Wednesday, May 15, 2013

What the Genomic Signature Says about the Domestic Dogs Ability to Digest Starch

     The latest craze in canine diets is the prey model formula.  If one is looking to improve the dental hygiene and therefore the overall health of one’s dog, then adding raw meaty bones to the diet is a must.   Dogs have alkaline mouths.  This makes them five times more likely to develop periodontal disease than humans.  When food sticks to the teeth the immune system views the food as a foreign body and releases white blood cells which in turn stimulate enzymes to destroy  not only the foreign bodies clinging to the teeth but gum tissue.  This leads to bone and eventually tooth loss.  Chewing on raw meaty bones helps dogs dislodge foreign matter from the teeth and strengthens surrounding musculature. 
     The Prey Model Diet for dogs; however, is built upon a fallacy.   It is based upon the diet of wolves which genetically are the domestic dog’s closest relative.  It is a carnivorous diet.  It avoids plant materials claiming that dentition and the digestive system of dogs indicate that they have not evolved to eat plant based materials.  Is this in fact the case?
      One of the areas the Prey Model Diet points to when claiming that dogs are strictly meat and bone eaters is the dentition.   It is surmised that the canine teeth which are long and pointed indicate that dogs are carnivores.  Are teeth alone, especially the canines, a good indication of diet?  The teeth to the right are a case in point.  Is this a carnivore or an herbivore? 
If you guessed carnivore you are wrong.  This skull shows the dentition of the Gelada baboon which eats grass.  In one study which measured the strength of canines in primates, it was found that the canines of primates were as strong as that of carnivores.  Most primates eat plant based diets.  This of course is a simplification as the dentition does tell one a great deal about diet and species, but one cannot determine what an animal can and cannot process by simply looking at the  canines. 

      If one looks at a cousin of man, Neanderthal, one sees that they possessed dentition very similar to our own; however, scientists have determined that Neanderthals were almost
exclusively meat eaters.  How could they and Homo sapiens effectively eat meat when neither have carnivore dentition?  Both Neanderthals and Homo sapiens chewed in a rotating type fashion which allows the effective break down of fibrous tissue.  However unlike Neanderthal, humans consumed a wide variety of food stuffs.  Although this is certainly not the only reason Neanderthals are now extinct while Homo sapiens flourish, by limiting themselves to one food source Neanderthals  limited their options when that source became scarce.

     This is the key for survival among wild canines as well.  The more varied the diet the more likely the species will survive to reproduce.  If we look at the diet of wild canines we find:
               
Species
Diet
Wolves
Carnivore, will consume plant materials
Dingo
Omnivore
Coyote
Omnivore
Ethiopian Wolf
Carnivore, will consume plant materials
Black Backed Jackal
Omnivore
Golden Jackal
Omnivore
Side-stripped Jackal
Omnivore
African Wild Dog
Carnivore
Dhole
Omnivore
Crab Eating Fox
Omnivore
Short Eared Dog
Carnivore, will consume fruit
Culpeo
Carnivore, will consume plant materials
Darwin’s Fox
Omnivore
Hoary Fox
Insectivore, will eat small rodents and plant materials
Pampas Fox
Omnivore
South American Gray Fox
Omnivore
Sechura Fox
Omnivore
Maned Wolf
Omnivore
Arctic Fox
Omnivore
Bush Dog
Carnivore
Red Fox
Omnivore
Swift Fox
Omnivore
Ruppell’s Fox
Omnivore
Kit Fox
Omnivore
Blandford’s Fox
Omnivore
Cape Fox
Omnivore
Corsac Fox
Omnivore
Bengel Fox
Omnivore
Pale Fox
Omnivore
Tibetan Fox
Omnivore
Gray Fox
Omnivore
Bat Eared Fox
Insectivore
Raccoon Dog
Omnivore
Island Fox
Omnivore
Results
Omnivore  26 species
Insectivore  2 species
Carnivore  6 species  of these  only 2 appear to be true carnivores, meaning they consume only meat and bone.



      This listing of canine species demonstrates that the vast majority of them are omnivores excepting Wild Dogs and Bush Dogs.  Gray Wolves which share a common ancestor with domestic dogs are primarily carnivores but have been observed consuming plant materials including fruit, vegetation and they also raid human garbage where available.  To base a domestic dog’s diet on a prey model diet based solely on their connection with wolves is erroneous.  Looking at the fossil record scientists now believe that dogs may have accompanied humans when they lived among Neanderthals in what is now Europe during the Pleistocene period.   At a site in Predmosti in the Czech Republic remains of dogs and man were found dating to 29,000 years ago. 
Canine teeth were found with holes drilled through them indicating they were worn as ornaments and the remains of one animal was discovered with a bone place between its teeth shortly after death.
[i] Thousands of years therefore separate domestic dogs from their nearest canine companion the Gray Wolf.  How have domestic dogs changed during this period?
      One area that changed at the genome level is the dog’s ability to digest starches.  Natural selection says that biological variation comes about through competition.  Favorable traits allow an organism to survive and reproduce.  These traits are inherited.  Overtime favorable traits passed on to offspring become common in that population.  This leads to later generations becoming distinct from their ancestors.  Has this happened with dogs in the area of digesting starches?
      A group of scientist recently identified “3.8 million genetic variants used to identify 36 genomic regions” that they feel are “targets for selection during dog domestication” in the gene sequencing of dogs and wolves.  They identified ten genes which they felt were associated with the dog’s ability to process starches as compared to wolves.  The scientists used pooled DNA from 12 wolves from differing locations on the planet.  They looked at the genetic material of 60 dogs from 14 different breeds.  They identified “3,786,655 putative[ii] single nucleotide polymorphisms[iii] (SNPs) in the combined dog and wolf data.  1,770,909 (46.8%) of which were only segregating in the dog pools.”  The scientists among other things looked for areas in the genes which had changed between the wolf and the dog.
     They discovered 10 genes which related to starch and fat metabolism.  They “proposed that genetic variants within these genes may have been selected to aid adaptation from a mainly carnivorous diet to a more starch rich diet during dog domestication.”  Humans begin digestion of food in the mouth through chewing.  Human saliva carries the enzyme amylase which begins the breakdown of starch.  Prey model diet supporters often claim that because the dog produces no amylase in their saliva, they cannot digest starches.  Dogs do not chew their food.  Digestion for dogs begins in the stomach and dogs produce amylase in their pancreas to aid in the digestion of starches.
     Somewhere in the distance past dogs began to duplicate the pancreatic amylase gene.  When the scientists looked at the gene in 136 dogs and 36 wolves they found that there was a 7.4 fold average increase in the expression in the dog as compared to the wolf.   Dogs can much more readily produce the amylase enzyme than can wolves.  Maltase-glucoamylase, a brush border membrane enzyme, also plays a role in the final steps of the digestion of starch.  When the scientists looked for differences between wolves and dogs in this area they found that dogs showed an increase in changing maltose to glucose when compared with wolves.  The scientists finally looked to see if the converted glucose was being absorbed through the membrane of the small intestine more efficiently by dogs than by wolves.  What they found was that only one of 19 wolves carried the inherited  gene sequence which allows the processed starch to be absorbed through the luminal plasma membrane while all dogs tested carried the haplotype[iv] with 63 being homozygous[v] and eight heterozygous[vi].    The scientist concluded “ we have presented evidence that dog domestication was accompanied by selection at three genes with key roles in starch digestion.”[vii]
     What does this mean for the diet of domestic dogs?  If one is looking for a diet based on wild canines than the evidence indicates that one would choose an omnivorous diet.  This diet allows for variety including fruits and plants as well as raw meat and bones.  Canines unlike felines taste sweets.  It is one of the reasons chocolate appeals so much to dogs and can lead to unintentional poisoning and even death.  Dogs can and do enjoy berries, water melon, carrots and many sweet tasting plant based products just as we enjoy them.  But more importantly they can digest them.  They have the enzymes needed to digest, absorb, and utilize starches.  Thousands of years separate dogs and wolves from their common ancestor.  Dogs adapted to living with man and sharing his diet and this adaptation is present in their genes today.




[i] Pat Shipman, “Do the Eyes Have It?: Dog Domestication May Have Helped Humans Thrive While Neandertals Declined,” www.americanscientist.org, accessed April 25, 2013.
[ii] A gene is putative when no action has been assigned to it.
[iii] Genetic variation in a DNA sequence occurs when a single nucleotide in a genome changes. This is called a mutation.  Successful mutations are those that enhance an animal’s ability to survive and reproduce.
[iv] Haplotype are genes which are close together on the same chromosome but are less likely to combine
[v] Homozygous means having two identical genes at corresponding locus (locations) on homologus chromosomes.
[vi] Heterozygous means having differing genes at one or more corresponding locus on a chromosome.
[vii] Erik Axelsson, Abhirami Ratnakumar, Maja-Louise Arendt, Khurram Maqbool, Matthew Webster, Michele Perloski, Olof Iberg, Jon Armemo, Ake Hedhammar & Kerstin Lindblad-Toh, “The Genomic Signature of Dog Domestication Reveals Adaptation to a Starch-rich Diet,” www.nature.com, Accessed April 15, 2013.

Friday, November 30, 2012

Achieving Genetic Diversity within the Pure Bred Dog Community

     There is a not so silent war raging between pure bred dog breeders and so called designer dog breeders.  It is a war of words and it gets nasty.  This post is not about creating a new trendy dog breed for financial gain.  It is about the health of dogs.  All dog breeds, almost without exception were yesteryears designer dogs whether pure bred dog breeders want to admit it or not.  The dog genome has been mapped.  Dog breeds fall into five different clusters, the vast majority of breeds falling into just one cluster.  What does this mean?  All these breeds have common ancestors.  One could illustrate it by thinking of dogs as being a basic white cake.  To make the cake more interesting one person might add chocolate frosting and roses, another strawberry frosting and gumdrops, still another chooses lemon frosting and orange peals.  All three cakes taste different but at the heart they are still just white cakes.   What one sees as breed diversity is simply the outside phenotype (the frosting) with a few behavioral modifications (the decorations.)
     It is only in the last century that we have fallen into the mystic of the pure bred dog.  It is fashionable to say I own a registered Golden Retriever or Border collie or Pekinese or now the Shih Poo.   The genetic problems seen today in pure bred dogs will appear in the designer dogs if their breeders go down the same path purebred dog breeders have been following for years.  Closed stud books lead to loss of genetic diversity and major behavioral and physical problems.  What does loss of genetic diversity mean and how can this trend be slowed or even eliminated?
     One study of genetic diversity of pure bred dogs using pedigree analysis found evidence of inbreeding in 9 of the 10 breeds sampled and the loss of genetic diversity >90% over six generations.   Two.one million dogs were studied during this research.  Part of the researcher’s conclusion states “On the basis of these results, we concur with LEROY et al. (2006) that remedial action to maintain or increase genetic diversity should now be a high priority in the interests of the health of purebred dogs. Possible remedial action includes limits on the use of popular sires; encouragement of mating’s across national and continental boundaries, and even the relaxation of breed rules to permit controlled outcrossing.”[i]  What does this study imply? 
      One of the arguments among pure bred dog breeders is that there is plenty of diversity out there because of population numbers.  But do x number of dogs equal diversity?  No.  It doesn’t matter if here are 50 dogs in the gene pool or one hundred thousand if the genetically the dogs are closely related. It is not distance or numbers which adds diversity.  Two.one million dogs is a lot of dogs and yet inbreeding was present in almost all of the pedigrees.  What does this mean?
     For pure bred dogs and their breeders it means the animals are more prone to genetically based health issues and a drop in fecundity. Closely bred dogs have more difficulties breeding and in producing viable offspring.  What then is the answer?  Controlled outcrossing. Two simple words that for pure bred dog breeders and most kennel clubs are considered dirty, sacrilegious, and worth starting at least a verbal battle over if not a physical one.  Why is controlled outcrossing sinful in the sight of breeders? And what can advocates of this simple effective means of breathing new life into what some scientist believe is on the road to extinction, the pure bred dog?
     Breeding dogs as it is practiced today involves inbreeding, line breeding and outcrossing within the breed itself.  To illustrate let’s put humans in the place of dogs for a moment.  Inbreeding is breeding two closely related individuals together such as mother to son, father to daughter, or brother to sister.  Genetic testing has revealed a five generation family tree for King Tut, with brother to sister couplings.  Two still born fetuses are believed to be Tut’s daughters by his half-sister. Both fetuses showed genetic abnormalities.  Tut suffered from a genetic bone disease which entails low blood supply to the bones and he had a club foot.  Continued inbreeding within this royal line led to much suffering and eventually the loss of viable offspring.  This is one example of what happens in humans when inbreeding is followed consistently.
     Line breeding entails breeding related individuals such as cousins.  The male descendants in the line of Queen Victoria of England suffered from Hemophilia B.  DNA testing of the recovered bone fragments of Alexei, the son of the last Tsar of Russia revealed the child suffered from the genetically inherited disease. Many of the ruling houses of this era were related to Queen Victoria and so the disease spread throughout these lines.  For example the three main players of WWI, King George V, Kaiser Wilhelm II, and Tsar Nicholas II were all first cousins.  Victoria was called the grandmother of Europe.  Her struggles to bring the ruling houses of Europe into one family through line breeding ultimately affected the health of them all.
     These examples of inbreeding and line breeding in humans are presented to demonstrate that where humans are concerned most individuals and probably 99% of pure bred dog breeders would agree that inbreeding in humans is a bad thing.  Incest is forbidden across most cultures.  Yet the same individuals fail to connect that continued line and inbreeding in dogs produces the same results seen in humans.  Genetically all species reproduce in the same manner whether they are human animals or canine animals.  What is the answer?  Most breeders would agree that outcrossing and genetic testing within the breeds will help eliminated inherited deficiencies? 
      This is not entirely true.  Pure bred dogs by definition are a closed gene pool.  There are no true outcrosses within breeds because as the above research shows, purebred dogs are related genetically.  Breeders are in fact line breeding when they think they are out crossing.  Most breeds can be traced back to a handful of distinct individuals.  Eliminating genetic carriers of disease does nothing more than decrease the gene pool still more.  The only way to introduce genetic diversity into these closed groups is through controlled out crossing.  What is controlled outcrossing?
     Controlled outcrossing is the breeding of a line of pure bred dogs to individuals of another breed (or a mixed breed dog.)  Doesn’t this make the offspring mutts?  Here’s the issue that has kept stud books closed to the determent of dogs and it is about exclusivity.  It is a form of eugenics.  When practiced within a human society it led to the atrocities of Nazis in WWII.  It was designed to purge inferior elements from the human race, the mutts of human society.  Rather than detrimental controlled out crossing or heterosis as it is called consistently produces healthier individuals with increased vigor and increased fecundity.  The old adage that mutts make better pets from an overall health point of view is probably true.
     What Basenji breeders did in in the 1970s and 80s, whether they considered it as an experiment in heterosis or not, is a good example of controlled outcrossing.  They went to Zaire and collected dogs to bring back to the United States including one bitch that was already in whelp.  Careful crossing between these African imports and American bred Basenjis began.  Were these individuals lovely examples of what Americans think of as the ideal basenji?  No, but with time and effort the individual offspring of these matings conformed more to the standard. This is what one individual reported on the results of this controlled outcrossing:
 Of the approximately 260 Basenjis having an Avongara or Esenjo in their pedigree, all have tested as outstandingly healthy! No other line has been so intensely tested as these two, and no other line has generated so many healthy animals. As per a list of the US Basenji Club:
Fanconi 0
Dysplasia 1
IPSID 2
Fanconi, PRA or IPSID when crossed with a purebred 2

With results like these, there’s really little left to discuss!
Author's Beloved Basenji, Pharlap
These crosses have been shown to be a complete success for the Basenji breed!”[ii]
    
This is controlled outcrossing and it works.
     What will it take to improve the lives of pure bred dogs?  It will take courage on the part of breeders.  It will take thinking outside of the box of popular rhetoric of what is or is not a pure bred dog.  It will take effort as it did with the dedicated Basenji breeders who spent years working to improve the phenotype of these crosses.  What it produces is a stronger healthier gene pool with added vigor and fecundity.

    



[i] F. Calboili, J Sampson, N Fretwell, and D. Balding, “Population Structure and Inbreeding from Pedigree Analysis of Purebred Dogs,” Genetics, May 2008, 179, 593-601.
[ii] “About the African Stock Project,” www.brassica-basenjis.de/b_africans-e.htm, accessed 11/30/2012.

Tuesday, October 30, 2012

The Grey, Wolf Depiction in the Popular Media


Recently I watched the movie The Grey and was again struck by how the media depicts wolves.  In spite of years of research into this shy, human avoiding canid we are still demonizing it in popular movies and books.  Why?  What is it about wolves that make them the target of such misinformation?  Why are they still the predator we love to fear?
     Our ancestors hunted the wolf to near extinction in the United States?  Our fairy tales depict them as killers.  Even in these most “enlightened” times controversy about their release back into their former habitats engenders passions ranging from indignation to pure hatred.  Why does the wolf pose such threat that grown men go weak in the knees at the thought of them skirting the edges of civilization?  Are they the revenge ridden killers depicted in moves like The Grey and Frozen?  Are they waiting in anticipation of their next juicy human meal?  Should plane crash survivors and ski enthusiasts tremble at the thought of being lost in a frozen landscape? What do the statistics tell us?
     Fifty-nine people have been killed by bear attacks in the U.S. since 1990.  Cougars have killed eleven.  During the last sixty years there have been over 350 injuries from alligator attacks.  One hundred and fifty people die from bee stings. Nearly eight thousand people are bitten by venomous snakes each year. Man killing man, 13,800 in 2011.  Number of wolf attacks in the last ten years?  Two!  One attack is controversial as indications of bear were also found at the site.  DNA evidence confirmed however that the other victim was indeed killed by wolves. (I want to express here that I feel deeply the death of Ms. Berner.  It must be absolutely terrifying to be attacked by any animal including man.  My deepest sympathy goes out to her family and friends.)  What does the statistical evidence indicate?  Wolves do not deserve their “Big Bad Wolf” reputation.  We are low to nonexistence on their list of valuable food resources.
     Why was Ms. Berner attacked and killed?  We will never know for sure, but there were several indicators at the scene to what might have happened.  Ms. Berner was jogging alone on a path with underbrush.  It seems that the wolves and Ms. Berner encountered each other in a blind curve.  The wolves should have been aware of Ms. Berner’s presence as the wind was blowing in the wolves favor.  At some point the victim turned to retrace her steps.  When encountering strange domestic dogs the big no, no is to turn and run.  It triggers a prey response.  Could this have happened in Ms. Berner’s case?  She was a small woman.  Did she start to scream?  I am certainly not making excuses for what happened, but after years of working with dogs I have learned you stand your ground, turn your body slightly away from the dog and do not make eye contact.  You never ever run.
     Once I was out with a group of women canvasing door to door.  When we were halfway up the sidewalk of one particular house, a large mixed breed dog came running around the house from the rear area.  This dog was bordering on the red zone.  The other women turned and ran for the car.  I stood still, lifted one arm and pointing directly at the dog, shouted “no.”  The dog stopped in its tracks.  I then slowly backed up, continuing to face the dog until everyone was safely in the car.  I have no doubt that had I not been there someone would have been badly bitten.  What would have happened in Ms. Berner’s case had she stood her ground we will never know.  We do know from the evidence that the wolves were not stalking her.  It was a chance encounter that ended tragically for both Ms. Berner and the eight wolves that were killed as a result, only one of which was subsequently proven to have taken part in the attack. 
     The Grey depicts wolves as being revengeful and relentless, even in the face of fire and human aggression.  They kill not for food but from some vaguely suggested desire to defend territory.  In Frozen the wolves hang around for hours waiting for the slim possibility that a human is going to fall from the sky.  None of these scenarios are even vaguely probable.  As I always tell my husband when watching a particularly foolish film “You must suspend reality.”  These moves take a lot of suspending. So why when it is obvious that humans are far more likely to dispatched by a bees than wolves, are wolves still viewed as venomous?
     First there is simple economics.  Wolves occasionally kill livestock and livestock equals dollars.  In an article discussing predation in Montana, wolves accounted for the second highest rate of death from predation in calves and lambs (coyotes get the number one spot.) However, the same report indicated an increase in predation from bear and mountain lions.  But who was blamed for even these deaths?  Wolves!  The reasoning being if wildlife management didn’t spend so much time concerned with wolves, they could take care of those other pesky predators.  Wolves it seems really are the root of all evil.  So what are the costs economically for allowing wolves to roam in one such state, Montana?
     There are 2.5 million cattle in Montana and 225,000 head of sheep.   With the average price for a feeder steer going from 150.00 to 220.00 a head and a lamb selling for 121.00, let’s just see how much wolf predation is costing the farmers of Montana.  Of the 2.5 million cattle in Montana in 2010, wolves took 458 calves.  Of the 225,000 head of sheep, wolves ate 796.  So wolves cost cattlemen (let’s be generous and say each calf killed was valued at 225.00,) $10,305.00.  They cost sheep herders $9,950.00.  About 1300 animals were lost in one state in one year from wolf predation.   However, if the rancher reports the kill within twenty-four hours and it is determined that the animal was indeed killed by a wolf, the rancher is reimbursed the fair market value of the animal.  A lot of the land these cattle and sheep are grazing on is publically owned and leased to ranchers at a minuscule rate. The livestock displace many of the wolf’s naturally occurring prey.  As one rancher put it “If it don’t benefit man, what good is it?”
     That statement brings us to the second reason wolves are so feared, ignorance.  Kentucky is without a wolf population yet a man recently claimed to have shot a wolf.  How did he know it was a wolf?  He stated that he knew it was a wolf because it was vicious.  Are wolves vicious?  What is the normal reaction of wolves when encountering humans?  Healthy wolves which have not become habituated to people avoid them.  When wolves are habituated to people such as from feeding at garbage dumps (one sees similar behavior in bears,) they are more likely to behave aggressively if they perceive the human as doing something unexpected or threatening.   They are also much more likely to be aggressive if the human is accompanied by a dog. Mark E.  McNay complied information on 80 wolf/human encounters in Canada, Alaska, and Minnesota.  What he discovered was that in 39 of the encounters healthy wolves demonstrated some element of aggression, 29 encounters proved nonaggressive and 12 involved rabid wolves.  Sixteen encounters resulted in healthy wolves biting people or their clothing.  McNay states that most of the bites were minor and none life threatening.[i]
      Habituated wolves can and do bite people but so does the family dog.  Dogs kill on average 12 people per year in the United States. We bring dogs into our homes and that is where most fatal dog attacks occur.  Wolves have killed (that we are aware of) one perhaps two people over the last ten years, dogs have killed well over 100 people yet we do not view dogs as vicious and expendable.  They are not depicted as soulless monsters seeking the destruction of helpless human prey.  Since gray wolves have been removed from the Endangered Species list, states like Montana are once more aggressively working to eliminate wolves from the lower forty-eight states. Before the ban on hunting there were around 650 wolves in Montana, 650 wolves compared to 2 million cattle and 200,000 sheep.  Wolves are neither furry angels nor fanged demons.  Do they benefit man?  Are they worth defending? Do we need them?  Perhaps the real question is, can we accept them for what they are, wild canids, nothing more nor less, which are part of the natural world.


 



[i] M. McNay, “A Case History of Wolf-Human Encounters in Canada and Alaska,” http://146.63.61.200/static/home/library/pdfs/wildlife/research_pdfs/techb13_full.pdf, accessed 10/30/2012.