Why Evolution is True is a blog written by Jerry Coyne, centered on evolution and biology but also dealing with diverse topics like politics, culture, and cats.
Poor Cyrus. I keep taking his space! But where am I supposed to sit?
Cyrus: The American occupier wants to take this sofa away from me.
Hili: You can settle on mine.
Cyrus: Amerykański okupant chce mi zabrać sofę.
Hili: Możesz się osiedlić na mojej.
Voilà: a gif from The Meta Picture. Their notes:
Pardus is a black leopard that is currently a part of the Cheetah Experience, a big cat centre that was founded in 2006 with the long-term goal of breeding cheetahs.
Pardus is very enthusiastic about people. Here’s what happens when Pardus notices his favorite zoo keeper is visiting.
Her name is Juhi Agrawal and she works for Cheetah Experience. They have Cheetahs, Lions, Leopards and other animals and Juhi has been able to work closely with them all.
Three notes:
1. The Cheetah Experience is located in South Africa, and is devoted to saving endangered species of cats.
2. The “black leopard” is simply a genetic mutation in the regular leopard, Panthera pardus (clearly the source of the name of the loving leopard shown above). The black mutation is recessive, meaning that the cat needs two copies to show the color variation. (The mutation is called “melanistic,” and increases the amount of black melanin pigment in the fur.) But in the right light you can still see the characteristic rosettes of the leopard’s coat, as you can toward the end of this video.
A similar mutation is found in jaguars of the New World, Panthera onca, but those mutations are dominant, requiring only one copy to turn the animal black. Black jaguars are also called “black panthers.” Black domestic housecats also have a single dominant gene that darkens their coats, and in the right light you can often discern a tabby pattern in the coat of an all-black cat, revealing its underlying genetics. (“Tabby-pattern” genes are also dominant, but are largely masked when a tabby also carries the “black” gene.)
3. I would love to be that keeper. Apparently one can touch some of the cats at this place.
h/t: John
A famous puzzle about classifying animals involves the abutting distributions of the hooded crow and the carrion crow in Europe. The two crows are considered members of different species, Corvus cornix and Corvus corone, respectively, and have been classified that way because they not only have different color patterns, but tend to mate with others of like pattern, as well as differing in their dominance behavior. Here’s what they look like:
Hooded crow:
The crows’ distributions abut abruptly along a line from north to south through Europe—the red line shown in the picture below, taken from the second reference at the bottom of the page. The caption gives information about where the birds were captured (one taken from each locality) and the genetic relationships between them:
Yet they are otherwise very similar, and do hybridize from time to time, so some biologists have considered them subspecies rather than species. The “biological species concept” (BSC) uses the idea of reproductive isolation as the criterion of species distinctness: if two groups inhabit the same area, but do not produce fertile hybrids (i.e., are “reproductively isolated”), then they are considered separate species.
Under that criterion, the presence of some fertile hybrids between these groups means that they aren’t strictly “species” according to the BSC, but in our book Speciation, Allen Orr and I use reproductive isolation as a relative criterion: the more two populations are reproductively isolated from each other, the more “species like,” they are, up to the point where there is no genetic interchange, at which point they can be called “good biological species.”
Under this criterion, these two crows are “species-like” but not “good species,” and how you name them becomes somewhat arbitrary.
But how much genetic difference is there between the groups? If there are extensive genetic differences, spread throughout the genome, that suggests that although there is interbreeding, the genes from one species don’t become incorporated easily into the genome of the other’s, so reproductive isolation is stronger (perhaps hybrids can’t find mates, or don’t survive as well as the parents). On the other hand, if the groups differ by only a few genes, one could more easily see them as subspecies, or “races,” or “ecotypes.”
To resolve this question, a large group of researchers used a number of scientific methods, including sequencing of most of the genome as well as looking at differential expression of the genes, in both groups of crows. The results, by J. W. Poelstra et al., were published in a recent issue of Science (reference and link below, but no free download), and were highlighted in a “news and views” piece in the same issue by Peter de Knijff (reference and link also below).
Here are the salient results, and I’ll try to be brief:
What does this mean? Are they good species or not? Well, it’s still a judgement call. There are some fixed genetic differences between hooded and carrion crows, but it looks as if hybridization has homogenized most of their genes, so reproductive isolation is far from complete. In fact, if you just classify species by overall genetic similarity, you’d call Spanish carrion crows a different species from German carrion crows!
What we have here are two partially isolated populations: interbreeding is limited by the fact that there are color differences between the types, and each type tends to mate with others of its color. That clearly means that there are differences in at least two types of genes: color genes, and genes for how one responds to the colors, which makes you more likely to mate with a bird having a color similar to yours. (There are probably differences in visual sensitivity to the patterns as well, which may explain the fixed differences in the DNA of “vision” genes.) The “response” or “preference” genes could be active in females (who do most of the mate choosing) males (who may decide which species to court) or both sexes.
The importance of the inversion is that it keeps these types of genes together, because inversions keep genes tied up in blocks. If an ABCDEFGHIJKLMN bird mates with an ABCDEKJIHGFLMN bird, there can be free genetic interchange (“crossing over” between the chromosomes, except in the inverted F-K region, because a cross-over in that region will produce sperm and eggs that yield inviable zygotes (they will have duplications of some genes and absences of others, leading to inviability).
Therefore, if one species has the first configuration, and the other the second, genes in the F-K region will tend to stay together. So if that inversion contains, in one species, genes for the hooded pattern as well as genes for preferring the hooded pattern, while the region in the other species has genes for the non-hooded pattern and genes for preferring the non-hooded pattern, the system will be stable.
If crossing-over were allowed, and the species-specific genes were not in inversions, you’d get hybrid birds having, say, a hooded pattern but a preference for a non-hooded pattern, and the species would soon lose their integrity for pattern and mate preference. Population geneticists have shown that, because of this, genes that are involved in speciation will tend to accumulate in inversions if there is gene flow between the populations during speciation. Since we know that there is gene flow between these groups, and they are not yet “good” species (they may never be), this observation is a striking confirmation of population-genetics theory.
So what do we call these things? Are they species or not? My preference is to consider them subspecies, as many biologists have before. Most of the genome is being exchanged between the hooded and carrion crows, so reproductive isolation is far from complete. But that is a judgment call using my definition of biological species as something of a sliding scale. Others will disagree, for no species concept will always work, if for no other reason that species are dynamic entities that begin as populations and only gradually become species. There will always be cases of species in statu nascendi, or gray areas that defy classification under any definition of species. (See chapter 1 of Speciation by Coyne and Orr if you want to see why we prefer to use the BSC.)
Although deKnijff’s piece tends to concentrate on the semantic problem—what do we call these birds?—I find the genetic results more interesting: that they maintain their distinctness due to only a very few genetic differences, and those differences are largely bound up in rearranged sections of one small chromosome.
So when my European readers (and I am, for another few days, a writer in Europe) see a hooded or carrion crow, be aware that you’re looking at a remarkable case of recent evolution, and a puzzle that has largely been solved by work published in just the last two weeks.
__________
Poelstra, J. W., N. Vijay, et al. 2014. The genomic landscape underlying phenotypic integrity in the face of gene flow in crows. Science 344: 1410-1414.
de Knijff, P. 2014. How carrion and hooded crows defeat Linneaus’s curse. Science 344:1345-1346.
Here we get conflicting statements from the state of Arizona vs. the executed man’s lawyer and a witness who reported in the Guardian. Joseph Wood III, convicted of executing his estranged girlfriend and her father, was put to death yesterday in Arizona by lethal injection. The procedure normally takes ten minutes. This one took nearly two hours. As the New York Times reports:
In another unexpectedly prolonged execution using disputed lethal injection drugs, a condemned Arizona prisoner on Wednesday repeatedly gasped for one hour and 40 minutes, according to witnesses, before dying at an Arizona state prison.
. . . But what would normally be a 10- to 15-minute procedure dragged on for nearly two hours, as Mr. Wood appeared repeatedly to gasp, according to witnesses including reporters and one of his federal defenders, Dale Baich.
Mauricio Marin, who witnessed it, reported in The Guardian:
The curtains opened. The medical staff checked the man’s veins. He said his last words – “God forgive you all” – and the lethal drugs began to flow, at 1.52pm. James Wood appeared to fall asleep, albeit strapped down to a table, and he looked straight ahead at the wall. The first 10 minutes went according to plan.
Then, a hard gulp. I looked over to my left: the priest praying the rosary. To my right: the family watching on. Then dead ahead: the side of Wood’s stomach appeared to move, even after the Arizona state prison’s medical staff had announced he was sedated.
I saw a man who was supposed to be dead, coughing – or choking, possibly even gasping for air. I knew this because Wood’s stomach moved at the same time, just like it would if you were lying down and trying to breath. Then another of those gulps – those gasps for air, movements just from the throat area and sometimes from the stomach, too.
I started looking at the priest’s watch to keep track of time. Five, 10, 20 minutes … an hour had passed. I started to wonder: Will this get called off? Will this ever stop?
I continued to scribble on my state-issued notepad, counting the gulps and gasps of the man on the gurney. I counted 660. This went on for over an hour and a half.
During that time, medical staff checked Wood six times in total, looking at his eyes, feeling for a pulse on his neck, informing us over the loud speaker that he was still sedated. His eyes were still closed.
My eyes turned to Wood’s attorney, Dale Baich, as he handed a lady a note and she left the witness chamber. I wondered what the lawyer had written, and as the door opened, it let in a bright light, for just a quick moment.
What seemed like an eternity passed – 20, 30, 45 minutes more, looking straight ahead – and finally the gulps and gasps started to slow, from about every five seconds or so, to about one per minute. Finally, the gulps and gasps stopped. A few minutes more went by. At last, the killing had stopped, too. A medical staff member checked Wood again one last time. Another few minutes still, and the warden pronounced the killer dead, at 3.49pm, one hour and 57 minutes after the execution had began.
In a move that I think is unprecedented, Wood’s lawyers asked for a stay of execution to both the federal district court and Judge Anthony Kennedy of the Supreme court an hour into the execution, as Wood was still alive. Both courts refused. (On Tuesday the U.S. Supreme Court also overturned a stay of execution ordered by a lower court, demanding details about the source of the lethal drugs and the training of those who administered them.)
What were the drugs? The Times notes:
Arizona officials said they were using the same sedative that was used in Oklahoma, midazolam, together with a different second drug, hydromorphone, a combination that has been used previously in Ohio. Similar problems were reported in the execution in Ohio in January of Dennis McGuire, using the same two drugs. He reportedly gasped as the procedure took longer than expected.
There are reliable ways to execute someone by injection. That involves using the same drugs that people take when they end their own lives legally, as they do in Switzerland. The drugs are barbiturates, and are guaranteed to cause sleep and then a painless death. But these aren’t used in the U.S. for executions, for their manufacturers won’t sell them for purposes of execution. This means that a variety of other drugs, produced by dubious “compounding pharmacies” whose names the executioners won’t disclose, are used—with variable and often horrible results. Moreover, persons trained to administer drugs, like physicians, are forbidden from participating in executions.
Naturally, the state of Arizona maintains that Wood didn’t suffer. They said he was snoring, that he was asleep. But how do they know what he actually felt? There is no way to know what a man who is gasping but appears unconscious is actually experiencing. I doubt he was simply “snoring” as he was dying.
And of course Wood’s botched execution was minimalized by both the Governor of Arizona and the victims’ relatives:
“This man conducted a horrific murder and you guys are going, ‘Let’s worry about the drugs,’ ” Richard Brown, brother-in-law of Debra Dietz, told The A.P. “Why didn’t they give him a bullet? Why didn’t we give him Drano?”
Gov. Jan Brewer of Arizona said that she was concerned about the length of time the execution took.
“While justice was carried out today, I directed the Department of Corrections to conduct a full review of the process,” she said. “One thing is certain, however: Inmate Wood died in a lawful manner, and by eyewitness and medical accounts he did not suffer. This is in stark comparison to the gruesome, vicious suffering that he inflicted on his two victims — and the lifetime of suffering he has caused their family.”
Drano? That is a caustic drain-cleaning chemical in the U.S. that people occasionally swallow to kill themselves, producing a horrible death. The point, though, is not to contrast the relative ease of the criminal’s death with that of his victims. The point is that when we take away from someone the only thing he has left—his earthly existence—we should not act as a country the way a criminal acts toward his victims. Do we want them to suffer. Of course there is plenty of mental suffering involved in knowing exactly when you’ll die, but what kind of people demand physical suffering as well? We should be better than vicious criminals!
Physicians will not participate in these executions, companies will not sell states the drugs we need for painless executions, and executions cost more than life in prison without parole. Further, capital punishment puts our country into the killing business. We are the only First World country to retain the death penalty (see below), and we can’t even carry it out properly. Isn’t it time to bring this charade to an end?
Here, from Wikipedia, are the countries that have abolished the death penalty (dark green; 97 nations) versus those that retain it in some form. Only the red ones (58 nations) have actually used it in the last ten years. Light green countries (8 nations) have it only for special circumstances like war crimes; tan countries (35 nations) retain capital punishment but haven’t used it in at least a decade:
Yesterday was a quiet day in Dobrzyn: working, eating, making cherry jam and pie, and napping. It rained much of the day, fortunately after the day’s cherry harvest was done. There is one more day’s picking left, but they want to wait until the fruit dries off. We also lost power (and thus internet) several times.
The upside of rainy weather is that the Princess stays inside (see below).
What else can you do when you see a cat on its back like this? BELLY RUB! So I did:
More jam was made (Malgorzata considered the first batch too runny, but this one was perfect):
And, of course, another cherry pie. Given the thoroughness of the pickers, pies have to be made before all the cherries are gone. I was ordered not to photograph this one as it was considered unsightly, but I flouted the orders. It was delicious; I’ve just had a slice for breakfast. As I’ve always maintained, pie is the perfect breakfast food.
Several people asked about the size of these cherries. Yes, they are large for morello (sour) cherries, at least compared to the ones I’m used to in the U.S. Here is one to human scale:
And for felids that are reading, to cat scale:
Match that, White Basket Cat!
Reader Charlie Jones from the University of Pittsburgh sent several pictures of a gorgeous Cecropia “silkmoth” (Hyalophora cecropia), first described and named by Linnaeus. Charlie’s notes:
These were taken in June 2008 just northwest of Cody, Wyoming, in Sunlight Valley (part of the Clarks Fork of the Yellowstone canyon). I particularly like the last photo that shows what a great plush toy these moths would make for a very small child.
According to Wikipedia, this is North America’s largest native moth, with a wing span up to six inches in females. Its range is in the eastern part of the US, from southern Canada to Florida, and west to the Rocky Mountains.
Note the “eyespots” on the wing above and below, a feature found in many moths and butterflies. Its evolutionary significance, I believe, is still not fully understood. Some say it’s a mimic of vertebrate predator eyes, like those of owls, that can scare away birds who are going after the moths.
Someone should indeed make a plush toy of this moth. Don’t you just want to pet that furry belly?
And reader Diana MacPherson sends photos of her chimpunks, or rather one young chipmunk (Tamias striatus):
A juvenile chipmunk decided to explore everything on my deck this morning including the hummingbird feeder. You can see the sequence I shot with the chipmunk eventually falling off completely. This one climbed all over my screen facing down (I’ve never seen the chipmunks do that) and kept looking in. If I had the door open, I’d be trying to usher the chippy outside right now. I did get decent photo when the chipmunk stood still for a bit, resting with legs draped over the deck.
Oops. . .
On the screen:
On the deck:
Interspecific love:
Yesterday Hili got fusses from Kaja:
Kaja: Hili, tell me, what’s your philosophy?Hili: It’s Stoicismus interruptus.
Kaja: Hili, powiedz mi, jaką ty masz filozofię?
Hili: Stoicyzm przerywany.