“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

Caturday felid unifecta: Free cat art show in L.A.

October 16, 2021 • 9:30 am

I’m running a Caturday felid post with only one item today, as I have three other tripartite posts lined up, but this one is time-sensitive, and if you live in Los Angeles you may want to go.

This is Colossal has announced a free Cat Art Show that runs in Los Angeles between October 14 and 24 at the Golden Pagoda (address here). The work of many artists will be featured, and the pieces are for sale, with 10% of the proceeds going to charity. And ALL THE ART IS OF CAT!

Here’s the announcement and some details:

More than 70 artists feature cats as their muse for a feline-centric group exhibition that scratches well beyond the tropes associated with the frisky creatures. Now in its fourth iteration, the Cat Art Show features sculptures, paintings, collages, and a variety of other works by artists from 16 countries—Ravi Zupa (previously), Lola Dupré (previously), and Aniela Sobieski (previously) are among them—that capture the feisty antics, adorable wide-eyed stares, and stealthy adventures of both domestic and wild breeds. The exhibition is the project of curator and journalist Susan Michals, who also wrote the 2019 book compiling hundreds of photos by cat-enthusiast and photographer Walter Chandoha.

If you’re in Los Angeles, stop by The Golden Pagoda between October 14 and 24 to see the quirky, spirited works in person, and check out the available pieces on Instagram. As with previous shows, 10 percent of all sales will be donated to cat care, with this year’s funds going to Kitt Crusaders, Faces of Castelar, and Milo’s Sanctuary.

The main page for the show also has explains it and enables you to sign up for free tickets (you have to be vaccinated or show a negative Covid test within the last 48 hours). If you go, send photos or report on the show below.

Here’s some of the artwork (and patrons) from previous shows:

The other pictures appear to show that this exhibition draws a big crowd, so go early and often!

h/t: Reese

Jack the Cat is healing nicely

October 3, 2021 • 12:45 pm

On September 18 I recounted the unfortunate fall of Jack the Cat, staffed by the daughter and son-in-law of my oldest friends, who live in Boston. For reasons unknown, Jack fell off a third-floor balcony and was very badly banged up: so badly that they didn’t think he would live. And if he did, he was likely to have a front paw amputated.

The good news is that Jack’s staff lived near Angell Memorial Hospital, the best animal hospital in the U.S., and they did a fantastic job with him.  And even better: he’s healing very well! He still has all his paws and got a thumbs-up after his first checkup. (Note added: The staff had pet insurance, which is fortunate as Jack’s care would have broken the bank!)

From the fall, Jack broke several bones in his paw, which were held together with thin pins, sustained breakage to both mandibular joints, and had a collapsed lung. Here’s his vet report (you can see more photos at the earlier link) :

Here’s Jack when he was groggy on painkillers with his buttons, pinned paw, and the Cone of Shame. Staff reports:

Our daughter has been very interested in Jack, enjoys multiple supervised visits a day with him – usually pets him gently

Here’s Jack in his carrier at the vet’s to get his first checkup (and those buttons removed, which were holding his jaw wired shut. Staff reports:

This pic is him at vet right before buttons removed. They also took sutures out of his arm, still has the pins/external fixator. Will be x-rayed 11/3 and likely have hardware removed then 🤞. His doctors are happy with his progress.

The three buttoms removed from Jack’s face:

All looks well for Jack; the very short video below shows that he’s eating much better now that he can open his mouth more than a centimeter. Staff reports:

Jack has been upgraded from bathroom to home office room, and he gets to hang with his dog brother and cat sister much more frequently in the new room. He’s still not allowed to roam free or jump up/down on the furniture. He wears the Cone of Shame when nobody is in room with him. If we’re in the room or he’s having couch/tv time with us, no cone.

 

Kink the Cat has gone missing

October 2, 2021 • 8:45 am

Reader Doc Bill is extraordinarily fond of his cat Kink, so named because of a bend in his tail (see last photo below). I visited Doc Bill in Houston five years ago and met this estimable cat, who sat next to me on the table at dinner (Doc Bill and his wife are great cooks!)

Now Kink has unaccountably disappeared from the front yard where he customarily sits, and it’s unexplainable. He was either kidnapped or a predator got him.  He may not come back, and that’s what Doc Bill is assuming. [He was chipped, so I am still holding out hope.]

So I am presenting Doc’s memorial for Kink below as a supplement to today’s Caturday Felid post, which will be up later. Doc’s words are indented:

Kink the Cat, so named because of the distinctive kink in his tail, was my constant companion for 15 years.  Kink was a very vocal cat with about a dozen different sounds from “hello, I’m here” to “food!” to “where are you” and more.  A very photogenic cat, Kink earned several awards from photography contests, including his most prized possession, an autographed and illustrated copy of WEiT.  Throughout his life Kink was devoted to the study of gravity.  Whether it was a bowl of food or a bottle of wine, Kink felt that not enough experimentation had been done.  The sound of things crashing to the floor was common in our house.
Kink disappeared from home last week suddenly and without a trace.  He was a homebody, not a wanderer.  He never missed breakfast.  Kink came into our lives by chance and left us with a mystery.  He will be missed greatly.
Photos:  Portrait from 2011; sitting on a sweater 2021; tail picture [showing the kink] 7-months old.

Jack the Cat improving rapidly, takes a short walk!

September 21, 2021 • 10:00 am

On my post about Jack the Cat two days ago, you probably thought he was in pretty bad shape—and he was. He had taken a very bad fall.

But he’s an intrepid moggie, and yesterday took a pretty substantial walk (vet’s advice), even putting weight on his injured front paw. A report from his staff:

We both think it’s a great tribute to Jack and his misadventure. It’s wonderful to have friends, family and strangers rooting for his recovery.

He started eating better yesterday and he’s up to walking around the house (short periods of time, no jumping) a couple of times a day. See attached video.

Go Jack! I am going over to visit him and his staff this morning, and hope to put up more photos on this post later on today.

Cat survives long fall by being netted in an American flag!

September 13, 2021 • 2:00 pm

Ceiling Cat bless America! This is a lucky cat who was saved by some nice people. The moggie was hanging precariously from a cable at Miami’s Hard Rock stadium the other day during a football game. The crowd is disturbed (listen to their moans), but some enterprising folks repurposed an American flag to catch the falling cat. It’s caught and was apparently uninjured.

I always wonder when a cat runs out on a baseball field or football pitch, and it gets caught and removed, what happens to it. Such cats, who are television stars, should be adopted, but I always worry about their fate. Could they be sent to a shelter and euthanized?

This particularly handsome cat should definitely be adopted. I tried to find out what happened to it, but found bupkes. If you know, please tell us in the comments.

 

h/t: Thomas

Readers’ wildlife photos

August 31, 2021 • 8:00 am

Today we have more African mammal photos from Delia Randolph, who lives in Kenya. Her captions are indented, and you can enlarge the photos by clicking on them.

Tommy’s Gazelle, same site on Mara where my last photos came from :

Grant’s Gazelle (Nanger granti)  same site.

Visitors often get Tommy’s (full name Thomson’s gazelle = Eudorcas thomsonii) and Grant’s confused. The black stripe on the Tommy is quite variable and some Grant’s have a black stripe, too. And though they are smaller than Grant’s this is also variable. How can you tell them apart? It’s easy. Grant’s have pants – that is the white goes above their tail.

Even ugly animals like spotted hyenas (Crocuta crocuta) are cute when they are babies.

And beautiful animals are even more cute when young! Common eland (Taurotragus oryx). One of my favourite biology writers, Jared Diamond, famously argued that African animals were uniquely difficult to tame. The docile eland proves this wrong: they have been successfully domesticated in Russia and South Africa.

The African bush elephant (Loxodonta africana) needs no introduction. Their cousins, the North African elephant (Loxodonta africana pharaohensis) were also domesticated by the Carthaginians (Hannibal famous crossing of the Alps with war elephants).

Re the photos below: Apologies in advance for any anthropomorphism or metooism.

Lioness having a little tiff with lioness (Panthera leo):

Lioness not speaking to lion:

Lioness making up with lion. And they lived happily ever after:

The babies 😊

Readers’ wildlife photos

August 20, 2021 • 8:00 am

Please send in your good wildlife photos, as the tank drops ever lower.

Reader Divy Figueroa and her husband Ivan Alfonso run an exotic-animal veterinary-care clinic in Florida (often going to the animals, as they treat all sorts), and also keep a number of reptiles (and two cats). Here we see one of their favorite turtles. Divy’s notes are indented, and you can enlarge the photos by clicking on them.

This is a  Malayemys subtrijuga, commonly known as the  Mekong Snail Eating Turtle, or as we call them, Snail Eaters. Guess what they eat? They are originally from Malaysia, but the story from the Indonesian locals is that they were introduced to Java and Sumatra by the Dutch to eradicate snails. Needless to say, the snails are still around, and so are the Snail Eaters, who thrived and are by now established in the area.

We took a trip to Java a couple of years ago, and got to see them in situ. Ivan wanted to study and document their habitat for a lecture he would be giving later that year, and we wanted to see if we could improve our husbandry skills and care.

These turtles are one of my favorite species in our collection. They are very docile and I love their cute faces.

After several years of infertile egg laying, we hatched three babies in a matter of months. Our firstborn hatched in October, and the second two hatched the following January.  We’ve had several successful hatchings since then, but these three little amigos are our pride and joy, and in a few more years should join the breeding group.

This is our firstborn, pipping out of his shell.

The three babies in my hand, right after the 3rd hatched. Notice the difference in size.


One of the babies begging to be fed.

The three, about a year after hatching.  The first-born will be the smallest once they reach adulthood, as males are smaller than females.

This is one of our adult Snail Eaters, and you can see that the babies are a miniature replica of their parents

A few of our adults on land.

Another pic of our firstborn as he was emerging from the egg.

A female looking to nest in her enclosure. This process can take several days—sometimes up to a week or more.

Snail-Eating habitat in Java. This picture was taken in July during the dry season, when the turtles normally hibernate-aestivate.

How did a picture of Jango get there? 😻

Some science listening from the BBC

July 30, 2021 • 10:00 am

Reader Dom called my attention to today’s BBC Science in Action program, which contains several items of interest. You can hear the 35-minute show by clicking on the site below and clicking “listen now”:

There are four bits:

Start – 12:20.  A discussion with Elizabeth Turner about her new evidence for 890-million-year-old animals (spongelike creatures), which I wrote about yesterday.

12:20-18:55.  A discussion with Cambridge University’s Dr Sanna Cottaar about the “Insight” probe on Mars’s surface and scientists’ attempt to deduce the structure of the planet.

18:55-26:45: Prof Lesley Lyons from the University of Missouri discusses the similarity of the genome of cats to that of humans, and how that could be used for medical purposes in humans. I’m not keen on this because it implies that they’re going to experiment on cats. As she says, “they’re bigger than mice and cheaper than primates”.

26:45-end:  A remembrance of Steven Weinberg, who died a week ago. There are extracts from two BBC interviews with Weinberg as well as discussions of his work by fellow scientists.

Readers’ wildlife photos

June 16, 2021 • 8:00 am

Once again I ask readers to consider sending me their good wildlife photos.

Today’s photos are of BIG CATS IN AFRICA, and were taken by reader John. His notes and IDs are indented, and you can click on his photos to enlarge them

Since you asked us to send more wildlife photos, here are some more. African cats this time, from Tanzania — Serengeti National Park and Ngorongoro Crater Conservation Area.

We were lucky to see a mother cheetah  (Acinonyx jubatus) and her offspring, I don’t know how old. My wife and I fell in love with cheetahs, so can’t help including several of them. It’s funny how the baby’s head and neck fur look like feathers.

(S)he’s looking at us:

These animals define the word svelte.

This female lion (Panthera leo) is wearing a “wire”, as they say on the police shows.

Two shots of leopards (Panthera pardus). This one was right next to the road.

Ans this one is taking a welcome afternoon siesta in a tree. We saw several of these.

These four lionesses (or is there a male there?) were the first creatures we saw in the Serengeti, so we figured they were a welcoming committee.

Our driver cheated some by going fairly close to this mother lion and her cubs — but not too close. One little one has light spots on its back legs. Is this normal?

I can’t see this one without feeling like reaching out and scratching its belly. It would be the last thing I ever did!

This is a rare one, that we saw only from far away, hence the bad quality of the photo, which is much enlarged. It’s a serval (Leptailurus serval). It’s maybe a good half meter tall and weighs less than 20 kg.