How molecular genetics will change dog breeding

The first complete sequence of the human genome was completed in 2003, taking 13 years and $3-billion. By 2007, the cost had dropped to about $10-million. Then, in 2007, the development of a revolutionary new technology (called “Next-Generation Sequencing, NGS) sent the cost plummeting. By 2009 the cost was down to $100,000, and there is every reason to expect that within the year, you can sequence your entire genetic code for $1000.  And it will continue to get even cheaper.

cost per genome

The line for Moore’s law on the graph reflects the cost of computer chips, which drops by half about every two years.  Note that the axes of the graph are a log scale, so the slope of Moore’s law is actually exponential. The cost of computing power is declining at an astonishing rate – and since 2007, the cost of gene sequencing has been going down even faster.

This has created a revolution in genetics. Things that were impossibly expensive only a few years ago are becoming affordable.  Nobody could spend $1-million to identify the defective gene causing a rare illness in a child, or even $100,000. But $5,000 is in the realm of possibility, and at $1,000 even an insurance carrier will cover it. Medicine is being transformed so fast that physicians can scarcely keep up with the new developments, and medical schools are rushing to add training in molecular genetics so doctors will be able to use all the new information. New medical journals are being created to publish the flood of studies suddenly coming from this new field (e.g., Molecular Genetics & Genomic Medicine, launched in fall 2012).

There is a similar revolution underway in the breeding of both animals and plants. For livestock breeders, it means they can now use genotype information to assess breeding stock, and they can determine the quality and characteristics of the offspring at birth – from a blood sample or cheek swab – instead of waiting until three years later at maturity. They can select for particular traits with much greater efficiency, because there is no guessing about what alleles the parents carry. (There’s a nice, basic review of how molecular genetics is transforming cattle breeding here.  ** You should read it, because this is coming soon to the world of breeding dogs!)

The first dog genome was sequenced in 2004, and in less than a decade the dog has supplanted the mouse as the model organism for the study of genetics. First, it turns out that humans are more similar to dogs genetically than they are to mice. And studying particular genes in mice required the breeding of special populations that were selected for particular genes, which took space, time, and money. In dogs, on the other hand, there are many genetic traits that are characteristc of individual breeds that can be studied with just a routine blood sample, taken from a family pet that goes home at the end of the day to sleep on the sofa. For scientists, there are no animals to house, no breedings to do or offspring to raise, very little trouble, and essentially no expense at all.

Together with modern molecular genetics, dogs are driving a revolution in our understanding of human genetics.  But along the way, we’re learning a lot about canine genetics that can be put to good use by dog breeders.   Identifying the gene behind a particular trait can now be done using cheek swabs from a few dozen animals in a few months or even weeks.  We can begin identifying the genes associated with non-Mendelian and polygenic traits.  This is information dog breeders can start using to take some of the guess-work out breeding, to make better predictions about the qualities in their next litter, and to breed healthier, happier dogs.

It’s an exciting time to be a dog breeder.  Things are possible now that you could only dream about even a few years ago.   Breeders need to start working as partners to the scientists, so that the science being done will be useful to the breeders and not just some data in a publication.  And scientists need to start partnering with the dog breeders, who know stuff about dogs that scientists will never learn any other way.

Dogs can help scientists, and the scientists can help dogs.  They should be best friends


Here are a few resources where you can learn more about the new developments in dog genetics –

Wayne, RK & EA Ostrander 2004 Out of the dog house: the emergence of the canine genome.  Heredity 92: 273-274

Ostrander, EA & RK Wayne  2005  The canine genome.  Genome Research 15: 1706-1716.

Parker, HG & EA Ostrander  2005 Canine genomics and genetics: running with the pack.  PLoS Genetics 1: e58

Neff, MW & J Rine  2006 A fetching model organism.  Cell 124: 229-231

Ostrander, EA 2007  Genetics and the shape of dogs.  American Scientist 

Spady, TC & EA Ostrander  2008 Canine behavioral genetics: pointing out the phenotypes and herding up the genes.  Am J of Human Genetics 82: 10-18.

Locating the genes for hip dysplasia in dogs (Psssst! Look in the kibble bag.)

There is probably no other non-lethal health problem except perhaps allergies that afflicts so many breeds of dogs as hip dysplasia.  It cripples dogs with pain, sometimes in the prime of their lives, and there is very little modern veterinary care can do about it.  It seems clear that it has some genetic component (it is thought to be polygenic) but there are clearly environmental (i.e., non-genetic) influences as well.  There has been some modest success in reducing its incidence in some breeds by screening programs, but for the most part it remains an intractable problem and the focus of many research programs.

Consequently, I was quite surprised to run across a paper (1) published way back in 2006 about a study that was able to substantially reduce in incidence and severity of hip dysplasia in Labradors – not by locating particular genes or implementing strategically-designed breeding programs – but by reducing food consumption.  (Download a copy here – pdf)   Conducted by Nestle Purina in collaboration with a slate of veterinarians and academics, the study used 48 Labrador Retriever puppies from 7 litters.  In each litter, puppies were paired and one assigned to the control group and one to the treatment group.  The control group was provided food ad libitum (unrestricted) starting at 8 weeks, and each puppy in the treatment group was fed 25% less than the amount consumed by its pair in the control group.  Their weight was monitored and hips x-rayed at regular intervals throughout the lifetimes of the dogs.

Dogs that were fed less had dramatically lower incidence of hip dysplasia.   How dramatic?  Have a look at these graphs (modified from Smith et al’s paper).

Dogs allowed to eat as much as they wanted showed evidence of hip dysplasia at younger ages than dogs fed less, and the difference between the groups got worse as they got older.  By 6 years of age, 50% of dogs in the unlimited food group had evidence of osteoarthritis, compared with only 10% of dogs in the restricted food group.  More than 50% of the dogs in the restricted food group still had radiographically normal hips at 12 years old; in the other group, 90% were arthritic.  Dogs fed 25% less food than their pair in the control group weighed about 25% less throughout their lives.  Heavier dogs had worse hips.

I was astonished to see these results.  By any scientific, medical, or veterinary standard, the effect of diet restriction on incidence of osteoarthritis in Labradors would be considered profound.  If somebody was to submit a grant proposal to test a treatment that promised to reduce the incidence of hip dysplasia in dogs – not by 10%, or even 25%, but 50% – I should hope it would receive very serious consideration for funding.  And what about the Canine Health Foundation and also the Orthopedic Foundation for Animals (OFA), which owes its founding to concern about the high incidence and crippling effects of hip dysplasia in dogs?  A browse of the information on their websites about the disease makes no mention of this study or the potential benefits of lifelong food limitation.  I showed this paper to a few breeders.  Most were surprised to see these data.  Some breeders, especially of large breeds, said they managed food intake of their puppies so they didn’t grow to fast, but they were worried about growth rate and not adult body weight.

“Less Food” – such a simple (and cost-effective!) way to substantially reduce the suffering of dogs, reduce veterinary bills for treatment, x-rays, and pain relief, and increase the amount of time the family dog can continue to lead an active life.  Millions of dollars are spent every year looking for sources and cures of disease in dogs so that we can offer them better lives.   Maybe we should direct some of this funding to an informational public service campaign to get this simple information to breeders and pet owners, and perhaps also some clear recommendations on dog food bags, maybe even brochures in veterinary offices.

I mentioned up top that there was also most certainly some genetic component to development of hip dysplasia, and that’s certainly worth talking about because there might be some surprises there as well.  Getting back to genetics, I’ll be addressing those in another post.

In the meantime, I’m taking a pound or two off my dog.

(1)  Smith, GK, ER Paster, MY Powers, DF Lawler, DN Biery, FS Shofer, PJ McKellvie & RD Kealy.  2006.  Lifelong diet restriction and radiographic evidence of osteoarthritis of the hip joint in dogs.



Carol Beuchat, PhD (USA) – Founder & Scientific Director, Canine Genetic Resources

Robert Lacy, PhD (USA) – Senior Scientific Adviser; Population Geneticist; Chicago Zoological Society

Grégoire Leroy, PhD (France) – Geneticist, AgroParisTech, Génétique et Diversité Animales

Heather Huson, PhD (USA) – Geneticist, USDA

Jennifer Mickelberg, PhD (USA) – Smithsonian Institute, Center for Conservation & Evolutionary Genetics

Katariina Maki, PhD (Finland) – Canine Geneticist, Finnish Kennel Club

Claudia Melis, PhD (Norway) – Canine Genetics, Norwegian Univ of Science & Technology

Pieter Oliehoek, PhD (Netherlands ) – Population & Conservation Geneticist

Terhi Mehtiö (Finland) – Conservation Geneticist

CA Sharp (USA) – President, Australian Shepherd Health & Genetics Institute

Laurie Bingaman-Lacky (USA) – Wildlife Biologist; Computer Systems/Data Management (ISIS)

Jeffrey Bragg (Canada) – Seppala Siberian Sleddog, Population Genetics of Dogs

Cara Bryan (UK ) – Population Biologist, AZA Population Management Center, Lincoln Park Zoo



Our goal is to create a central, permanent, and freely accessible database of the pedigree history of every purebred dog.  This is an international, cooperative effort that will bring together pedigree information that is presently scattered among kennel clubs around the world and consolidate it so that the entire history of a breed will be traceable from founders to present day dogs.



Purebred dogs are increasingly afflicted with genetic disorders that negatively affect health, lifespan, behavior, and the ability to lead a full, happy life.  The technology to explore the causes of disease at the molecular level is improving rapidly, and because the canine genome has become an excellent model in which to study the basis of many human diseases, the current interest in canine genetics will continue to increase.

Locating the genes that underlie genetic disorders in dogs can identify cause and function, but this doesn’t eliminate the deleterious consequences to health.  Breeders use test information to minimize the risk of producing affected offspring, but as the number of genetic disorders increase, the breeding options diminish.  As breeders select away from unwanted genes, the genetic diversity of the gene pool declines, which increases the probability that other deleterious genes will begin to be a problem.  In a way, the best efforts of breeders to minimize the health risks of the puppies they produce by testing and careful selection only continue to make matters worse over the long term.



The solution to this problem is to improve the genetic health of the dog.  In some cases, this can be done by locating isolated populations, perhaps in another kennel or even another country, that contain unique genes that can be reintroduced into the larger breeding population.  It might be accomplished by bringing dogs together from field and bench lines that have been genetically separated for perhaps generations.  In the most desperate situations, where extinction of a breed is possible, outcrossing to another breed can be the only option left to save a breed.

To make the best possible breeding choices, breeders need information about the genetic structure of their breed.  Producing this information requires a pedigree database that is as complete as possible back to founders, but for the majority of breeds this is not available.  The single most important tool needed by breeders to improve the genetic health of their dogs – a complete pedigree – is not available.



Obviously, this mission is enormous.  There are hundreds of dog breeds, many of which will have millions of dogs in their history.

To start this project, we have opted to begin with breeds that are relatively small, relatively recent (in terms of being a registered breed), and which have a good network of breeders who will be able to cooperate in the construction of the database.  Each breed has a volunteer coordinator who will serve as the contact person for that breed and will oversee the process.  The breeders themselves have a better chance than an outsider of negotiating with breed clubs and other breeders for access to records they might maintain.  Our hope is that Kennel clubs will recognize the value of this resource as it develops and be willing to cooperate.  In the interest of making progress quickly, we are taking a grass roots approach and breeders themselves are crowd-sourcing the information.

Where will we put the data?

Creating a database of this size and making it accessible to anyone in the world will require substantial computer resources, both hardware and software, and the personnel to manage it all.  Starting from scratch, setting this up would take months or even years.

Instead, we are working with ISIS, the International Species Information System, which has for decades maintained the global database of managed animal populations in zoos, captive programs, and wildlife reserves, as well as endangered species in conservation programs both in captivity and in the wild.  Their existing infrastructure is already well-suited to our needs, and they have the computer, scientific, and administrative expertise needed to support it.  ISIS is a non-profit organization, and we envision that funding to support them as hosts could come from annual subscription fees from kennel clubs, breed clubs, and other types of canine organizations, as well as fee-for-service options available to breeders for particular personalized analyses.  Grant support, charitable contributions, and other sources of funding will also be explored.

What will we do with the data?

There are obvious benefits to having a single, comprehensive database of pedigree information that will allow breeders and researchers to trace the lineage of any dog of interest.

But the real value of this resource is that it will enable for the first time genetic analyses that can unlock a trove of information that would otherwise not be available to either breeders or researchers.  I have discussed examples of some of these in previous blog posts, and the availability for the first time of a database like this will open the door to many more.

Most breeders have neither the computing resources nor the expertise to do much beyond simple pedigree analysis.  Therefore, we have gathered together a group of population geneticists that have the expertise to assist in analysis and interpretation of genetic data for breeders.  This team includes some world-class experts in population and conservation genetics, with expertise not only in the analysis of canine pedigrees, but also in genetic management of captive populations and the design of breeding programs to restore and manage genetic diversity.  (see above)

Their goal will be to extract the data describing the genetic structure of the breed (things like actual and potential genetic diversity, effective population size, effective number of founders, coefficient of inbreeding, and kinship).  This standard information for each breed will be available to breeders online and updated regularly.  Additional analyses can be provided as appropriate such as the genetically most valuable animals in a population, estimated breeding values that incorporate information about many different traits, and cluster analysis to identify genetically-similar groups of animals.

Incorporation of health data

Test results and health data for dogs are in many independent testing laboratories and organizations around the world.  This prevents examining all the data available for a breed worldwide.  It also makes it difficult to link the health data with the pedigree.

Our second major goal is to provide a parallel, comprehensive compilation of the health, testing, and genetic information for dogs.  This will likely be more difficult than organizing the pedigree information, but the potential benefits are huge.  It will require partnerships with testing organizations to provide the information and keep it up to date.  Information that is confidential will be coded so that it can be used in analyses while maintaining privacy.



We are working with staff from ISIS to provide a customized interface suitable for entry and management of the data for dogs.

Volunteers have begun the process of compiling the pedigree databases for more than 20 breeds.

We have assembed a team of population geneticists that will assist with the population genetics analyses and work with breeders to provide additional information and analyses as necessary to address the problems of particular breeds.  We also have members of the fancy who can assist in educating breeders about breeding strategies to minimize genetic problems and leverage information from the databases.

We are ready to proceed as soon as the first pedigree database is completed.



We need breeders that will volunteer to coordinate the collection of pedigree data for their breeds.  If you would like to do this, please contact me privately.  There is a list of breeds already in process below..

Ultimately this will be a fee-based service with global support (although access to the pedigree database should be free to breeders).  During development, however, we must depend on other sources of support.  If you would like to offer financial support for this effort, or would be interested in being involved in fund-raising, website design, development of educational materials, please contact me

We welcome your feedback and questions.



Amanda Pough (USA)   Canaan Dog

Amanda Kelly (Canada)  Toy and Standard Manchester Terriers

Beverly Cabral (USA)   Polish Lowland Sheepdog

Brenna Spencer (USA)   Field Spaniel

Celeste Pongrácz (Hungary)   Pumi

Celeste Pongrácz (Hungary)   Mudi

Dan Nechemias & Lois Claus (USA)   Tibetan Mastiff

Dawn Saunders (UK)  English Toy Terrier

Diana McCarty (USA)   Podengo Medio & Grande

Gina Spadafori (USA)   Flat-coated Retriever

Janet Lee Evans (Canada)  West Highland White Terriers

Jean Gaucet-Hargis (USA)   Collie

Jean Gaucet-Hargis (USA)   Keeshond

Jo Ann Secondino  (USA)   Icelandic Sheepdog

JoAnn Stoll (USA)   Russell Terrier

Joan Weiskopf (USA)   Bedlington Terrier

Joaquim & Temple DaSilva   (USA)   Portuguese Pointer

Karen Hinchy (USA)   Chinook

Kay Lawson (USA)   Xoloitzcuintli

Linda Ford (USA)   American Water Spaniel

Lynn Higgins (USA)   Norwegian Lundehund

Patty Gregg (USA)   Airedale Terrier

Peri Norman (USA)   Belgian Tervuren

Rainy Browning (USA)   Miniature American Shepherd

Stacy McWilliams (USA)   Rat Terrier

Susannah Thyni (Sweden)   Azawakh

Vivi Snellman (Finland)   Kromfohrländer

Zoe Bolin (USA)   Black & Tan Coonhound






Do we really need new Basenjis?

It doesn’t happen often, but the AKC has opened the Basenji stud book to allow the introduction of new African imports.  One of the compelling reasons to do this is that the small number of founders of the breed and subsequent inbreeding (which, of course, is inevitable in a closed gene pool) has reduced genetic diversity.  There is abundant evidence in many, many animals (and even plants) that diminished genetic diversity has many deleterious effects – reduced fertility, greater infant mortality, shorter lifespan, diminished resistance to diease, and increased incidence of genetic diseases.

But how compromised is the genetic diversity of the breed?  And how many new dogs would be needed to significantly improve the breed’s genetic health?  It is neither cheap nor easy to bring back a basenji from Central Africa, and there are safety concerns as well.  A complete analysis of the population genetics of the breed would be able to address these questions, but that has never been done for this breed.  So how can we address these questions?

One thing we can do is look at the trend in coefficient of inbreeding (COI) over time from the inception of the breed, using data for dogs from founders up through about 1990 (and a few scattered individuals after that, but the more recent data is still incomplete).

(Apologies for  the watermark on the graph.)

This graph tells the tale.  Over this entire span of time, there are dogs with calculated COI’s of zero.  But after the first 10 years or so, there are very few dogs with COI less than 5%, and after 30 years (~1969) all but a scattering of points are > 10%.  By 1979, the average COI is about 30%, and there are many dogs above 40%.  To give you some perspective, 25% is the COI of a full-sib mating (or father-daughter, eg).  Conservation geneticists working with endangered species consider a COI of 5% as cause for concern, and 10% the level at which a species is in serious peril of extinction as a consequence of inbreeding.  You can compare this graph with similar ones in the papers by Oliehoek on Icelandic Sheepdogs, and Malik on Nova Scotia Duck Tolling Retrievers (which we reviewed in earlier blogs).  By any measure, the degree of inbreeding in the Basenji population in about 1980 would be considered extreme.  A handful of dogs from Africa were added to the stud book in the 1980’s, and it will be interesting to see the effect these had on the genetics of the registered population when those data are available.  But my scan of the data suggests that they were not well-integrated into the breeding population, so there is likely to be little overall improvement in the genetics of the population.

From the information at hand, and extrapolating to the present, it appears that the registered population of Basenjis could indeed use some new blood.  But how many new dogs should be added?

My colleague Bob Lacy and I addressed this question in an essay that will be appearing soon in a number of the Basenji breed magazines.  So that it is freely available, I have copied it below.

In a nutshell, a sustainable population of Basenjis that are freely interbreeding should have no fewer than 20 individuals in the worse case, and 50 should be considered the minimum for management purposes.  But purebred dog breeders doe not allow their animals to freely interbreed – they are selectively bred, and these breeding choices will result in changes in the gene pool of the breed.  So, a healthy population of pedigree Basenjis would need to have substantially more than 5o dogs, perhaps hundreds.  Bob and I discuss the reasons for this in some detail in our article.

So, the original question: “Do we really need new Basenjis?”

The answer:  Absolutely, yes.


How Many Founders Does it Take to Make a Breed?  A Reply to Thompson

Robert C. Lacy, Ph.D. * and Carol A Beuchat, Ph.D.

*Senior Conservation Scientist, Chicago Zoological Society; Committee on Evolutionary Biology, University of Chicago; Science Advisor, SSC Conservation Breeding Specialist Group, International Union for the Conservation of Nature
In response to the paper by Thompson (2012), we wish to provide some information about issues relevant to managing the genetic health of the pedigree Basenji population. Thompson provides a valuable introduction to the principles underlying genetic management of breeding programs for rare and valuable populations. One of us (RCL) has been involved in the development and application of these concepts and methods for the preservation of endangered species for the past 30 years, and we agree with Thompson that many of the principles that have been developed for optimal management of threatened species have value also for the management of breeds of domesticated animals. However, there are also differences in the goals and feasible methods that should be considered when adapting the lessons from endangered species management to breed management. Below, we address some of the issues raised by Thompson that might need clarification or further explanation.


1) When numbers such as 5-15 founders, or no fewer than 6, have been provided by conservation geneticists as the minimum number necessary to build a viable population, the context has been emergency efforts to sustain a wildlife population or species, and the emphasis is very much on a “minimum” number. Even when the possible loss of an entire species is at risk, it is debatable (and it is vigorously debated!) if it is worth putting resources into trying to build a breeding population from fewer than 6 founders. As Thompson notes, a recommendation of 20 effective founders is typical as the starting point to rescue a population at risk of extinction (Lacy 1989). Beyond the recommended minimum of 20 effective founders, zoos must carefully consider the incremental benefit of starting with larger numbers of founders, because of the considerable cost – sometimes including even the potential to seriously damage the remaining wild population by over-harvesting – of importing an additional 10 to 20 individuals of a large wildlife species that is likely difficult to capture, handle, and transport.


2) General statements about minimum number of founding individuals necessary to build a viable closed population are based on models of population genetics that assume an “ideal” population where breeding is either random or will be managed to preserve genetic diversity using a breeding strategy designed for this purpose.  An example of this would be a captive zoo population of a species where reproduction is carefully managed to minimize loss of genetic diversity and changes from the original, wild traits over generations.  The strategy pursued in such a management plan would be to maintain equal genetic contributions of all founders to subsequent generations, as this would maintain the maximum amount of the original genetic diversity.

In populations of animals (whether species or breeds) where management of reproduction is not focused purely on the preservation of the full range of characteristics (good and bad) of the founders, the assumptions underlying the “ideal” estimate (as above) are not met. Some of the variation brought into the population via the founders will likely be lost in the first few generations, and the number of founding individuals will need to be greater in order to provide an adequate genetic base for future breeding. Indeed, even in breeding programs for endangered species in zoos, we know that in spite of our best efforts some initial “potential founders” will not contribute to future generations, so that we need to start with more – sometimes many more – wild-collected animals to achieve 20 effective founders.


This would likely even more so be the case in a population of purebred dogs for several reasons.  A breeding plan designed to maintain as much of the founding genetic diversity as possible would require the collective cooperation of all breeders as it must use all existing reproductive dogs in an optimally designed and rigorously managed breeding scheme.  But dog breeders have specific breeding priorities of their own, such as selection for particular traits in their dogs (e.g., color, leg length, behavioral traits), or preferences to use particular individuals in their breeding program.  Their breeding options might also be constrained by geography, or by available space and other resources. The presence of known genetically based health issues will also influence breeding decisions, and selection against genes that can cause health problems (while sometimes necessary) further reduces the variation across the rest of the genes as well, because the selection by definition reduces the number of breeders contributing to the next generation.  Thus, it seems highly unlikely that all custodians of breeding individuals could fully cooperate with a breeding strategy designed to ensure equal contributions of all founders to subsequent generations. With selective breeding, the genetic diversity in the founding population can be substantially reduced in just a few generations (Oliehoek, Bijma, & van der Meijden 2009; Maki 2010).

3) If a large number of founders cannot be obtained initially, or if some of those lineages are lost or under-represented in subsequent generations, or if breeder goals will necessarily include selection for desired traits and against genetic problems, then low and declining diversity of the population can later be increased or restored through the addition of new founders – if available – to the breeding stock. This can bring back genetic variants that once represented the species or breed but were lost by chance, reverse incidental fixation of deleterious genes and accumulated inbreeding, and provide the diversity necessary for continued modification and improvement through selection.
4)  Full analysis of the population genetics of the (worldwide) pedigree of Basenjis has not been done, so there is no information about how well the genetic diversity of founders has been maintained, or about the degree of inbreeding in the existing population.  A genetic analysis using pedigree information for all dogs back to founders could provide substantial insights as to the value of any additional founders.  This information would also allow breeders to make the best possible decisions about the use of their breeding stock by identifying populations of dogs that are most critical to maintain in the breeding population, and the degree of imbalance in the contributions of founders to the current generation (Lacy 1989; Ballou & Lacy 1995).

5)  Basenjis are one of the (very) few breeds where a large population of animals from which the founders were originally drawn still exists in Africa, and these animals have not been subject to an organized breeding program, so mating has likely been more or less random.  Consequently, we can expect that in such a population, a diversity of genetic alleles will still be present.  Selecting animals randomly from this well-mixed gene pool is most likely to yield a genetic subsample that reflects the actual genetic diversity in the native African dogs. If the selection of animals is not random (for example, certain traits are desired, or some traits simply do not result in dogs that will be successful breeders if brought out of Africa), or if the dogs cannot be collected across the geographic range (possibly resulting in some lineages in Africa being sampled several times), then a larger number of new founders is required to obtain a good representation of the diversity of the breed.

6)  We assume that the desire to increase the genetic heterogeneity of the pedigree Basenji population is motivated at least in part by concern about the possibility of unacceptable levels of genetic diseases in the future as a consequence of the small size of the founder population and subsequent inbreeding.  Such problems have arisen in many breeds (canine and otherwise) that descend from small numbers of founders or have small breeding populations, and can be difficult to counter once the problems become prevalent enough to be to make it clear that restoration of genetic variation is needed.  However, one issue breeders might be concerned about is that the addition of new animals can introduce again to the breeding stock potentially deleterious genes.  We do not believe that this problem will be significant enough to override the benefits of restored genetic variation. The problem is not that deleterious alleles exist – as it is the case that all animals carry some deleterious recessive alleles and a few new ones arise by mutation every generation – but rather that in a small population or one with few founders some of the deleterious alleles can be expressed in homozygous condition in a number of animals. It should be noted that natural selection continues to work on wild populations, and with much greater force and efficiency that in populations under our care, so that deleterious alleles will have been held to very low frequencies.  In a large, genetically diverse population, therefore, the probability of producing offspring that are homozygous for the disease allele is very low.


Especially for Basenjis, which in Africa are subject to strong natural selection when they fend for themselves, it is reasonable to expect that in the absence of evidence to the contrary, the animals should be genetically healthy, and a checkup from a veterinarian should satisfy to catch anything that might become a problem.  Again, the key to managing health issues is maintaining the genetic diversity of the breeding dogs.  If a deleterious allele does become common enough to be a problem for the breed, selection against that allele might be practiced, but we need to recognize that such selection will also reduce the genetic diversity across the rest of the genes, and any beneficial traits carried by the dogs that are removed from breeding will be lost (Lacy 2000). Thus, having high diversity within the breeding stock is essential both to minimize expression of deleterious traits and to allow selection to be practiced when desired without inadvertently jeopardizing the genetic health of the breed.

7)  Thompson (2012) discusses the often-cited number of 50 and correctly notes that this refers to a recommendation for a minimum effective population size, not the minimum number of founders. For the reasons discussed above, achieving the recommended 20 effective founders, might require fewer or more than 50 initial imported animals. The recommendation of 50 as a minimum effective population size derives from a desire to minimize the accumulation of inbreeding subsequent to the founder generation.


The definition that Thompson gives for effective population size is correct only under very specific and idealized circumstances. Effective population size is not, in general nor in most populations, “the current number of breeding individuals in a population that contribute genes to succeeding generations.”  Effective population size is the number of breeding animals in a theoretical random breeding population that would experience the same rate of change in allele frequencies, or the same degree of inbreeding, as seen in the actual population (Lacy 1995).  The number of breeding animals will be close to the effective population size only if breeding is truly random.  Of course, in any real breeding program, breeding is far from random and some lineages contribute more to the population as a whole than others, because breeders select for specific traits or are limited in their choice of sire.  In pedigreed dog breeds, the effective population size will likely be substantially smaller than the actual number of breeding animals, and this leads to more rapid loss of the genetic diversity that was brought in via the original founders.


The recommendation of a minimum effective population size of 50 is equivalent, mathematically, to a recommendation to keep the rate of increase in the coefficient of inbreeding below 1% per generation. This recommendation arises from the centuries of experience of animal breeders regarding what level of inbreeding can be accepted for a moderate number of generations without incurring risk of genetic damage in the form of higher frequency of genetic defects and lower overall average fitness of individuals. High levels of inbreeding have well documented deleterious effects including reduced fertility, decreased litter size, lower birth weight, lower survival, decreased resistance to disease, and decreased tolerance of environmental stress (Charlesworth & Willis 2009; Keller & Waller 2002; Lacy 1997; Ryan et al. 2002). Not every inbred animal will be affected, but the probability of problems increases and the average level of performance declines. Moreover, it is not predictable which lineages will suffer from inbreeding problems, and selection programs aimed at reversing inbreeding problems usually have only limited effectiveness (Lacy 2007).


8) Whenever possible, within breeding programs for rare wildlife species we start to seek out new animals to boost genetic diversity again whenever the cumulative mean inbreeding level increases to about 5% or more.  When cumulative inbreeding levels reach 10% or higher, we consider the need for new animals to be urgent.  For example, the Association of Zoos and Aquariums recently decided to open up breeding of even endangered species to exchange with private breeders who are not accredited members nor bound by association policies that require registry of animals in studbooks, when the breeding population mean inbreeding rises above 10% — unless a plan is in place to quickly bring in new founders to restore the lost variation to the more tightly controlled population.


Thompson (2012) mistakenly describes the goal of 90% of the diversity of the source population (equivalent to cumulative inbreeding no greater than 10%) as the goal for starting a population, whereas the 90% criteria is actually widely applied as the limit for acceptable genetic decay over the long-term (e.g., 100 years) for a viable population designed to sustain and represent the source population. I.e., 10% loss of diversity is not the benchmark for an acceptable starting point, but rather is often defined as an end point below which a population should not be allowed to descend, or as the point at which quick action should be taken to obtain new founders to restore variation. While conservation biologists do aim to start breeding programs of wildlife with at least 20 effectively contributing breeders (i.e., 97.5% of source diversity), we recognize that after a number of generations of propagating a small breeding stock, we often cannot avoid losing some or even much of the diversity that had been present in the founders. The goal of never dropping below 90% of the source population diversity drives both the recommendation to start with much more diversity than this, and the recommendation to maintain an effective population size greater than 50 so that further losses are no more than 1% per generation. A simple calculation shows that if the starting diversity is about 97.5% and 1% is lost in each subsequent generation, then the population can be sustained above the 90% goal for only 7-8 generations. Although this short-term strategy often is acceptable for endangered species breeding programs that are designed to be a temporary reserve for a species until they can be returned to a better protected wild habitat (e.g., as has been done with condors, black-footed ferrets, Mexican wolves, and red wolves), presumably people who sustain special breeds of dogs are interested in longer term preservation. Therefore, good genetic management will require more initial founders, a much larger breeding population allowing slower inbreeding, more rigorous control over breeding based on pedigree rather than expressed traits, and/or periodic replenishment of diversity with new founders.


9) Inbreeding levels in some dog breeds are already substantially higher than 10% (Leroy et al 2009; Leroy 2011). Although we are not aware of the value for Basenjis, we would expect that it is probably higher than 10% as well. For perspective, a mean inbreeding level of 10% is the equivalent of having the genetic diversity that would be provided by only 5 founders – which would not seem to be a very good representation of the breed.  So for the pedigree Basenji, which is an unmanaged population (i.e., there is no single authority responsible for making breeding decisions), and which has limited opportunities for introducing new breeding stock on a regular and continuing basis, we would recommend that breeders should not forego the opportunity to add new animals whenever dogs representing the breed can be added to the breeding programs.  This will help to maintain the genetic diversity in the population as a whole in the face of the conflicting demands on breeders.

For all purebred dogs (and wildlife species, for that matter), the goal is healthy animals that represent the breed well and can continue to respond to selection.  Selecting only for breed-specific traits without also actively working to sustain the underlying genetic diversity needed to produce a healthy dog would ultimately result in failure.  Two well established and even fundamental principles of genetic management are that (1) accumulated inbreeding almost inevitably causes reduced fitness and performance in a sexually reproducing species, and (2) variation is necessary to allow successful selection for desired traits or against deleterious traits. With adequate knowledge of the ancestry and current genetic structure of the breed, and some prudent breeding strategies, breeders can achieve their breeding goals while protecting the health of their animals and safe-guarding the future of the breed.  Pedigree analysis software is available for assessing the effective population size, the loss of genetic variation to date, the rate of accumulation of inbreeding, and the potential benefits of adding new founders (Lacy, Ballou, & Pollak 2012). Genetics management advisors who are experienced in pedigree analysis for zoos would likely be available to assist by providing analyses and advice to Basenji and other dog breed groups. Regularly updating the genetic analysis of the population as new individuals are added by birth or introduction, and revisiting the breeding plan in light of new information, is the best strategy to assure the health of the breed for the long term.


Ballou, J.D.. & R.C. Lacy.  1995. Identifying genetically important individuals for management of genetic diversity in pedigreed populations.  Pp 76-111 in J.D. Ballou, M. Gilpin, & T. Foose (eds).  Population Management for Survival & Recovery: Analytical Methods and Strategies in Small Population Conservation.  Columbia Univ. Press, NY.

Charlesworth, D. & J.H. Willis.  2009.  The genetics of inbreeding depression.  Nature Reviews 10:783-796.

Keller, L.F. & D.M. Waller.  2010.  Inbreeding effects in natural populations.  Trends in Ecology & Evolutions 17: 230-241.

Lacy, R.C. 1989. Analysis of founder representation in pedigrees: Founder equivalents and founder genome equivalents. Zoo Biology 8:111-124.

Lacy, R.C.  1995. Clarification of genetic terms and their use in the management of captive populations.  Zoo Biology 14:565-578.

Lacy, R.C. 1997. Importance of genetic variation to the viability of mammalian populations. Journal of Mammalogy 78:320­‑335.

Lacy, R.C.  2000.  Should we select genetic alleles in our conservation breeding programs?  Zoo Biology 19:279-282.

Lacy, R.C. 2007. Understanding inbreeding depression: 20 years of experiments with

Peromyscus mice. Pages 327-329 in F.W. Allendorf and G. Luikart. Conservation and the Genetics of Populations. Wiley-Blackwell, New York.

Lacy, R.C., J.D. Ballou, & J.P. Pollak.  2012.  PMx: software package for demographic and genetic analysis and management of pedigreed populations.  Methods in Ecology and Evolution 3:433-437.

Leroy, G.  2011.  Genetic diversity, inbreeding and breeding practices in dogs: results from pedigree analyses.  Veterinary Journal 189:177-182.

Leroy, G., E. Verrier, J.C. Meriaux, & X. Rognon.  2009.  Genetic diversity of dog breeds: within-breed diversity comparing genealogical and molecular data.  Animal Genetics 40:333-343.

Maki, K.  2010. Population structure and genetic diversity of worldwide Nova Scotia Duck Tolling Retriever and Lancashire Heeler dog populations.  Journal of Animal Breeding and Genetics 127:318-326.

Oliehoek, P.A., P. Bijma, & A. van der Meijden.  2009.  History and structure of the closed pedigreed population of Icelandic Sheepdogs.  Genetics Selection Evolution 41:39.

Ryan, K.K., R.C. Lacy, and S.W. Margulis. 2002. Impacts of inbreeding on components of reproductive success. Pages 82-96 in: W. V. Holt, A. R. Pickard, J. C. Rodger, and D. E. Wildt, eds. Reproductive Science and Integrated Conservation. Cambridge University Press, Cambridge, UK.

Thompson, J. 2012. How many founders does it take to make a breed? The Modern Basenji 2: 26-27.

Population genetics suggests dire straits for Tollers and Heelers

Maki, K. 2010.  Population structure and genetic diversity of worldwide Nova Scotia Duck Tolling Retriever and Lancashire Heeler dog populations.  J Anim Breed Genet 127: 318-326.  (pdf


For those that asked about other examples of the application of population genetics analyses to dog breeds, here is another excellent paper that does this for two uncommon breeds, Nova Scotia Duck Tolling Retrievers and Lancashire Heelers.  Like Oliehoek did in his study of Icelandic Sheepdogs (see the previous posts beginning here), Maki gathered up the pedigree data for essentially the entire worldwide registered populations of these breeds back to founders – a total of almost 29,000 dogs for Tollers, and nearly 5,000 for Heelers.

For the Tollers, there were 22 original founder dogs and for Heelers 155 founders, but in both breeds only a fraction of the offspring were bred (13% of Tollers were bred, 25% of Heelers).   As a consequence, the average inbreeding coefficient of Tollers rose rapidly right at the start and reached 25% within 15 years of founding.  It has fluctuated slightly since, reaching as high as 30% at one point.  The average degree of inbreeding increased more slowly in the Heelers (remember, there were more founders, which will slow the rate of inbreeding) and appeared to have stabilized by the time of the study at about 10%.

The consequence of inbreeding is a reduction in the genetic diversity of the breed.  In both Tollers and Heelers, more than 90% of the genetic diversity present in the founders has been lost, leaving Tollers with genetic equivalent of only 2 dogs and only 6 for Heelers (“founder genome equivalents”).  The Lancashire Heelers are prone to eye problems but are otherwise generally healthy (  Tollers have a few disorders that are common in other breeds as well (hip dysplasia, progressive retinal atrophy), but more seriously there is now genetic evidence of a seriously compromised immune system resulting from loss of haplotype diversity (Hughes et al 2010; Wilbe et al 2009).  The immune system is the body’s defense against the world.  It’s job is to beat back all the harmful things nature can throw at an animal.  A compromised immune system leaves the animal defenseless against viruses, bacteria, parasites and other pathogens, and susceptible to a large array of potentially severe autoimmune disorders.  It’s a very complicated system, and to be broken even a little is very serious.

First, let me say that these genetic problems are certainly not unique to these breeds.  Many studies are finding similar problems in other breeds, but the papers I have commented on here are the most complete and are presented in a way that should be understandable to a dog breeder without advanced training in population genetics.

The loss of genetic diversity in both Tollers and Heelers is a result of several things, among them the relatively small founding populations and the use of some dogs more than others in breeding, both of which are common to many other breeds.  But I think the biggest problem has been that the kinds of information about population genetics that are presented in this paper have not been available to breeders.  The changes that occur in the genetics of the breed over time are a consequence of the activities of many individual and usually independent breeders.  Without the ability to coordinate breeding strategies, or oversee changes in the population genetics of the entire (world-wide) breed in real time, loss of genetic diversity can occur despite diligent efforts by the majority of breeders to use breeding strategies they feel are in the best interests of the health of their dogs and offspring.

As breed populations inevitably become more and more inbred, the need for current information about population genetics will become more urgent, but breeders have no way to know this and no way to get it.  I have found that for the few breeds I have looked into, complete pedigree records back to founders are simply not available.  But even if they were, the kinds of analyses used here would need to be performed by somebody familiar with the statistical techniques, and redone on a regular basis, something the average dog breeder simply can’t do.

I’ve been working with Dr Bob Lacy, an expert in population genetics and endangered species management, to perform analyses like this one on several breeds that are relatively small and for which we have a reasonable chance of gathering up all the pedigree data without a heroic effort.  I’ll be posting progress as these move forward so people that are interested can follow along.  I hope we will ultimately have some model analyses to show as examples, as well as some breeders that have learned enough by going through the process to continue to carry out the analyses on a regular basis for their own breed.

Watch this space…!


Wilbe, M, P Jokinen, C Heranrud, LJ Kennedy, E Strandberg, H Hansson-Hamlin, H Lohi, & G Andersson.  MHC class II polymorphism is associated with a canine SLE-related disease complex.  Immunogenetics 61:557-564.

Hughes, AM, P Jokinen, DL Bannasch, H Lohi, & AM Oberbauer.  2010.  Association of a dog leukocyte antigen class II haplotype with hypoadrenocorticism in Nova Scotia Duck Tolling Retrievers.  Tissue Antigens 75: 684-690.

Where are the genes hiding? Fancy math reveals in Labradors, Wolfhounds, and Bedlingtons

If you’ve worked your way through the paper on Icelandic Sheepdogs (ISD) from previous posts (part 1 and part 2), you ran into a mathematical technique called cluster analysis.  It’s a little complicated, but basically it’s a way of grouping things by similarities in various traits.  In the ISD paper, cluster analysis was used to group dogs by genetic similarity.  It revealed that most of the dogs in the pedigree population clustered together in one large group, with the rest of the dogs being distributed over a number of  smaller groups.  These smaller groups represent little puddles of genetic diversity – dogs that are genetically slightly different than dogs in other groups – and theoretically at least, breeders could dip into these other populations as a source of genetic material to add to their breeding lines.

In a post on the ISD discussion, someone asked two very good questions.  1) Could there be differences in disease incidence between groups of dogs within a breed? – e.g., working dogs vs bench dogs, or even dogs from different breeding lines.  2) Can we have recognizible breeds and still maintain genetic diversity?

In answer to both of her questions, the data suggest “yes”.

A very interesting study was published some years ago in which researchers used cluster analysis to figure out how particular diseases are distributed in populations of dogs (1).  They paired pedigree databases with data for occurrence of specific disorders for three breeds: elbow dysplasia in Labradors, portosystemic shunts in Irish Wolfhounds, and copper toxicosis in Bedlington Terriers.  The Labrador data were for 252 dogs owned by the Royal Dutch Guide Dog for the Blind Association that were screened for clinical signs of fragmented coronoid process.  Seventeen percent of these dogs were found to be affected.  For the Wolfhounds, 613 dogs registered between 1985 and 1992 were screened for the presence of a congenital portosystemic shunt, which was found in 4% of this group.  For Bedlingtons, 155 dogs registered between 1977 and 1985 were screened for hepatic copper toxicosis by biopsy when the dogs were a year old, and 46% were found to be affected.

Cluster analysis allowed the researchers to isolate groups of dogs in each breed that were more closely related to each other (at least the 0.125 level of relatedness) than to dogs in other groups.  They could then look for patterns in the distribution of these disorders across these genetically distinct clusters.

In Labradors, there were 31 small clusters of dogs that had a relatedness within each cluster of at least 0.125, and were genetically distinct from the other clusters.  From the dendrogram of the clusters (these funny tree-like graphs as below), it was clear that the cases of elbow dysplasia were all found in only five groups of dogs that were closely related to each other.  In these 5 clusters, the incidence was greater than 27%, while for all the others it was zero.  (Remember, the overall frequency in the population was 17%.)

Cluster analysis of Labrador Retrievers in this study. The fraction of dogs with affected elbows is indicated by shading.


Likewise, the dendrogram for the Wolfhounds showed that they grouped into 14 clusters (also with relatedness within clusters of at least 0.125).  Portosystemic shunts occurred in only four clusters, but these groups were not clumped together in the dendrogram.  All other clusters were free of the disease.

Cluster analysis of Irish Wolfhounds. The fraction of dogs with a congenital portosystemic shunt is indicated by shading.


The Bedlington Terriers split into 12 clusters of related individuals, and copper toxicosis occurred in all of them.  The gene for this disorder appeared from this analysis to be widely distributed in the breed, and indeed, subsequent genetic studies revealed that to be the case.  Just about the time this paper was published, the gene was identified and a DNA test is now available (2).

Cluster analysis of Bedlington Terriers in this study. The fraction of dogs with copper toxicosis of the liver is indicated by shading.


The first sentence of the Discussion from this study sums it up well:

“This study has evaluated cluster analysis as a method for studying the relatedness of purebred dog populations, for resolving the complex structure of these populations to estimate their level of relatedness and genetic heterogeneity, and for assessing the genetic background of disease.”

What this study shows so clearly is the enormous amount of information that can be leveraged from just pedigrees and some data on occurrence of a particular trait or disease.  They were able to accomplish this using relatively small subpopulations of the entire breed, but they note that the most accurate estimations of genetic similarity among individuals would be obtained using pedigrees that extend back to founders.

“A knowledge of the distribution of an inherited disease among clusters of related animals may help to provide the means to select against disease, while maintaining the heterogeneity of the population.  The clusters of dogs at risk may also provide a basis for the selection of animals for molecular genetic studies to search for markers of the genes underlying the disease.”

With this kind of information, breeders can do a better job of eliminating deleterious genes from their breed without taking a huge toll on the overall genetic diversity.  What a powerful tool!

This paper was published in 1998.  Oliehoek made brilliant use of it in his study on Icelandic Sheepdogs to identify sources of genetic variability that could be incorporated into the breed population .  Why haven’t we seen many more studies like this??

The paper this discussion is based on (below) is not freely available online because of copyright restrictions.  If you would like to obtain a copy for your own educational purposes, contact me privately and I can supply a copy.

1)  Ubbink, GJ, HAW Hazewinkel, J Rothuizen, J van de Broek, & WTC Wolvekamp.  1998.  Cluster analysis of the genetic heterogeneity and disease distributions in purebred dog populations.  Veterinary Record 142: 209-213.





What population genetics can tell you about your breed

> I’ve moved my summary and some comments on the previous post to a new blog post here.  If you haven’t already, you might want to read my introduction to the reading group, and also my introduction to this paper and why it’s relevant to ALL breeds of dogs.  If you don’t have a copy of the paper, here’s a link to the download – <

Oliehoek, PA, P Bijma, & A van der Meijden.  2009.  History and structure of the closed pedigreed population of Icelandic Sheepdogs.  (PDF download)

Okay everybody, let’s see if we can make some progress on this. You should all have the beginnings of a list of jargon definitions and/or a copy of the paper I posted above, and you’ll be adding to it as we go. I think most of you will have at least a sense about what Pieter Oliehoek and his colleagues set out to do from your reading of the introduction and conclusions of the paper.

Let’s start with that. The Icelandic Sheepdog is like many other uncommon breeds –

1) It was founded with a relatively small number of dogs (36);

2) It became a registered breed fairly recently (~1955);

3) For much of its history as a registered breed the total population was small (< ~500 dogs until about 1990);

4) There has been a rapid increase in registrations in recent years as the breed has gained a following and been introduced to new countries (see Figure 1);

5) At the time of the study, the current population numbered about 2500 dogs, many times the size of the founding population.


Oliehoek knew that a small, closed population will inevitably suffer from inbreeding, resulting in inbreeding depression which is reflected in reduced resistence to disease, reproductive problems (reduced fertility, smaller offspring, smaller litter sizes, higher mortality, etc). Also, with loss of genetic diversity in breeding populations, there will likely be an increase in the incidence of inherited disorders, because it becomes more likely that an individual will just by chance be homozygous for a deleterious allele.

Knowing that breeding of Icelandic Sheepdogs had not been managed in any way as it grew in popularity, Oliehoek suspected that an analysis of the breed might reveal some evidence of significant inbreeding.

They gathered together the pedigrees for all the registered dogs in the world back to founders (a total of 4680 current and ancestor dogs) and subjected them to special analyses that were able to reveal things about the breed that would have been difficult or impossible to learn any other day.

They found that not only were the dogs were extremely inbred, but the situation of the breed was dire.

1) In just the first 10 years after registration, the breed lost more than 50% (!!!!) of its initial genetic diversity (Figure 2);


2) The astonishing decline in genetic diversity was a consequence of breeding practices that resulted in increasing levels of inbreeding over time;


3) At the time of the study, the entire worldwide population of 2554 dogs had the genetic diversity expected from only 2.2 founders;

4) The average coefficient of inbreeding of the existing dogs was about 25%; that is, the entire population was as closely related as siblings (Figure 3);

This is grim news. Starting with 36 unrelated dogs, inbreeding has reduced the breed to the genetic equivalent of about 2 individuals as closely related as siblings. To save the breed from potential extinction as a consequence of inbreeding, the genetic diversity in the population(s) of breeding dogs needs to increase.

Using a very clever analytical technique called “cluster analysis”, Oliehoek was able to sort the existing dogs into groups of individuals that were similar genetically. He was able to identify 8 groups, two large ones, four of modest size, and two that were very small. You can see these in Figure 6. Note that the longest bar is really 10 times longer than depicted so the graph would fit on the page. So it’s a VERY big group – in fact, 85% of the entire population. These groups also reflected the fact that dogs in different countries (so were geographically isolated) tended also to be genetically distinct (Figure 9).

What this means is that the breed population is not genetically homogeneous. That is, there are little subpopulations of animals in different countries that carry alleles not found in the other groups. In a carefully managed breeding program, these little puddles of diversity could be used to bring the genetic diversity in the breeding population from the equivalent of 2.2 founders up to as much as 4.7. But while it is possible to improve the situation of the breed somewhat, it was unlikely to happen without extraordinary cooperation among breeders, and at best the improvement would still leave the breed in dire straits.

The good news is that when this study was published, the Icelandic Sheepdog breeders used this information to modify breeding strategies to protect the smaller populations of genetically unique animals from extinction, and minimize the additional loss of genetic diversity from the breed.

Genetics of Icelandic Sheepdogs

Oliehoek, PA, P Bijma, & A van der Meijden.  2009.  History and structure of the closed pedigreed population of Icelandic Sheepdogs.  (PDF download)



I picked this paper to start with for a few reasons.

1)  The topic – genetics of purebred dogs – should seem immediately relevant and interesting.

2)  It will introduce most of you to a field – population genetics – that you probably know little about.  So it will be new to you, but for those that invest the time, the payoff will be huge.  Population genetics will open your eyes to an extremely powerful way of learning about the genetics of dog breeds, one that will enable you to learn things about the genetic structure of your breed that you could never get at any other way.

3)  The techniques used will be new to you and might at first be difficult to understand, but the research in this study is excellent, the paper is well written, and what you learn from this will provide a solid foundation for your understanding of population genetics and how it can be applied to problems in purebred dogs.

4)  Finally, this paper is so, so relevant now.  Genetic problems in purebred dogs seem to be spiraling out of control, and finding a solution to this problem will require an understanding of why this is happening.  This paper will be the start to that understanding.

If you are a dog breeder, I promise you – this will be the MOST IMPORTANT paper you will ever read about dogs.  Stick with it and it will start you on the road to understanding how to tackle the seemingly intractable genetic problems in your breed.

MY ADVICE – The techniques used in this study rely on mathematics and statistics.  You probably won’t have a clue what they’re talking about in the Methods section.  Don’t worry, for now you don’t need to.  We’ll work to understand the concepts, then the underlying methods will make more sense.

So for now, here’s what you should do:

– Read the Abstract and Background sections.

– Skip the Methods.

– Skip the Results and Discussion.

– Begin reading again at the Conclusion, which will summarize the findings of the study.  The authors will use some acronyms that you won’t recognize, and for now just skim past them.  Read the parts that are plain English and make sense to you.  Have a look at the Figures they refer to; some you will understand, and some you won’t at first.  That’s fine.  Skip the Table for now.

The goal on your first read is to understand what the study is about and what the authors found.  I think you will immediately see the relevance of this study to the breeder of pedigree dogs who is faced with declining genetic diversity in their breed.

When you feel comfortable with generalities of the paper, start reading again at Results and Discussion.  As you read, the authors will introduce some specific terms used in population biology (e.g., genetic diversity, potential diversity, average mean kinship, etc).  As you come to these, make a list on a separate piece of paper with the abbreviation and the name of the term; this way, when they are used again later in the paper you can refer to your list to remember what they are (believe me, that’s what I do!).  Read slowly, but don’t labor.  If you don’t understand something after thinking about it for a few minutes, leave it and you will come back later.

WARNING – I expect you will find this paper difficult to read.  I did, and I’ve read it many times now and learn something new each time.  But this is the paper that opened my eyes to the absolute importance of understanding population genetics if we are ever to be successful in dealing with the health problems of dogs.  We will work together to understand it as we discuss it together here.

SCHEDULE – After you download the paper, you can start reading.  Read the beginning and end (as above) at least twice.  Before you go on, you can come here to ask questions.  If you don’t understand what the paper is about, getting through the details will be deadly.  Mark your paper up with highlighter.  Make notes on the graphs.  Write questions in the margins, then come here if you can’t answer them.

There are no stupid questions.  We will all help each other.

Introducing: The Dog Genetics Reading Club

The purpose of this reading club is to read and discuss recent research into dog genetics that might be of interest to dog breeders and anyone else interested in the biology of dogs.  We can modify the format as necessary as we go along to suit the needs of the participants, but to begin we will all read a paper then reconvene here to critique, discuss, ask questions, and review any aspect of the study of interest.  This kind of reading group is common in academic settings like graduate school because it’s a great way to keep up with current research, hone critical thinking skills, and interact with others that share an interest.  Critical questions are encouraged; personal attacks will not be tolerated.  This is a place for communication and learning.  It should be fun, challenging, and interesting.   What you get out of it will depend on what you put into it.  My hope is that over time we will develop a community that will include both the dog fanciers wrestling with breeding decisions and the researchers who are working to understand all aspects of dog genetics.

We will read papers that might focus on a particular breed, but this discussion will not be breed-specific.  Instead, I will try to choose papers that will present research questions that are relevant to any breed and that will be interesting and useful for anyone interested in the genetics of dogs.

I am not a geneticist by training.  My background is in vertebrate physiology, but I know I can master a discipline with time and hard work, and so can you.  Genetics has jargon, unfamiliar techniques, lots of mysterious looking acronyms, and focuses on tiny little bits of stuff that you will never actually see.  But I’m learning, and so will you.  Persist here and a new world will open to you.

Please limit your posts here to comments relevant to the paper we are reading.  If you have suggestions, comments, or any other general feedback, please send directly to me by email so we don’t clutter up the thread about a paper with stuff that’s not relevant.

So, if you think you’re ready, check out the first paper we’re going to read.

SHOOT THE DOG™: Dogs doing what dogs do

Most dog photography is of dogs in “pet” mode.  The photographer is using a relatively short lens and is interacting directly with the dog while shooting, often keeping the dog’s attention by waving a yummy treat in front of his face.  This results in a photo with the dog looking towards the camera with total love and devotion, eyes large and tongue lolling as he tries to figure out what cute thing he needs to do to be rewarded with the bait.  This is the dog in total pet mode, which is the only way many people ever see their dog.

There’s another way to photograph dogs.  Under the veneer of domestication is the original canine beast, with its instincts and desires largely intact but suppressed when interacting with people.  Releasing and photographing that inner dog is often no harder than putting a long lens on the camera, taking off the leash, and shooting whatever happens.  This is the kind of photography that I really enjoy.

I live on the west coast and frequently take advantage of a beautiful beach as a shoot location.  Most dogs love to run, but none more than whippets.  They are lean, mean running machines, with long legs, well-muscled thighs, the leanest possible body, and everything streamlined from nose to the tip of the tail.  Take off the leash, give them room to run, and the show can be spectacular.

This is once again the lovely whippet Chanel, whom I have photographed many times.   She’s one of my favorite subjects because, despite being a top-ranked show dog, her inner canine soul is very much intact and wonderful fun to photograph.  We had her one afternoon on a beach in Southern California shooting some posed photos for her show career, and when we were done let her play on the beach until well after sundown.  She could have taken off down the beach and been hopelessly out of sight in minutes (a real danger with most sighthounds), but she’s as loyal as a retriever and ran up and down the beach at top speed in front of us until all she could do was collapse on the cold sand with a huge smile of satisfaction on her face.

I got many wonderful shoots from that shoot, but this one to me is the essence of whippet.  Sprinting flat out with all her energy, mental and physical, directed intensely forward, she is still the picture of grace and effortless elegance.  It’s breathtaking to watch.  It’s a whippet being a whippet.

The Queen meets a King


This handsome and elegant Smooth Fox Terrier is Dodger (CH J’Cobe Vigilante Justice), who swept the dog world off its feet in 2010 and retired from his American show career as the top dog in the country as well as the top-winning Smooth Fox Terrier of all time.  Still very much in his prime, he then went to Brazil for a year and blew the competition away there as well.

He was already topping the charts in June 2010 when I caught him while he was on the west coast at the Great Western Terrier show in Long Beach, CA.  Handler Amy Booth asked if I would take some photos and I jumped at the chance.  We were at a park right on the water, adjacent to the berth for the retired cruise ship, RMS Queen Mary.

I wanted a clean shot of the dog with blue sky and an uncomplicated coastline, but we let him move around a bit and he wandered over to a spot where the Queen Mary was going to be in the background.  I really didn’t want a big white (distracting) boat behind the dog.  I kept trying to adjust my position to get a better angle without success.  I wasn’t going to get that boat out of the background without moving the dog.  Then, Dodger turned his head and front towards the camera, leaving a sliver of blue sky between his body and the ship, and that was the money shot.

Dodger won Best In Show at the terrier specialty not only that day but the next.  When I look at this shot, I can’t help but think that this spectacular dog found his own place in the presence of royalty.


Fun or Fight? Quiz 2 Redeaux

In the photo for Quiz 2, most people thought it looked like the dogs were having a less-than-friendly encounter, more like fight than fun.

The nature of the interaction becomes very clear when you can see the rest of the encounter.  Below are about 50 photos shot over about 4 minutes, in sequence with the shot I posted in Quiz 2.

The shot I pulled out for the quiz is very dramatic, but these dogs are clearly having a wonderful time.  The Jack seems quite welcome to join in, despite his preference for sneak attacks on the achilles.  So, were there enough clues in the quiz photo to indicate that the dogs were playing, and what were they?  How can we learn to see them?

On the suggestion of dog trainer friend, I’ve spent some time with Brenda Aloff’s excellent book, “Canine Body Language: A Photographic Guide“, which goes into great detail about the nuances of posture and facial expression in dogs.  Certainly you are aware that your own sometimes subtle facial expressions and posture are revealing – raised eyebrows, squinting, a twitch in the corner of the mouth, dilated pupils, blinking, looking away, lowering the head, etc are all part of our non-verbal language.  Similarly, tiny changes in ear position, a slightly lifted paw, staring, squinting, or wide open eyes, the tension in the lips, carriage of the tail, and so many other things are used by dogs to communicate with each other and reveal their emotional state.

It takes practice to see these (often fleeting) signals in dogs, and these photos certainly have convinced me that I’ve been missing most of what dogs were saying to each other.  I highly recommend Brenda Aloff’s book, and after some study I think you’ll start to see many things in these photos that you missed before.

Please let me know what you think about this “Fun or Fight” series, and I welcome any suggestions.

If you haven’t already, have a look at Quiz 3.

A Chessie for the bay

The Chesapeake Bay Retriever is the quintessential water dog among the sporting breeds.  It’s a sturdy dog with an even sturdier coat, and a non-nonsense approach to the task at hand.  This is an American breed, developed to be masterful in the hunt of waterfowl.

This is Coupe (GCh Quailridge’s Coupe De Ville), photographed at one of my favorite places, the lovely beach in Ventura, California.  He is a fine example of the breed, with the unique and unmistakable silhouette of a Chessie.  The color and texture of his coat look magnificant in this late afternoon light, and his keen expression suggests a dog of intelligence and determination that would be ready to hunt on a moment’s notice.  This was shot just moments before sundown when the last of the lingering light illuminated his beautiful head and glowing eye.

Coupe was the top Chesapeake in the country in 2011.

Fun or Fight? Quiz 1 Redeaux

There were some great comments to the photo in Quiz 1 (you can read them here).

Most people thought the dogs were playing based on body position and balance, tail carriage, the lack of tension in the face of the brown dog (no wrinkling on the muzzle), and the non-aggressive face of the dane and the fact that she’s not in a defensive posture.

So, to answer the question, here are some more photos of the interaction –

From these, you can clearly see that this is play, even though the brown dog has grabbed a bit of skin in the second shot.  The Dane, who is a bitch about 15 mo old, has her teeth carefully protected by her lips, and neither dog is trying to get away from the interaction.  Actually, it looks very much like a dance, with the brown dog taking the role of the friendly aggressor and the Dane as the “prey”, dodging and jumping in response to the other dog’s moves.

Here’s where I need to give a disclaimer.  I’m a dog photographer, not a professionally trained canine behaviorist (although I am a PhD biologist).  When I started taking photos at the local dog park just for fun, I was amazed to see the behavior of the dogs that had happened too quickly for me to follow by eye.  There were lots of teeth, bulging eyes, and athletic moves that were really fascinating for me to see.  It seemed to me that there was lots of information in these photos and that it would be useful to share them in some way.  That’s how I came to start this “Fun or Fight” series.

If people find this interesting and useful, I’ll continue to develop it.  Please let me know if you have any suggestions.

You can subscribe to these posts either by email or RSS using the tools in the sidebar.  And please do share this with your friends on Twitter and Facebook.

You can leave more comments on this series of photos below.  And check out Quiz 2!

Fun or Fight? Quiz 1


Welcome to the first “FUN OR FIGHT?” Quiz!  (If you missed the Introduction to these quizzes, you can read it here.)

These quizzes are going to test your understanding of dog behavior and communication.  Below is a photo taken at a dog park.  Decide whether the dogs are playing or fighting (or thinking about playing or fighting), and identify the clues you used to come to this conclusion.  You can enter your responses in the Comments box below the post, and you can also comment on other posts (maybe you disagree and why).  Everybody is welcome – the pet owner as well as the professional trainer.  The more people participating, the more we can learn.

I’m hoping there will be some lively discussion and a useful learning experience.  After a few days for comments, I can also post additional photos from a particular interaction if necessary to provide more information.

Have fun!


To see the followup, click here.


How well do your understand dog behavior?   Understanding what your dog is thinking, feeling, and trying to communicate can be harder than you think.

If you don’t know what to look for in your dog’s behavior and body language, you might not be able to tell the difference between fun and a fight, or whether that dog is saying “Nice to meet you” or “I’m about to kill you.”

See how well you can read dog behavior. Put on your dog hat and check out QUIZ 1.

The kindly Cardigan Corgi

The Herding Group is a hodgepodge of flashy breeds with charisma and coat (e.g., Bearded Collie, Rough Collie, Old English  Sheepdog, Sheltie, German Shepherd), and “the rest” – understated, workmanlike, low-profile (in both senses of the term) breeds like the Australian Cattle Dog, Corgis, and Vallhunds.  Among the latter, I’ve always had a soft spot for the Cardigan Corgi.  The Pembroke always seems to have a mischievous twinkle in the eye, like he’s hiding a secret or has the inside on a joke that he’ll tell you if you lean in close.  To me, the Cardigan seems like the shy cousin who is just as clever as the Pembroke but doesn’t care if you know it; who knows his job and loves his people, but responds to praise with “Aw, shucks”.  I especially love the sincerity in the Cardigan Corgi’s face, and the warm, soft eyes that reflect self-confidence without arrogance.

Continue reading The kindly Cardigan Corgi

SHOOT THE DOG™: Add the 4th dimension to your photography

running dog

We think of photography as capturing “a moment in time”, but how long is a moment?

With a fast enough shutter speed you can freeze action without blur, and the resulting photos can allow us to see events that happen too quickly to see with the eye.  But the camera can also record events happening over time in a way that we also cannot see.  By reducing shutter speed you can capture that fourth dimension, and the resulting photos can be magical.

If you want to have some fun, experiment with different shutter speeds and you’ll be amazed at the new perspective this can add to your photography.  And even better, slow shutter speeds will allow you to shoot after dark.  I captured both of these images after dark.  In the first one, I’ve caught an Australian Shepherd looking back over his shoulder while running.  In the second one, my English Springer Spaniel is being chased by a Jack Russell Terrier, and the image captures both their speed and their playful interaction.running dogs

It’s great fun to shoot at really slow shutter speeds because you never know what you’ll get and the results can be really amazing.  When the light is fading and you think it’s time to pack it up for the day, try slowing down the shutter and maybe you’ll capture something magical.

2012 Dog Photography Calendar

My new 2012 Dog Calendar is hot off the press, featuring photos that will appear in my forthcoming book, DOGSPLAY: The Joy of Being A Dog (due out any day as well).

These are wonderful photos of dogs having fun that I think you’ll really enjoy looking at over the next 12 months.

You can have a look and order a copy here!

Hot Gothic Dogs From Russia

Dogs Gothic

Dog – Black Russian Terrier – MOSKVORECHIE YASON – World Winner, Crufts Winner, Interchampion, Champion of 34 Countries, 5x BIS, 40xCACIB, IPO-1
Russian Handlers 2012 Calendar – “Gothic and Lolita“.  Photographs by Oleg Bochkov

I first met the Russian dog photographer Oleg Bochkov at the AKC/Eukanuba show several years ago, and since then he’s been a regular at that show and Westminster.  He’s the Editor of the Russian dog show magazine HotDog, which covers shows all over the continent.  Oleg’s latest creation is his annual calendar of Russian dog handlers, and this year he knocked it out of the park.  These aren’t stuffy handler-with-dog photos.  The theme of this year’s calendar is “Gothic and Lolita“, and to pull it off he assembled a creative team in his studio for makeup, hair styling, clothing, props, and lighting.  The result is a collection of stunning images of show dogs and their handlers unlike anything you’ve ever seen.  The calendar will be available at all the big shows in Europe in 2012, and Oleg will also have them at Westminster.  If you want a copy and won’t be at a show where they’re available, drop Oleg a note and I’m sure he can work out how to get a copy to you.  Check out his  calendars from previous years at 2009, 2010, and 2011.

SHOOT THE DOG: 10 keys to becoming a better dog photographer

Lola French Bulldog

Becoming good at anything requires time and effort.  You might be born with natural talent, and that might allow you to get better faster and achieve a higher level of competence, but the path will still be uphill.  Musicians and singers, painters and poets, all that achieve success got there by making a significant investment in honing their skills.

Continue reading SHOOT THE DOG: 10 keys to becoming a better dog photographer

SHOOT THE DOG™: Using perspective

German Shepherd

The difference between a good photograph and a great one is often the little “tricks” used in the setup and camera work.  I wanted to get a shot of Gavin (GCH CH Lakota’s Hitman Of Cantar) gaiting that would knock your socks off, and since we were near the beautiful beach in Ventura, CA I decided to head to the water to come up with something interesting.

Continue reading SHOOT THE DOG™: Using perspective

The elegant whippet


I was digging through old photos looking for a particular image and I came across this one, shot almost exactly a year ago.  This is Tawny (GCh Sporting Fields Bahama Sands) bred by Debbie Butt, and who was on the west coast for a show with her handler (and Debbie’s daughter) Amanda Giles.  I love photographing whippets and had never done a portrait of this dog, so I grabbed Tawny and Amanda and scouted the showgrounds for a place to shoot.  Tawny and Amanda were waiting to go into the ring, so we had perhaps only 10 minutes to get the shot.

Continue reading The elegant whippet

Being Thankful

Wild Turkey

I’ve been away from my blog for awhile.  Blogging takes creative energy, focus, and steady commitment, and I’ve been lacking all three.  In my last post, I was so excited to announce what I thought would be the appearance of my first book of photographs, in the form of an eBook.  Then my computer died, and so did the momentum.  At the same time, my recovery from shoulder replacement surgery last July took a turn, the result of getting decked by a bulldog at the local dog park (how ironic!).  The metal implant fractured my upper arm bone and yanked my still-healing shoulder muscles, and I’ve been in pain ever since.  It’s been a real bummer.

I finally have my new computer.  And this Saturday I will have a second operation to get my shoulder back on track.  My rehab starts over from the beginning, so 6 weeks in a sling, 6 weeks out of sling but no lifting anything heavier than a coffee cup, then physical therapy starting with a one pound weight.  I won’t be at the AKC/Eukanuba show, and if I’m at Westminster it will be without a camera.  Bummer, bummer.

But I will be back to blogging, because it’s one of the few things I can do with both hands that doesn’t entail lifting anything.  Once I’m past the week or so of post-surgery pain, I’ll be able to type.  So I’ll be focused like a laser on doing this book, and it will be a real, printed-on-paper book, with a version also available as an eBook that anybody can afford.  ($0.99! No shipping!).  I’ll also get back to my Shoot The Dog posts for those interested in the “how-to” behind getting great photographs of dogs.

I won’t be taking any photographs for a few months, and since that’s how I make my living, I’m going to have to come up with some new, creative ways to make a living from the thousands of photographs I’ve already taken.  Necessity is the mother of invention, and in addition to a book or two I have a few other ideas that I’ll explore.  And I welcome your ideas, too – ordinary, wacky, outlandish, whatever.  I’m all ears.

Today, I am so grateful for my wonderful friends, who have enriched my life in so many ways.  I wish all of you the happiest Thanksgiving holiday and a wonderful feast with your friends and family.


I’m so excited to announce my first eBook of photography, DOGPLAY: The Amazing Ways Dogs Play, which will become available on 1 November on Amazon for (only!) $0.99.

DOGPLAY: The amazing ways dogs play

These are astonishing images – of teeth, tugs, nips, and bulging eyeballs (but especially TEETH!) – of dogs in their own world playing as dogs do, in the rough and tumble of mock battle and having more fun than pigs in a mud wallow.

I’ve photographed thousands of dogs over the years, and I’ve seen lots of photos of dogs, but these are the most extraordinary images I’ve ever taken, and the most amazing photos of dogs I’ve ever seen.   If you’re a regular follower of my blog, you’ve seen a few of these in my HOW DOGS PLAY posts.

For DOGPLAY, I’ve compiled a collection of about 30 of my favorite photos as an eBook that you can view in stunning color on your iPad, iPhone, Android, Amazon’s new color KindleFire, or any other devices running the iBook or Kindle apps or Adobe Acrobat (pdf).

DOGPLAY will be available on Amazon on 1 November for only $0.99.  Why am I selling it for only $0.99?  Because I want it to be affordable to anybody who loves dogs, anywhere in the world.

If you don’t want to wait until November to order, you can preorder a copy now from my website and DOGPLAY will be sent to you automatically the instant it becomes available.


This Basset Hound can really fly

I love photographing dogs outdoors in beautiful settings, but there are some great shots to be had indoors as well.

I got this terrific shot of a Basset Hound at an indoor dog show last year.  There were lots of spectators and I couldn’t find an open spot next to the ring where I could see the action.   I finally squeezed under a table at the far end of the ring, and after deciding it was too uncomfortable to shoot all scrunched over, I finally gave up and lay down flat on the floor (in the dog hair and various unidentified liquids).
Continue reading This Basset Hound can really fly

The lapdog Bully

French Bulldog

Meet my friend Wooly Bully (GCh Lebull’s New Hope Wooly Bully).

Bully (to his friends) is a French Bulldog, a breed that probably originated in England, where the English Bulldog was bred down to a size more suitable as a lap dog.  Some of these smaller dogs were taken to France, and apparently it was love at first sight because they became so popular that they came to be known as the “French” bulldog despite their British heritage.
Continue reading The lapdog Bully

SHOOT THE DOG™: Visualizing speed

Running dog

I was going to go forward from the last SHOOT THE DOG post on shutter speed to discuss aperture and how it can affect the look of your photos. But I took some photos at the dog park the other day that are great for illustrating the effects of shutter speed on action photography.
Continue reading SHOOT THE DOG™: Visualizing speed

SHOOT THE DOG™: Speed control

In my last post to SHOOT THE DOG, you learned how the exposure meter of your camera works and why it sometimes does a good job of creating a properly exposed photo, while other times it doesn’t.  I hope you’ve invested in a gray card to keep in your camera bag – I can’t think of any other piece of photographic paraphernalia that will cost so little and give you more bang for your buck while you learn to see the world the way your exposure meter does.  If you’re comfortable with everything to this point, you should be ready to take full control of your camera.

Photographs are created by light.  To create images that will look the way you want them to, you need to be able to control how much light enters your camera.  Too much, and the film or digital sensor is overwhelmed and the image is way too bright or simply white; too little, and the image is very dark or even black.

The amount of light that enters the lens is controlled by a diaphragm made of metal blades.  The blades can move to create a hole in the center that lets light enter the camera.  The hole is called the aperture, and you can control how large or small it is with a setting on the camera, just as your eye can control the diameter of the pupil of your eye – larger to let in more light, and smaller to let in less.



Continue reading SHOOT THE DOG™: Speed control

The Big picture

Big (Ch Flatbrook Royal Point Attitude JH)
Big (Ch Flatbrook Royal Point Attitude JH)

The Wirehaired Pointing Griffon is a breed you don’t hear much about. It was devloped in Holland in the 1870’s by Eduard Karel Korthals, who wanted a hunting dog that would stay close to the hunter on foot, could hunt any game in any terrain in any weather, and would come home at the end of the day to fill the role of family and companion dog. Korthals largely succeeded, and those who know the breed will tell you there is no better dog for a companion as well as a hunting dog.
Continue reading The Big picture

The magic moment

The Manchester Terrier might be the best kept secret in the Terrier Group.  Handsome in an understated way, with a slick black coat and stylish mahogany tan accents on the head, chest, and legs, he is civilized – cuddly even – at home, but all terrier when he’s on duty keeping the grounds free of small vermin.
Continue reading The magic moment

SHOOT THE DOG™: Black, white, or gray

If you’re working on improving your photography, you’ve been shooting 1,000 pics a week as I suggested in the first blog in this series (SHOOT THE DOG: Oh Romeo, Romeo), and hopefully you can now hit that shutter release with speed and precision even if the rest of the buttons and dials on your camera still remain a mystery. (If you haven’t done this, grab your lens and get out there. Just do it!)

In my last post (SHOOT THE DOG: Total exposure), I asked you to go outside and do a little experiment that would help you understand how your exposure meter works.  I told you that the meter is calibrated to indicate perfect exposure for the middle gray (18% gray) of a photographer’s “gray card”.  To show you this, I went outside to the shade on my patio with a white mailing envelope, the black case for my iPad, and my photographer’s gray card.  Here’s a shot of these things taken with my camera in full program mode (envelope on the left, gray card in the middle, and iPad case on the right):

Continue reading SHOOT THE DOG™: Black, white, or gray

SHOOT THE DOG™: Total exposure

When you shoot a photo, you have to get the exposure right or you won’t get the shot you were hoping for.  If you shoot in an automatic or program mode, most cameras now can do a pretty good job most of the time.  But there are lots of situations where the camera makes the “wrong” decision about the appropriate settings and the shot is underexposed, or overexposed, or blurry, or a funny color, or in some other way not what you wanted.

If you don’t understand how your camera works, you won’t be able to figure out what went wrong and how to fix the problem.  But if you know your camera, you can choose the settings that will produce an image that is exactly what you want.

The thing we need to tackle first is getting the exposure right.

Continue reading SHOOT THE DOG™: Total exposure

The catch

If you’re a student of photography, you will probably have heard of Henri Cartier-Bresson.  He studied painting in his youth, but in mid-life he became interested in photography and went on to become famous for his candid images of ordinary life, the earliest form of street photography.  He was especially fascinated in the camera’s ability to “fix eternity in an instant”.
Continue reading The catch