Shar-pei - the eyes have it

Have what?

Well, quite often entropion - the turning in of the eye margins causing damage to the dogs' eyes.

It is a direct consequence of the wrinkling/skin folds that have become a defining feature of the Westernised version of the breed but was never a feature of the original Shar-pei (see here).

And, indeed, it is is so bad that "tacking" is routine in the breed -  a procedure in which the vet places sutures around the eye when the dogs are pups to prevent the eye surface being injured by the inward rolling of eyelashes.

This often does the trick; sometimes, though, Shar-pei need more surgery to correct the entropion when they are older.

Shar-pei breeders are so de-sensitised to this that tacking (and entropion surgery) is not considered a big deal in the breed. In fact, in the twisted logic adopted by some breeders, tacking is actually considered a sign of a responsible breeder. And although the Kennel Club dictated a few years back that dogs that have had their eyes tacked cannot be shown, insiders tell me that an awful lot of show dogs will have had their eyes tacked as pups. It is hard to prove one way or the other.

But there are some breeders taking a stand and one in particular I'd like to praise.

Three years ago, I blogged this photograph, as featured in a book by the photographer Tim Flach. As you can see, this very wrinkled eight-week-old pup is sporting a stitch above her right eye - a "tack".

It turned out that the pup was bred by a UK-based breeder called Ines Alarcao. She took quite a lot of stick at the time and has since withdrawn from showing.

But she's kept breeding Shar-pei and she recently sent me these pix of her current litter of eight pups. Here they are at six weeks old. They all have clear eyes and not a single one has had to be tacked. They also have fewer wrinkles and bigger ears (breeding for very small ears in Shar-pei has led to tiny ear canals prone to ear infections).

Have a look at these photos and then see below for what Ines says about these pups.

It's a big improvement - at least in terms of their conformation.

I asked Ines how she had achieved it:

"I bought two girls from different lines four years ago , with reasonable eyes and not many wrinkles and good ears. I have mated them with guys with the same features. One of them produced a blue boy with excellent eyes, the other produced a girl with good eyes too, and  I have now mated these two together and produced this guys.   Some people say that good eyes are a matter of luck. Not true! But I had to find it through trial and error. I am keeping two girls from this litter , I bought another one that has got less wrinkles and more traditional features, and I have another 6 mth-old girl that i bred and kept with really good eyes. My new breeding program will  be based on them."

Now these pups are still too immoderate for me. And, in my opinion, this breed is too inbred and has too many inherent health problems (notably Familial Shar-pei Fever) to be able to justify breeding it at all.

But I really was pleased to see these pix. A step in the right direction.

Lola the Bulldog: tu-tu much

Now I'm all for a good party. And I don't have any inherent objections to dogs being dressed up.

But let's not pretend that this is for the dogs, eh? Especially when the party girl has to be taken out every 10 minutes and be blasted with air-conditioning to stop her collapsing (see from 10.31).

See how Lola tries to take the matter into her own hands at 11.15 minutes in with a blatant attempt at suicide.

Suspect this video will be taken down pretty quickly... enjoy, or otherwise, while you can.

Pedigree Cats Exposed

Extreme cats at the Supreme Cat Show at the National Exhibiton Centre in Birmingham today.

We didn't just fuck up dogs.

We tried very hard to persuade the BBC to commission Pedigree Cats Exposed but after much deliberating, they turned it down. "Too like the dogs" was their verdict.

Well exactly. 

Haven't quite given up yet. 

What has cheap genome sequencing done for dog science lately?

So you have the full sequence of a couple few dog genomes, and a wolf genome to boot. (Yes, these days sequencing is cheap enough that genomics researchers can do this. There are more errors in these less expensive, “shallowly sequenced” genomes than the one that we use for the standard canine reference, but even with errors, you can still get the whole genome to play with.) So you have these genomes. And you are curious about domestication. What makes a dog different from a wolf? These genomes each are made up of millions of nucelotides, so when you do a straightforward comparison between dog and wolf, you get hundreds of thousands of differences in nucleotides, ranging from single nucleotides that are different to long stretches where chunks of the genome are repeated in one species but not the other. And what to make of the differences between pairs of dogs — are those important too? It can seem an overwhelming problem.

Luckily, in addition to having fast and cheap access to full genome sequences, we also have powerful computers for analyzing these sequences (and one of my favorite parts of my PhD program is that I get to use my programming skills in addition to my biomedical skills). What people do is think of patterns that suggest that certain areas are the interesting ones, and tell computers to look for those areas. It turns out that if you have a couple of genomes of animals of the same species, you can compare them to find regions where there is very little variation between animals. This suggests that this area is important — everyone has to have exactly the same sequence here, because anyone who has any differences is less fit and less likely to survive to pass on their genes. This is called a selective sweep, because at some point in the past, this change swept through the genome and everyone eventually got the identical copy of this region.

For an added bonus, if you have the ancestral species — in this case I am obviously talking about wolves, which are ancestral to dogs — you can compare this region in that species. If you find that this region is the same in all the dogs but different in the wolves, you have an area which is highly suspicious for being involved in domestication. So you can ask a computer to go find some of these low variation regions for you,

There are a lot of statistical tests that you can do to convince yourself that this area has sufficiently low variation to be interesting, but that area doesn’t, and it has been my pleasure this week to be reading about those in great detail. (Being a grad student rocks, but then sometimes there is statistics.) But the most recent papers I have been reading have pretty much done away with statistical tests to convince themselves that certain areas are involved in domestication. What they have done is to use stats to find areas that are just potentially interesting, and then they actually go look at the areas and see what they see. What known genes are in that area? Anything that could have to do with domestication? Yes? So let’s see how that gene differs in a whole bunch of dogs and wolves. The same in all the dogs, and different from that in all the wolves? Awesome. So what does this gene actually do? Can we understand how the genomic change between dogs and wolves — the mutation — changed the protein? Did it change the protein’s function? Or maybe dogs make more, or less, of that protein. Labs have just been selecting specific genes from these areas and investigating them intensely and seeing what they find out.

The best example of this approach (and the one I find the most interesting, because it was done in dogs, not pigs or chickens like the other papers I have been reading) was published early this year. You have probably heard it if you are interested in dog domestication, because it made a big stir by declaring that dogs had evolved to be better at digesting starch than wolves.

Axelsson E., Ratnakumar A., Arendt M.L., Maqbool K., Webster M.T., Perloski M., Liberg O., Arnemo J.M., Hedhammar Å. & Lindblad-Toh K. (2013). The genomic signature of dog domestication reveals adaptation to a starch-rich diet, Nature, 495 (7441) 360-364. DOI: 10.1038/nature11837

But when you read about this paper, did you know how they figured out that dogs are better at digesting starch? They did one of these low-variation genomic scans. They found some interesting regions. They looked at what genes were in these regions. They found a lot of genes involved in digestion, so they decided to chase that first. (They also found some interesting genes that work in the brain, and hopefully we will see a followup paper on that soon.) They focused on a few genes and tried to figure out what they did and how they had changed between dog and wolf. In at least one case they found that dogs just expressed a lot more of a particular protein than wolves do, and that protein is involved in digesting starch.

There are a lot more regions to look at in dogs, and there are some interesting things to hunt down in tame foxes, too, of course. We are in a fascinating time for genomics. The technology is becoming so inexpensive that we can actually look at the code of genomes belonging to individual animals more more readily than we could just a few years ago, and this is a game-changer. There should be many more discoveries to come soon about the mechanics of canid domestication!

Frenchies: breathtaking

Now one would think that given the current focus on French Bulldogs that the breed club would have been able to furnish one for the breed stand at Discover Dogs yesterday that had, you know, nostrils.

But no. There wasn't a nostril between them.

Cataracts too... perhaps just an older dog

Dogs pant through their mouths - but they breathe through their nostrils. To get an idea of what this feels like, close your mouth and pinch your nostrils. Even the slightest pressure feels awful. Increase it and it's impossible not to feel panic.

This is what too many in this breed has to endure. The restricted airflow means the dogs have to make an increased effort to breathe which leads to (or is accompanied by) a host of airway pathology, often requiring surgery.

Stenotic nares - before and after surgery

The breed Club had a lot of info on the stand on Frenchie health and they talk such a good game re health that the Kennel Club has just taken them off their high profile breeds list despite there being little concrete evidence that this breed has improved (see here).

But ask yourself this: if they were really that concerned, would they have allowed these dogs to be put on display as examples of the breed?

I can only see two other possible reasons:

Either they are ignorantly unaware of the suffering caused by breeding dogs with stenotic nares like this.

Or there aren't any Frenchies with normal nostrils.

Not of course that the public, equally culpable in all this, gives a shit. The French Bulldog breed stand was packed with lots of people cooing over the cute little dogs with the smushed-in faces.

Registrations for this breed are going through the roof.

There were just 349 French Bulldogs registered with the Kennel Club in 2003. Last year there were  4648 and, in just the first three quarters of this year, 4843.

I will be attending this event tomorrow... looking forward to it.

Bassets... too true

Spotted at the Kennel Club's Discover Dogs Show in London today.