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.
Stephen Barnard is back with some lovely photos from Idaho—including mallards! His notes are indented:
First, a couple of photos of some elk (Cervus canadensis) I found in my backyard after I came home from a weekend trip. This group is part of a larger herd of at least 100. It appears to be dominated by one bull. I find the expressions on the faces in the second photo amusing.
The next day, a couple of photos of two bull elk, part of the large herd, sparring and trashing one of my wheel lines. I had to chase them off.
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A ring-necked pheasant (Phasianus colchicus), one of two cocks romancing a hen. These are probably stocked birds (for hunting) that wandered onto my place. They don’t survive the winters in good numbers.
Migrating mallards [Anas platyrhynchos] by the thousands, finding refuge in Loving Creek. They’re hunted intensively, so they’re very spooky and they flush when I get out and about in the morning. They fly onto neighboring properties where Elmer-Fudd-like hunters are lying in wait in their blinds. Sunday mornings are especially loud. Shouldn’t these people be in church?🙂
In the morning (not every morning, but a few) I’ll see thousands of mallards in the sky over the barley fields, looking for a safe place to land. Quite a sight. They come in waves from Canada and Alaska. Mallards are doing well.
My dogs, Deets and Hitch, used to be gun shy, but they’re gotten used to it. Here’s a lagniappe photo of Hitch on the run.
It’s almost Halloween, which is tomorrow; today it’s Tuesday, October 30, 2018, and once again National Candy Corn Day, celebrating the Worst of All Possible Candies. Made of perfume and paraffin, this candy has no rival in confectionary dreadfulness.
Speaking of Halloween (the source of all c—y c–n, today’s animated Google Doodle (click on screenshot below) is the outfit’s first multiplayer game: you can play with up to six other people throughout the world. See the explanation at C|Net.
Meanwhile in Washington, Trump advisor Kellyanne Conway put her metatarsals in her mouth on Fox News, once again lying about Trump’s leadership against hatred. Do remember that Trump’s daughter Ivanka and her husband (who are Jewish) had to persuade the President to denounce anti-Semitism after the Pittsburgh attack. But more invidious is the second clip, in which Conway blames the anti-Semitic hatred in the country, which led to the Pittsburgh shooting, on the nonbelievers and anti-religious: “This is no time to be driving God out of the public square.”
Conway tries to frame Pittsburgh shooting as really being about "anti-religiosity" writ large.
"The anti-religiosity in this country that is somehow in vogue… making fun of people who express religion, the late night comedians,.. It's always anti-religious." pic.twitter.com/yw6ZvY1CIQ
On this day in 1485, Henry VII was crowned King of England, beginning the Tudor reign. On October 30, 1831, Nat Turner was arrested for leading his bloody slave rebellion (55-65 people were killed, 51 of them white). He was soon caught, hanged and his body cut into pieces. On this day in 1938, when my father was 20 years old, Orson Welles and his Mercury Theater broadcast his radio play of The War of the Worlds, causing anxiety in many Americans who thought the play was a real news broadcast, announcing the invasion of Earth by Martians. My dad remembered people rushing out into the streets in panic. On this day in 1942, reports Wikipedia, “Second World War: Lt. Tony Fasson and Able Seaman Colin Grazier drown while taking code books from the sinking German submarine U-559.” And two years later, Anne Frank and her sister Margot were moved from Auschwitz to the Bergen-Belsen Lager, where they were to die of typhus shortly before the war’s end.
One year after that, in 1945, Jackie Robinson, playing for the Kansas City Monarchs, signed a contract with the Brooklyn Dodgers, becoming the first black man to play major league baseball. On October 30, 1961, because Stalin supposedly “violated Lenin’s precepts”, Father Joe’s body was moved from being on view in Lenin’s tomb to a burial site with a plain marker. Finally, on this day in 1995, the citizens of Quebec voted very narrowly (50.58% to 49.42%) to remain a province of Canada. I wonder if such a vote will ever occur again.
Notables born on this day include John Adams (1735), Alfred Sisley (1839), Paul Valéry (1871), Ezra Pound (1885), Charles Atlas (1893), Robert Caro (1935; still working on the last volume of his great biography of Lyndon Johnson), Grace Slick (1939), Henry Winkler (1945), and Stephanie Izard, our own Chicago chef (1978).
Those who died on this day include Kitigawa Utamaro (1806), Egon Schiele (1918), Harry Houdini (1926), Indira Gandhi (1984), River Phoenix (1993, only 23 years old), Studs Terkel (2008) and Ted Sorensen (2010). Here’s a lovely print by Utamaro, “Cat Dreaming”:
And another: “Wild Chrysanthemum: Woman and Cat”:
Meanwhile in Dobrzyn, Hili saw a bug:
Hili: Look, it’s walking.
A: What’s walking?
Hili: I don’t know, you’ll have to ask an entomologist.
In Polish:
Hili: Patrz, chodzi.
Ja: Co chodzi?
Hili: Nie wiem, trzeba zapytać entomologa.
Humor of the day from reader Neil: Amish salsa!. He notes:
Saw this in my local grocery store (run by Amish). The Amish will appropriate Mexican culture but they won’t appropriate buttons, cars, or birth control. Go figure.
Somebody tell the Culture Police!
Tweets; the first sent by reader Nilou. The comments indicate that it’s eating and not a fake animation. This starfish twerks even better than James Pond:
Do you know about social credit in China? Listen to this, and then read an explanation here.
Here's a dystopian vision of the future: A real announcement I recorded on the Beijing-Shanghai bullet train. (I've subtitled it so you can watch in silence.) pic.twitter.com/ZoRWtdcSMy
I continue with another exhibit from Zagreb’s Museum of Broken Relationships, a truly remarkable place. Each item was donated by someone involved in a “broken relationship” (mostly romances but some parent/child relationships), and the donor wrote an explanation of the circumstances.
Here’s a token from a long but ultimately broken love:
How could I have missed this? As the tweet below (h/t: Grania) indicates, it’s NATIONAL CAT DAY! And the hashtag #NationalCatDay is full of swell pictures.
In honor of this day, the first five readers who send me a photo of their cat, along with two sentences giving its name and some salient facts, will have them posted here. Be quick about it. (I’ll add them to this post.) One picture per reader, please.
NOTE: The submissions are now closed; we have five magnificent felines below (actually, seven):
And here we go. #1 is from Luana Maroja, who sent two cats in one photo:
Here my cats: Sushi and Wasabi – they are not related but both came from the same feral colony in VT (near Bennington). Sushi (dilute calico) was born without a tail and is polydactyl – her mother was a black cat with tail and polydactyl which makes the father orange and white without tail – the litter was 3 tail-less to 1 tailed (expected for dominant tailess would be 1:1).
From reader Robin:
Clementine is not allowed on the kitchen counter. Ever. Except maybe at the very edge. From her staff, Robin in Boca Raton FL
From reader Darryl Ernst:
This is her highness Coco Chanel. In this picture she is telepathically communicating to me that she is so amazing in every way that I really should be giving her all of my attention instead of paying attention to the book I am trying to read. So demanding! I’m sure she is sometimes exasperated by the seeming denseness of her human staff. We try!
From Michael Glenister:
These are two cats I’m fostering at the moment: Thing 1 and Thing 2. Thing 2 at the back has two spots on his shoulders, a goatee, and is generally more cuddly.
And the last one, from reader Amy Tovar:
This is my new kitten. I was finally ready for a new cat after Kitten (see Spot the orange cat post) died last year. We named him K2 as an homage to Kitten. Still haven’t settled on spelling…
K-two, K-too or K2. K2 probably isn’t the best as this was the street drug that many people have over-dosed on. never thought I wanted a kitten but he is hilarious and goes full speed non-stop until he finally falls over completely exhausted.
I had to go to the on-campus bank today, and was struck on my walk at how lovely the fall is here. Here are a few snaps I took along the way; these are taken with my iPhone camera as I didn’t bring my Panasonic Lumix along.
It’s a sad situation that the tiger (Panthera tigris), the world’s largest and arguably most magnificent wild cat, is heading towards extinction in nature. Fewer than 4,000 of them remain in the wild, and there are more in captivity than are roaming free in nature. Their current range is only 7% of the territory they occupied before humans killed them and destroyed their territory. Here, from Wikipedia, is a map of their present versus historical ranges. Sad, isn’t it?
One strategy for saving the tiger is to recognize subspecies, which are populations of the species that are recognizably different, either genetically (usually through inspection of DNA sequences) or through morphology (morphological differences, of course, often reflect genetic differences). Subspecies used to be called “races,” and still are by some people, but the term “race” is now in bad odor because of its past misapplication to our own species.
The designating-subspecies strategy here is two-pronged, with one prong scientific and the other political. The scientific rationale is that because populations differ genetically, saving different populations that are genetically diverse is a way to conserve overall genetic diversity in that species. Why? It’s sometimes not clear, but reasons given are to enable the species to recover if populations go extinct from inbreeding (a loss of genetic diversity), to conserve populations that look different and thus could be considered to have diverse appeal, and to save rare alleles that might prove adaptive under environmental change. I consider this strategy ill-conceived for reasons I’ll mention below.
The political reason is simply because some conservation laws, like the U.S.’s Endangered Species Act of 1973, allow a population to be listed as threatened or endangered if it’s not an entire species but simply a subspecies: a genetically different population. If you want to save a species, then, one way is to help save its constituent subspecies, regardless of the genetic rationale above. All that’s required is that a population be designated a subspecies because it is genetically different from other populations, and then that subspecies cannot be touched. Exactly how different a population must be to be regarded as a subspecies is not clear, and is subject to discussion and argument by biologists.
The use of the “subspecies” category thus gives conservationists a way to save species by saving their populations, even if the genetic rationale supporting it is weak. But because most conservationists and many biologists, including me, see saving species as an intrinsic good, regardless of genetic differentiation, we can use the “genetic differences” regulations as a way to do what we really want to do: save species as wholes regardless of how genetically different their populations are. And that surely holds for the vanishing tiger.
In other words, it’s in the interests of species-loving biologists to designate as many subspecies as possible as a way to save species, regardless of whether we agree with the “saving genetic diversity” argument. (As I said, I don’t really buy into that argument.) Thus you can use even tiny genetic differences, perhaps as little as a single gene causing change in, say, color—or even a diagnostic difference in DNA sequence of unknown function—as a way to designate subspecies and thus save species.
Now some biologists do think that we need to conserve genetic diversity within a species, and sometimes they might be right. But more often I think it’s a tactic to enable them to do what they feel impelled to do: stave off the destruction of threatened species by any means possible.
I hasten to add, though, that investigating population differences is of interest in its own right. For instance, we can get an idea whether those populations might be reproductively isolated (no gene exchange because of biological differences), and thus true species rather than subspecies. Or the genetic differences might give us some idea of the history of the species and the evolutionary relationships among populations. Or you might be able to identify illegal wildlife traffickers by looking at the DNA of material they’re selling.
An increase in tiger subspecies—or rather, a genetic confirmation of traditional subspecies— comes from a new genetic survey of the world’s tigers by by Yue-Chen Liu et al., just published in Current Biology (paper here, pdf here; reference below; ask if you can’t get it). There’s also a summary of the study in this week’s New York Times (click on screenshot below).
The upshot of the paper:
Tigers are genetically depauperate, probably because of a reduction in species size to around 50,000 during Pleistocene glaciation.
Nevertheless, sequencing of mitochondrial and nuclear DNA of tigers shows clear genetic differentiation among populations, and the well-demarcated populations (genetically, not morphologically) correspond to the six subspecies already recognized: the Bengal tiger, the Amur tiger, the South China tiger (only one specimen used), the Sumatran tiger, the Indochinese tiger, and the Malayan tiger.
Here’s a phylogeny of the tigers based on 11,600,055 autosomal variants, showing that they fall into six neat groups (consult the paper for caption and methodology) corresponding to the different subspecies already recognized (colors). Mitonchondrial and X-chromosomal analyses give similar phylogenies, and the numbers at the branches show that these are significantly demarcated using bootstrapping methods:
Below is a cluster analysis of tiger genomes using the “ADMIXTURE” program. The data are based on nearly two million variants on the autosomes. The different colors recognize units that the program can distinguish under assumptions of different numbers of clusters, with the number of clusters to look for set from 4 to 6. As you see, under the assumption of 5 clusters you get five subspecies, and with 6 clusters you get six subspecies. (This is not a trick, but a way to recognize hierarchically differentiated populations.)
Gene flow among populations was extant but low, reflecting the fact that they’re geographically isolated and have been so for some time. They aren’t considered different species because there is some gene flow and because hybrids, at least in captivity, are readily formed and are fertile.
These differences aren’t so readily discerned using morphology, since tiger subspecies generally lack diagnostic physical traits, though there are some average differences in size, shape and color (see here for a summary). That is, you can’t unambiguously put a single tiger into one of the six subspecies using morphology alone, but you can do it using just a few genes.
These findings, while confirming traditional classification, go against the suggestion of some biologists that there are only two subspecies of tigers. Those biologists say that having only two subspecies is better than having more, because the recognition of some very small subspecies, like the South China tiger, would make them “face extinction”. (This baffles me unless those researchers don’t think we should make an effort to save this population.)
Some of the DNA data give evidence that population differences arose by natural selection (this comes from the pattern of the variation associated with these regions). As the paper notes, “We identified multiple genomic regions that are candidates for identifying the adaptive divergence of subspecies. The body-size-related gene ADH7 appears to have been strongly selected in the Sumatran tiger, perhaps in association with adaptation to the tropical Sunda Islands.”
But genetics does confirm the populations previously recognized by average trait differences. That’s not a novel finding, but the genetically diagnostic differences, say the authors, will help us conserve the species. As they say in the paper (my emphasis):
Because many of the conservation policies and measurements regarding the tiger, including coordinated captive breeding programs and legislations in several tiger range countries, are based on “subspecies taxonomy,” an appropriate description of subspecies is vitally important.
Considering the subspecies concepts presented above, the genome-wide signatures of phylogeographic partitioning and evidence for long-term restriction of gene flow and adaptive divergence jointly allow us to elucidate tiger evolution and corroborate six phylogeographic units. These findings provide the strongest genetic evidence for subspecies delineation in tigers to date, evidence stronger than that used to define subspecies in nearly any felid reported thus far. These population units correspond precisely with the geographic subspecies named much earlier. . .
Understanding the tiger’s natural history from a genomic perspective provides a data-driven foundation for subspecies recognition, conservation strategic planning, and management actions. Our general goals are to reverse the species’ decline by maximizing the efforts to preserve the genetic diversity, evolutionary uniqueness, and potential of the species Panthera tigris.
The New York Times article echoes the conservation importance emphasized by the study’s authors. But, as I implied above, recognizing six subspecies rather than two is important mainly because it gives biologists a legal handle to save tigers in general. The genetic differences between populations, as diagnostic as they are, are in my view not sufficient reason by themselves to save all populations. Sufficient reason to save the populations, though it won’t fly with governments and laws, is simply because we need to save as many tiger populations as we can, because they add to our world, because they were here before us, and because we have no right to wipe out a dwindling species for our own selfish needs. Despite their fierceness, tigers can’t fight human development. Most nature-loving biologists simply want any way to save tigers, and genetics (again, this is my opinion) gives them an excuse—but not a good population-genetic reason. Any one population of tigers surely contains enough genetic variation to replenish all the other populations, whether that variation be common or rare. And, of course, new mutations occur.
Here’s what one of the authors say in the NYT piece:
A system recently proposed by some scientists that would classify the world’s tigers into two subspecies would harm the world’s remaining tigers rather than benefit them, said Shu-Jin Luo, a geneticist at Peking University who led the study. Preserving what is left of tigers’ genetic diversity will require ensuring that all remaining subspecies are taken into account, she and her co-authors argue.
“If you think that all tigers are genetically homogeneous, you might say if you lose the Amur tiger, you still have the Bengal tiger — and that’s O.K. because they’re very similar,” Dr. Luo said. “But that’s not O.K., because now we know that tigers are not all alike.”
No, tigers are not all alike; they differ on average in appearance, and in DNA sequence, some of those differences probably being the result of geographically varying natural selection. But what do we gain by saving subspecies because they have genetic differences. What, indeed, are the genetic differences we’re trying to conserve? Genes for morphology? Those differences are inherent within in any one subspecies, so you could constitute any extinct population simply by either selecting variants within another subpopulation, or transplanting members of extant populations to areas of extinction, where selection will act eventually to create a new subspecies (it may be different from the old one). Are we trying to save variants that might be adaptive in the whole species, enabling it to respond to new selective pressures? If so, those variants are probably latent in several populations, so you don’t need to conserve them all. Are we trying to prevent inbreeding? Well, there’s no evidence that extinction is caused by inbreeding in this species, and to save them that way requires crossing members of different subspecies, which wipes out the differences we’re trying to conserve in the first place.
What I’m not saying here is that because the rationale for conserving genetic variation in tigers is weak, we shouldn’t try to save every subspecies. No, what I’m saying is that the genetic-variation excuse is a way that some biologists, chafing under legal restrictions, try to save every member of a species, no matter how many subspecies there are. Having six rather than two subspecies of tigers makes it easier to save them all, but what if the genetic variation analysis had shown just two, or four, distinct subspecies? Would it be less pressing to save tiger populations? I doubt that even conservationists would agree. And that shows that we’re using political rather than sound genetic rationales to save endangered species.
My message here is just this: we should save all the tigers because tigers are an inherent good. If we have to do that by recognizing subspecies, well, that’s the way we have to do it. But we shouldn’t pretend that we need to save subspecies to “conserve genetic variation in tigers”. That rationale is very weak, and makes conservation dependent on subjective criteria like the frequency of DNA variants that may not even play a role in adaptation—now or in the future. I think it’s time for conservation geneticists to tell us exactly what kind of genetic variation they want to save, and why. (There’s very little written about this.) And it’s time for biologists to admit that for many of us, our interest is not in conserving genetic variation, but in saving every tiger possible. The subspecies ploy is one way to do that, but it’s still a ploy.
We should save all tigers because of they are dwindling but magnificent; because of this:
(From the NYT): Tigers in a park in Hailin, northeast China. A century ago, about 100,000 tigers roamed Asia’s habitats. There remain only about 4,000 in the wild worldwide.CreditVisual China Group/Getty Images
The way to save tigers is not to designate subspecies and then use various schemes to conserve genetic variation, but to save the habitat in which tigers live and to keep people from poaching them.
Bruce Lyon has returned from Europe with some swell pictures, including many birds. His notes are indented:
A selection of alpine and montane birds from my recent visit to France. I was in France to work on papers with my former graduate student Alexis Chaine, now a researcher at a research station at Moulis in the foothills of the Pyrenees. We were able to fit in a couple of natural history trips during my visit, including trips into the mountains. Here are photos from a day we spent visiting the Pic du Midi de Bigorre, one of the highest peaks in the area (9500 feet). From the bottom of the mountain, a two-stage tram ride takes you to the top. Once there, you are restricted to a large fenced in viewing platform, complete with a restaurant (with very decent views)
The views were spectacular, and although bird diversity was not high, the species we saw were very charismatic high elevation species not seen lower down. The Pyrenees had different feel than the other mountain ranges I have seen. A lot of the terrain seemed smoother than other mountain ranges, and had more vegetation.
Below. View from the mountain top showing the tram that ferries people up and down the mountain. The habitat looks lifeless but it was actually pretty birdy at times.
Below. The Pic du Midi Observatory. According to Wikipedia, a large telescope here was “funded by NASA and used to take detailed photographs of the surface of the Moon in preparation for the Apollo missions”. I am not sure what the tower is about, perhaps weather data? The French government also encourage research at the site and colleagues from the Moulis CNRS research station brought some low elevation lizards to a lab at the top of the mountain to study short-term physiological response to changes in altitude.
Below. The Wallcreeper (Tichodroma muraria) is a much sought after mountain bird in Europe (and a nemesis bird because it is often missed). This small songbird, a relative of the nuthatches, forages by climbing around sheer cliff faces looking for small insects. We got very lucky—within 30 seconds of exiting the tram we made our way to the edge of the viewing platform and I noticed a small gray bird working a cement pylon. It turned out to be Wallcreeper.
Below. After feeding for half a minute, the Wallcreeper flew off, showing us its spectacular colorful wings and weird loopy butterfly-like flight. I did not get a flight shot but one cannot discuss this bird without showing a flight shot so I ‘borrowed’ this image from the internet (unnamed photographer). NOT MY PHOTO!
Below: We also saw Alpine Accentors (Prunella collaris), charming little birds that live and breed in social groups on the rocky slopes of high mountains.
Below: More accentors. These birds have an interesting mating system—they are polygynandrous, which means that both males and females mate with more than one member of the other sex. Males then help feed at the nests of more than one female.
Nick Davies, a behavioral ecologist from Cambridge University, studied this species in the French Pyrenees with several colleagues. Davies did famous work on the closely related Dunnock (Prunella modulars), which also has a polygynangrous mating system. The researchers wanted to know if the Dunnock mating system is unique—does Dunnock ecology explain the mating system, or do other accentors living in very different habitats also share aspects of the same mating system? If relatives share the mating system, then phylogenetic history would be an important explanation. Davies studied Dunnocks in the Cambridge botanical gardens so the idea was to look at a close relative that lives in a very different setting, so they studied Alpine Accentors in the Pyrenees. It turns out that the mating system of the Alpine Accentor and the Dunnock are similar in many ways, which showed that the mating system is influenced by phylogeny and cannot be explained solely by an evolutionary response to local ecological conditions.
Below: Speak of the devil—at the end of the day when we descended the mountain to find a very tame Dunnock feeding beside our parked car. It clearly did not want us to leave the area with a focus solely on its high elevation relative.
Below: On the mountain we also saw the White-winged Snowfinch (Montifringilla nivalis), another iconic high-elevation species. Like the accentor, this bird was abundant and tame—at the end of the day small flocks of both species were feeding at our feet, looking for food scraps people had left on the viewing platform.
Below: I was delighted to see the snowfinch because it seems very similar ecologically and morphologically to the Snow Bunting (Plectrophenax nivalis), an arctic songbird I studied for my Masters with Bob Montgomerie at Queen’s University. The color pattern in flight is quite similar in both species—these two species are not closely related so it seems this plumage resemblance might be a case of convergent evolution. I also find it interesting that males of both species display to females with aerial flight song displays and both species nest in cavities in the rocks. The two photos below, pinched from the web, show that that birds look quite similar in flight (snow bunting on left, snowfinch on right).
Below: A group of Red-billed Choughs (Pyrrhocorax pyrrhocorax ) visited the mountain top a few times. These are corvids (crow and jay relatives) but they have a distinctive sickle-shaped bill. We watched them foraging and they used their long curved beaks to poke in the soil and in cracks in the rocks. The choughs never came very close but I did manage to get an OK flight shot.
Below: We also saw several Griffin Vultures (Gyps fulvus), very large vultures whose shape silhouette reminded me a bit of California Condors. Wingspan is 7-9 feet. This is Old World vulture that is unrelated to the New World vultures, so any resemblance is due to convergent evolution.
Another Griffin Vulture that nicely shows the ‘slotted wings’ with finger-like primary feathers at the wing tips. Slotted wings have evolved independently in various birds that soar using thermals to gain lift—New World vultures, Old World vultures, other raptors like eagles, various storks, cranes, and to some extent American White Pelicans. From what I have read, each feather acts as a mini airfoil that creates smoother airflow at the wing tips at slow flight speeds. This results in a reduction of stall speed so that the birds can circle very slowly, and therefore make very turn tight turns to remain in the highly localized thermals, without losing lift and stalling.
