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For most of my life, we have thought of snakes as being closely related to lizards. Both snakes and lizards are squamates (the order Squamata), but all my childhood reptile books placed snakes as being part of a distinct suborder called Serpentes.

However, taxonomy has moved onto a cladistic model, where we group organisms based upon their common ancestry. A clade is defined as including all descendants of a common ancestor, and keeping snakes a specially defined entity distinct from lizards is problematic.

A recently published paper on the Komodo dragon genome reveals why this is a problem for a cladistic classification model.  The authors compared the genomes of komodo dragons with the Burmese python, several species of lizard and lots of other tetrapods.

A phylogenetic tree was drawn from the comparisons.

komodo dragon genome phylogenetic

The Burmese python does not fit outside of the “lizard” clade. It fits within that clade, and if we are to use cladistic classification, then we must place snakes within lizards.

Snakes are a particularly specialized form of lizard, and as it should be noted, they are not the only legless lizards known. There are glass lizards and worm lizards (some of which are not entirely legless) that have a similar sort of body design to the snakes.

Snakes are the most wildly distributed legless lizards, but we probably should recognize them as lizards and not some sort of special grouping distinct from lizards.

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beowulf

Humans have an aversion to inbreeding. We find the idea of two humans from the same family marrying and having children quite disgusting.

We also know that wild dogs have strong inbreeding avoidance behavior. Wolves and African wild dogs generally avoid mating with blood relatives. Most domestic dogs will mate with their relatives without reservation, and inbreeding has been a tool that dog breeders have used for centuries to establish type and promote homogeneity in their strains.

I have been a critic of inbreeding domestic dogs, but I now realize that I was cherry-picking the science a bit and playing up to human aversion to inbreeding to give a fully nuance and accurate understanding of what inbreeding can do to domestic dogs.

Inbreeding does tend to reduce MHC haplotype diversity over time, which can make dogs more susceptible to various maladies.  It also can increase the chance of deleterious recessive alleles from being inherited homozygously.  All of these are potential risks from inbreeding.

However, I would be remiss to say that inbreeding has not always been a horrible.  Indeed, certain breeds have been founded through a rigorous inbreeding and selection process that surely cannot be thought of as entirely disastrous to the strain.

A few years ago, I came across a book called Working Sheep Dogs: A Practical Guide to Breeding, Training and Handling by Tully Williams. In the text, Williams refers to Kyle Onstott’s work on dog breeding in which Onstott mention an experiment at the Wistar Institute involving rats. A “Miss King,” writes Onstott, bred rat siblings for twenty generations with a strong selection for vigor and stamina, and after twenty generations, she produced a strain of rats that were longer-lived, larger, and generally healthier than the average laboratory rat.

Onstott was a dog breeder and novelist, and his book on dog breeding was considered revolutionary when it was published in 1962. It is called The New Art of Breeding Better Dogsand I have been trying to get my hands on a copy.  However, I was able to glean from the names mentioned in Williams’s quote of Onstott that the “Miss King” of the Wistar Institute is Helen Dean King.  Dr. (not “Miss”) King was one of the early researcher on the question of inbreeding, and one of leading lights of the Wistar Institute’s rat breeding experiments.

I was able to find her study in which she was able to create the super rats strain through inbreeding, and yes, she was able to do so through rigorous selection for vigor.

In dogs, it is difficult to find a similar experiment, but then I realized one was quite literally staring me in the face.

Most are unaware that German shepherd dogs are all quite closely related to each other. Yes, they appear to have a lot genetic diversity, because we have all these quite different working and show-bred forms, but they all derive from a very similar inbreeding experiment to the one that Dr. King performed at the Wistar Institute.

Max von Stephanitz based the breed upon a Thuringian sheepdog named Horand von Grafrath, which he then bred to Bavarian and Swabian/Württemberg sheepdogs. He then tightly bred upon the progeny. Indeed, the entire breed is based off of three grandsons of Horand. They were Beowulf, Pilot, and Heinz von Starkenburg. They were bred mostly to other descendants of Horand, and there was strong selection for temperament and vitality in the population. It is in these foundations of the breed that wolf may have been added, but the breed still derives from these three grandsons of a single dog.

We can have lots of debates about this in the comments, but the German shepherd dog as an entire breed is fairly healthy for a large breed dog.  In that inbred population, the deleterious allele that leads to a degenerative myelopathy was part of the founders, and the breed itself does have that issue.  Some eye issues were also part of the founding population.

However, if inbreeding were always such a terrible thing, every dog in the breed would be a genetic basket case. Regardless of what one might think about show dogs, the working police and military dogs derive from this exact same inbred population, and it would be folly to say these dogs lacked vigor or were universally unhealthy and unsound creatures. Indeed, it can be argued that the most useful dog ever bred was the German shepherd dog. It has that much utility in a variety of situations.

Now,  I am not saying that inbreeding problems don’t exist. I am saying that we need a nuanced understanding of what inbreeding can do to dog populations, and it is not universally a horrible thing.

Inbreeding and rigorous selection can be a good thing for a strain.  Of course, I know there are breeds that do need some genetic rescue. The Doberman pinscher was founded in much the same way as the German shepherd, using a much more diverse group of domestic dogs in the foundation strain. However, the breed suffers so much from inherited DCM that it an outcross program could very well be justified.

But those of us who advocate rationalism and science in understanding and caring for dogs must keep an open mind. We must look at all the objective science and avoid appeals to human prejudice.

That’s what I’ve tried to do here. I am correcting some of my earlier errors, and I hope this helps lead to a more nuanced view of the subject.

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dare stacked

The little Tasmanian devil is turning into a little lady.   She’s about to enter the “teething ears” phase in which she will look quite ridiculous.

 

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dare platz

Dare is learning very quickly. She has learned the difference between “sit” and “platz” (I prefer the German for her for that command), and the difference between the markers “yes” (you did the right thing!) and “good” (keep doing what you’re doing, like remaining in a sit or down position). She also has a good enough puppy recall that I can call her off the cat, which is her favorite playmate.

She has tons of ball drive for a puppy. She is already fetching toys and bringing them back to hand, which is amazing considering how many golden retrievers I know that have no natural or play retrieve to speak of.

I really enjoy training this breed. I find them far easier than any gun dog.

She is also learning valuable lessons from other dogs. If she gets rowdy playing with the whippets and runs over sleeping Erika, Erika will correct the puppy for her rudeness.  She has acute awareness of other dogs’ body language.  She respects the elder dogs, but she also enjoys playing with them.

She has a genetically sound temperament, but she is getting the upbringing she truly deserves to become a super dog. I cannot be prouder of this little pup.

fetching dare

 

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gsd wolf

So in the early days of this blog, I was wrong about something.  I wish I had never written a word about German shepherd structure and hips,  because I was essentially parroting nonsense that I’d read somewhere without asking for documentation. The rear angulation of the dog is not related to hip dysplasia. There are plenty of dogs with “extra: rears that have OFA excellent hips.

Also, although one can get worked up about “hock walking,” no one is actually intentionally breeding a German shepherd to walk on his hocks. The goal is to produce flowing side movement, where the dog opens up in the rear and shoulder.  Some dogs may walk on their hocks, but if the dog is just going to be a pet, it’s not a major welfare issue. We have some studies on GSD longevity that show that skeletal and spinal issues are a major reason why they die, but those studies do not provide a break down about the dog’s actual conformation or if the dog died of a condition called degenerative myelopathy, which is a genetic condition that results in the dog’s spinal cord degenerating when it is an older dog.

I know there will be people who refuse to believe a single word I’ve written in these two paragraphs, and they will comment away about what an idiot I am for changing my mind. I honestly don’t care. I have looked at the same evidence you have, and I don’t find it convincing.

At the same time, though, people who have written and promoted the position that I once held about German shepherd structure have unintentionally set the breed up for failure in pet homes.

When we go on and on about how terrible the show dogs are, the pet buying public will naturally turn to breeders who have dogs that lack the rear angulation. The vast majority of German shepherds bred without this angulation are those bred for bite-work or for bite=work competitions. These are wonderful dogs.  It was one of these dogs that turned me into a lover of the breed.

But they are not for everyone. These dogs have lots and lots of drive. They are smart. Some have really high defense drive and little social openness. Some poorly-bred ones are sketchy, and yes, some poorly-bred show dogs are sketchy freaks too.

But when the best dogs of this type are very high drive dogs and the worst are potentially dangerous, you are setting the public up for a disaster. People are getting super working dogs that need constant work and training just to feel content in the home, and the owners work 40 or 50 hours a week.  People are also getting dogs that are neurotic and potentially dangerous.

This is not what most people want when they get a German shepherd, but because people like the me from a decade ago would go on and on about the “crippled” show lines, it has become received wisdom that the pet buying public should not buy a dog bred for conformation.

This is problematic, because most people would be better off with a conformation-bred dog. The reason is that dog shows themselves do place several unintentional selection pressures on breeding stock. A show dog is forced to deal with many, many dogs and lots of people walking around. All of these dogs are intact. Some may be in heat.  Further, every show dog must accept fairly extensive grooming (even whippets!, and they must be able to receive an examination from a judge.

A dog that has a poor temperament simply cannot go through these selection pressures, and although there are dogs that have weird temperaments that do succeed in the ring and do get bred, the general average is for a dog that is far more mentally stable than the typical pet dog.

Also, because no one is breeding show German shepherds to break through windshields to get bad guys, no one is breeding for crazy drive and pain tolerance. The show dogs do have a quite a bit more drive and a need for exercise than the typical pet dog, but their needs are much easier for the typical family to meet.

I say this as someone who loves working line GSD and who will happily own another. I say this as someone who deeply cares for this breed.

But I think we have done a poor job by our constant haranguing of the show dogs in this breed. It is not serving the breed, the dogs, or the public well.

And it is also creating divisions between breeders, the people who should be standing together to ensure that every puppy goes into a loving home and that our favorite disciplines and activities for our dogs remain legal.

So I do feel a lot of guilt for what I have written. The best I can do is correct the errors from here on out.

And if you want a pet German shepherd, check out a breeder who specializes in good conformation stock. You’re far more likely to get what you really want than if you deliberately go searching for “straight-backed” dogs on the internet. The really ethical working dog breeders will steer you away from their dogs anyway, but the working dogs aren’t the first place to look for a pet.  I’m sure there are working GSD breeders who are getting tired of the inquiries from people who are just seeking pets.

So all this rhetoric about crippled show dogs has done a very poor service to the breed. I am deeply sorry that I participated in it.

 

 

 

 

 

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xolo

The dog world is always an interesting place to observe human behavior.  A few days ago, someone posted a coated Xoloitzcuintli (“Mexican hairless dog”) on an FB group, and I happened to mention the new evidence about the genetics of this dog breed.

This breed has a strong connection to the Mexica/Aztec identity in Mexico. The dog has a Nahuatl name, and when we discuss the Americas pre-Conquest, the civilization that existed in Mexico  was certainly the equivalent of anything in the Old World.

The mutation that causes hairlessness in these dogs has been traced to Mexico around 4,000 years ago. It is conferred by an incomplete dominant allele, and thus, it was able to spread from Mexico into South America, where hairless village dogs still exist in some areas.  Later, these hairless dogs were crossed with various toy breeds to found what has (laughably) been called “the Chinese crested dog.”

Further, we have really good evidence that shows that the indigenous dogs of the Americas were replaced with a genetic swarm of European dogs. This means that the xoloitzcuintli, though it has this mutation that originated in the Americas, is mostly European dog in its ancestry.

What is even more shocking is that a genome-wide analysis that traced the origins of many dog breeds found that the xolo fits in a clade that includes the German shepherd, the Berger Picard, and the Chinook. When a prick-eared regional Italian sheepdog called a Cane Paratore is added to the analysis, the xolo and the Peruvian hairless dog fit closer to that breed than the GSD and Picardy shepherd.

If one thinks about the history of Mexico, the Spanish became deeply involved in turning Mexico into a great place for herding cattle, sheep, and goats, and it would make sense that the typical dog that would have been brought over would have been an Iberian herding dog that is probably quite closely related to the Cane Paratore.

So more analysis was performed with an emphasis on Italian dog breeds. Some of the clades changed position, but xolos and Peruvian Inca orchid dogs remained in this clade closely related to the German shepherd, the various Italian herding dogs, the Berger Picard, and the Chinook.  The Catahoula leopard dog, a celebrated cur dog from Louisiana that is said to have derived from French and Spanish herding dogs brought over by colonists, were found to be closely related to the xolos.

This means that the dog called the xoloitzcuintli is mostly rough pastoral dog from the Iberian Peninsula, and it is not an ancient American breed.

I mentioned all this information on that Facebook group, and it was as if I blasphemed against the Almighty.

Sadly, we have almost lost an entire lineage of domestic dogs. The Conquest of the Americas and the resulting Columbian Exchange changed the genetic fortunes of humans and animals on these continents.

And though people would love for the xolo to be this untouched pure strain of dog. It simply is not.  In fact, it is very heavily admixed with southern European herding dog to the point that the dog is almost entirely that in ancestry. If that hairless trait were not dominant, it likely would have disappeared in the Mexican village dog population, and there would not have been any suggestion that these dogs were anything special.

So by a fluke of the allele, a mostly European herding dog-derived village dog from Mexico became the ancient dog of the Aztecs.

Yep. I ruined that one, too.

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dog_food_brands_named_most_frequently_in_dcm_cases_reported_to_fda

I don’t like posting dog food controversies on this blog, simply because dog food leads to lots of fights.

A few years ago, it was revealed that dogs had more copies of gene that leads to the production of amylase than wolves do. Amylase is used to convert starches into simple sugars, and dogs with these extra copies would be better able to get nutrition from grains.  These extra copies made it easier for dogs to live in human societies that were shifting from hunter-gatherer to the modern agrarian exist.

That study means that dogs can do well on a diet that is rich in grains.  Many members the raw feeding movement,  swear that dogs must be fed only meat and organs. Some dogs do have a real difficulty digesting grain-based dog food, and they certainly would do better on this diet. However, in the raw feeding community, there is a generally held belief that virtually all degenerative disease in dogs can be traced to having corn or some other grain in the diet.

That controversy is still raging, though not in scientific circles. The real controversy with grains and dog food right now comes from the discovery of a linkage between feeding grain free dog food and dilated cardiomyopathy (DCM).  Grain free dog foods have been all the rage in recent years. They provide the convenient kibbles, but unlike grain-based kibble, some sort of legume is used to create the mixture.

Last year, there was deep suspicion that dogs fed a grain free diet were having issues with DCM, and a few days ago, the FDA released a study that shows a very strong linkage between these diets and contracting DCM.

The current hypothesis is that the legumes interfere in some way with he excretion and production of taurine, which creates a taurine deficiency that leads to the DCM.

More research needs to be done, of course.  Taurine is not considered an essential amino acid for dogs, but it very well might be.

Maybe, though, the best thing to feed a dog is a scientifically formulated dog food from a long-established company, one that has performed decades worth of research on its products.

Until we know for sure, maybe it’s safer to feed dogs one of those brands.

I certainly think so.

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