Month: July 2014

A tale of two crows

July 24, 2014 • 10:09 am

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:

Hooded Crow ok

Carrion crow:


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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:

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Speciation battleground. On either side of the narrow hybridization zone (dark brown), the carrion crow (Corvus corone) (dark area) and hooded crow (Corvus cornix) (pale area) ( 2) maintain their marked phenotypic differentiation, despite apparent lack of genetic differentiation. Genome-wide admixture analyses (inset at bottom) show that German carrion crows most closely resemble (80%) hooded crows, and are quite distinct from Spanish carrion crows. Sampling sites for the present study ( 6) are shown as circles. Sp, Spain; Ge, Germany; Po, Poland; Sw, Sweden.

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:

  • The hooded and carrion crows were barely different genetically. Of over 8 million DNA positions that were variable within the two species, they were “fixed” between them in only 83 places (i.e., one could diagnose with certainty the two species by looking at only 83 places out of millions in the genome, while the rest of the DNA bases gave no diagnostic information about whether a crow was hooded or carrion.
  • Similarly, gene expression (as measured by the gene product, messenger RNA) barely differed between members of the two species. The percentage of all genes expressed differently ranged from 0.03% to 0.41% depending on the tissue—less than half a percent difference between hoodeds and carrions. As one might expect, most of the genes that differed in expression were those involved in plumage color, the most obvious difference between the species.
  • Surprisingly, 81 of those 83 fixed differences between the “species” mapped to one small region of a single chromosome: chromosome 18. That region represents only 0.28% of the total genome: about one quarter of one percent. The figure below shows the fixed genetic differences between the species (indicated with red arrows) across the genome, with each chromosome given by either a light blue or dark-blue color. You can see that most of the differences cluster on chromosome 18.

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  • The genes in that very small region included “transcription factors” (genes that control the expression of genes elsewhere in the genome); these factors appeared to control pigmentation and vision.
  • The genes that differed in that region were probably contained in an “inversion”: a section of the chromosome that has been turned around in one of the two species since the common ancestor.  That is, if the common ancestor had gene order ABCDEFGHIJKLMN on its chromosome, one of the two descendants had an inversion that made the gene order something like ABCDEKJIHGFLMN, with the region F-K turned around. This happens when a chromosome breaks in two places and re-forms, but with the broken bit inserted backwards.
  • A few genes on other chromosomes also affected differences in pigmentation and probably vision as well.
  • Finally, as shown in the diagram at the top of the species’ ranges, carrion crows from Germany were more genetically similar to hooded crows from Poland and Sweden than to crows of their own species (carrions) from Spain. This probably reflects a historical phenomenon: the Spanish crows were isolated during the last glaciation, while the German crows expanded their ranges eastward out of a glacial refugium to eventually contact the hooded crows that were west from their refugium. Genetic interchange between the adjacent populations have made them more genetically homogeneous, despite their differences in the inverted region of chromosome 18.

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.

Another U.S. execution botched

July 24, 2014 • 6:28 am

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:

Capital_punishment Screen shot 2014-07-24 at 6.36.51 AM

Thursday: Dobrzyn

July 24, 2014 • 4:02 am

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).

Hili 1

 

Hili 2

 

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):

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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.

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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:

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And for felids that are reading, to cat scale:

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Match that, White Basket Cat!

 

 

Readers’ wildlife photographs

July 24, 2014 • 12:43 am

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.

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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.

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Someone should indeed make a plush toy of this moth. Don’t you just want to pet that furry belly?

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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.

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Oops. . .

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On the screen:

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On the deck:

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Interspecific love:

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Fox noms, damages, and absconds with GoPro camera

July 23, 2014 • 11:58 am

This video shows two things:

1. These cameras are pretty indestructible.

2. This fox’s teeth are in good shape.

The backstory from GrindTV:

You could say that Jonathan VanBallenberghe was outfoxed by the critter he was trying to videotape recently during an expedition to Round Island, Alaska.

VanBallenberghe was part of a group from the University of Alaska, capturing footage to showcase the wildlife of Round Island, which is at the northern end of Bristol Bay. He had set his camera on the ground, hoping for a low-angle closeup of a red fox approaching on the trail.

But the fox had its own idea. It decided to run off with the camera, and use the expensive device as a chew toy.

“My friends were photographing and filming sea lions when I spotted this fox come along,” VanBallenberghe states in the YouTube video description. “So I stupidly put my GoPro on the ground in hopes of getting a closeup. When the fox ran off, I thought I’d never see my camera again.”

Viewers can see the fox grab the camera, and the inside of the critter’s mouth as it gnaws on the unit with incredibly sharp and pointy teeth.

After several minutes of looking, VanBallenberghe and a friend locate the camera, with its face plate torn and the lens area badly damaged.

“It turns on and records, but the lens is messed up and I’ll need to have it repaired,” VanBallenberghe states. “I’m glad the fox itself didn’t get hurt or swallow anything that could have harmed it.”

The film project director told the Alaska Dispatch that the 30 or so red foxes on Round Island enjoy an ample food supply, thanks to an abundance of voles and other small animals.

Perhaps out of boredom, they sometimes kill voles without eating them, and are “used to going after little things just for entertainment.”

The GoPro is a little think with a blinking red light. In hindsight VanBallenberghe should have known better. But he did retrieve his camera, and some very unique footage.

“I don’t care really,” he said of the damaged camera. “I’m excited to have something different.”

h/t: Scott

Afghani mullah rapes ten-year-old girl; family wants to kill her

July 23, 2014 • 8:53 am

There is no explicit statement in the Qur’an (I don’t know about the hadith) urging or sanctioning “honor killings,” but it’s now become a feature of Islamic culture, and has been justified on religious grounds (in Jordan, attempts to strengthen laws against honor killing were opposed and turned back by Muslim leaders for religious reasons).

Virtually every case  (I’ll add here “that I know of”) of “honor killing” is done by Muslims, and is committed against women, either for being raped (the excuses here are that a raped woman must have been a temptress, provoking the uncontrollable lust of men, or that a raped woman is no longer a virgin and thus not a candidate for marriage), for consorting with an apostate, for having extramarital or premarital sex, and so on. Often young members of the family, like boys, are assigned to do the deed, with the idea that they’d get off easier if they were young.

Such women (men, of course, aren’t often the subject of honor killings) are killed in a sick and perverted attempt to restore “honor” to the family defiled by, say, having one of its daughters raped. One would think that if you have to restore honor through violence (something that I do not favor, of course), you’d kill the rapist, or at least men involved in such episodes. But that rarely happens. That’s because it’s women’s sexuality that is supposedly besmirched, not the male’s; and that cult of “purity” also comes from religion.

Now, in Afghanistan, which has become increasingly more radical and misogynistic since the ultrareligious Taliban has made gains, comes one of the most odious cases of incipient honor killing I’ve heard of.

As The New York Times reported on July 19, a ten-year-old girl, weighing just 40 pounds and prepubescent, was raped by a mullah (a religiously educated Muslim man, usually with high standing). His name is Mohammad Amin.

The rape was so violent that it nearly killed the girl. The mullah has confessed, but said that he thought the girl was 17 (yeah, that explains why she weighed 40 pounds and had no secondary sexual characteristics), and has offered to marry her.  The girl was placed in an shelter for women to protect her, as her family threatened to “honor” kill her. But, and the idiocy continues, now the police have taken the girl out of the shelter and returned her to her family.  Unless somebody intervenes, she’s doomed to die—for the “crime” of being raped by a much older man. One can’t even use the excuse that she “tempted” him.

Here are some facts (these are direct quotes from the Times). It’s unbelievable that people can behave this way:

  • The girl’s own testimony, and medical evidence, supported a rape so violent that it caused a fistula, or a break in the wall between the vagina and rectum, according to the police and the official bill of indictment. She bled so profusely after the attack that she was at one point in danger of losing her life because of a delay in getting medical care.

  • The case has broader repercussions. The head of the Women for Afghan Women shelter here where the girl took refuge, Dr. Hassina Sarwari, was at one point driven into hiding by death threats from the girl’s family and other mullahs, who sought to play down the crime by arguing the girl was much older than 10. One militia commander sent Dr. Sarwari threatening texts and an ultimatum to return the girl to her family. The doctor said she now wanted to flee Afghanistan.

  • Most of the anger in Kunduz has been focused not on the mullah but on the women’s activists and the shelter, which is one of seven operated across Afghanistan by W omen for Afghan Women, an Afghan-run charity that is heavily dependent on American aid, from both government and private donors.

    “People know this office as the Americans’ office,” Dr. Sarwari said. “They all think the shelter is an American shelter. There isn’t a single American here,” she said.

    “W.A.W. is not American-run,” said Manizha Naderi, its executive director. “Every single staff member is an Afghan. They are from the communities we work in. Our only concern is to make sure women and girls are protected and that they get justice.”

  • When Dr. Sarwari, who is a pediatrician, arrived to pick up the girl at the hospital, a crowd of village elders from Alti Gumbad, the girl’s home village on the outskirts of the city of Kunduz, were gathered outside the hospital; the girl’s brothers, father and uncle were among them. Inside, Dr. Sarwari encountered the girl’s aunt, who told her she had been ordered by her husband to sneak the girl out of the hospital and deliver her to the male relatives outside. “She said they wanted to take her and kill her, and dump her in the river,” Dr. Sarwari said.
  • In the hospital room, the doctor found the girl’s mother holding her child’s hand, and both were weeping. “My daughter, may dust and soil protect you now,” Dr. Sarwari quoted the mother as saying. “We will make you a bed of dust and soil. We will send you to the cemetery where you will be safe.”

  • Dr. Sarwari has accused prosecutors and religious officials of siding with the accused rapist and ignoring the child’s plight.

    “There are a lot of powerful people behind the mullah,” Dr. Sarwari said. The girl’s family knows they cannot do anything to Mr. Amin, she said, but “the girl is easy. They can get to her; she’s their daughter.” She said she feared the girl would either be killed, or forced to recant her accusations against the mullah.

    Women for Afghan Women arranged for the girl to get medical treatment, and after she healed, she was returned to the shelter in Kunduz, about two weeks ago, until the police returned her to her family last Tuesday. Those caring for the girl said she had been terribly homesick and wanted to return to her family, but no one had the heart to tell her they had been conspiring to kill her.

I don’t see any way that this girl’s life will be saved now that she’s in the hands of her family. The girl is doubly victimized: by a pedophilic imam who uses his position to rape a child, and by her family, who doesn’t care very much about the rapist iman, but really, really wants to kill their daughter. It makes me weep that people can be so bestial—so twisted—that they can do this. And blame religion, too, for this is an endemic trait of Islam, though it’s also sometimes seen in non-Islamic cultures (I’m having a hard time finding cases of honor killings not involving Muslims, but citing one or two won’t disprove the relationship).

The imam has been arrested, but he’ll likely either get off or get the usual very light sentence. All we can do is fight against the forms of religion that sanction this behavior, and donate to Women for Afghan Women.  Their numerous programs are described on the site, and this video shows some of the suffering inflicted on Afghan women:

You can donate here; I didn’t hesitate a second.