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Archive for February, 2012

From Science Daily:

Coyotes today are pint-sized compared to their Ice Age counterparts, finds a new fossil study. Between 11,500 and 10,000 years ago — a mere blink of an eye in geologic terms — coyotes shrunk to their present size. The sudden shrinkage was most likely a response to dwindling food supply and changing interactions with competitors, rather than warming climate, researchers say.

In a paper appearing this week in Proceedings of the National Academy of Sciences, researchers studied museum collections of coyote skeletons dating from 38,000 years ago to the present day. It turns out that between 11,500 and 10,000 years ago, at the end of a period called the Pleistocene, coyotes in North America suddenly got smaller.

“Pleistocene coyotes probably weighed between 15-25 kilograms, and overlapped in size with wolves. But today the upper limit of a coyote is only around 10-18 kilograms,” said co-author Julie Meachen of the National Evolutionary Synthesis Center in Durham, North Carolina.

“Within just over a thousand years, they evolved into the smaller coyotes that we have today,” she added.

What caused coyotes to shrink? Several factors could explain the shift. One possibility is warming climate, the researchers say. Between 15,000 and 10,000 years ago, global average annual temperatures quickly rose by an average of six degrees. “Things got a long warmer, real fast,” Meachen said.

Large animals are predicted to fare worse than small animals when temperatures warm up. To find out if climate played a role in coyotes’ sudden shrinkage, Meachen and co-author Joshua Samuels of John Day Fossil Beds National Monument in Oregon measured the relationship between body size and temperature for dozens of Ice Age coyotes, and for coyotes living today, using thigh bone circumference to estimate body size for each individual.

But when they plotted body size against coldest average annual temperature for each animal’s location, they found no relationship, suggesting that climate change was unlikely to be the main factor.

If the climate hypothesis is true, then we should see similar changes in other Ice Age carnivores too, Meachen added. The researchers also studied body size over time in the coyote’s larger relative, the wolf, but they found that wolf body sizes didn’t budge. “We’re skeptical that climate change at the end of the Pleistocene was the direct cause of the size shift in coyotes,” Meachen said.

Another possibility is that humans played a role. In this view, coyotes may have shrunk over time because early human hunters — believed to have arrived in North America around 13,000 years ago — selectively wiped out the bigger coyotes, or the animals coyotes depended on for food, leaving only the small to survive. Stone tool butchery marks on Ice Age animal bones would provide a clue that human hunters had something to do with it, but the fossil record has turned up too few examples to test the idea. “Human hunting as the culprit is really hard to dispute or confirm because there’s so little data,” Meachen said.

A third, far more likely explanation, is dwindling food supply and changing interactions with competitors, the researchers say. Just 1000 years before the sudden shrinkage in coyotes, dozens of other species were wiped out in a wave of extinctions that killed off many large mammals in North America. Until then, coyotes lived alongside a great diversity of large prey, including horses, sloths, camels, llamas and bison. “There were not only a greater diversity of prey species, but the species were also more abundant. It was a great food source,” Meachen said.

While coyotes survived the extinctions, there were fewer large prey left for them to eat. Smaller individuals that required less food to survive, or could switch to smaller prey, would have had an advantage.

Before the die-off, coyotes also faced stiff competition for food from other large carnivores, including a bigger version of wolves living today called the dire wolf. After bigger carnivores such as dire wolves went extinct, coyotes would have no longer needed their large size to compete with these animals for food.

The findings are important because they show that extinction doesn’t just affect the animals that disappear, the researchers say — it has long-term effects on the species that remain as well.

“In a time of increasing loss of biodiversity, understanding the degree to which species interactions drive evolutionary change is important,” says Saran Twombly, program director in the National Science Foundation (NSF)’s Division of Environmental Biology, which supported the research.

“Species interactions are delicate balancing acts. When species go extinct, we see the signature of the effects on the species that remain,” Meachen said.

This is an interesting find, but I need to make some clarifications. There are coyotes that weigh 25 kilos that are alive right now. 25 kilos is 55 pounds, and the record weight for a coyote was somewhere in the neighborhood of 65 pounds. A big Eastern coyote can be over 50 pounds in weight. It’s not necessarily common, but the upper limit for coyote size is higher than this study is claiming. Coyotes in the West tend to be smaller than those in the East, and those in the East are pretty skilled at forming packs and killing deer. Those in the West are smaller, and the smallest individuals are those that live in southern Mexico and Central America, which are in the 15 to 20 pound range.

Wolves also greatly vary in size. The smallest subspecies of wolf in North America is the Mexican wolf (Canis lupus baileyi), and it’s about the size of a golden retriever. The smallest subspecies in Eurasia is the Arabian wolf (Canis lupus arabs) which weighs as little as 25 pounds.

Both wolves and coyotes likely derive from an ancestor that was the size of a modern Western coyote. This ancestor is usually posited as Canis lepophagus, which lived in North America from 10 million to 1.8 million years ago, and it may actually be the ancestor of all dogs in the genus Canis and the two dog that should be in the genus Canis, the African wild dog and the dhole.

In North America and Eurasia, wolf and coyote/jackal sized animals have evolved at different times over those 10 million years.

It’s not clear if the coyote derives solely from ancestors that never left the Americas, or if they derive from Eurasian ancestors that they share with the golden jackal and Ethiopian wolf that came back into North America.  The earliest wolf-like Canis that appeared in North America  was Canis edwardii, which lived from about 5 million years ago to 300,000 years ago. Canis edwardii has sometimes been posited as an ancestor the red wolf, which we now know to be nothing more than a recent hybrid between the modern wolf and the modern coyote.  Others, including Ron Nowak, have contended that the coyote, red wolf, and Holarctic wolf derived from the later Eurasian wolf known as Canis mosbachensis.

Now, all of these have been posited, but there is another evolutionary tree that has been posited for evolution of Canis, which someone on Wikipedia managed to put together. It’s not made up. It actually comes from Tedford and Wang’s analysis of how Canis evolved in North America (Tedford and Wang pdf).

In this analysis, the ancestor of all Canis is Canis ferox, a species that was endemic to Central Mexico from 10.3 to 5.3 million years ago. In this analysis, the species is the ancestor of the African wild dog, Xenocyon lycanoides, is also derived from Canis ferox.  The dhole is probably derived from this ancestor, too.  The close relationship with these two extant species and the interfertile Canis strongly suggests that they should be included in the genus Canis. And so should Xenocyon.

Xenocyon was a wolf before there was a wolf. It hunted large prey, while the smaller Canis species, like Canis mosbachensis, were forced to have something like the Western coyote and golden jackal niche. In How the Dog Became the Dog, Mark Derr uses Nowak’s paradigm to claim that that the extinction of large Xenocyon from Eurasia gave the Canis mosbachensis an opportunity to fill the wolf niche. This is precisely the niche that Eastern coyotes are filling in the absence of wolves.

With this analysis, the large wolf lineage begins in Asia. The ancestor of Armbruster’s wolf (Canis armbrusteri), which is the ancestor of the dire wolf, is derived from the same lineage as Canis lupus. Both of these might actually be nothing more than earlier subspecies of Canis lupus.

So however Canis evolved, it has produced large wolf-like canids and small jackal and Western coyote-like canids at different points in history.

This study shows that modern Western coyotes have evolved a smaller size in response to fewer prey resources and increased competition from Canis lupus in a very short time period.  Dogs can change their size relatively rapidly when exposed to selection pressures. We’ve seen this in Eastern coyotes, domestic dogs, and even red foxes in England. So this finding doesn’t surprise me in the least.

The dog family is very successful. Whereas our species has been successful because we rapidly can develop new technology, dogs have been successful because their body size and shape can rapidly adapt through the generations when exposed to new selection  pressures.

This is what happened to coyotes at the end of the last Ice Age.

Now let’s see how big Eastern coyotes and British red foxes will get as they adapt to new niches that have been opened up for them in the absence of wolves.

 

 

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First of all, I am a United States citizen who has watched Pedigree Dogs Exposed: Three Years On.

I know what you’re thinking.

It was only recently show on the actual BBC, so how on earth could I have seen it already?

We have our ways. Over at BorderWars, Chris will show you how, and he now has links to the first Youtube uploads of program. These will likely be taken down soon, so I’d get over there posthaste.

Now, there is a lot of good in this documentary.

Well, initially, Jemima Harrison promised to put up a positive and optimistic portrayal of what breeders are doing to solve problems.

And in the case of Fiona, the LUA Dalmatian, she did. Fiona’s breeder is portrayed as the forward thinking breeder that she is, and she  makes a nice point. Not a single one of these dog breeds was created by nature. Their bloodlines are not written in stone, and if modern science says we need to sully the purity of these bloodlines for increased health, we should do it.

The other breeds discussed in the documentary don’t have very good stories.

The Cavalier King Charles spaniel may be utterly ruined. The incidence of syringomyelia in the breed has increased. A large majority of those bred in the UK will be affected by the disorder in some way by the six years old– and virtually all of them have mitral valve disease by the time they are ten.  Carol Fowler, the campaigner for Cavalier health in the first PDE, now says it may no longer be responsible to be breeding any dogs of this breed.  The risks of a breeding producing dogs with these disorders is so high that it may no longer be ethical to produce them. That’s very sad.

And the UK boxer population is going down virtually the same route. Dr. Bruce Cattanach has discovered that juvenile kidney disease in boxers has an hereditary basis, and he was able to trace this disease to a single popular stud boxer. And then he traced it to a single top show kennel in the UK. Because these dogs win a lot of shows, their studs are in high demand, which means that a huge proportion of boxers produced in the UK are going to derive from these dogs. And they are likely doomed to die at very young ages.

And then there’s the pug. I actually learned quite a bit about exactly how awful it is for a dog be bred with such a brachycephalic face. I have often mentioned that these dog have a hard time breathing and cooling themselves, but I didn’t know that the big sinus in a dog’s muzzle is quite crucial to its cooling system.  In normal dogs, this sinus is pretty large, but in pugs, it is almost vestigial, and the dogs cannot cool themselves at all.

Pugs have such a hard time breathing that many cannot sleep well lying down. They always want to have their heads propped up a bit. The documentary shows the classic Youtube video of a pug falling asleep sitting up, which is something we all think is cute.

But it’s not. The truth is these dogs would like to sleep like normal dogs, but they just can’t breathe properly.

The documentary then shows a German veterinary surgeon who specializes in correcting the various problems associated with the brachycephalic dogs and their airways– which is now called brachycephalic airways syndrome. The surgeon is shown working on a pug. He makes its nostrils larger, and he pares back some of the soft palate in the back of the throat. He opens up the airways more. The same airways that bizarre selective breeding has clogged up.

Even though this film used a lot of recycled footage, I think it was a better documentary than the first.

I think its real strength is that Harrison clearly divided the problems with purebred dogs into the two distinct categories that should not be confused.

One of these is gene loss through inbreeding. I think she made a good attack on breeders who do really, really tight breedings. However, I don’t think that’s the biggest issue. The problem isn’t that these breeders are doing these kind of breedings. The problem is that these dogs exist within closed off populations, and an elite number dogs produces a huge chunk of the puppies born every year. Even if people are  not doing very tight breedings with their own dogs, the dogs within in a breed will become more and more related over time. And all of the dogs within a breed will descend from the same founders– unless you’re talking about Africa basenjis, Tibetan lhasa apsos, and COO salukis, which may not be as closely related to the dogs in the closed registry populations.

I know that Jemima Harrison knows these facts, and she has written about them extensively. I just think that people need to know that inbreeding in dogs isn’t just that people are doing tight breedings. It’s that the systems in which dogs are registered are forcing the populations of these breeds into more genetically depauperate gene pools.

This is what is causing the problems with Cavaliers and boxers in the UK.  Elite stud dogs are transmitting their defective genes into a larger and larger proportion of the breed, which is itself founded from a finite number of dogs. No new blood is being brought in, and the bloodlines are becoming saturated with genetic diseases.

This would happen in any closed or relatively closed registry population.  It would not matter if the dogs were bred for show or for work.  Disease would wind up saturating the population over time.

There was also no discussion of MHC haplotypes in the film, but from my own experience, this discussion tends to be ignored by those who just don’t want to hear it. It is Kryptonite for the closed registry system and for virtually all defenders of very tight breedings. That’s because the only way to keep MHC haplotypes diverse and heterozygous is to test for them before breeding.

And very few people are doing that. The tests are only now becoming available, and as far as I know, only one breed club is actually encouraging its members to do these tests– the Dandie Dinmont Club of America.

You can’t seen immune genes, so they are very easily lost.

And if seeing is believing, then we get to the second category of purebred dog problems:  health and welfare problems that result from exaggerated and unhealthy conformation.

The documentary focused mostly on the problems of brachycephalic breeds, including the pug and bulldog.  The initial documentary covered these problems in greater detail, but the scene involving the German vet opening up the pug’s airways really showed how extensive the problems are with their extreme brachycephaly.

The only issue I had with the film was her call for a big regulatory agency that would oversee  the welfare of all dogs in the UK.

I worry that such an agency would be very prone to regulatory capture.

What would happen if an agency were given teeth to go after bad breeders and this agency wound up being run by people who want to engage in a witch hunt against anyone who intentionally crosses two breeds?

I don’t know what procedures exist to prevent regulatory capture in agencies in the United Kingdom, but the US has very little control over it. Lobbyists regularly wind up heading agencies that they once lobbied for.

So we have to be a little bit careful here.

I think the best way to take these people down is to keep on educating people about what is actually happening within the institutions that claim to be looking out for the best interest of dogs.  The public needs to know that dogs are in a lot of trouble because of the strictures and paradigms that rule them.

And the only way to save them is to ditch the strictures and paradigms.

***

Jose Cruz of the Chatham Hill Kennels has uploaded the entire documentary onto the RDW  Blog Readers group on Facebook, so you can watch it there!

You have to join the group to see the posts and watch the film, but I’ll let you in :).

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Basically, this show is about four people who wander around the backwoods somewhere in America, listening to eyewitness accounts. One of these people is a skeptic. Two are believers, one of which also models as the sasquatch for scaling purposes.

The other isn’t just a believer. He’s more or less a bigfoot fanatic.  Matt Moneymaker pretty much thinks any sound or sign in the woods is bigfoot sign. He’s got a great imagination.

He also knows so many exotic things about bigfoot that you’d think he were something like the Jane Goodall or Dian Fossey of the sasquatches.  That’s probably why he’s president of the Bigfoot Field Researchers Organization and you aren’t.

He’s actually a bit like Cliff Clavin.

Here he is explaining to Renae, the professional scientist and skeptic of the team, why bigfoot doesn’t attack cattle:

Source.

See, bigfoot doesn’t attack our cattle, so we won’t kill their deer.

That arrangement works out so well.

I’ve never heard of an American killing a deer to eat.

That’s just a totally foreign concept.

And I’ve never heard of sasquatch killing a cow, so they must really have things worked out perfectly.

He also thinks that bigfoot is the cause of many deer and car collisions.

Yep. Sasquatches use cars to kill deer!

It makes perfect sense!

I just wonder why you never see a bigfoot picking up the deer that it chased into traffic to kill.

 

 

 

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I’ve written several posts about dog domestication and how the foundation of modern Western “breed” dogs has distorted our ability to figure out where dogs originated.  For several  years, it was strongly contended that dogs were derived from East Asian wolves and that there was only a single domestication event. Most of this studies that point to East Asia as the place of origin have used either mitochondrial DNA and–most recently– y-chromosome analyses. However, a study that examined the largest part of the genome of dogs and wolves found that most domestic dogs share genetic markers with Middle Eastern wolves.  And of course, the oldest of all dog remains are found in a region that runs from Central Asia to Belgium– the earliest, in the Altai Mountains of Siberia, dates to 33,000 years before present.

How can these different findings be reconciled?  I think the best way is simply that dogs were domesticated over a long process that involved several different populations of wolves.  Mark Derr in How the Dog Became the Dog lays out a very complex scenario in which humans and wolves associated with each other over tens of thousands of years.  For most of this time wolves living near humans had little morphological differences from wolves not associated with humans, but then, during the Last Glacial Maximum, the wolves associating with humans began to develop the morphological traits associated with domestication. These same forces created a general gracilization in humans, and they likely had the same effects on the wolves that were living with and relying upon humans for sustenance.  The shortened muzzle trait, which has been found in several specimens that are over 30,000 years old, is perhaps the earliest trait to have developed in the wolves that became dogs. Derr posits that the region running from the Carpathians to Central Asia would have been where the first anatomically distinct dogs would have been found– and that is precisely where the oldest dog remains to date were found. (The manuscript for How the Dog Became the Dog was submitted months before this discovery was published.)

For whatever reason, the dogs that descend from Middle Eastern wolves wound up contributing the most to modern dog lineages, though there is some influence of East Asian wolves in East Asian dog breeds, just as many Scandinavian dog breeds also descend from the a mitochondrial DNA matriline that originated in a European wolf bitch. When wolves were more common, they exchanged genes with dogs and the wolves that became dogs– and vice versa.

All of these issues are very complex and are often contradictory. And they are further exacerbated with a real methodological problem that exist in most genetic assays of domestic dogs:  they tend to include too many Western breed dogs. Western breed dogs are genetically depauperate compared to the village dogs of Asia and Africa, which have both proven to be quite genetically diverse. Because the African dogs are more genetically diverse than those of Asia and also possess Middle Eastern wolf genetic markers,  it is very unlikely that dogs were domesticated in East Asia in a single domestication event.

Now, what if we had a parallel domestication from which we could compare to the domestication process in dogs?

Well, it turns out we do.

Dogs are the oldest domestic animal. There is no debate about it.

However, the question of what the second domestic animal was has always been debated.  The debate is between two species:  the goat and the sheep. Evidence of domestication for these two species occurred from 9,000 to 11,000 years ago. I think the bulk of the evidence suggests that sheep were the earlier of the two species. The first evidence of domestic sheep appears  around 11,000 years ago in the Middle East, which means that sheep domestication predates the large-scale horticultural societies that would develop in the Fertile Crescent by about a 1,000 years.

We’ve known for a while that sheep are pretty genetically diverse even as domesticates, but the extent of that diversity was only recently revealed in a study that was recently released in PLoS Biology. This study examined over49,000 SNP’s in over 2,800 sheep from  74 breeds.

The study found that these sheep breeds had more diversity than most dog breeds. Many sheep breeds have effective populations in excess of 300 individuals.  The various breeds of sheep we have are the result of breeding for just a few traits, and the two most widespread traits, wool and hornlessness in both sexes, are the result of dominant alleles that are easily transmitted across populations. Sheep breeds were largely not created through inbreeding. They were mostly created through selectively breeding from a genetically diverse population. Sheep were likely domesticated over a large range over a relatively long period of time. There was no greater diversity in the Middle Eastern sheep breeds than those from other places, and what’s more, there was a lot of crossbreeding between breeds over the years.

The study is entirely about sheep, but I think it shows a real weakness in the genetic studies I’ve seen in domestic dogs. Most studies on domestic dogs do not fully account for the amount of loss in genetic diversity that exists in breed dogs. However, almost all dogs in the West are either breed dogs or derived from crosses between breeds. It has been calculated that modern breed formation may have taken away over a third of all the genetic diversity in domestic dogs, which are still a pretty genetically diverse population.

They become even more so when non-breed village dogs from Africa and Asia are included in the analysis.  Dogs from these populations actually suggest that dogs were domesticated in the way sheep were. However, because most dogs in the West derive from dogs that were intensely inbred and/or kept in closed registry populations, a lot of dog genetic diversity was squandered.

Sheep also show that breeds can be founded from genetically diverse populations. Inbreeding is not a requirement for breed formation or maintenance. In the oldest dog “breeds,” like the greater tazi landrace, there is still a lot of genetic diversity when the landrace as a whole is considered one breed. However, when one considers these dog to be separate entities, as they typically are in the West,  they don’t have much. These dogs existed for thousands of years with selective breeding from a genetically diverse population, just as domestic sheep breeds have been. But within the Western closed registry framework, they have lost a lot of that diversity.

Dogs were not created by inbreeding wolves. Sheep were not created by inbreeding wild mouflon.  Instead, through domestication, certain traits were selectively bred from animals presenting novel mutations. Inbreeding would fix these novel traits more quickly, but the genetic evidence shows that most of the oldest forms in dogs predate modern breed formation. That is, dogs like sighthounds, mastiffs, and mountain dogs that existed thousands of years ago didn’t appear by inbreeding but through selective breeding from diverse populations.

The intense inbreeding and linebreeding that exists within the closed registry system for most domestic dogs in the West has created a major distortion in our understanding of how dogs were created.  Dogs that exist within those populations are not very representative of dogs throughout their history.  But the dogs of Africa and Asia point to the possibility that was once there.

If sheep breeders can produce wool, milk, and meat animals that have produced so effectively over thousands of years without resorting to using genetically depauperate populations, why can’t dog breeders?

I think the answer lies in two places:  the Victorian blood purity cult that is the modern dog fancy and the traditions of how dogs are bred. Both of these things have almost metaphysical reasons for existing as they do, for both fly in the face of what modern science says about the importance of genetic diversity in maintaining sustainable, healthy populations.

The other problem that exists with dog genetic diversity is that the economics simply don’t work anymore.  When breeds were being founded, they weren’t as different from landraces. Wealthy individuals kept scores of dogs in their breeding programs, so they had large founding populations. Most people can’t do that today, which is one reason why virtually every breed that has been founded after the Second World War and then placed within a closed registry system has had severe health problems. Further, I don’t think most people want to do the intense culling that one must use to use very tight breeding effectively.  In those days, there was a lot of culling of the weak.

Today, we have situations where it is hard to maintain genetically diverse populations in dog breeds. Crossbreeding is not allowed in any of the established registries, and the blood purity cult won’t allow such heresy to go without fatwas. Dogs that are born through crossbreeding may only participate in competitions if they are spayed or neutered, and their genes never contribute to the next populations. There are some exceptions to the blood purity cult, like the Dalmatian backcross project and the use of Central Asian tazis in the UKC saluki. But in general, blood purity is seen as an ideal. Further, many dogs that are purchased from breeders are given spay-neuter contracts, and more and more municipalities are passing mandatory spay and neuter.

All of these factors are pushing dogs into more and more genetically depauperate populations that, over time, will become less healthy– regardless of what sort of culling and “selecting against disease” continues to happen within the system.

Sheep were lucky.  Because almost every sheep that exists today has some practical purpose, there was never a big push to turn them into fancy animals. By the time of the Industrial Revolution, the bulk of dogs in the West were no longer needed for anything, except as sporting animals and objects of conspicuous consumption. And those factors led to the big push to “improve” them through “scientific” breeding, which was often little more than inbreeding or very tight linebreeding.

Perhaps the best juxtaposition of two dogs that can explain what happens when dogs from genetically diverse populations become “improved breeds” can be found in AKC salukis and tazis from Central Asia. Tazis from Central Asia can live into their twenties, but the average lifespan of a Western breed saluki is something in the 11 to 12 year range.

The tazi was developed from a genetically diverse population, while the saluki is a Western cutting off of dogs of that general type into something called a breed.

If dog breeds had been able to continue on as selectively bred from diverse populations in the West, the results would have been different.

For the very simple reason that large predators tend to exist at lower densities than their prey, fewer wolves would have been involved in dog domestication than would wild sheep have been involved in their domestication– at least in the initial stages. However, over time, we could be talking about a large number of wolves working their way into the dog population, so it may have been a wash.

But sheep very clearly show us that we don’t have to inbreed to create and maintain breeds.

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This followed an epic tug-of-war, and then Miley let Rhodie have her raccoon.

Rhodie runs with the raccoon.

Rhodie takes refuge on the couch. (Where Miley can't go.)

Rhodie gloats.

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Willie and Maddie posing

Here are Willie and Maddie:

Maddie is 14, and she lost her eye to glaucoma.

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Rhodie is growing up. She’s all legs.

She shows a lot of the Italian greyhound blood that was put into the old fox terrier.

Compare:

Alphonse De Lamartine by Decaisne. Mostly white Italian greyhounds.

Willie and Rhodie juxtaposed. She's that much taller than him already. I couldn't get a better photo of them standing together.

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