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Archive for April, 2019

box turtle

Possibly the greatest debate in all vertebrate taxonomy is classifying the turtle. If you were to ask an expert about where turtles belong, well, it will depend upon the expert and which papers this expert has recently read.

That’s because the literature on turtles is definitely divided. Morphological comparison studies, some of which have used rather complex statistical analysis of characters, have generally placed them closer to Lepidosaurs.  The most common Lepidosaurs are squamates, which are better known as snakes and lizards, and there is another Lepidosaur order with exactly one species left in it. Rhynchocephalia is this order, and it includes exactly one extant species, the tuatara of New Zealand.

Molecular studies have generally placed the turtles either into or close to Archosaurs.  Extant Archosaurs are the crocodilians and birds. All dinosaurs and pterosaurs were also Archosaurs, and birds, which are the only living dinosaurs, are certainly Archosaurs.

One would think that molecular studies would solve this problem, but it really doesn’t.  The problem is that turtles evolve quite slowly, and trying to figure out divergence times based upon mutation rates could result in inaccurate conclusions.

So no one really has a way to resolve this conflict.

And if you were to ask me, I would say, well, I don’t know. We have some ideas, but they are in conflict. And we have no way to resolve them at this time.

But that’s science for ya.

 

 

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felis lybica

As I have noted many times on this blog, I think that the only way to correctly classify the domestic dog is as form of gray wolf. I am okay with regarding them as a divergent subspecies, but Pierotti and Fogg make a pretty good case that we really cannot define a domestic dog subspecies, because that subspecies would have to include everything from truly feral dogs to pekingese. I think that the wolf genome comparisons also show that creating a special dog or dingo species distorts the monophyly of Canis lupus.

Some will argue with me on this one, but you will have to use a species concept that is totally not based in cladistics or one that allows for a huge amount of gene flow between the two species.  An ecological species concept can work, but then you’re going to be forced to split up Canis lupus into many different species. Arabian wolves are simply aren’t ecologically equivalent to arctic wolves. So I think creating a special dog species is problematic from a systematics perspective.

However, I’ve been asked several times what I think about how to classify the domestic cat. Almost every authority in cats uses the name Felis catus to describe the domestic cat, while Canis familiaris is slowly being replaced by Canis lupus familiaris.

The revised taxonomy of Felidae  that was released in 2017 does change how we classify wildcats. Classically, we recognized a single species of wildcat, Felis silvestris. The domestic cat is derived from a Near Eastern population, which was classified as Felis silvestris lybica.  There was another wildcat that lives Western China that was sometimes recognized as Felis sivestris bieti or Felis bieti. The big taxonomy debate in this genus was where to include this Chinese mountain cat into the greater wildcat species or have it be a species of its own.

The new taxonomy changes quite a bit of this. Felis bieti is now recognized as species, but Felis silvestris now refers to only European and Caucasian wildcats.  Felis lybica is the new scientific name for the wildcats living Africa, the Middle East, South Asia, and some parts of Central Asia, where it is sympatric with the Chinese mountain cat.  The fact that lybica and bieti exist in the same area without much gene flow is apparently the reason for elevating bieti to a species.  The reason for splitting up silvestris, though, had do with a deep mitochondrial DNA divergence between European and Caucasian wildcats and the rest of the wildcat species. Apparently, these two forms split from each other 173,000 years ago.

This revised taxonomy is really, well-supported with data, and I generally think it is right in its conclusions. However, I do think it made an error with this genus.

It retained Felis catus as a full species.  The same logic that says dogs are Canis lupus familiaris says that you cannot have a special domestic cat species either.

So the best way to classify domestic cats is as Felis lybica cata. You will probably only see this name written on this space, because unlike the literature on dogs, there is a noted deep adherence to Felis catus in the literature on domestic cats.

I honestly don’t know why there is such an adherence, because domestic cats are not that different from Felis lybica.  They come in more colors and coat types, but most domestic cats can live just as wildcats do. That’s why feral cats are an ecological hazard in so many places. They are quite effective predators, the ultimate mesopredator that found a niche living under the nose of man.

We don’t have as many good nuclear DNA studies on the various small cats as we do on various forms of the gray wolf complex, and this may be why there is a tendency to avoid a cladistic classification for the domestic form.

But if we’re doing this for dogs– and for good reason– we should be doing the same for cats. And the same for pigs and domestic mallards and domestic jungle fowl.

 

 

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feral dog

Most feral domestic animals revert to a form that is roughly similar to their wild ancestor. You can see this quite dramatically in feral pigs. They generally evolve into a form that is about the same size and even coat type of the Eurasian wild boar. City pigeons look very much like the rock dove or “rock pigeon” that is their wild ancestor after just a few generations of breeding without human care.

Because village and pariah dogs tend to be mid-sized, it has been assumed that the wild ancestor of these dogs surely would have been on the smaller side as well. Therefore, the gray wolf simply could not have been an ancestor.

What actually drives the size of freely breeding and feral domestic dogs isn’t that they have some ancient alleles that force them into returning to an ancestral form.  The truth of the matter is that ecological niche and caloric restraints have a lot more to do with this phenomenon.

Dogs are unique among domestic animals in that they are the only domesticated form of large carnivoran. We have never domesticated any other species of large predatory mammal except for those Pleistocene Eurasian wolves that are at the base of domestic dogs.

Most domestic dogs are poorly adapted to living as predators, and they really don’t have to be. When dogs go feral in societies with extensive agriculture, they readily scavenge and hunt small prey. They dabble in various levels of omnivory.  Some dogs might be good at hunting deer, but deer are a lot harder to catch than garbage and groundhogs.

There is an extensive literature on mammal predator size and prey choice. The best known researcher looking at these issues is Chris Carbone, and in a 2007 paper called “The Costs of Carnivory,” which was published in POLS Biology, Carbone and colleagues looked at body mass of mammalian predators and their prey choices. If a predator weighed more than 20 kg, it hunted large vertebrates. If it weighed less than that weight, it hunted invertebrates or small vertebrates.

Larger predators get a much higher net energy gain by targeting large prey, and this large prey allows them to maintain their larger body size.

Feral and freely-breeding domestic dogs are not hunting large vertebrates. It is much easier for them to scavenge as mid-sized creatures. Natural selection would favor a moderate size, because any dogs that retained the large dog or large wolf alleles in the population would have a harder time feeding itself efficiently on these resources alone.

There are, of course, exceptions to this rule. In Uruguay, there was a population of feral mastiff-type dogs, which are called Cimarrón Uruguayo. These dogs were introduced by Europeans as working dogs, but some of them went feral. They were able to maintain their large size because they hunted livestock and game, and they were such a problem that the government placed bounties on them.  These dogs were living in a feral existence for at least 250 years, but they were able to retain a large mastiff phenotype. The feral mastiff is now being transformed into a standard breed.

However, the general rule is that village and pariah dogs tend to be significantly smaller than wolves, but this smaller size cannot be used to deny that dogs are derived from gray wolves. This smaller size is just more efficient for the ecological niche of feral and village dogs.

And it is poor reasoning to assume that dogs cannot be wolf derivatives simply because they do not evolve back into a wolfish form once they go feral.  Dogs have been domesticated for a long time, and their domestication is quite unique.  As the only large predator we have domesticated, ecological pressures create a different sort of animal than the original wild ancestor.

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dragon eats goat

Komodo dragons are the world’s largest lizard.  They are supersized monitor lizards that first evolved in Australia four million years ago.  One million years ago they arrived on the Wallacea Islands, where they fed upon a dwarf species of elephant. That elephant went extinct 50,000 years ago. The mainland Australian population of these lizards went extinct around the same time as those dwarf elephants.  The main prey of Komodo dragons now consists of introduced ungulates that arrived on those islands between 7,000 and 10,000 years ago.

That means Komodo dragons spent 40,000-43,000 years without large terrestrial prey sources, and if that is the case, how did they survive?

Well, a new paper in the journal Global Ecology and Conservation attempts to answer that question.

Apparently, Komodo dragons are an odd mix of the best ectotherms and the best of endotherms.  As ecotherms, they have the ability to rely upon limited food resources, and it just so happens that the oceans around their last island redoubts are quite diverse marine ecosystems. So the dragons would have plenty of marine food that they could scavenge. They also have the ability to reduce their growth rates to compensate for the lack of large prey species on the island, a trait that has been shown in the subfossil record. Remains of dragons that date to these lean millennia show that dragons were significantly smaller then than they are now.

Also, unlike most ectotherms, Komodo dragons, like virtually all monitor lizards, have the ability to adjust their behavior and try new food sources. When tourists scared off the ungulate prey of Rinca Island, the dragons simply started hunting macaques and raiding scrubfowl nests.

Further, the dragons could also live nicely as cannibals. Smaller dragons get eaten by the larger ones, and because the dragons produce far more offspring than could ever reproduce, the excess dragon young could have fed the adults quite well.

Humans also never really thought of these arid and semi-arid islands as good places to set up large scale agriculture, and because these islands were also devoid of native prey species, humans were not widely using them as places to hunt until deer, buffalo, and pigs were introduced.  When humans did settle the islands, there were enough dragons in the population that had “shy personalities” that kept them from causing conflicts with humans. These “shy” dragons are disproportionately female, and they could have passed these more retiring traits onto their offspring, which is why Komodo dragons are not killing people left and right. People likely killed off the bolder males when they first began to settle these islands, and in a species were the sex ratio tends to be biased in favor of males, any trait that would have increased a female’s survival would have definite consequences in the population genetics of the species. That means that the “shy” trait could have easily become expressed in the population, simply because humans would have low tolerance for aggressive behavior.  Dragons today generally avoid people.

Finally, females of this species are capable of reproducing via parthenogenesis. Males in this species are larger, and if conditions became so bad that all the large males died off, some of the females would still be able to reproduce anyway.  Because of how the lizards’ sex chromosomes work, they can only produce male offspring when they reproduce this way, which could be a way to restore males to a population that lost them through a lack of food resources.

Komodo dragons were once quite widespread across Australia and several nearby islands, but now they exist only on the islands of Wallacea. These islands are named for Alfred Russel Wallace, a co-discoverer of evolution by natural selection. Wallace noticed that the native animals of Sunda, which is the Malayan Peninsula and the Malayan Archipelago, are fundamentally different from the native animals of the islands just to their east.  The animals of Sunda generally have an Asian origin, while those of the islands to the east are more of Australian origin. The line between these islands is called the Wallace Line.

The dragons of Wallacea are of Australian origin. Their current main prey sources are all most of Asia origin. So in the Holocene, humans broke down Mr. Wallace’s Line, and the dragons grew back into their larger form. This larger dragon was the same one that hunted the megafauna of the Australian mainland, playing second fiddle to only the larger monitor called megalania (Varanus priscus).

I have often wondered what it would have been like to have seen the mammoths that lived on Wrangel and St. Paul Islands. These mammoths were the last survivors of a species that range over much of Eurasia and North America until 10,000 years ago, but they continued to survive on St. Paul Island for 5,600 years. They died off on Wrangel Island only 4,000 years ago, and they only died out because of a weird genetic mutation similar to the rex mutation in rabbits that made it harder for them to insulate their bodies on that cold island.

But by several accidents of their biology, the Komodo dragons have not undergone the same fate. They still exist as a relict population.

We have a hard time living with large predatory animals. They tend to inconvenience our way of life pretty badly. However, the people of these islands do benefit from the dragons. They attract a lot of tourists and their dollars. There is real economic benefit to having such creatures roaming about.

But I don’t know how long this can last.  Because the dragons have these shy behaviors where they avoid humans, increased tourism on these islands could greatly stress them, making it harder for them to thrive and breed. These concerns came at about the same time of a mass arrest of an animals smuggling ring that had 40 dragons in its possession, which has led the Indonesian government to ban tourists from coming to Komodo Island in 2020.

If the islanders cannot make money from tourists, though, it is very likely they will try to make some money selling the dragons to smugglers, and if authorities are not on top of things, the Komodo dragon might not survive the Anthropocene.

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Mule deer dreams

mule deer stott

One of my dreams is hunt mule deer in the West. I don’t care where in the West. I just want to go out on into that big country, wander around the rocks and cliffs and sage brush, climb out onto a high vista, and glass the scenery for antlers.

I am from the land of white-tails. White-tails are the ultimate habitat generalists, and in “settling” and “civilizing” these Eastern lands, we have create a paradise for them. They can wander the forest devouring acorn after acorn, and they can grow fat and glossy in the fields of soybeans and corn.

The mule deer is a different animal. It migrates from higher elevations to lower ones. It likes much more open forests and grasslands and sagebrush steppes.

Current taxonomy says that the various forms of mule deer and the two subspecies of black-tailed deer represent a single species, but the black-tails are creatures of the Pacific Coast forests. They are different entity in my mind, though I’m sure the deer exchange genes where one form’s range runs into another without any consideration of human classification.

These arid and semi-arid land mule deer, though, are what has me fascinated. The mature bucks are rather large and impressive, more so than the equivalent white-tails. But I do not think of them so highly because they are larger. I think of them so highly because they have a Western mystique. They are not such habitat generalists in the way white-tails are.

They are beings of a more specific landscape, a landscape that is under threat in part because oil and gas development, housing speculation, and overgrazing by livestock are taking their toll. The spread of cheatgrass, which grows into lovely fire tinder, is also to blame. The fires that spread from its stalks wipe out the sagebrush, which the mule deer rely upon to feed them through the winter.

So the white-tail basks in the glory that is our civilization, as the mule deer continues to retreat and withdraw from it. And in this, I find their true appeal.

I hope that when I will get a chance go West on a mule deer hunt before it is too late. I can see a time when the deer will become so hard-pressed that hunting opportunities will be curtailed, even abolished. I hope that we will be wise in our understanding what is happening to these deer before they lose the range and forage on which they so clearly depend.

To hunt mule deer is to go nearer to the wilderness, perhaps even into it.  It is an odd little romantic dream of mine at which I’m sure some Westerners will laugh.

But these deer still exist in the sage and rocks and grasses. They are the setting sun, casting away beyond the Western horizon, beckoning me across the continent to cross the prairies and the mountains.

And someday, I hope to. Before it’s too late.

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This video shows coyotes hunting very much like larger wolves, but it also shows you an odd thing about mule deer.

Mule deer stick together. Mule deer that are not related to a fawn will come in to defend it, while white-tail does defend only their fawns. This makes some sense. White-tails evolved in dense forests where it was pretty easy to hide fawns, while mule deer evolved in open country. Kin selection would favor the genes of mule deer that were willing to come in and defend fawns of related does.

So this is really amazing footage, which shows can cooperatively hunt very much like wolves. These are Western coyotes, which typically aren’t thought of as pack-hunters, but under certain conditions, they absolutely can work as a pack.

I like the way this elk hunter clearly stated that we shouldn’t kill every coyote we see and definitely sees a place for them in the ecosystem.

Mule deer aren’t as numerous as they once were. They have definite habitat requirements, unlike white-tails, which live in virtually every town in the East. Since wolves have been extirpated from most of the West, is it possible that increased coyote numbers could be affecting mule deer populations (even at the margins)?

We know that when wolves came to Yellowstone, they cut the coyote population by half.  Wolves are not major predators of pronghorn, but coyotes take many of their fawns.  When wolves kicked the coyote numbers down a bit, the pronghorn population began to recover significantly.

Wolves certainly do hunt mule deer, but in the West, they have options to go after elk and moose.  Coyotes might take elk and moose calves, but they aren’t likely to be a problem for most mature individuals.

Maybe something similar is going here, but I should caution that the real problem facing mule deer in the West is habitat loss, and although predator control can fix the problem at the margins, it won’t solve the habitat problem.

 

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marsh rabbit

One of the most interesting aspects of North American wildlife is the wide diversity of rabbit species. The most common rabbit species in the Eastern and Midwestern US is the Eastern cottontail (Sylvilagus floridanus), but it only one many North American rabbits.  The genus of cottontails, Sylvilagus, includes many regional and specialized forms. In the Allegheny mountains, there are Appalachian cottontails (S. obscurus), and in parts of New England and New York State, one can find the New England cottontail (S. trasitionalis).  In the West, we have desert cottontails (S. audubonii) and the mountain cottontail (S. nutallii) in the interior, and the brush rabbit (S. bachmani) along the Pacific coast.

However, those are pretty banal bunnies. Over the past week or so, though, I’ve seen the video clip from the CBC showing a swamp rabbit swimming strongly to evade predators, So I thought I would take some time to talk about our “water rabbits,” the two species of cottontail have evolved to live in the Southeastern swamps and marshes.

From Southeastern Virginia to Florida and as far west as Mobile Bay, the short-eared marsh rabbit (S. palustris) lives makes its home among fresh and brackwater marshes and swamps.  They live among the cattails and mangroves and thickets of black gum and magnolia. They tend to be smaller than Eastern cottontails, which can also appear in similar environments, and their tails are usually shorter and are almost never fully white.

The swamp rabbit (S. aquaticus) by contrast is the largest cottontail species, averaging double the mass of an Eastern cottontail.  It is much larger than the marsh rabbit. The only states where both of these species are found are South Carolina, Georgia,  and Alabama, but there isn’t much range overlap. This rabbit likes cypress swamps and lowland river floodplains. They range as far north as southern Illinois and Indiana, but they are particularly common in the Mississippi Delta.

These two species are considered sister taxa, and these two rabbits are placed in the subgenus Tapeti. This subgenus includes mostly cottontails from Mexico on south, and these two water rabbits are the only two members of these subgenus found in the United States. This classification has been determined through a limited mitochondrial DNA study. 

Of course, I would like to see more studies of the various cottontail rabbits’ genomes, but this classification is the only one currently accepted.

I should note that one subspecies of marsh rabbit (Sylvilagus palustris hefneri), which is found in the Lower Keys of Florida, is considered an endangered species.  It is named for Hugh Hefner, whose corporation donated a substantial sum to research this rabbit.

This rabbit is vulnerable because of predation by feral cats, as well as other invasive predators, such as boa constrictors and fire ants. Invasive plants have also destroyed the undergrowth that these rabbits use to hid from their predators. Many of these rabbits are also victims of traffic.

Maybe this rabbit would get better attention as an endangered species if conservationist played up its connection to Hugh Hefner. We could call it “The Campaign to Save the Real Playboy Bunny. ”

The swamp rabbit has a following among beagle houndsman in much of its range, and these rabbits are taken as monster trophies in much the same way that Eastern deer hunters who have hunted white-tails their whole lives will go west in search of a monster mule deer.  The old way of hunting both swamp and marsh rabbits was to burn them out of their marsh grass hideouts, but wildlife management agencies regulate the hunting of both species.

So when you see that clip of the swamp rabbit swimming think of both of these rabbits. They are amazing creatures, perfectly adapted to living near water and using their strong swimming abilities to evade their most aggressive predators.

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