According to our readers, the Ivory-billed Woodpecker is everywhere! Here: seven independent sightings!

April 21, 2022 • 8:30 am

The other day I posted a video in which a researcher claimed to have sighted an Ivory-billed Woodpecker in the wet bottomlands of Louisiana. It didn’t prove to me that the bird still exists, but raised my Bayesian probability that it does.

One reason why researchers haven’t yet accepted the existence of the bird is that there are still no unequivocal identifying photos or videos of this bird in the wild. The more recent photos and videos are tantalizing, and make me think that it’s more probable than not that Campephilus principalis has not yet become an ex-species, singing with the Choir Invisible. But I’m still not convinced.

Yet over the last two days, a bunch of readers—seven, to be exact—have made comments asserting confidently that they have seen this bird. None of them have expressed doubt. My first response would be “No you haven’t: you’ve seen a Pileated Woodpecker”.  If Ivorybills were that common, showing up in people’s backyards (!), then we would have good evidence by now.

So, go to the thread here; I’ve posted all the sightings that readers claim to have made. And feel free to answer those claims (or comment on them), but be polite. My response was “find a bird expert IMMEDIATELY, tell them, and get some good photos.”  Birders can contact me if they want me to email the claimants telling them how they have to document the bird. Better yet, birders should VISIT all these people NOW.

Here we go. The first one has my response:

Another:

But wait! There are several more!

This one gives a phone number. Ornithologists and birders—GET ON IT!

 

For others who want to claim they’ve seen the real Ivorybill, here’s how to tell it from the similar (but smaller) Pileated Woodpecker. Look for the white “saddle” formed by the folded wings, as well as the sexual dimorphism.

 

Here’s the real bird from an Audubon website:

(From website): A colorized rendition of a photograph taken by Arthur Allen of an Ivory-billed Woodpecker at a nest in Louisiana’s Singer Tract, 1935. Photo: Cornell Lab of Ornithology

Do we have more evidence that the Ivory-billed woodpecker is not extinct?

April 19, 2022 • 1:00 pm

About a week ago I put up a post summarizing a new paper in bioRχiv by Latta et al. reporting the likely persistence of the Ivory-Billed Woodpecker (Campephilus principalis) in an area of bottomland forest in Louisiana. Thought to have been extinct since about 1940, this largest American woodpecker was regarded as one of conservation’s great losses, like the Carolina Parakeet or the Passenger Pigeon.  Interest was revived after the publication of a 2005 paper in Science by Fitzpatrick et al., based on photographs and calls, suggesting that individuals of species still remained. But attempts to replicate those sightings failed, and disappointed birders were more convinced that the Ivorybill was indeed gone.

But now we have the Latta et al. report of living Ivorybills, and I find it a bit more convincing than the Science paper of 2005. The more recent report was based on a decade’s worth of drone and trail-camera footage with suggestive images showing the unique field marks of this bird, including its large size, its unique “manspreading” and laid-back stance on trees, and its white saddle and black-and-white wing markings. See my earlier post for the data that convinced me that there’s a decent chance this bird is still alive, though its restricted habitat would surely make it “endangered.”

The article below, from EcoWatch(click on screenshot) is of interest not because it gives new data, as it doesn’t (it’s a news report), but because it includes some newly released videos  taken in Louisiana in 2006 and 2008—between the two periods of research that led to the paper) that show more suggestive evidence of living ivorybills, including size, stance, its method of flying (sometimes folding up the wings), and white coloration.

Watch the YouTube video below and come to your own conclusions. (I’m sure birders will be more skeptical than I, and that’s great.)

The supplementary page cited on the YouTube page, which has additional video, shows that work was done largely by one Michael D. Collins, not an author of either paper. What we have, then, is one man giving his observations and measurements, and concluding that he’s seen Ivorybills rather than the smaller relative the Pileated Woopecker.  But the work was not trivial!

Now the will to believe is strong, and people want to think that the Ivorybill is still alive. But after watching the 24-minute video below, I have to say that my priors that the Ivorybill still exists have increased a bit.

Still, nobody is going to accept that this species is still alive until we get much better videos and  photos.  But have a look! Collins actually gives better location data than either paper cited above, which will of course entice the area to be flooded with birders. That may not be good, which is why those other papers did not divulge the exact location of their observations.

Is the Ivory-billed Woodpecker still with us?

April 11, 2022 • 10:00 am

UPDATE: I have removed the photos from the new paper as the authors have copyrighted them and won’t give me permission to use them. , but you can see them at the site.

 

In 2005, a paper in Science by Fitzpatrick et al. produced a flurry of ornithological excitement. The paper (click on screenshot below) adduced evidence that the Ivory-billed Woodpecker, Campephilus principalis—thought to have been extinct in the US (and elsewhere) since about 1940was actually persisting in wet lowland forests of the South.  This was based on sightings and recordings of calls, but the photographs weren’t that convincing. Nevertheless, the authors declared that the bird persists: click on the screenshot to read.

This magnificent beast, the third largest woodpecker in the world, used to have a fairly broad range across the South, but was limited to wet lowland forests with very old trees. Loss of habitat caused a big popuation decline, and fewer and fewer sightings were made. Here’s a photo of a male from Louisiana in 1935, and another, showing both sexes, is colorized below:

A colorized rendition of a photograph taken by Arthur Allen of an Ivory-billed Woodpecker at a nest in Louisiana’s Singer Tract, 1935. Photo: Cornell Lab of Ornithology

As you can see from the second photo, one distinctive feature of this bird is the sexual dimorphism in crest color: males have red crests and females black ones.  Ivorybills also have a distinctive white “saddle” on their back, and white patches on the wings. These features, and the larger size of the Ivory-billed, distinguish it from a similar species, the pileated woodpecker (Dryocopus pileatus), the largest woodpecker known to exist in the U.S. (many of us have seen them).

Here’s a comparison of both species that I showed when I wrote about the Ivorybill in 2010. Note the white saddle of the Ivory-billed, absent in the pileated, and the sexual dimorphism of the crest. Also, there are differences in facial coloration. It is the superficial similarity of the ivory-billed to the pileated that has led people to declare that, after seeing the latter (they co-occurred), the former was still around.

Audubon’s painting:

And a drawer of preserved ivorybills from Harvard’s Museum of Comparative Zoology (again note the sexual dimorphism):

Ivory-billed woodpeckers at Harvard’s Museum of Comparative Zoology. Image: Damir Frkovic © 2009/Small Change Productions

But over the years after 2005, repeated forays into Louisiana bottomland—the people who see these things tend to keep the locations secret as the places would get overrun with birders and gawkers—failed to turn up convincing evidence of the bird (a really good couple of photos or videos would do). And despite a movie made about the “rediscovery”, Ghost Bird (and a presentation on YouTube), people lost confidence that this elusive bird was still around, and interest waned. Except among a small group who have just published a paper.

On September 29 of last year, the U.S. Fish and Wildlife Service declared the Ivorybill, along with 22 other species, extinct.

And so, apparently, this woodpecker joined the passenger pigeon and Carolina parakeet as one of America’s most famous extinct bird species. It was declared an ex-woodpecker, singing with the Choir Invisible.

But wait—not so fast! I was alerted to a new paper by this tweet from Matthew, linking to a paper that gives pretty convincing evidence that the Ivory-billed Woodpecker is still around, though not numerous.

I’ve read the paper, as have two of my ornithological colleagues, and both declare that the evidence in the paper below is fairly strong. Click on the screenshot to read it, and download the paper here.  Do note that this is an unpublished manuscript, and appears on bioRχiv. It must be reviewed and published before its credibility can increase.

What’s the evidence? Well, the authors scoured a 93 km² (36² mi) area of Louisiana bottomland and mosaic upland for ten years, using both high-flying drones (for 3 years) and trail cameras, and came up with a number of photos, as well as recordings and videos (the photos are the evidence they present. There were 438,000 camera hours of watching and about 1590 drone flights. The evidence, as they say above, is multifarious. It includes these features:

PHOTOS REMOVED AT AUTHORS’ REQUEST

1.) Morphology:  Photos show the white saddle and a dimorphism of crest color, though the photos are admittedly not great. Here are a couple from the paper (captions from the paper; also, see the paper for the videos). I’ve put an arrow by the white saddle:

Enlarged: left column is an Ivorybill photographed years ago in Cuba (where they once lived as well), and the right column shows a new photo and enlargement:

The bird they photographed is also larger than related species photographed on the same tree. Here’s another photo.

There are also apparent differences in crest color seen in some photos like this one, with one member of a pair having a red crest and the other a black one:

 

2.) Behavior. The ivorybill has a different morphology of feet and legs from that of other woodpeckers.  This results in a very different stance of the ivorybill when it’s sitting on a vertical trunk.

From the paper:

Most intriguing is that these images depict the distinctive morphological adaptations of the feet and legs of Campephilus woodpeckers as compared with Dryocopus woodpeckers like the Pileated Woodpecker (33). The phenotypically similar Pileated is one of the most unspecialized of the truly arboreal woodpeckers, while the Campephilus woodpeckers are characterized by pamprodactyly, a pedal morphology that enables the forward rotation of all four toes (33). The specialized modifications in the highly arboreal Ivory-billed Woodpecker are not so much in the structure of the toes as in the position of the legs. The feet are held outward from the body and are directed diagonally upward and sidewise (Figure 7), with both feet wide apart and more anterior relative to the body (33, 34). Usually the angle between the tarsi and the horizontal plane is ≤45˚, and often seem to be pressed against the tree trunk. This is very different from the condition seen in most woodpeckers, as, for example, the Pileated Woodpecker, where the legs are held more or less beneath the pelvic girdle, the joints are fully flexed, and the tarsi are held well away from the tree trunk. This generally results also in a more obtuse angle of the intertarsal joint (where the leg bends between the tibiotarsus and the tarsometatarsus), and is evidence of the better scansorial adaptations of the Ivory-billed Woodpecker compared to the PileatedWoodpecker (33). This obtuse angle is visible from a distance, is readily seen in our images (Figures 6, 7), and can be a useful identification clue in situations where lighting or distance makes it hard to observe plumage details with clarity (35). Combined with feet extended diagonally upward and to the side of the body, the stance of the birds appearing here are consistent with that of a Campephilus sp.

In other words, the ivorybills show what a feminist ornithologist might call “birdspreading”, with a wide stance, legs angled upward (not below the pelvis, as in the pileated), and feet forward. Two photos (A and D below) are from this study. No other woodpecker stands like this.

Fig. 7: Comparison of photographs taken of apparent Ivory-billed Woodpeckers in Louisiana from this study (A, D), with a colorized Ivory-billed Woodpecker, also from Louisiana, but taken by Arthur A. Allen in 1935 (B), and a Pale-billed Woodpecker (Campephilus guatemalensis) are directed diagonally upward and sidewise, with both feet wide apart and forward. The angle between the tarsi and the horizontal plane is ≤45˚ and there is an obtuse angle of the intertarsal joint. Photos (B) and (C) are from the James T. Tanner, and the Arthur A. Allen papers, respectively, courtesy Division of Rare and Manuscript Collections, Cornell University Library.

I encourage you to watch the two video clips (successions of trail-camera photos), which you’ll find here.

There are several other behavioral indices that these are ivorybills.  Comporting with historical observations, the birds seen recently fly high and far, having big home ranges. They are also fast. All three of these features differ from the pileated, whose flight is quoted as being “rather slow, but vigorous and direct.”

Finally, while pileateds forage alone, the authors of the present paper saw three of the putative ivorybills foraging just a few meters apart—perhaps a family group. This of course is one anecdote, but it adds to the evidence.

The authors conclude (and I agree, along with some birders), that they have indeed seen living individuals of Ivory-billed woodpeckers.

But some ornithologists aren’t convinced, and for good reason: the evidence, while pretty good, is not strong enough to be dispositive. When I asked my colleague Steve Pruett-Jones what it would take to convince ornithologists that the species isn’t extinct, he said this:

Well, I’m not really sure. It would vary with the person I guess. Clear, unmistakable photographs or a video would do it.
The paper in question has not yet been peer reviewed and so there may be additional criticisms that come to light.
The criticisms of the earlier reports (over the last 10 years) were generally along the lines of ‘without a clear photograph, you can’t completely rule out a pileated woodpecker’.
This criticism or skepticism is also rooted in the belief/assumption that there are so many birdwatchers now, and there are so few large intact flooded areas where the bird could survive, that if it was still alive, it would have been seen by more people.
Steve, who is fairly convinced by the evidence, also sent me a link to the only summary of this new paper I’ve seen, from revkinbulletin.  It does give criticisms, including some by ecologist Stuart Pimm. They don’t dismiss the evidence, but Pimm argues that the amount of habitat left for these birds is so small that some individuals must have crossed open areas and been seen by birders.

The conclusion is that old chestnut of scientific conclusions: “More work needs to be done.” But one thing is for sure: this new work (which is ongoing) will make birders think twice about declaring the ivorybill extinct, and will spur new efforts to find it. Of course without a concerted effort to save or increase the habitat (wet bottomland forest), seeing the bird is not the same thing as saving it.

h/t: Steve

Vox analogizes invasive species with human immigrants

November 30, 2021 • 9:15 am

I suppose it was inevitable that “invasive” species—species that take over a new area, often far from their native habitat—would be compared by the “progressive” Left to human immigrants, and thus the impact of these species minimized or even lauded. That’s the conclusion you can draw from the headline at the uber-woke Vox website below.

Actually, the article isn’t all that bad, as it does point out that some invasive species destroy ecosystems and must be controlled; other species are moving due to climate change; draws a distinction between true invasives and those deliberately introduced (see Wikipedia’s list of 100 of the World’s Worst Invasive Alien Species; the name “alien will alienate many here, lacking only the adjective “illegal” to enrage the woke); calls attention to the cruel way many invaders are destroyed (poisons can cause an agonizing death), and raises moral issues that should be considered (how do we trade off the death of sentient animals, or nonsentient plants, against native habitat and wildlife)? Those are all things to consider.

But the tenor of the article is one of equating human immigrants with invading species. As a biologist, I admit my biases that when trading off an invader that destroys native species and ecosystems, I give precedence to the natives. Each extinct species is a book that tells us not only about its ancestry, but also can impart fascinating facts about biology. Think of the Hawaiian Islands, where 95 out of the 142 endemic bird species (those found nowhere else) have gone extinct, not just because of habitat damage but because of introduced predators like rats and mongooses who destroy eggs, or feral pigs that destroy habitat. My solution would be, if possible, to get rid of the predators and pigs (as humanely as possible) and try to stem habitat loss.  Problems like this exist all over the world, and unless you have no appreciation for nature at all, you must think about invasion vs. conservation.

I have to say, though, that although the Vox article gives lip service to some truly damaging invasive species (e.g., cats and foxes that kill Australian marsupials), they tend to downplay many cases, like the interbreeding of coyotes with endangered red wolves (see below), my impression is that the article is written by a Leftist who favors open borders for the U.S. But of course the most invasive species of all, and the greatest danger to native species, is Homo sapiens.

Read and judge; you might take issue with my claims above.


As I said, the article isn’t as bad as it could be, but that’s not saying much when it comes to Vox.  Here’s a list of sentences and phrases where author Bolotnikova explicitly use the human/invasive species analogy:

For example, invasives can be considered a threat not only by killing or outcompeting native species but also by mating with them. To protect the “genetic integrity” of species, conservationists often go to extraordinary lengths to prevent animals from hybridizing, environmental writer Emma Marris points out in her book Wild SoulsFreedom and Flourishing in the Non-Human World. Consider the effort in North Carolina to prevent coyotes from breeding with endangered red wolves, which bears uncomfortable parallels to Western preoccupations with racial purity that only recently went out of fashion.

Good Lord! Only those who are looking for offense would find these “parallels”. Wolves and coyotes are different biological species, for one thing.

. . .That’s why some scientists look askance at the influence of invasion biology and argue that the field has a baked-in, nativist bias on documenting negative consequences of introduced species and preserving nature as it is. Invasion biology is like epidemiology, the study of disease spread, biologists Matthew Chew and Scott Carroll wrote in a widely read opinion piece a decade ago, in that it is “a discipline explicitly devoted to destroying that which it studies.”

Historically, the term has erroneously expanded to the idea of, “‘If you’re not from here, then you are most likely going to be invasive,’” Sonia Shah, author of The Next Great Migration: The Beauty and Terror of Life on the Movesaid on a June 2021 episode of Unexplainable, Vox’s science-mysteries podcast. Conservation policies have been crafted around the idea that if something is not from “here” — however we define that — “then it is likely to become invasive, and therefore we should repel it even before it causes any actual damage,” as Shah says, which is part of the nativist bent that pervades ecological management.

Now these are uncomfortable parallels, but they’re between human immigration and animal invasions (animals are often moved deliberately by humans). This could—and may well have intended to—be an argument for letting immigrants go wherever they want. But wait! There’s more!:

. . .What’s more, the very notion of “invasion” draws on a war metaphor, and media narratives about non-native species are remarkably similar to those describing enemy armies or immigrants. For example, a recent news story in the Guardian about armadillos “besieging” North Carolina described them as “pests” and “freakish.” It also gawked at the animal’s “booming reproduction rate,” an allegation that, not coincidentally, is leveled against human migrants.

Well, we use invasion and war as metaphors for disease to. Is the “battle against covid” an alt-right slur on immigration?

We always have to be wary of teaching “indigenous knowledge” as equivalent to Western science. (New Zealand is having a real issue with that right now.) Here’s a confusing paragraph about that:

Indigenous knowledge is increasingly being recognized as essential to conservation, write Nicholas Reo and Laura Ogden — Dartmouth University professors of Indigenous environmental studies and anthropology, respectively — in an ethnographic study of Anishinaabe perspectives on invasive species. (The Anishinaabe are a group of culturally related First Nations peoples in the Great Lakes region of Canada and the US.) Anishinaabe ideas, Reo and Ogden found, reflect a worldview that sees animals and plants as belonging to nations with their own purposes and believes people have the responsibility to find the reason for a species’ migration. The authors’ sources recognized parallels between the extermination of species deemed invasive and the dark history of colonial violence against Indigenous peoples. The interviews “helped me recognize the ways in which different philosophies of the world shape our ethical response to change,” Ogden says.

But do the Anishinaabe try to find out the reasons for species migrations? If they do, then they have to use modern science. If they don’t, then this is irrelevant to the issue of conservation.

Finally, the article couldn’t resist using the word “diaspora”, which is usually applied to Jews but refers to any people dispersed widely from where they originally lived. This is the first time I’ve seen it applied to animals:

In Tierra del Fuego, at the tip of Chile and Argentina, a particularly dramatic novel ecosystem is taking shape. In 1946, beavers were introduced there in a futile attempt to create a fur industry. Instead, the animals proliferated and munched down the region’s Nothofagus — southern beech — forests, creating dams and ponds. “They are these miraculous world builders,” says Ogden, who wrote an essay imagining the beavers not as invaders, but as a diaspora. (Beavers have also been a boon for ducks and other marine species.) The invasive species paradigm, Ogden adds, is devoid of nuance, history, and politics; she prefers a concept that gives expression to the moral complexity of the beavers’ presence in South America, as well as the fact that they had no choice in being moved there.

Ecologist Dan Simberloff, however, deems this invasion a “disaster” for the native habitat.

As I said, this article is not without merit. It raises questions about invasive species (do they really damage native habitat or fauna?) that laypeople may not have considered, but, believe me, biologists have considered. But there are moral questions that biologists haven’t considered: is it worth the lives of 10,000 beavers, for instance, to save the Patagonian forests? Biologists say “yes”, for we’ll always have beavers, but Patagonian forests (or Hawaiian birds), once gone, are gone for good.  (Yes, the beavers should be exterminated humanely, which I suppose the Vox article would consider “genocide”.)

But in general, this article, conflating the problem of human immigration and crossing of politically determined borders with the invasion of animals and plants into novel areas, is a good example of the naturalistic fallacy. We learn nothing about how to deal with human immigration from studying invasive species. Not only that, but if you want to be more accurate in your analogy, you’d liken invasive species not to Central Americans crowded at the American border, but to Cortéz genocidal extinction of the Aztecs.  After all, human immigrants don’t wipe out the population into which they meld.

Here are four extinct species once on Oahu, one of the Hawaiian islands:

 

h/t: Luana

“Black tigers” in a small Indian reserve suggest random genetic drift

October 17, 2021 • 9:15 am

The two greatest forces changing the frequency of gene variants in a population are natural selection and genetic drift. You’d better be familiar with natural selection by now, but genetic drift isn’t widely appreciated by non-evolutionists. It’s simply the change in frequency of genetic variants due to chance alone: the random sorting and representation of variants from one generation to the next, due not to any inherent increment or detriment to reproduction conferred by the genes.

Teaching genetic drift to students often involves letting them represent a population by choosing marbles out of a sack. If you have ten marbles in a sack, five red and five blue (representing a population with equal frequencies of two genetic variants), and choose five to be the genes in the parents of the next generation (population size must be finite), then you might get three red ones and two blue ones. You then make a new sack with the new population’s frequencies—6 red marbles and 4 blue ones. The frequency of the red variant has risen from 50% to 60%. Lather, rinse, and repeat, and you’ll see the frequencies of the marbles change each generation due to chance alone. Given enough time, all the marbles will be the same color, and then no further change can occur (this is called “fixation”). Thus we see gene-frequency change (which most of us define as “evolution”) occurring, but there’s been no natural selection, no deliberate choosing of marbles of one color. I often gave my students examples of gene frequency change in one population and said “what would you do to determine if this is due to selection?” (Answer: set up replicate populations. Selection will always drive the same variant to high frequency, while with drift you will get diverse and opposite changes among the replicate populations.)

The smaller the population, the greater the changes in gene proportions will occur (i.e., the stronger the “genetic drift”). In fact, if the population is small enough, genetic drift can overcome natural selection, increasing variants that actually diminish reproduction.  When you see small populations with high frequencies of odd variants, or even deleterious ones, you might begin to suspect the action of drift. Inbreeding can be seen as a form of genetic drift in a small population of restricted size, which is why one sometimes sees high frequencies of genetic diseases or defects in small populations of humans (here are some examples in the Amish).

The paper below, from the latest Proceedings of the National Academy of Sciences, shows a likely case of genetic drift involving a gene variant that causes bigger and darker stripes in tigers in India. You can read it by clicking on the screenshot below, or get the pdf here (the full reference is at the bottom of post).

There’s also a PNAS commentary on the paper above if you want the short take. Click on screenshot below, or get the pdf here.

India is home to two-thirds of the world’s tigers, and natural populations are often fragmented because of habitat destruction, and can also be small because of past hunting. A sampling of Indian tigers from wildlife reserves and zoos showed that one area, the Similipal Tiger Reserve in Odisha, had a high proportion of darkly striped tigers called “black tigers”. This is not the same as the melanism we see in black leopards and jaguars—both called “black panthers” though they’re different species. Below is a black tiger (right) compared to a “normal” tiger (click all figures to enlarge them.)

Below is a map showing where the authors sampled tigers. Circles are natural populations, and squares are zoos or captive reserves. The size of the circles and squares represents the sample size of tigers. I’ve put an arrow pointing to the area of interest, the Similipal Tiger Reserve.

Black tigers are seen only in Similipal Tiger or in small reserves or zoos.  The pie charts also show the frequencies of individuals that have zero (yellow), one (orange) or two copies of the mutant gene causing the unusual pattern (black color). The diagram below shows that black tigers “m/m” are found only in the wild in Similipal, but are also seen in two zoos, where they’ve probably been selected for breeding because they’re unusual. Further, the black tigers in the zoos all were founded by at least one ancestral individual from Similipal.

For some reason that one small wild population has a high frequency of the black variant (“allele”). (There are a minimum of 12 adult tigers in Simlipal, which is a minimum estimate. But there can’t be many more than that, as the rangers can identify the tigers.)

(From paper): Fig. 2. Distribution of the genotyped individuals. A total of 428 individuals were genotyped at the Taqpep c.1360C > T mutation site. Wild tigers are shown with a circular marker, and captive tigers (NKB, AAC, and Mysore Zoo) are shown with a square marker. The size of the square/circle indicates the number of individuals genotyped from a given area. In addition to the 399 Bengal tigers shown on the map, we genotyped 12 Amur, 12 Malayan, and five Sumatran tigers from Armstrong et al. (40) These are not shown on the map to allow the figure to focus on sampling within India. The fraction of the three genotypes in samples from the three populations in which pseudomelanistic tigers are present is shown with the pie chart. Similipal is the only population of wild tigers to have pseudomelanistic tigers, and the other two populations are of captive tigers. All wild tigers were homozygous for the wild-type allele at Taqpep c.1360C > T site except for Similipal individuals.

The researchers got samples of captive tiger DNA easily, but getting wild tiger DNA is hard. That involved tracking the tigers and collecting their feces, saliva from prey, or shed hairs. Sequencing can tell you immediately whether you have tiger DNA or something else. I’m not quite clear about how they managed to distinguish the tracks or prey of individual tigers in the wild from that other tigers, but differences in the DNA from different samples would tell you how many tigers you’re dealing with.

If it is indeed a single gene causing blackness, it behaves as a recessive; that is, you have to have two copies of the mutant form to be a black tiger. With no copies or only one copy paired with the “normal” allele, you have the normal tiger pattern. Here’s a genealogy of color from breeding records of captive tigers. Orange represents normal-patterned tigers, while black are “black tigers.” Circles represent females and squares males.

You see that two orange tigers can produce a black one; in these cases the orange tigers each carried one copy of the recessive “black” allele; they were “heterozygotes”.  This doesn’t absolutely establish that it’s a single recessive gene; it would strengthen the case if they mated two black tigers together and got all black offspring, which is what you predict from a recessive gene.

From paper: (From paper): (B) The pedigree of the captive tigers sampled for this study. The individual labels shown in red are for the tigers whose genome was sequenced for this study (NKB17 is not shown in the pedigree). The genotype values are indicated for the individuals sampled and successfully genotyped at the mutation site (+/+ for wild-type homozygote, +/m for heterozygote, m/m for mutant homozygote, and x/x for missing genotype). Squares represent males, and circles represent females. Pseudomelanistic phenotype is represented in solid black shapes. The dashed line shows the presence of the same individual at two spots in the pedigree.

But how do they know that the black pattern is caused by a single gene? The authors’ whole-genome sequencing found one gene whose variants comported completely with the color: if you had two copies of the mutant, which has a DNA sequence that eliminates formation of the protein coded by that gene, you were black, but if you had no copies or only one, you were normally colored.  This gene is called Taqpep, which has been implicated in making dark variants in other cat species (see below). The full name is “transmembrane amino-peptidase Q”, and the mutant form, which doesn’t function at all, is called Taqpep pH454Y. We’re not sure how the “normal” gene works in pattern formation: the enzyme is involved in degrading other proteins, and also helps form the placenta in humans!

What we do know is that other mutant felids with darker and broader stripes also have mutations in the Taqpep gene. Below is a figure from the commentary paper showing homozygous mutations in that gene in the tiger as well as in the domestic cat and in the cheetah, where it produces cheetahs with dark blotches instead of spots (see below). Each of the three Taqpep mutations is different, so here we have an example of “convergent evolution,” independent species arriving at similar appearances via independent mutations. These mutations must have occurred since the common ancestors of the three cats, which lived 11.5 million years ago for all three, and 8.8 milion years ago since the ancestor of the domestic cat split from the ancestor of the cheetah.

(From paper): Fig. 1. Convergent evolution of broadened stripes/spots in cat species. The phenotype has arisen independently in the domestic cat (Felis catus), cheetah (Acinonyx jubatus), and tiger (Panthera tigris). (A) The phylogeny on the left depicts the relationships among the three species; numbers above branches indicate the divergence times (in million years ago) among their respective lineages; a timescale is shown at the bottom (tree and node dates are from ref. 17). In each of these species, the phenotype is caused by unique mutations in the Taqpep gene, whose positions in the encoded protein are indicated below the respective branch. Coat pattern images are modified from the photos provided in the original articles: ref. 10 for domestic cat and cheetah; ref. 8 for tiger. (B) Schematic of the Taqpep protein indicating the positions of the five pattern-altering mutations shown in A (color coded per species).

Below, a “king” cheetah (right) next to a normal cheetah:

Why the dark tigers in Similipal? Given that the gene is rare elsewhere except in zoos, and that the Similipal population is small, genetic drift is a likely explanation. The mutation could be “neutral” (i.e., conferring neither a reproductive advantage or disadvantage compared to “normal tigers”, or it could even be slightly harmful. If the dark form were selectively advantageous, you’d likely see it in many Indian populations as it increased in frequency. (Further genome analysis shows no sign that the gene has risen in frequency due to selection, but we can’t say that with absolute assurance.)

In fact, the authors did a simulation assuming that the Similipal population was isolated from other populations 10-50 tiger generations ago, and concluded that the population was likely founded by only a couple of tigers: two or three. In Similipal the frequency of the “dark” gene form is about 58%, while the light gene form is at about 42%. If there were random mating, you’d thus expect (0.58)² dark tigers there, or about 34% of all tigers. As you can see for the Similipal pie chart above, that is pretty close to what you get.

This would, then, be a good example to use when teaching about genetic drift, which is a difficult concept to teach well, involving mathematics that students don’t like. But when teaching you always need examples, and we can demonstrate drift in the lab using sacks of marbles or computer simulations. But it’s better to have examples from nature, and this is one that I’d use when teaching, as it satisfies the conditions for drift, there appears to be no selection favoring the black gene, and the population is known to be small and isolated.

The only other question is that of conservation. The Similipal population is endangered, and could be increased by bringing in other tigers. That would reduce the frequency of the black gene and of black tigers. It all depends on what you want to save: the tiger itself or the pattern? I’d go for the tiger, as the pattern genes will always be around in low frequency in the gene pool, but the tigers may disappear.

______________

Sagar, V. Christopher B. KaelinMeghana NateshP. Anuradha ReddyRajesh K. MohapatraHimanshu ChhattaniPrachi ThatteSrinivas VaidyanathanSuvankar BiswasSupriya BhattShashi PaulYadavendradev V. JhalaMayank, M. Verma Bivash PandavSamrat MondolGregory S. BarshDebabrata Swain, and Uma Ramakrishnan. 2021. High frequency of an otherwise rare phenotype in a small and isolated tiger population

ZeFrank on Merlin Tuttle

March 23, 2021 • 2:45 pm

I must have my constitutional, but I’ll leave you with this video about the life and work of a great naturalist and biologist, Merlin Tuttle. Tuttle (born 1941) devoted his career to studying and saving bats. His various efforts are shown in the film, and have occurred worldwide.

Donate to his foundation, which you can do here. Bats are wonderful creatures and good for the planet.

h/t: Mark

John Muir gets canceled

September 1, 2020 • 9:30 am

This article on the cancellation of John Muir, outdoor lover and founder of the Sierra Club, appeared in the Pittsburgh Post-Gazette (click on screenshot below), but I also found the same piece in the National Review. (The author, John Fund, is the National Review‘s national-affairs reporter.) Yes, the National Review is a conservative magazine, but investigate the facts for yourself if you’re dubious.

 

The pieces begin with the revelation that Muir was not immune to the bigotry of white people of his time—he made racist statements. But he’s also being tarred for his association with other bigots AND, according to a statement on the Sierra Club website by Michael Brune, Muir even recanted many of his bigoted views. But that doesn’t matter, for the Sierra Club is intent on flagellating itself.

Brune:

The most monumental figure in the Sierra Club’s past is John Muir. Beloved by many of our members, his writings taught generations of people to see the sacredness of nature. But Muir maintained friendships with people like Henry Fairfield Osborn, who worked for both the conservation of nature and the conservation of the white race. Head of the New York Zoological Society and the board of trustees of the American Museum of Natural History, Osborn also helped found the American Eugenics Society in the years after Muir’s death.

And Muir was not immune to the racism peddled by many in the early conservation movement. He made derogatory comments about Black people and Indigenous peoples that drew on deeply harmful racist stereotypes, though his views evolved later in his life. As the most iconic figure in Sierra Club history, Muir’s words and actions carry an especially heavy weight. They continue to hurt and alienate Indigenous people and people of color who come into contact with the Sierra Club.

But is that the case.  If Muir changed his mind—and the article at the top shows how he came to recognize that white people committed genocide on Native Americans. So why do his words continue to “hurt and alienate” people? Do people even know about Muir’s earlier attitudes, what his words were, or how he changed? I doubt it.

It’s even more unfair to tar Muir for being friends with Henry Fairfield Osborn (an famous paleontologist, which isn’t mentioned above), who helped found the American Eugenics Society after Muir’s death. If you’re to be canceled not just because of your own words, but because of your association with someone who had racist attitudes in the late nineteenth centuries, then virtually all white men from that era are guilty and complicit.

But wait! There’s more. No environmentalist organization is free from these taints. I’ve added a link to Nelson’s article in the excerpt below (also from the paper’s piece):

The debate over John Muir is only the beginning of a purge sweeping the environmental community. In Crosscut magazine, Glenn Nelson wrote a piece last month headlined “Toppling John Muir from Sierra Club Is Not Enough.

Mr. Nelson called for dramatic efforts to “overcome a violent history of exclusion” by environmental groups. He said the next focus should be on the National Audubon Society, whose namesake, artist John James Audubon, “was an enslaver who opposed the intermingling of races.” The fact that Audubon may have himself been born to a black Creole woman in Haiti is less important than the fact the Audubon Society “has not reconciled its association with a man who, like Muir, embraced racist ideas and activities.”

If we are to expunge from their place of honor all the historical figures who changed their views later in life or who held views that were common in their time, where will it stop?

The rest of the piece is a series of whataboutery citations of others who weren’t canceled. For example, Fund notes that Martin Luther King, Jr., who wrote an advice column for Ebony magazine, once told a gay teenager to get rid of his “culturally acquired” gayness. Of course he didn’t get canceled. But King wasn’t a bigot, either. Still, that part of the article is largely irrelevant, though it does call out a certain hypocrisy in the Cancel Culture.

We have two issues here. First, how hard do we come down on people like Muir and Audubon who expressed views common in white men of their time but are now seen as odious? In my view, not as hard as people are doing. For, as Steve PInker has amply demonstrated, morality has evolved and improved over the past several centuries. While it’s historically salient to recognize that men like Muir and Audubon did express a common white bigotry, it doesn’t seem fair to single them out—as opposed to everyone else—and then cancel every aspect of their legacy. It’s unfair to expect people brought up in a certain culture to overcome it by becoming super-moral. (Animals named after Audubon will be the next to go.)

This is especially true when Audubon, uncharacteristically, recognized his errors later in life and corrected them.  The claim that the bigotry of these men still hurts people seems to me exaggerated and, as usual, is undocumented and unevidenced. The assertion alone is taken as the evidence. 

The other issue, largely unconnected, is whether conservation organizations are either excluding people of color or have created an atmosphere that makes them unwelcome. If that is the case, it would seem to have little with John Muir’s bigotry. Nelson’s article makes a case worth hearing that yes, there has been both deliberate and unwitting exclusion of minorities from outdoor groups. And this article in Orion Magazine argues that Native Americans have been treated pretty shabbily by the National Park Service.

So, the eagerness of organizations like the Sierra Club to flagellate themselves for century-old words or attitudes of their founders is unseemly: a form of au courant virtue signaling. But if those organizations could do meaningful outreach to those who don’t often get opportunities to get into the wilderness, they should. After all, we’re all evolved humans, and, if E. O. Wilson be right, we all have a degree of “biophilia.” Surely those who don’t get the opportunity to exercise it should be exposed to the great outdoors, and although the main object of the Sierra Club is to appreciate and preserve wilderness, everyone should be given that opportunity.

Readers’ wildlife photos

August 24, 2020 • 7:45 am

The tank is a bit lower than I like, so I importune readers with good wildlife photos to send them in.

On July 10, reader Mark Jones recounted conservationists’ success in breeding white storks (Ciconia ciconia) to release in the wild, and sent some photos. Today he adds a verbal and photographic update (his pictures). Mark’s caption and quotes are indented:

An update on the white stork chicks at the Knepp Estate in West Sussex; the four surviving chicks (out of six I think) have now all fledged their nests and have been seen out and about. Fingers crossed that the re-wilding continues its current success. The quote from the White Stork Project:

“24TH JULY 2020: “Our fourth and final chick from 2020 took its first flight and fledged the nest today. This is the single chick from nest 2 who has been growing well.  After losing the other two chicks, the parents put all of their energy into raising this chick. It has been seen flying in the fields near the nest and has also been seen with the adults in the nearby enclosure where we have our static population.  It is great to see it integrating with the rest of the flock.”

As mentioned before, Knepp is doing an extensive back-to nature experiment in farming, with free roaming herbivores (cattle, ponies, pigs and deer) and a ‘hands-off’ approach to the land. This has resulted in an explosion of biodiversity in this corner of Sussex, apart from the storks. This all seems highly sustainable ecologically, but I’m not sure how sustainable financially it is; it is partly paid for by glamping and safari trips . Anyway, it’s lovely to see properly diverse meadows for a change, so I hope it’s not idealistic to think a lot more land can be farmed this way.

There have been three nests (all built by the storks themselves, not manmade as I may have indicated before) this year and two have produced chicks. Apparently the eldest chick in the nest photographed has already flown with the parents at least once, but the others are still to fledge the nest.

The photos:

The nest in the top of the tree, with the three chicks standing up.

One of the parents arrives with food.

A sequence showing the mum (or dad, perhaps someone can tell?!) flying into the nest delivering something to eat, judging by the chicks’ reaction, although I couldn’t see what.

The three chicks side by side.

The oak tree (spot the nest) with some of the free roaming Exmoor ponies grazing below.

A fly-by from one of the adult storks.

Readers’ wildlife photos

July 10, 2020 • 7:45 am

Today we have installment #2 of Mark Jones’s photographs (#1 was yesterday). The photos document the return of the stork to England. You can read about their comeback in this article, which notes that the species hasn’t bred in England for hundreds of years: the last documented breeding was in fact in 1416! Yet everyone loves storks, and the conservationists’ goal is to get thirty pair breeding in nature by 2030.

Mark’s words are indented:

It is over 600 years since we have had white storks (Ciconia ciconia) in England, so imagine my excitement when, as I was photographing one of my favourite trees near my home, three of them flew down and landed on it! We just don’t see birds this size in Sussex, so it came as a bit of a shock. A complete stroke of luck, and I was also testing a new 300mm lens at the time.

These storks come from a rewilding project at Knepp Castle (www.whitestorkproject.org), which is having a bit of success at the moment with some chicks being raised and drawing the sightseers. But this is the first time I’ve seen them in Rudgwick (about 10 miles from Knepp as the stork flies). If you look closely you can see that all the storks are ringed, with a GB ‘number plate’.

Anyway the lens performed reasonably so I hope you like this selection.

Incidentally, for more context this is the tree that I was making a long exposure photo of; now with added storks.

 

Trump administration weakens Endangered Species Act

August 13, 2019 • 10:00 am

Everything the Trump administration does seems aimed in the wrong direction, but as a biologist, I’m really pissed off at this latest bit of stupidity. Read the NPR or NYT articles below (click on screenshots) to see the latest debacle:

NYT:

Here are some of the changes. The new regulations:

  • weaken protections for species listed as “threatened”: one step below “endangered”;
  • allow future listings to be based partly on economic assessments (the NYT says, “for instance, lost revenue from a prohibition on logging a critical habitat”) rather than on science alone. This is a first, and something the original Act aimed to avoid.
  • make it easier to remove species from the “endangered” list;
  • limit the nature and amount of habitats are considered when deciding whether a species is listed as “endangered”. Environmental groups claim that this will make it harder to protect species at risk from warming climates, which alters where they live and how much space they occupy; and
  • give the government a lot more discretion about interpreting the phrase “foreseeable future” when deciding whether to list species. This would allow the government to largely ignore impending threats to species’ existence, one of them being climate change. In other words, what could happen in the future can be ignored when deciding which species to save.

The Trump administration claims that this will “help conservation efforts” (Interior Secretary David Bernhardt) and “ease the regulatory burden on the American public, without sacrificing our species’ protection and recovery goals” (Commerce Secretary Wilbur Ross). Those are, of course, lies. This is not about conserving species, but about making it easier for ranchers, oil drillers, and developers to take over land at the expense of its animal and plant inhabitants. Not a single change increases protection for species.

The motivations for this change are transparent, and become even more transparent when you see that, as NPR reports, “Republican lawmakers and industry groups celebrated the revisions. . . .”  Frankly, the government’s defense of these changes, which are a pack of lies, and its refusal to even acknowledgethe real motivations, sicken me. This is just one more REM bout in the continuing nightmare that is Trump.

But not everyone is going gentle into this bad plight. According to the Associated Press, both Maine and Massachusetts, along with several conservation groups, said they’ll sue the government over these latest changes. Should we sign petitions? See the next post.

h/t: Ken