Archive for February, 2015

The really cold temperatures must be messing with the time stamp. Neither of these two videos came from 2068.

These are melanistic Eastern gray squirrel, and there aren’t many of them in West Virginia.


Two of them here, and you can see where black color is an advantage in deep cover:


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Blue jay for breakfast

The frigid last day of February brings a blue jay in to eat some beef fat.




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10 eggs go into the Janoel mini-incubator. It is European and uses the Celsius.






The other is a Little Giant. It was made in America and uses Fahrenheit. 10 eggs also went into it.







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Let there be Rouens!

Duck eggs have arrived!

Rouen eggs

28 days. Then little Rouens.

Rouens are domestic mallards that reach fairly large sizes, but they retain the wild mallard’s plumage.

I think all of the domestic mallards that retained this color were Rouen crosses that were sold as wild mallards.

Here are some adult Rouens:

rouens adults

Pretty familiar eh?

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Feral donkeys on Bonaire.

Feral donkeys on Bonaire. 

The Nubian wild ass hasn’t been seen in the wild since the 1950s. The subspecies has been presumed to be extinct. It lived in the Red Sea Hills and the Atbara region of Sudan.

Based upon ancient mitochondrial DNA analysis, it was revealed that there were at least two wild populations that are the source for domestic donkeys. The Nubian wild ass was the source one of the clades of donkeys, and the other came froma mystery population. Somali wild asses, the other extant subspecies of African wild ass that actally still can be found in the wild, is not a source for mitochondrial DNA diversity in domestic donkey.

I say all of this right up front, because what I am about to discuss are the limits of using mtDNA analysis to determine the relationship between populations, especially when one is trying to figure out whether feral population has some taxonomic distinctness.

The Dutch Empire still holds steadfastly to some islands in Caribbean. Among these is Bonaire, which is located just north of Venezuela. On that island is a population of feral donkeys, and the current excitement is the possibility that these animals might be pure Nubian wild asses.

If they are, they could be the very last of their subspecies, which is pretty amazing.  Keep in mind that there is no real historical context I can think of that connects an island off the coast of Venezuela with Sudan. Now, it’s certainly true that the Dutch colonists were connected to an empire that was all over the Indian Ocean, and the same can be said about the British and Spanish, who also occupied the island at various points in its history.

But even if they were connected across these maritime empires, why would anyone bring wild donkeys to an island and turn them loose?

And that brings us to the evidence for the Bonaire donkeys being Nubian wild asses. This is where mtDNA alone analysis can cause problems.

Researchers at Texas A & M performed an mtDNA analysis with samples from some Bonaire donkeys, samples from Nubian wild asses that were part of museum collections, sequences from four Somali wild asses, and one sequence from a domestic donkey that was available from the National Center for Biotechnology Information.

The results showed that the Bonaire donkeys were very close to historical Nubian wild asses and very different from the Somali wild asses and the domestic one.

I looked at the cladogram set up from the mtDNA analysis, and my curiosity was piqued. The domestic donkey’s mtDNA didn’t fit with the Nubians, but we do know that a lot of domestic donkeys actually do descend from Nubian wild asses. Nubian wild asses are a source for their mtDNA diversity, as I mentioned earlier.

But this NCBI sample wasn’t from the Nubian population.  Remember that the study I linked to earlier showed that some domestic donkey mtDNA sequences came from an undocumented population that was neither Somali nor Nubian. This particular sample could have come from that mtDNA lineage in domestic donkeys, but if they had included those that had Nubian ancestry, my guess is things would get complicated fairly quickly. The domestic donkey was used as a control, when in reality the best research method would have been to include a lot of samples from domestic donkeys in the study.

For some reason, this just wasn’t done.

Occam’s razor suggests to me that these donkeys aren’t Nubian wild asses after all. If more samples of domestic donkey are included in the analysis, I bet there will be several of them that come up very close to Nubian.

This is why we have to be careful of mtDNA-only studies, and the researchers at Texas A&M may not be aware for the new data on donkey domestication. Some donkeys have Nubian wild ass mtDNA, and others have mtDNA from a mystery wild ass population, which is not of the Somali subspecies.

We need more evidence to see if what the Bonaire donkeys are, but I think it is a very giant leap to call them the last Nubian wild asses.

Of course, what prompted this study is that late last year, the government of Bonaire was going to institute a donkey cull, which, of course, upset animal rights groups. With this analysis by Texas A&M in hand, the government was forced to halt the donkey cull.

However, the evidence that these donkeys are “pure Nubian wild asses” is nowhere near as convincing as it sounds.

I would like them to be. Don’t get me wrong.

But I’m not betting on it.


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Wisdom from the Serbs

earth stars

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Don’t invite disaster

"A Wolf-Hound" by Paulus Potter. Maybe the same breed as in Ireland, but this dog was Dutch and was alive in the seventeenth century.

“A Wolf-Hound” by Paulus Potter. Maybe the same breed as in Ireland, but this dog was Dutch and was alive in the seventeenth century. 

“Though men in the mass forget the origins of their need, they still bring wolfhounds into city apartments, where dog and man both sit brooding in wistful discomfort.

The magic that gleams an instant between Argos and Odysseus is both the recognition of diversity and the need for affection across the illusions of form. It is nature’s cry to homeless, far-wandering, insatiable man: “Do not forget your brethren, nor the green wood from which you sprang. To do so is to invite disaster.”

–Loren Eisley,  The Unexpected Universe.



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I am nothing more than a fluttering, sputtering avatar of carbon.*

I am nothing less than a fluttering, sputtering avatar of carbon.

I am the product of luck and chance and accident, and in this way I am wonderfully made.

I have been given the gift of consciousness. I am aware of myself. I am aware of mortality. Someday all the fluttering and sputtering will come to an end, and the elements which comprise me will pass on into the universe from whence they came.

But while I can still sputter and flutter, I shall.

I know that when my time comes, I will regret that I have not laughed enough or loved enough, that I was perhaps too stingy with the dollar and not as patient with fools as I should have been.

When the avatar flutters and sputters its last, I shall be no more, but I will live on in the memories of those I have known.

I will probably have a bit of immortality from the madman scribblings I’ve done. and I’ll probably be known for a few other things as well.

I am a Naturalist. I don’t just mean it in the sense that I know about natural history.  I am true philosophical Naturalist.  All that exists is Nature. I have no deity but Nature, which is to say that I have no belief in a deity at all.

Science reveals Nature’s secrets to us, but our limited, often vainglorious little minds can never comprehend it all. What we have not understood we have historically shoved some mythological explanation into that place where our true knowledge stops.

In other words, if we didn’t understand it, we made it up.

And that just isn’t good enough for me.

Every day, a bit more of Nature’s truth is revealed to us through the painstaking efforts of the scientists.

With each amazing discovery, the mythology seems trite, even a bit egotistical, not at all reverential of the true mystery of what it means to be alive in the universe.

To be truly reverential means taking more than a step back. It means truly realizing the tenuous nature of existence. It means coming to terms with the reality that it wasn’t all built for you, and the universe owes you nothing.

It certainly doesn’t own you an explanation.

To confront the reality of existence is to lie out naked and vulnerable and ignorant and naive before an impersonal universe that cannot love or comfort you in any way.

It is a scary prospect for many, and it may be for most of us. This may be the reason why religion will go on and on, regardless of what scientific findings reveal to us. We just can’t be that vulnerable.

I choose to be vulnerable. I want to know what I can know.

And that’s the best I can do before I’ve fluttered and sputtered my last.

For reality is magical and mysterious, but it has a wonder to it that our imaginations, even at the brightest and most vivid, cannot possibly conjure.

So here I stand, this fluttering, sputtering avatar of carbon, vulnerable before the cosmos, fighting against my primate lusts and rages and egocentric delusions, wanting to know, wanting to make things better, yearning for truth and justice.

If I could not do this every day, there would be no reason to live. Just give up on the species and the planet and watch it burn.

But I cannot reconcile myself to that possibility.

We are truly doomed otherwise, and whatever gift it is to be conscious and alive in the universe is nothing more than a gift stupidly squandered.

So let us be. Let us truly be. Let us think about what it means to be, and be truly reverential of this most amazing fact.


*I am aware that other elements besides carbon comprise my body. Allow me this term as a metaphor, please.

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Egyptian jackal or African wolf with golden jackal and wolf-like features.

Egyptian jackal or African wolf with golden jackal and wolf-like features. From “Roosevelt in Africa” (1910).

One the strange ironies about dogs is that we have set up a system in which populations are maintained without regular influxes of new blood. However, at no point in the evolutionary history was this ever the case.

Some dog fanciers maintain breeds as if they were distinct species, and in some breeds, one can find lore that they are derived from sort of wild canid that has nothing to do with wolves or the rest of dogdom. Chihuahuas are supposedly domestic variants of the fennec fox. The Japanese chin was said to be distinct species that belonged to its own genus.

But no matter how you slice it, domestic dogs are all one species, and what is even more important, the more we have found out about the genome and that of their closest relatives, the harder it becomes to think of them as a distinct species from the wolf.

And if that weren’t such a revelation, it really gets more bizarre when we have no learned that wolves, golden jackals, and coyotes are not the cut-and-dry species we assumed them to be. In Eastern Canada and the Northeastern US and Midwestern US, we have discovered that wolves and coyotes have hybridized a whole lot more than we realized. We have also found evidence that golden jackals and wolves have hybridized in Bulgaria. Both coyotes and golden jackals can cross with wolves or domestic dogs and produce fertile offspring.

To make things more complicated, it turns out that wolves and golden jackals have continued to exchange genes since the two species separated. A recent genome-wide study of modern dogs, wolves, and golden jackals revealed that Eurasian wolves and golden jackals continued to mate with each other after their initial separation. The authors found substantial gene flow between golden jackals and Israeli wolves, as well as the ancestral population to all wolves and domestic dogs.

Most North Americans are aware of the taxonomic controversies involving coyote and wolf hybrid populations, including the red wolf and the proposed “Eastern wolf” species, but it turns out that this problem also exists in the Old World.

There is now a debate as to whether certain sub-Saharan  and North African golden jackals are golden jackals or wolves. A few years ago, there were several studies that suggested that the mitochondrial DNA of certain African golden jackals were actually those of a primitive wolf lineage. There is still some debate as to whether these animals are wolves or jackals, and some of the proposed wolves have been found to hybridize with golden jackals in Senegal.

In utter ignorance of the natural history of wild Canis, domestic dog fanciers have spent the past century to century and half splitting up gene pools under the delusion that this somehow preserves them.  Never mind that for most of their suggested 2 or 3 million years on the planet, wild wolves have continued to exchange genes with their closest relatives. When species hybridize, it was always thought that this would be a negative, but in truth, hybridization can be source of genetic rescue. In the case of Eastern coyotes, crossing with wolves can introduce new genes for more powerful jaws and larger size, which make them better predators of deer. It can also introduce new MHC haplotypes, which can provide the animal with enhanced immunity to disease.

One way of looking at golden jackals and coyotes is they are actually themselves primitive wolves. This might sound a bit heretical, but if you were to go back into time and find the ancestor of all wolves, golden jackals, and coyotes, it would look more less like a golden jackal or coyote.  I would argue that these animals represent a sort of generalized template from which larger, more specialized forms can evolve. One of the problems in sorting out wolf, coyote, and jackal lineages from the fossil record is that at various times through their history on the planet, different lineages have evolved larger wolf-like sizes or have produced coyote or jackal-like forms to fit the niche in question.

A recent comparison of golden jackals, African golden jackals that might be wolves (Canis lupus lupaster or Canis lupaster), black-backed jackals, modern wolves, and the extinct Canis etruscus and Canis arnensis revealed that those the proposed African wolves had skull morphologies that were closer to known golden jackals and black-backed jackals. If these lupaster canids are actually wolves and not jackals, then we would have never been able to guess their identity upon morphology alone.

So while the dog fancy has been splitting hairs and arbitrarily dividing up gene pools, science has revealed that the wild dogs haven’t been doing the same.

Canis is not a closed registry.

Even the boundaries between wolves and golden jackals and between wolves and coyotes are blurry, and of course, this leaves out the rather significant gene flow that has occurred between domestic dogs and wild wolves. Black wolves and wolves with dewclaws on the hind legs are the result of dogs and wolves mating “in the wild.”

Science has found all of these wonderful things out, but the dog fancy remains stuck in another era.

Maybe someday it will move beyond the closed registry system and instead of offering up the bromide of “breed preservation,” it will adopt a system of “breed management,” which strives to maintain genetic diversity within a breed and allows regular influxes of outside blood.

That is what nature has allowed with the wild Canis.

That is the actual story of the animals of this genus. It is not one of one lineage remaining pure for millions or even thousands of years.

It is about significant hybridization.

And Canis is not the only genus with this hybridization issue. Ducks in the genus Anas hybridize quite a bit, and it is well-known that many species of whales and dolphins hybridize with their close kin as well. All of these animals are fairly mobile organisms, and their mobility is likely why they retain so much interfertility.  They simply cannot be reproductively isolated from their closest relatives long enough for them to lose chemical interfertility.

It is not something that should be thought of as an evil. Instead, it’s actually a major strength. It is one our own species utilized when we exchanged genes with the Neanderthals and Denisovan people, and if there were another human species alive today, we would likely be able to cross with it.

But because we are so alone in this world, it is difficult for us to understand the concept of a species complex. We are the only humans left.

But dogs and wolves are not the last of their kind.

The gene flow between wild and domestic and among the these three species of Canis is something we have difficulty imagining.

But it is the story of dogkind.





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White coyote steals a Red Bull

It’s not an albino, but the video delivers otherwise:


Since Red Bull gives you wings, maybe he’s hoping that flying will give him a heads up over the roadrunner.

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