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Archive for the ‘wolves’ Category

I’m so glad these taxonomy issues are being raised on a popular science Youtube series:

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This is “Mr. Ethiopian wolf,” pretty much the world’s leading expert on the species:

There is a very interesting discussion in the Q and A portion about the introgression of dog genes into Ethiopian wolves and why that’s not necessarily always a bad thing.

The current research is working toward a full genome sequence of the Ethiopian wolf, and if they are like coyotes and “Holarctic” wolves, I bet there will be some surprises in store.

 

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I have to admit that I am bit of a Joe Rogan Experience fan. I generally watch the podcasts that are about politics, hunting, and animals. I’m not really into pugilism stuff.

I actually came to Steven Rinella’s work through Joe Rogan’s program, and a few years ago, he mentioned something about Dan Flores and his work on the “American Serengeti,” which is actually a book by Flores that I have not read.  It is about the megafauna of the North American Great Plains, and it is a topic I’m somewhat interested in.

But as you know from reading this blog, I am a big coyote fan. I have had an experience with a male coyote in the woods, which I blogged about right after it happened I blogged about right after it happened, and I’ve written some more literary accounts of this encounter (but not for public consumption yet).

I then heard that Flores had a book about coyotes that came out, and I decided to read it.

And I didn’t like it.

I found that he adhered way too much to the paleontology of canids and pretty much ignored all the latest molecular data. At one point in the book, he makes the comparison that the genetic difference between a coyote and wolf is like the genetic difference between a human and an orangutan.  I think that assertion comes from an mtDNA study from 1993, which was the first to say that dogs were wolves and that “red wolves” had no unique mtDNA haplotypes.  It posited a 4% difference in the mtDNA sequence from wolves and coyotes, which is pretty accurate.  (Ironically, this study comes from Robert Wayne of UCLA, whom Flores largely discounts in his interview with Rogan at about 22 minutes.)

But mtDNA studies are notorious for leading people astray when we’re dealing with closely related species that can and do hybridize. For example, initial studies on mtDNA in European wolves found no evidence of dog hybridization, but because virtually all matings between dogs and wolves in the wild involve a male dog mating with a female wolf, the influence of dog genes in European wolves never could be accurately measured. Mitochondrial DNA is inherited only from the mother, and thus, it misses a lot of genetic information.

More recent full-genome analyses have revealed a greater than 99 percent genetic relationship among wolves, coyotes, and domestic dogs. That’s not at all equivalent to the genetic distance between humans and orangutans. In fact, we know that domestic dogs, coyotes, and wolves readily hybridize and produce fertile offspring, and no hybrids between a human and orangutan has ever been documented.

Flores pretty much rejects off-hand the more recent genome-wide studies that have found red and Eastern wolves to be hybrids with wolves and coyotes because Robert Wayne and his colleagues do not use morphological studies or pay much attention to the fossil record of canids in North America.  And the Fish and Wildlife Service adheres to the red and Eastern wolf paradigm.

I’m going to defend Wayne and his colleagues here.  You really need to be careful about morphological studies in canids.  That’s because canids can evolve quite rapidly, and there is a great tendency toward parallel evolution in the family.  I can remember when it was seriously discussed that the bush dogs of South America were a potential close relative of the dhole, based solely upon their “trenchant heel dentition.”  We now know that the bush dog is very much in the South American canid clade, probably a close relative to the maned wolf.  Until very recently, it was believed that the diminutive coyote-like golden jackals of Africa were the same species as the golden jackal of Eurasia, but a recent mtDNA study suggests a much great variance– enough to consider them separate species.  The similarities between the two forms of golden jackal likely resulted from parallel evolution.  The African “golden jackals” are actually much more closely related to wolves and coyotes, and the name “golden wolf” has been suggested for them.

This tendency to evolve rapidly is something we see in the domestic dog. Every single kennel club critic blog posts photos of dog breeds from different periods to show how much breeds change through selective breeding.  Nature selectively breeds, too, and dogs in the wild can rapidly change to fit new niches.

These issues are going to confound virtually every study on canid evolution.  This is one reason why we have nothing resembling a consensus on dog domestication. It is very hard to figure out when a sub-fossil wolf is a dog or is too much like a wolf to be a dog.

This is why I trust molecular studies far more than paleontology, and it is why I think the Fish and Wildlife Service is largely misguided in trying to hold onto the red wolf paradigm. It is possible that a recent wolf and coyote hybrid is going to look a lot like an ancient wolf-like canid, and the amount of convergence between the two can be enough to fit character-based analysis that paleontologists and anatomists use.

Also, the Fish and Wildlife Service is government, and in the US, government moves quite slowly.  I think it is going to take some time before the molecular data finally corrects these errors, but it doesn’t stop them from being errors.

The comparison of full genomes of wolves and coyotes that came out last summer pretty much ended this debate. Unless you’re going to argue over fossils, which is a dubious undertaking, I don’t think we can say that red wolves, Eastern wolves, or coyotes are what we thought they were.

Granted, Flores probably had the book at the publisher’s by the time this study came out, but the fact that he adheres to the old paradigm because Wayne and Wayne’s colleagues didn’t look at the fossils is pretty troubling.

If I were to rewrite Flores’s taxonomy, I would argue that coyotes have nothing to do with Canis edwardii.  That species was an early North American wolf that went extinct, and it could have been related to virtually any species in the genus Canis, including really divergent things like black-backed jackals.

The comparative genome study found that the most recent common ancestor of the wolf and coyote didn’t live 3.2 million years ago, as Flores asserts. Instead, it lived around 50,000 years ago, and it probably was living in Eurasia at the time. This animal was probably an archaic form of Canis lupus or maybe Canis mosbachensis.

When this animal crossed in North America, ancient North American wolves already dominated the landscape. There were also coyote-like forms of wolf, which likely weren’t coyotes at all.  The packing hunting wolf niche was already occupied by dire wolves and ancient North American dholes, so this radiation of the Eurasian wolf had to become more of a generalist to survive. The larger wolves, like the dire wolf, and the various forms of large predatory cat killed this ancestral coyote, and over time, it evolved into a smaller jackal-like canid.  This is how the coyote likely evolved the fission-fusion strategy of existence that Flores writes about. When the numbers are high, coyotes form stable packs and have relatively few young. They hunt mid-sized prey. When numbers are lower, they hunt rodents and lagomorphs, and female coyotes actually have a hormone change when the numbers are low and produce more ova during their estrus cycles. The females mate at 10 months instead of 22 months, and with more ova produced and more bitches breeding, the population can easily recover from a dire wolf or Smilodon attack. This is also why killing coyotes can actually force their numbers up, and it is one reason our intense persecution of coyotes has resulted in them spreading North, South, and to the East,

This is something that would have evolved in a mid-sized canid in the presence of many other large predators.  The fission-fusion strategy has just recently been confirmed in the Cape subspecies of black-backed jackal, which is another smaller canid that has evolved around large predators.

The Cape black-backed jackal is sort of the coyote of Southern Africa.  It is  generalist predator and scavenger, and it actually does cooperatively hunt small antelope species. It also kills sheep and goats.

It is not, however, closely related to wolves or coyotes. It is a very divergent form of Canis, which may actually be given its own genus (Lupelella) in the near future.  It has evolved coyote-like strategies for survival entirely in parallel with the coyote of North America.

This tendency toward parallel and convergent evolution in wild dog species is something that really messes up paleontology and morphological studies, and that is why the genome-wide studies are such compelling evidence. I’m dead-certain that many dinosaur specialists would love to have genomes from descendants of T. rex or the triceratops.

But those animals, like the ancient wolf- and coyote-like canids of North America, have left no descendants.

And what we likely have is a very diverse Holarctic wolf species that includes mid-size convergent jackals, massive megafauna-hunting wolves in taiga of Canada, the desert wolves of South Asia, and the all the weird domestic dogs that we have now.

That’s every bit as amazing as the older paradigm. Of course, I’m a bit of a rogue for suggesting that we include coyotes in the wolf species, but it seems to be right if we hare to adhere to cladistic classification.

This poor understanding of genetic studies actually ruined what could have been a great book on coyotes.

If you’ve ever looked into a coyote’s eyes, it is like looking into the eyes of a very bright dog.  They have so many dog-like mannerism that is hard not to see the similarity.

But you’re actually looking into the eyes of a super wolf.  This is the wolf that took all we could throw it at, and it thrived beyond our wildest expectations.

In Anthropocene, the meek do inherit the earth.

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dire wolf mesomelas

Yep. This was an April Fools’ prank.

That’s okay. I had one pulled on me last night at the cabin where we were fishing. About 10 o’clock last night, my dad shouts “Oh my God! There is a bear in the trash!”

By the time everyone had rushed to the windows to see– and I had just been roused from slumber– it was soon revealed there was no bear.

Yes, and just as there was no bear, all that was in the post about the dire wolf’s genome being closely allied to black-backed jackals is utter nonsense.

But I have always imagined that this was a possibility, because I think our assumption that dire wolves were very closely related to modern wolves really hasn’t been tested out empirically.  We have some phylogenetic trees drawn from paleontological analysis, but one must be very careful of these studies. Parallel evolution is a very common occurrence in canids, and I’ve come to the conclusion that everything one reads about paleontology and canids needs to be taken with a grain of salt.

So yes, it’s an April Fool, but it is a definite possibility.

Oh, and please don’t hate on my dodgy “photoshop.”

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dire wolf mesomelas

It was always assumed that the dire wolf and its kin, the endemic extinct North American wolves, were very closely related to modern wolves.

However, the genome of the dire wolf was just sequenced by a team of independent researchers at the Russian Institute of Cytology in Saint Petersburg.  The team of geneticists and paleontologists was led by Boris Yudin. The team wanted to have access to the remains of dire wolves at Rancho La Brea, but they were instead able to obtain access to several skeletons that were being held at the Indiana Museum of Natural History.

“It was very hard to get access to the specimens,” says Yudin,  who has always been fascinated by Pleistocene North American megafauna, “But once we did get access, the DNA sequences were quite easily obtained from the shoulder bones.”

“We were able to get one full genome sequenced, and then we began to compare this genome with other species in the genus Canis,”  says Yudin, “and using a Bayesian analysis, we were quite shocked to learn that the dire wolf wasn’t really a wolf at all.”

Most paleontologists had believed that the dire wolf was a sister species to the modern gray wolf, and if this assumption were true,  the dire wolf genome would be most similar to this species.

However, the dire wolf didn’t share an affinity with the gray wolf. Instead, it shared a much stronger relationship with the black-backed jackal, a species of canid found in East and Southern Africa, which is quite genetically distant from other wolves and jackals.

“There is even a debate as to whether the black-backed jackal even properly belongs in Canis,” says Yudin, “It is so genetically divergent.  But our research found that the dire wolf and the black-backed jackal are sister tax.”

Using the genetic differences between the dire wolf and the black-backed jackal to calculate when they last shared a common ancestor,  Yudin’s team estimated that the two species split only about a million years ago. Black-backed jackals and their current living closest relative, the side-striped jackal, are believed to have diverged from the rest of Canis some 5 million years ago, and the same is true of the dire wolf.

“The two divergent African jackals and the dire wolf form a clade, and if we are to classify the  two jackals outside of Canis, then the same will have to be done with the dire wolf,” Yudin points out.

“Within the dog family, the tendency towards parallel and convergent evolution cannot be underestimated.  We now know there are jackals and wolves that exist now and have existed that come out of divergent lineages. This is the most important discovery,” says Yudin.

So now we have the golden wolf of Africa, which is a convergent form of jackal out of the wolf lineage, and we have the extinct dire wolf, which was a divergent jackal that evolved into a wolf.

Yudin’s team plans on extracting the genome of the Armbruster’s wolf, which is conventionally believed to have been the direct ancestor of the dire wolf.  If this is true, then the Armbruster’s wolf will also share an affinity with the black-backed jackal.  The team also is beginning an analysis of Pleistocene coyote genomes from across the United States.

“It is an amazing time, ” says Yudin. “Many discoveries to be made.”

Disclaimer:  Please do not post this story as authoritative until reading this post that acts as a follow-up. 

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coyote profile pic

I am a coyote lover. No two ways about it.  I have always been interested in wolves and dogs, but in the past couple of years, I’ve had encounters with Eastern coyotes.  And they are every bit as fascinating. Western man has thrown every single weapon he could contrive at them, and all they have done is spread all over the continent.

So it was with great joy when I got a chance to read Dan Flores’s  Coyote America. I had heard the author interviewed on Steven Rinella’s podcast a while back, and I was really fascinated about what he had to say about Pleistocene megafauna on the North American Great Plains.

I also knew he was writing a book on coyotes, and I wanted get his take on them.

I’ve just started reading the book. I really enjoy his discussion about Native American traditions with coyotes. I am a damned, no-good Easterner, so I know very little about those traditions.

But I do have a quibble. It’s a friendly quibble. In one part of the book he describes coyotes as being as genetically distinct from wolves as humans are from orangutans and that the two species split from a common ancestor some 3.2 million years ago. He uses a lot of the paleontological data from Xiaoming Wang, who is a great canid paleontologist, who posits that coyotes evolved from directly from Canis lepophagus and that they are wholly a North American lineage.

Now, this is paleontology, and it’s not exactly the best way to determine evolution relationships between very closely related canid species. The reason why is that canids have a tendency toward parallel evolution. For example, the bush dog of South America has dentition that is very much like the African wild dog and the dhole, and at one time, it was suggested that the bush dog was actually a species of dwarf dhole. We now know from genetic studies that it is actually a close relative the of the maned wolf, and it is well-nested in the South American canid clade.

It is definitely true that coyotes resemble African golden jackals, but similarities in appearance have led to error here.  Molecular geneticist have recently found that African golden jackal is actually much more closely related to coyotes and wolves than it is to the Eurasian golden jackal. That means that two animals we thought were the same species actually turned out to be two.

And when it comes to the relationship between coyotes and wolves, molecular geneticists had long assumed that the two species split around 1 million years ago.  In countless dog domestication articles, the molecular clock has been calibrated around a 1-million-year-old split between wolves and coyotes. I have always thought that was weird, because the paleontology studies suggested a much older divergence.

Well, a recent comparison of wolf and coyote genomes from across North America revealed that the actual separation time was something more like 50,000 years ago. That means the animals we’re calling coyotes now aren’t the same thing as those million-year-old fossils.  Those animals are of evolutionary dead-ends that just happened to have a very similar morphology to a coyote in much the same way that African and Eurasian jackals do. Of course, we cannot get genetic data from such old fossils, but it could be that some of these dead-end canids might be more closely related to black-backed and side-striped jackals, which really did diverge from the rest of Canis a really long time ago. They are more divergent from the rest of Canis than the African wild dog and dhole are, and the dhole and African wild dog have their own genera.

If coyotes and wolves diverged only 50,000 years ago, then this raises an interesting taxonomic question. All extant wolf lineages diverged in the past 44,400-45,900 years, as a recent study comparing wolf genomes revealed.  These means the genetic difference between a wolf and a coyote is not much more than the greatest genetic variance between wolves. (Generation time are roughly similar in both wolves and coyotes).

This means that the creatures we’re calling coyotes now actually derived from the Eurasian wolf. The reason this animal looks so much like a jackal isn’t because it represents a primitive North American Canis lineage, but because the larger, pack hunting wolf from Eurasia couldn’t live very well at middle latitudes in North America. At the time, dire wolves were occupying this niche. There were also dholes coming into North America, which means that the pack-hunting wolf of Eurasia really had some strong competition. That means that these wolves evolved more toward the generalist jackal body-type and ecological niche. They did so in parallel to the Eurasian and African jackals.

This is very similar to what happened to the first radiation of Eurasian lynx into North America. Eurasian lynx are pretty large, weighing as much as 70 pounds, but they found the mid-sized cat niche already locked up in North America. So they evolved into the smaller bobcat. It just happened millions of years before the wolves that became coyotes came into the continent.

The fact that wolves and coyotes are this closely related and have exchanged genes so much across the continent raises some important questions about what a coyote is. The comparative genome study on wolves and coyotes showed that the animals called the Eastern wolf and the red wolf, which Flores considers valid species in the book, are actually hybrids between wolves and coyotes. I’ve long been a skeptic of the red and Eastern wolf paradigm, but this study actually makes me question coyotes.

One could actually argue that coyotes are a subspecies of wolf. This is a controversial thing to say, but it was once controversial to say that dogs and wolves were the same species– and now there is growing acceptance (at least among scientists) of this fact.

It is certainly true that all wolves, jackals, African wild dogs, and dholes do descend from a coyote-like North American ancestor.  But to assume that coyotes are directly derived from this ancestor is a major error, and one that has been falsified in the molecular studies.

If my interpretation of the genetic studies is correct, the coyote should be called the “thriving wolf.” Unlike the bigger ones, it was able to survive all that we threw at it. The more we persecuted it, the greater its numbers became, as did the vastness of its range. It is an adaptable, resourceful survivor, and that makes it the perfect “American avatar” to use Flores’s construction.

So that is what a coyote is.  It is the wolf that thrives.

 

 

 

 

 

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They aren’t the most genetically distant canids from wolves. That would be the Urocyon species.

Reproductive technologies in domestic dogs will lead the way.

I have this bizarre fantasy of someone setting up a ranch in the Southwest for the purpose of rewilding maned wolves. The oldest fossil remains of maned wolves actually do come from the Southwestern US,but the species is now confined to South America.

 

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