgi/Basenji mix.”

But it’s much more complicated. The genes—and there may be hundreds—that work together to make a Corgi look like a short-legged Shepherd may be completely different than those responsible for a Basset Hound’s low-slung carriage. With some exceptions, scientists cannot yet connect genetic dots to specific traits. But they have discovered something tangible that measures some of the differences between breeds: genetic patterns of organization displayed on a scatter graph that answer the question, “What’s the same and what’s different?”

A scatter graph provides a symbolic visualization of DNA, wherein each individual dog contributes one point. The resulting pattern indicates the type and strength of the relationship between individuals. The more the points cluster around each other, the more alike they are.


Until only a few years ago, scientists couldn’t identify the differences in genetic material that might explain profound variations in the Canidae clan. From wolf to West Highland White Terrier—they all looked the same under the microscope. Then, in 2004, Elaine Ostrander and her colleagues at the Washington-based Fred Hutchinson Cancer Research Center published data indicating that as much as 30 percent of the dog’s genetic material accounts for breed variation (Science, May 2004).

In addition to simplifying methods used to find markers for breed-related disease, the researchers identified patterns of “breedness” and tracked the history of breed DNA. At the same time, by following mitochondrial DNA, genetic material passed down from mother to offspring without changing, they traced the breed’s journey.

Depending on how much time is attributed to a generation and how many generations are involved, scientists can estimate how much time has passed. Based on this tracking, it has been suggested that it took 5,000 years to develop and refine a handful of the world’s 350-plus breeds, and about 400 years to create the rest.

Research indicates that four distinct breed groups are ancient: (1) Middle Eastern Saluki and Afghan, (2) Tibetan Terrier and Lhasa Apso, (3) Chinese Chow Chow, Pekingese, Shar-Pei and Shih Tzu; Japanese Akita and Shiba Inu, (4) Arctic Alaskan Malamute, Siberian Husky and Samoyed. Although the 13 breeds look different, they are so closely related that they are represented by a single genetic cluster. It’s likely they all originated from the same stem-parent—proto-breed, if you will—who roamed the Asian continent.

As humans migrated from one place to another, this ubiquitous proto-breed trotted along, bringing with her the ingredients needed to cook up all the breeds we’re familiar with today. Her offspring performed work unique to each geographical region, such as hunting, hauling or guarding. Isolated and mating only with each other, “accidental” breed types exhibiting consistent shape, color and behavior emerged.

No matter what historians might claim—scent hound to sight hound, bird dog to bad dog—evidence produced through genetic research indicates that all remaining breeds have been concocted in the last 400 years. Although closely related to one another, they can be identified as distinct based on the way their DNA separates.

How They Do It
Sue DeNise, vice president of genomic research at MMI Genomics Inc., which developed the Canine Heritage Breed Test specifically for mixed-breed analysis, talked to us about how her company analyzes canine DNA. “We’ve been doing testing for AKC parentage verification for a long time,” she notes. “We initially started working in the cattle business, looking for genetic markers in order to trace what was important to cattle breeders. Out of that whole-genome association study, we had purebred and crossbred cattle, so we asked, ‘What can the markers tell us about underlying traits in breeds of cattle?’” Their discovery paved the way for the companion animal program, which was modeled on what they learned with cattle.

“We look at ’breedness‘ among dogs. Our canine database is built with 10,000 samples of 108 breeds. We ran 400 markers to identify the best markers for a ’breedness‘ test against 38 breeds. We created a panel of 96 pieces of DNA that split dogs into their identified pure breed. In our preliminary test, we found that individual purebred dogs cluster with other purebreds.” Initially, MMI chose 38 AKC registered breeds from their database, selected for their popularity based on number of registrations. Recently, as DeNise notes, they increased the number to 108 breeds. This jump in breed recognition required testing thousands of markers to identify the just over 300 markers that characterize these 108 breeds.

Constructing Breeds
Like all species, domestic dogs are on an evolutionary journey, starting at wolf and going somewhere yet to be determined. We tinker with evolution, but might be surprised to find out we don’t control it. Our concept of a breed—that individuals within the breed look alike—is nothing more than a snapshot of the DNA time line, taken while we’re doing the tinkering.

Breeds are created a number of ways. In simple terms, when breeders interfere with natural reproduction and rigorously select for traits favored by humans, specialized breeds like Retrievers, Spaniels, Hounds and Terriers are the result. Saving spontaneous mutations in a litter of dogs, repeating the breeding to get more of the same mutation, and breeding those dogs back to one another has resulted in the English Bulldog, Chinese Crested and Inca Hairless. More recent breeds, such as the Airedale, Australian Cattle Dog and Doberman, are the result of crossing older breeds to make new ones.

When kennel clubs closed gene pools in the late 19th century to suspend change in registered dogs, breeds drifted toward a more uniform stereotype. Until the early 1800s, an assortment of dogs with similar talents who could produce somewhat similar offspring were awarded the right be called a breed. Breeds evolved, flourished and disappeared when jobs were eliminated. Tumblers, who mesmerized prey by “winding their bodies about circularly, and then fiercely and violently venturing on the beast,” disappeared when guns came into widespread use. Turnspit dogs, who made a living running on a wheel to turn meat so it would cook evenly, received their pink slips when technology improved cooking methods.

By and large, Victorian society was not so pragmatic; sentimentality and commercial opportunity were catalysts for saving unemployed breeds from their inevitable demise. As a result, many Terrier breeds went from killing varmints in the barnyard to killing time in the Victorian parlor in less than a decade.

Whereas previously, a breed was a regional product maintained and preserved by a small community of knowledgeable people, commercial interest in the well-bred pet dog initiated a shift in breeding practices during the Victorian era. The old-money kennels operated as a pastime by the wealthy gave way to a large number of small, commercially operated kennels run by entrepreneurs of modest means and experience.

Germane to this tale is that, according to the unwritten rules governing canine physiology, anatomy and behavior go hand in hand. One cannot be changed without affecting the other. Victorian enthusiasts who were busily adding aesthetic traits to utilitarian breeds were creating not only subtle variations in type, but in many cases, modifications in behavior as well. As utilitarian breeds went from working hard to hardly working, many exhibited new physical and behavioral characteristics that were compatible with their augmented duties as companion animals. Breeders claimed the “sub-breeds” as their own, made up new names and registered each one.

However, no matter how they’re sliced and diced, reducing and suppressing genes so they aren’t expressed doesn’t mean they’ve been eliminated. They’re still lurking and, depending on the method used to analyze the DNA, the lurkers often show up in the results.

Deconstructing Breeds
The problematic aspect of analyzing mongrel DNA is that breeds were not all created at the same time. As DeNise explains, “As new breeds are developed, they may not appear as uniform as older breeds. When older breeds are crossed to create a new breed, there is some period of time before the new breed develops a unique DNA pattern of its own. In these cases, the more ancient breed sometimes appears in the new breed. The number of generations required to have a uniquely identified breed created from crossing of older breeds depends on the number of breeding animals in the new line, the severity with which the breed owners apply the standard, and the amount of introgressing [inbreeding, or breeding immediate relatives; line breeding, breeding close relatives; and backcrossing, breeding sibling to parent] allowed by the registration agency.”

Most people assume all mixed-breed dogs had a purebred ancestor at some time in their recent heritage. But in fact, this is not necessarily the case. When you run a mongrel’s DNA through a computer program, the algorithms attempt to group breeds together on a scatter chart. If the heritage of the dog is such that it is not in MMI’s database of 108 breeds, the program tries to find varieties that are most alike. Because at least one or two of the handful of ancient breeds are in every modern dog, sometimes the program will identify an ancient breed in the mix. “In the report we send to the client, we use the terms ‘primary,’ meaning the majority of the DNA matches a breed; ‘secondary,’ meaning less than the majority of the DNA but a strong influence nonetheless; and ‘in the mix,’ meaning the least amount of influence,” DeNise notes. That’s how you might get an obscure breed in the report. For instance, a 35-pound mongrel with a tablespoon of Husky and a teaspoon of Border Collie may also have a dash of Borzoi, because before gene pools were closed a century ago, Huskies were crossed with coursing hounds to add speed.

Don’t Judge a Pup by Her Cover
As MMI Genomics states on their certificates, “Your dog’s visual appearance may vary from the listed breed(s) due to the inherent randomness of phenotypic expression in every individual.” What this means is that you may look nothing like your parents, but you have Grandma’s great legs and Great Uncle Harry’s turned-up nose. All in all, though, no matter how genes are mixed and matched, your family members resemble one another. However, if Grandma was an Afghan Hound and Great Uncle Harry was a Pug, “random phenotypic expression” can be pretty extreme.

Researchers are intrigued by data that suggest expressed traits are somehow turned “on” and “off” by other genetic components, thus causing the wide variations in canine form and behavior. For instance, it’s possible that many breeds have the genetic potential for a black tongue, but only a few breeds have the molecular mechanism to switch that color on. So that black-tongued mutt may not have any Chow in the mix after all.

On the other hand, the results may show that a quintessential Heinz 57 has the genetic makeup of a single breed and it could be one she looks nothing like.

DeNise explains it this way: “In a population of any breed, there are dogs that are carriers but don’t exhibit phenotype [observable characteristics]. If you reduce the size of breeding population—creating what we call a bottleneck—you start increasing the frequency of deleterious traits, like dwarfism or white coat. If we looked at the DNA of, for instance, a group of white mini-German Shepherds, they would probably cluster with German Shepherds. After they’ve intermated for five to six generations, we may not come up with that. They would cluster with each other. If breeders were changing allele frequencies quickly, you could do it very fast.

“There are always contradictions that make you say, ‘Huh, that’s really weird.’ One odd thing that happens is due to some sort of random assortment of genes in mixed-breed dogs. The algorithm may identify a breed that is not consistent with the physical appearance of the dog. We sometimes get an indication of this when the certificate is printed with the picture of the dog provided by the owner, and the certificate is reviewed by our customer service department prior to mailing it to the pet owner.”

A 90-pound, wiry-haired mongrel who swims, chases balls and makes goo-goo eyes like a Golden Retriever and whose only pedigreed relative is a very distant Chihuahua confounds the process, but says a whole lot about the complexity of canine genetics and why some scientists devote their careers to studying canine evolution. Extreme variation in anatomy and behavior is unique to the domestic dog. If humans were an equally anomalous species, we’d weigh between 20 and 650 pounds and range in height from three to 10 feet. In dogs, adaptations change with such speed that scientists suspect there may be a clue in the canine genome that could reveal how evolution works.

Sorting It Out
Before they launched the project, MMI tested DNA from a street dog rescued from a Thai village. You’d think there would be no clusters of any kind, but the computer identified Chow and Akita in the mix. This isn’t surprising, because the free-living common village cur who populates most of the developing world may be the closest living relative to the original proto-breed. Findings suggest that Thai pooch stores a sizable chunk of the original genetic blueprint of every single living dog in her DNA. The question is, how much?

MMI can’t as yet define the percentage of “breedness” in mixed-breed dogs. One reason is that some breeds cluster loose and others tight. Why this happens isn’t clearly understood. German Shepherds, Standard Poodles and Collies cluster tight. Miniature Poodles cluster tight, but Toy Poodles cluster loose. Within their breeds, Labrador Retrievers and Beagles often cluster as two different groups. According to DeNise, “Labs from the United Kennel Club that are bred specifically for hunting and AKC Labs do not necessarily cluster as one breed. And AKC Beagles and Beagles bred specifically for research don’t cluster together either.”

She adds, “In my opinion, it’s possible that a population that increases rapidly doesn’t cluster as well as those populations that have remained static. This is because, as you increase a population to accommodate breed popularity, people breed everything, including animals that may not exhibit all the physical characteristics that are desirable.”

And even when dogs look alike, they can display behavioral differences. As DeNise notes, “We understand so little about how behaviors are coded. Many behaviors are learned, but there are probably multiple genes that are responsible for herding, birding, heeling—these kind of hard-wired behaviors.”

Scientists are eager to tease out genetic connections to breed-associated motor patterns. When wolves hunt, they display these behaviors sequentially: orient > eye > stalk > chase > grab-bite > kill-bite > eat. Artificial selection, however, extracts and segregates these patterns in incomplete sequences. In certain breeds, individuals perform the abbreviated motor pattern repeatedly. A Pointer who stops dead in her tracks and stands stock still with her front leg held rigid in mid-stride to indicate the presence and position of game is the lofty goal of bird-dog breeders. To wolves, it’s just a good meal interrupted.

Combinations of canine anatomy and behavior push and pull one another along in a rhythm of interconnected patterns in relationships that may not be as random as they appear. Like principal components of an automobile in which the size of the engine and the weight of the body directly affect efficiency, it appears that dogs, too, have integral parts wherein one component is proportionate to the other.

Researchers don’t fully understand the relationship, but they are making headway. As reported in Genetics (June 2008), a team of scientists identified a few single genes that regulate systems controlling skull shape, weight, fur length, age span and behavior. Because mutts are combinations of DNA from different breeds, they may hold the answer to how the genes influence multiple traits.

Scientists suspect that many evolutionary secrets are hidden in the dog genome. For dog lovers, deconstructing Molly or Max’s mixed-breed heritage is an interesting intellectual mystery to be discussed at cocktail parties or the dog park. For scientists, their genetic material is nothing less than an instruction manual for species building. Whereas populations evolve over the course of millennia through the process of natural selection, dogs can change so rapidly and abruptly that they represent evolution at hyperspeed. How it happens remains a puzzle. Now scientists are looking to mutts to find the missing piece.



News: Guest Posts
Downton Abbey Dog: Right Breed, Wrong Color
And more flubs in period films

In period movies, dog breeds, just like fabric on the furniture, should be accurate to the period. Only a few contemporary breeds look exactly as they did 100 years ago.

Downton Abbey, the early 20th century story of the aristocratic Crawley family and their servants, with its authentic Yorkshire country house and period decor, is accurate down to thread in the costumes. But oops. No one thought to research what Lord Crawley’s loyal dog would actually have looked like. And Pharaoh (played by Roly) would not be a light cream–colored yellow Labrador Retriever.

Ben of Hyde (above), born in 1899, was the first recognized light-colored Lab—not really yellow but rather a dark butterscotch color. Prior to Ben, Labs were black, usually with white markings. The light cream–colored coat we see in every opening episode as Pharaoh trots along side his master, is a much later 20th century look.

When it comes to dogs in period films, historical inaccuracy is a pet peeve of mine. Here are some winners and losers:

The Last of the Mohicans (1992)—Set in 1757, takes place in the Hudson River Valley, includes two American Black and Tan Coonhounds pretending to be Blue Gascony Hounds.

Mrs. Brown (1997)—The story of widowed Queen Victoria, her servant, Scottish Highlander John Brown, and their extraordinary friendship that apparently left no time for any of her 88 dogs. Nary a single dog appears on screen. We don’t even hear a proxy dog barking off screen.

Howard’s End (1992)—A typical Merchant Ivory production, historically accurate from turn of the century wardrobe to wallpaper, is a tale of social class, theosophy and two poorly placed four-month-old yellow Labrador Retrievers.

Apocalypto (2006)—The story of the demise of the ancient Central American civilization features two hungry Xolo dogs that check out a smoldering campfire for leftovers. Accurate depiction, but seconds of screen time is hardly enough.

Sense and Sensibility (1995)—At a time when Spaniels were a soupy mix of similar shapes and sizes, the movie depicts Spaniels just that way.

Spaniels were a generic sort of working bird dog until the end of the 19th century.

Amazing Grace (2002)—The story of religious social reformer and abolitionist William Wilburforce. The 18 historically accurate Regency period dogs include in order of appearance: Papillion, Border Terrier, Collie, little black dog, little Terrier dog, another Collie, yellow Lurcher, grey Lurcher, little white dog, Irish Red and White Setter, and another field dog that looks suspiciously like a contemporary Springer Spaniel groomed with an electric trimmer. I didn’t say the movie was perfect.

This is what Reverend Wilburforce’s Collie would have looked like.

To read my entire diatribe about historically inaccurate dogs in period films, click here.

News: Guest Posts
A Cautionary Tale About Breed Standards
Jane Brackman, PhD

In the beginning was the word and the word was dog and the people made more dogs and used more words to differentiate those dogs until they had more than 400 different kind of dogs and more than enough words to explain the differences.  —Doctor Barkman

Breed standards are one of the tools breeders use to suspend change in purebred dogs. But breeds evolve anyway, even when standards remain unchanged. How is that so?

Exaggerated traits come and go with fashion. If the standard says the skull should be “very short from the point of the nose” to the eye (Bulldog), or “egg-shaped” (Bull Terrier), fashion will dictate the length and shape of the head. A note of caution though—breeds are not mix-and-match combinations of thousands of small parts where you pick and choose what you want. They’re more like combinations of genes, pre-packaged in bundles and shuffled around. A whole lot of genetic stuff, good and bad, goes along for the ride when a breeder pulls out a trait.

This is what a Bulldog looked like in 1900...

...and today.

A Bull Terrier in 1900...

...and today.

If the standard says, "The ears are extremely long," in a hundred years the ears will be really, really long.

This is a Bassett Hound in 1900...

...and today

Some breed haven't changed much in a century.

This is the German Pointer in 1900...

...and today.

A standard is a handy tool for dog show judges who need to evaluate dogs in competition, but it doesn’t suspend change. It’s really just a lexical snapshot of a breed on its way to being something else. Breeds evolve. It’s the breeder’s job to make sure they evolve in a healthy way.

To learn more, read the entire article about how standards influence purebred dogs in unintended ways.

Good Dog: Studies & Research
Trait Relationships and Genetics in Dogs
Mapping the genetic relationships between physical traits in purebred dogs

Dogs come in countless shapes and sizes and exhibit more diversity than any other land mammal on earth, a fact that makes them especially appealing to geneticists. In the last decade, scientists working at more than 100 laboratories worldwide have made significant progress in painting a detailed picture of the complex relationships between physical traits, behavior and disease in purebred dogs, and the ways genes contribute to the striking differences seen across breeds.

Searching for related traits isn’t a new idea. Literature indicates that as far back as the fourth century BC, people were looking for something physical, like tail carriage or ear length, to predict something intangible — courage or sagacity, for example. The Greek philosopher Xenophon, describing the interests and values of sporting men, said that tan-colored dogs with black muzzles were esteemed as the best hunters. Early 16th-century New World explorers differentiated Indian dogs from wolves by the curve of their tails and their vocalizations. The 1785 edition of the Sportsman’s Dictionary advised serious huntsman: “Coal black dogs prove incomparable hounds.” On the other hand, the future was dubious at best for those dogs unlucky enough to be covered with spots: “Forego white hounds with black spots as they are never the best hare hunters.”

New genetic research indicates that yesteryear’s cynologists were on the right trail, but barking up the wrong trees. Dog breeds are not mix-andmatch combinations of thousands of small parts; rather, they are more like combinations of genes prepackaged in bundles and shuffled around.

So, yes: traits are linked to one another, but with caveats. As scientists and statisticians note, correlation is not causation — just because two phenomena are related, it doesn’t necessarily mean one causes the other. Sometimes, it’s merely coincidence. The rooster crows when the sun comes up, but contrary to what the big chicken thinks, he isn’t the reason it rises.

Molecular Conversations
Genetic interactions are less like a game of marbles, in which one gene strikes another and something happens, and more like a Rube Goldberg contraption: something seemingly simple is actually the result of a long list of intricate, complicated and extraneous events. Of the thousands of genes in the genome (dogs have about 19,000, compared to humans’ approximately 23,000), an inordinate number are involved in communicating with one another, sending information that either activates or represses a “dimmer switch” in other genes. Although numerous genes act alone, thousands play multiple roles during development, telling the cells of an embryo what kind of living creature it is to become.

This molecular maneuvering isn’t readily visible in most mammals. For instance, a human with a genetic variant that codes for extra height may grow to be 10 percent taller than the population average. But dogs are an entirely different story. The same type of genetic code in Canis lupus familiaris may result in a dog that’s 40 percent taller than the population norm.

Coded for Variety
Mapping a genome is like revealing the image on the front of the jigsaw-puzzle box. You know it’s a picture of a Boxer, but you don’t know how all the interlocking pieces fit together to make the picture. Some solutions may be fairly clear, but, for the most part, our understanding of the way genes function is still based on a lot of guesswork.

In simple terms, geneticists use mega-computers to compare and contrast DNA patterns, looking for discrepancies. Patterns with omissions, transpositions or substitutions provide more precise information to help scientists assign meaning to genomic variations. They then match the anomaly in the DNA to the trait of interest.

This is how researchers identified genetic deviations that account for breed differences. In 2004, Heidi Parker, Elaine Ostrander and their colleagues at the Washington-based Fred Hutchinson Cancer Research Center published data indicating that as much as 30 percent of the dog’s genetic material accounts for breed variation (Parker et al. 2004). Whether it codes for breed-specific size, shape, behavior or disease, or the 57 parts that make up the Heinz mutt, the metaphorical genetic needle hides out in one-third of the genomic haystack.

Foundation Traits
Depending on how much time is attributed to a generation and how many generations are involved, scientists can determine breed age. Although closely related to one another (some more closely than others), breeds can be identified as distinct based on the way their DNA segregates, or separates during gamete formation. Data suggest that the most ancient breeds are dogs that looked similar to modern-day Basenji, Saluki, Afghan Hound, Tibetan Terrier, Lhasa Apso, Chow Chow, Pekingese, Shar-Pei, Shih Tzu, Akita, Shiba Inu, Alaskan Malamute, Siberian Husky and Samoyed. All the others — from Affenpinscher to Slovakian Rough-haired Pointer to Yorkshire Terrier —were created in the last 400 years.

Scientists suspect that many foundation traits differentiating ancient dogs evolved only once. Perhaps they were embedded in the genome of the nowextinct wolf species that begat domestic dogs. For instance, achondroplasia (short-limbed dwarfism), a defining trait in 19 breeds, including Dachshunds, Corgis and Bassett Hounds, is the result of a single evolutionary event (Parker et al. 2009). This means that mongrel dogs with short limbs are not necessarily mixes of short-limbed breeds. Rather, it’s the other way around: short-limbed dogs were accompanying our ancestors long before Doxies and Corgis were engineered less than 400 years ago.

Brachycephalia (disproportionate shortening of the muzzle) is another foundation trait. A Boxer wouldn’t be mistaken for a Pug, nor a Bulldog for a Pekingese, but they all share brachycephalic head types. Archeological evidence from ancient gravesites indicates that brachycephalia existed long before the formation of modern breeds. And indeed, a single genetic variation causes this trait, no matter how different the breeds look (Bannasch et al. 2010).

The challenge comes in teasing out the handful of genes associated with these foundation characteristics when the breeds that share them are vastly different. To do so, researchers devised a method to map dog traits developed under extreme selection: find the marker in a single breed and it will provide a clue as to where it will be found in all dogs. Because size differences are magnified in certain breeds, looking for genes associated with size was a starting point. Information gleaned from archeological sites indicates that small stature in dogs appears to be an ancient trait.

Genetic Messengers
Diminutive breeds can be as small as six pounds, whereas some giants weigh in at just under 200 pounds, and height can vary from less than six inches to as much as three feet. Even so, all puppies are born almost the same size, with short muzzles for nursing and stout legs for pushing siblings out of the way at mealtime. Why does one turn into a calm 180-pound giant and the other into an excitable eight-pound lap dog?

Studying the genetic make-up of 526 dogs from 14 small breeds, including the Chihuahua, Toy Fox Terrier and Pomeranian, and nine giant breeds, including the Irish Wolfhound, Saint Bernard and Great Dane, scientists pinpointed a specific gene-sequence variant in the canine genetic code associated with small size (Sutter et al. 2007). They concluded that a single gene that encodes an insulin-like growth factor is common to all small breeds and is nearly absent from all giant breeds, implicating it as a major influence on small stature in dogs. But there are exceptions. Though at some stage of early growth, all little dogs get the genetic memo to stay small, some dogs, like Rottweilers, are born with the small-stature variation but grow large in spite of it, indicating that in certain cases, something overrides the message associated with small size.

This is not to say, however, that a single gene controls size. In genetics, big is not the opposite of small. In other words, a dog who doesn’t carry the small gene is not necessarily destined to be big. Researchers found several other gene variants that affect size to various degrees; large size is linked to three of them.

In science, every answer prompts new questions. Having found the genes associated with smallness, scientists were eager to find other traits that might be related to size. For example, little dogs live longer than big dogs. Or so it seems. Is there a genuine connection between size and longevity and, if so, where is the link in the DNA? Longevity has been documented only since the mid-1980s. However, because life span was never selected for by breeders, any link in the DNA between size and life span would be a result of random chance rather than artificial selection.

Researchers found no evidence indicating that the largest individuals within a breed die earlier than smaller ones (Jones et al. 2008; to date, studies have been done on only a few breeds. Anecdotal evidence indicates this may not be the case in other breeds). But when they mapped traits across certain breeds of extreme size difference, they found that the genetic subset that influences size also plays a role in longevity. As the authors wrote, “This peculiar inverse correlation between longevity and size … is strictly a between-breed phenomenon and provides an excellent example of a trait that can be approached with across-breed mapping … [A] subset of loci, which control body size, also contribute to longevity, with some playing a greater role in the aging process than others.”

Is temperament linked to longevity? A 1997 analysis of rates and causes of death in more than 222,000 insured Swedish dogs provided baseline mortality data on 250 breeds from birth through 10 years of age (Bonnett et al. 1997). Using the population-based study and then attributing temperament traits to breeds, researchers found evidence suggesting that a breed’s typical boldness is also related to longevity (Careau et al. 2010).

Extreme Selection
In 2003, researchers found evidence indicating that dogs engineered for the chase, with long thin legs for running, have narrow heads and long muzzles because the width of the leg bone and the length of the skull are controlled by the same group of genes (Chase et al. 2003). Recently, scientists in the same labs published additional findings (Jones et al. 2008): two aspects of size and shape of the muzzle are linked; tail length, ear erectness and size appear to be related; and ear and tail shapes are linked, as are head and neck size. In addition, they identified a candidate gene associated with the degree of tail curvature and short coat.

Geneticists suspect that many multiple- trait relationships were developed under extreme selection and are linked to a few single genes that regulate systems controlling most types of growth, some of which have been favored by breeders, and others — like longevity — the result of unintended consequences. Breed development is rapid because, as noted earlier, most selected traits are tied to a few big bundles of prepackaged traits; very few characteristics are offered a la carte. Unless breeds have truly unique features (like the Lundehund’s triple-jointed polydactyl toes), most breeds could be recreated by bringing together the right combination of genes from related breeds.

The Brain Game
Characterizing behavioral traits is an inexact science at best. Ask 10 experts to define fear-aggression and you’ll likely get 10 different descriptions. However, a few behaviors are magnified to the point of being easily characterized: the intense gaze and stalking movement certain herding breeds use to move livestock; the stylized position pointing dogs take to indicate the presence of game; the retrievers’ act of fetching game and returning it to the hunter. Strung together in sequence, these behaviors make up the bulk of the predatory response wolves employ to hunt and survive. But, in some amazing way, artificial selection extracts and segregates fragments of the sequence.

Scientists wondered: if a truncated motor pattern is exaggerated in a breed, will it be amplified in the DNA? The answer appears to be yes. Findings indicate that genes associated with herding, pointing and boldness are found in areas linked to brain development (Jones et al. 2008), and two gene variants tied to herding are in the same location as genes linked to schizophrenia in humans. This is not to say that Border Collies are borderline schizophrenics. But it does stand to reason that candidate genes associated with extreme behaviors include some that may be expected to play a role in regulating those behaviors. Genes tied to pointing are in the same area as cranial nerve development, and boldness is linked to genes that encode proteins affecting specific neural connections and signal transduction (the mechanism that converts a mechanical/chemical stimulus to a cell into a specific cellular response). Whereas small dogs are genetically predisposed to excitability, boldness has no relationship to size.

Health Linkages
In canine physiology, form, function and behavior are mixed up in ways we don’t fully understand, and it’s becoming increasingly apparent that health is part of the formula, too. For example, just as certain cancers tend to occur at higher rates within specific breeds, certain orthopedic diseases are linked to a dog’s size. Researchers found that the incidence of two specific polygenic orthopedic diseases (those affected by multiple genes) — hip dysplasia and patellar luxation — are allied with the same gene variant that’s associated with size (Chase et al. 2009). Additionally, scientists discovered that pancreatitis, which occurs more commonly in small dogs such as Cocker Spaniels, is also related to the size-gene variant. Selecting for growth rates may not be the cause of disease. Rather, it’s possible that size extremes upset the balance of genes that control disease.

Breeders and scientists are working hard to discover what and where the problems are and how to solve them. How much influence does any one trait have on another? Do early-onset health issues like allergies predict the debilitating illnesses dogs experience later in life, such as Addison’s disease, arthritis or even cancer? In a survey of blind guide-dog handlers conducted by the Morris Animal Foundation in 2008, we discovered that working Golden Retrievers have a less than 30 percent cancer rate, compared to a 62 percent cancer rate in the general breed population. Remarkable! Guide dog schools drop 75 percent of Goldens from their programs before the age of two due to any number of health issues, including chronic allergies. It’s possible that allergies are predictors of cancer, but that hypothesis hasn’t yet been studied.

Breeders want to know if they can remove deleterious genes that predispose dogs to fatal diseases and still hold on to desirable traits that create the essence of a breed. Getting rid of genes responsible for disease may dramatically change the way pedigreed dogs look and behave. Consider, for instance, the possibility that eliminating spinal degenerative disease will introduce inconsistency in tail carriage and gait, or that identifying markers for elbow dysplasia and removing carriers from the breeding population will affect the width of the chest, resulting in an appearance contrary to that described by breed standards, or how a breed is expected to move and even behave. If so, will we be willing to re-examine the definition of a breed as dogs who share characteristic appearance, function and a common gene pool, a Victorian-era mandate meant to suspend change in pedigreed dogs? What scientific findings in this decade will determine the breeding of dogs in the near future? Finding genetic traits and identifying their relationships to one another will assuredly be at the top of the list.

Culture: Reviews
Inside of a Dog: What Dogs See, Smell and Know
Scribner, 368 pp., 2009; $26
Inside of A Dog by Alexandra Horowitz

If we want to get inside of a dog’s mind, to know how it feels to be that dog, then we must first understand how he sees his subjective universe, or “umvelt.” This is the premise of Alexandra Horowitz’s nearly flawless book, Inside of a Dog: What Dogs See, Smell and Know.

Groucho Marx once quipped,“Outside of a dog, a book is man’s best friend. Inside of a dog, it’s too dark to read.” Horowitz turns on the light, climbs inside and shows us what goes on inside of a dog. She teases apart our anthropomorphic notion that dogs are like us. Then, basing her narrative on an exhaustive list of canine studies (she cites 185 references), she reconstructs the dog, piece by piece. For example, she writes, “To understand the dog umwelt, then, we must think of objects, people, emotions— even times of day—as having distinctive odors.” Horowitz adds that because dogs “see” smells, they must remember in smells as well. “When we imagine dogs’ dreaming and daydreaming, we should envisage dream images made of scents.” They are not chasing bunnies; they are chasing bunny odor.

Writing about science in a vernacular to which non-scientists can relate is tricky. Too erudite and you lose your regular folks. Too folksy and the science loses its application. Horowitz takes the middle road. Using her “dog-person” voice, she focuses on what the research means rather than the technical intricacies of its methodology. References are in the back of the book according to chapter and include empirical research, observational studies, books and personal conversations.

A psychologist with a PhD in cognitive science,Horowitz touches on smell, vocalization, vision, play, sense of self, cognition and the interaction between dogs and people. She’s organized the book based on a dog’s point of view. For instance, the chapter about olfaction is titled “Sniff” and includes sections such as You showed fear and Leaves and grass.

Horowitz enhances her already detailed description of canine knowing with poetic accounts of the relationship she has with her own dog, Pumpernickel. In the chapter about olfaction, she writes, “Since I’ve begun to appreciate Pump’s smelly world, I sometimes take her out just to sit and sniff.We have smell-walks, stopping at every landmark along our route in which she shows an interest.”

If you’re just looking for answers to some timeless canine questions, you’ll find them here, too. Why is a dog’s nose wet? To catch odor molecules. Why does a dog scratch the ground after he defecates? To spread the odor. Do dogs know what size they are? Yes. Do dogs laugh? Maybe. Do dogs “pack”with their human family? Not really—as she writes, “We and our dogs come closer to being a benign gang than a pack.”

If you think you know your dog, think again. Horowitz peels away the layers of pre-conceived notions and gets to the core of canine-ness to reveal that Canis familiaris is anything but familiar.