genetics – Pain In The Bud

A Missing Genetic Sequence Leads To Orange Fur In Cats. Could It Be Responsible For Behavioral Differences Too?

Scientists have uncovered the elusive mechanisms behind coat color expression, opening the door to a new question: is fur pigment connected to personality?

When Professor Hiroyuki Sasaki retired, he wasn’t done with science. He just wanted to use it to better understand his cats.

The Japanese geneticist raised more than $73,000 from Japanese and international cat lovers and put together a team, including partners from the US. Then he began the hard work of scrutinizing feline DNA to find out why some cats are orange, and why most all-orange cats are male while virtually all calico and tortoiseshell cats, whose coats have splotches of orange, are female.

It turns out there’s no genetic instruction telling the fur to take on an orange pigment — it’s the absence of a segment of DNA, which governs pigment production, that does it.

In other words, ginger cats are mutants.

Most fully-orange cats are male because the mutation removes the DNA segment in the X chromosome. As males have X and Y chromosomes, they only need the mutation in the single X chromosome for their coats to express in that shade.

Lots of cat lovers swear that coat color and temperament are connected.

Females have an XX chromosomal arrangement, so they need the mutation in both chromosomes to turn tangerine. If the mutation only shows up in one chromosome, you get patches of the color instead of a consistent coat.

That explains why 80 percent of ginger cats are male, and why only one in 3,000 calicos and tortoiseshells are male. A male cat would need an extra X chromosome, XXY, to be born with a calico or tortoiseshell coat. One of the side effects, however, is sterility.

Scientists estimate only one in a thousand male calicos/tortoiseshells can reproduce and pass their unique mutations on.

It’s not just coat color either. The mutation impacts skin and eye color, which is why a ginger cat might have a pink nose compared to the terracotta shade of a void cat or a silver tabby.

Are orange cats really more friendly and silly?

So how does this relate to temperament, and the many people who attest to a particular personality associated with orange cats? Some people say ginger tabbies are more loyal, affectionate and social than cats of other coat colors, but they’re also more prone to doing boneheaded things.

The stereotypes have picked up steam online, where people often share memes depicting orange felines as earnestly derpy, but they may be on to something — or at least, it can’t be ruled out until we know more.

Ginger cats are not the sharpest claw on the paw, according to popular memes.

Because of the missing piece of genetic code, a specific gene, ARHGAP36, isn’t “expressed.” Like so many genes, scientists don’t fully understand everything ARHGAP36 impacts, or how alterations can lead to unexpected changes elsewhere.

“Many cat owners swear by the idea that different coat colours and patterns are linked with different personalities,” Sasaki told the BBC. “There’s no scientific evidence for this yet, but it’s an intriguing idea and one I’d love to explore further.”

Header image via Pexels

Were Cats Really Domesticated By The Egyptian Cult Of Bastet?

While the sensational claims have spawned headlines around the world, a closer examination raises more questions.

According to dozens of articles, a pair of new studies throws doubt on the commonly-held view that cats self-domesticated 10,000 years ago by helping themselves to rodents invading human grain stores.

The conventional wisdom for some time has been that house cats are the domesticated ancestors of felis sylvestris lybica, the African wildcat. Their genomes are nearly identical, it’s often difficult even for experts to tell the species apart, and they’re much more tolerant toward humans than the comparatively hostile felis sylvestris, the European wildcat.

But two new papers are raising eyebrows for their fantastic claims that feline domestication was actually human-driven and began about 5,000 years ago in Egypt.

Specifically, the papers claim cats were sacrificed en masse by the cult of Bastet, an Egyptian feline goddess, guiding the species toward domestication in a way that doesn’t quite make sense with what we know of evolution.

Bastet was originally depicted with the head of a lion, but the imagery around her evolved as she became a more prominent deity in the Egyptian pantheon. Later glyphs depicted her with the head of a domestic cat or African wildcat.

There are two main elements to the new claim:

The earliest grave in which a cat was buried with a human was dated to about 10,000 years ago, and was found in Europe. But an analysis of the cat’s remains indicate it had DNA somewhere between a wild cat and a domestic feline. That, the authors claim, throws into doubt the idea that cats drifted into human settlements, drawn by the presence of rodents.
If domestication was closer to 5,000 years ago, that would coincide with the rise of the cult of Bastet, the Egyptian cat goddess, around 2,800 BC.

Instead of the feel-good, fortuitous sequence of events the scientific community has accepted as the likely genesis of our furry friends, the authors of the new papers claim aggressive and fearful traits were essentially murdered out of the feline population by Bastet cultists who sacrificed cats in large numbers and mummified their corpses.

Neither paper has been peer-reviewed yet, and experts on ancient Egypt, genetics and archeology have already begun pushing back.

The new timeline, they say, doesn’t quite add up, with cat mummies found throughout different periods in Egyptian history, not just during the height of Bastet’s popularity in the Egyptian pantheon. Bastet’s popularity came approximately 700 years later than the authors claim the sacrifices began, and early imagery of the felid goddess depicts her with a lion head. It wasn’t until later centuries that Bastet was represented with the features of a domestic cat.

The powerful Pharaoh Budhotep I, considered an apocryphal king by some, sent a fleet of ships to the Americas to bring back turkey, according to legend. Credit: The Royal Buddinese Archaeological Society

Separate from timeline concerns is the lack of historical evidence. Cats were revered in ancient Egypt, and while there are an abundance of cat mummies — as well as the mummified remains of many other animals — that does not mean the cats were ritually sacrificed.

Indeed, archaeological, hieroglyphic and anthropological evidence all show cats enjoyed elevated status in the Egypt of deep antiquity, long before the nation became a vassal state of the Greeks, then the Romans.

Cats were associated with magic, the divine and royalty, and cats who were the favored pets of Egyptian elites were given elaborate burials. Like Ta-miu, Prince Thutmose’s cat who is known for her grand sarcophagus decorated with images of felines and prayer glyphs meant to guide her to the afterlife.

Cats were sacred companions to the Egyptians

When cats are found buried with humans, the more common explanation is that those cats were the pets and companions of those humans. If the authors of the two new papers want to prove their claim that cats were ritually sacrificed by the tens of thousands — slaughter on a scale that would influence evolution — they’ve got a lot more work ahead of them. (And the burden of proof rests squarely with them, as the originators of the claim.)

Not only does their research attempt to change the origin stories of kitties to an ignominious tale of human barbarity, if we take their assertions at face value, we’re talking about a case of “domestication by slaughter.”

While it may be true that the earliest evidence of companion cats outside of North Africa revealed hybrid DNA, that doesn’t cast doubt on the commonly-accepted view of feline domestication, it strengthens it. Domestication is a process that takes hundreds of years if not more, and it occurs on a species level, so it makes perfect sense that cats found in burial sites from early civilization would be hybrids of domestic and wild. Those felines were of a generation undergoing domestication, but not quite there yet.

A detail from the sarcophagus of Ta-miu, Prince Thutmose’s beloved cat.

Ta-miu, Prince Thutmose’s beloved cat, was buried in an elaborately decorated sarcophagus with glyphs and offerings meant to guide her to the afterlife. Thutmose, son of Amenhotep III and Queen Tiye, lived in the 14th century BC.

Killing off docile cats?

Which brings us to another significant problem with the claim: if the ancient worshipers of Bastet were selecting the most docile and easiest-to-handle wildcats for their sacrifice rituals, as claimed, then they would be influencing evolution in the other direction.

In other words, they’d be killing off the cats who have a genetic predisposition toward friendliness, meaning those cats would not reproduce and would not pass their traits down. It would have the opposite effect of what the papers claim.

So despite the credulous stories circulating in the press and on social media, take the assertion with a grain of salt. Something tells me it won’t survive peer review, and this will be a footnote about a wrong turn in the search for more information on the domestication of our furry buddies.

Cats would like human civilization to return to the good old days.

After 10,000 Years, Dire Wolves Walk The Earth Again

The surprise announcement came from Colossal Biosciences, a company best known for its project to bring back the woolly mammoth.

A US biotech company shocked the world Monday when it announced the births of three dire wolf puppies, bringing back a species that hasn’t lived for more than ten millennia.

Or a version of that species, at least.

Scientists with Colossal Biosciences extracted DNA “from a 13,000 year old tooth and a 72,000 year old skull and made healthy dire wolf puppies,” Colossal CEO Ben Lamm said in a statement.

Of course, it wasn’t that simple.

The dire wolf, Aenocyon dirus, was heavier, stockier and had thicker fur than modern-day gray wolves. In addition, its bite was incredibly strong, generating more force than any living species of canid.

To create the dire wolf puppies, Colossal used the genomes reconstructed from the tooth and skull, spliced them with gray wolf DNA, and made 20 gene edits in 14 genes. Healthy embryos were implanted in three surrogates — large, mixed-breed dogs — and were successfully delivered.

Romulus, one of two male dire wolf pups born late in 2024. Credit: Colossal Biosciences

Remus, who was born at the same time as Romulus. Credit: Colossal Biosciences

Whether the new puppies are officially dire wolves is up for debate and beyond the scope of this post, but just like humans and chimpanzees share 98.7 percent of their DNA, dire wolves and gray wolves share 99.5 percent of their DNA.

The species also existed concurrently with gray wolves and there was interbreeding between the populations, meaning gray wolves already have dire wolf lineage.

As a result, the puppies may be more dire wolf than some are willing to admit. Just how far a “de-extinction” project has to go for the animals to qualify as their namesakes will be debated for years, and there are innumerable questions for which we won’t have answers until the pups grow and scientists monitor their behavior in addition to their physical health.

They won’t behave precisely the way their ancestors did, since they are growing up in a captive environment with teams of specialists constantly monitoring them. The wolves are “essentially living the Ritz Carlton lifestyle of a wolf. They can’t get a splinter without us knowing about it,” Colossal’s chief science officer, Beth Shapiro, told the New York Times.

Whether bringing back dire wolves is a “good” thing is also a topic for another day, at least as far as this post goes. You may disagree, and feel free to say so in the comments, but this is a subject you could write half a library of books on, encompassing ecological, moral and philosophical questions that don’t have easy answers.

It’s made even more complex by the situation we find ourselves in, with our own behavior and relentless expansion killing off more than 70 percent of the world’s wildlife since 1970, according to the World Wildlife Fund. The company wants to use its technology to help critically endangered species, like the red fox, avoid extinction.

Colossal has partnered with leaders in the fields of genetics and bioethics, as well as organizations that specialize in animal welfare. The puppies are in a sizable, custom-built facility in an undisclosed location, secured by “zoo grade” barriers, and the company enlisted the help of the SPCA to create an environment appropriate for them. Colossal says their care regimen will include socialization and the development of pack dynamics.

A newborn dire wolf pup. Credit: Colossal Biosciences

The company has well-publicized projects to bring back woolly mammoths and the dodo, and ultimately, its founders say they want to restore balance in places where apex predators have been brought to extinction by human activity.

“This project demonstrates the awesome potential for advances in genetic engineering and reproductive technologies to recreate lost diversity,” Andrew Pask, a Colossal board member and professor of biosciences at the University of Melbourne, said in a statement. “Apex predators are critical to stabilizing entire ecosystems and their loss from the landscape can have profound impacts on biodiversity.”

The pups are named Romulus, Remus and Khaleesi. That last name is in homage to the character Daenerys Targaryen (Emilia Clarke) from the book series A Song of Ice and Fire, and Game of Thrones, the television adaptation. Dire wolves play a major part in the narrative, and the series is credited with bringing the long-extinct animals back into the popular imagination.

Jon Snow (Kit Harrington) discovers an orphaned dire wolf pup in the first season of Game of Thrones. The pup, who grows into a fierce and massive adult wolf named Ghost, plays a pivotal role in many major events in the series. Credit: HBO

Khaleesi, a female dire wolf, named after the character Daenerys Targaryen from Game of Thrones. Credit: Colossal Biosciences

Buddy — Er, Budhotep — Is Apparently Descended From Royal Pharaonic Felines

Sheba and a geneticist who specializes in cats are looking for felines descended from ancient Egypt’s royal buddies.

“You may call me Budtum Ra Budhotep Bhufu Amun Buddeses, human. Now serve me!”

Bud’s already enormous ego just got a little bigger after I used Sheba’s Pharaoh Cat Finder to analyze his pharaohness.

The online tool says he’s up to 75 percent pharaoh:

I didn’t do it entirely out of altruism to give the little guy an ego boost. The winner of the Pharaoh Cat contest gets a lifetime supply of Sheba, and Bud’s been eating Sheba for 10 years. We’ve never endorsed any particular cat food here on PITB, partly because every cat is different, some have special nutritional needs and what works for one furry overlord may not work for another.

But as food motivated as he is, Buddy cannot scarf down more than half a can of wet food at a time, and he’s an enormous pain in the Bud when it comes to leftovers, so Sheba’s Perfect Portions saves me from wasting food.

While the online Pharaoh Cat Finder tool looks like it may be RNG combined with clever marketing, there’s a genetic basis for the search. The company is working with Dr. Leslie A. Lyons, a geneticist who specializes in the DNA of our furry little friends at the University of Missouri’s Feline Genetics and Comparative Medicine Lab.

The legendary funerary mask of pharaonic feline Buddankhamun Budstet Ra Budshepsut, Buddy’s royal Egyptian ancestor. Credit: The Grand Museum of Magnificent Feline Stuff

Lyons was part of a research team that extracted DNA from mummified cats buried in ancient Egyptian tombs and sequenced their genetic code.

While the project verified that the Egyptians domesticated cats long before they began mummifying them and affording them revered status, Lyons says a DNA sequence from the ancient felines “has only been found in cats in Egypt and the U.S., unlocking even more questions to be explored.”

“We are looking at mitochondrial DNA only found in these pharaoh cats and a few cats in the U.S. So it’s really hard to find these cats, hence this hunt with Sheba pet food,” she said. “We’re on that quest to find the cats that went from Egypt into the U.S. and are the divine cats of the pharaohs. They should be worshiped like they were.”

The Temple of Amun Bud is guarded by gold statues of domestic cats instead of sphynxes. Credit: National Gallery of Buddesian Artifacts

I don’t think there’s any doubt that the aptly named Dr. Lyons is on team cat.

So here’s to hoping Bud gets a lifetime supply of Sheba, and Dr. Lyons is successful in her quest to find the elusive pharaoh cat lineage. In the meantime, we should probably start work on an impressive new pyramid here in the US, lest we disappoint our new feline pharaoh.

Wordy Wednesday: Critically Endangered Orangutan Babies

The palm oil and logging industries have killed so many orangutan mothers, there are now more than a dozen major orangutan orphanages in Borneo and Sumatra. The pressure on orangutans, with whom we share 97% of our DNA, shows no signs of abating.

Orangutans are critically endangered, and the biggest threat to their continued existence comes from the agricultural sector, which has razed 55 percent of the species’ habitat in recent decades.

Jarang, a baby orangutan born in 2023. Credit: Blackpool Zoo

Logging companies clearing irreplaceable, old-growth jungle to claim more land for palm oil plantations have no compunction when it comes to flattening jungles despite the presence of orangutans hiding in the trees. The loggers often shoot the large apes on sight, leaving terrified, traumatized babies still clinging to their dead mothers, or taking them to sell as pets.

Of those left to die, the lucky babies are rescued before they starve and are brought to one of the many orangutan orphanages in Borneo and Sumatra, where they attend “school” to learn how to do everything from climb to forage. It takes at least eight years to teach them how to survive on their own, which is about the time it takes orangutan mothers to do the same job in the wild.

The unlucky babies end up as local pets, sold off to entertainment troupes or shipped off to places like Dubai, where wealthy clients will pay a premium for them.

Caretakers must start by teaching rescued orphans the most basic things, like how to climb and move through the jungle Credit: Borneo Orangutan Survival Foundation

Logos, an orphaned baby orangutan who was rescued in 2023 by the Jakarta Animal Aid Network (JAAN) Credit: International Animal Welfare Fund (IAWF)

Baby Galaksi (Indonesian for galaxy), was found wandering the jungle without his mother in 2021 by a villager in Borneo. He’s now in a “school” that teaches orphaned orangutans how to do everything from evading predators to discerning edible fruit from harmful and poisonous varieties. Credit: Samboja Lestari Orangutan Rehabilitation Centre

So what is palm oil, and why are countries in Asia bulldozing ancient jungles and forests to clear room and make more plantations?

Per the WWF:

“Palm oil has been and continues to be a major driver of deforestation of some of the world’s most biodiverse forests, destroying the habitat of already endangered species like the Orangutan, pygmy elephant and Sumatran rhino. This forest loss coupled with conversion of carbon rich peat soils are throwing out millions of tonnes of greenhouse gases into the atmosphere and contributing to climate change. There also remains some exploitation of workers and child labour. These are serious issues that the whole palm oil sector needs to step up to address because it doesn’t have to be this way.

…

Palm oil is in nearly everything – it’s in close to 50% of the packaged products we find in supermarkets, everything from pizza, doughnuts and chocolate, to deodorant, shampoo, toothpaste and lipstick.”

Palm oil is in constant demand, and it’s an easy to grow, incredibly efficient crop. Indonesia and Malaysia, the only two countries in the world where orangutans exist, produce 85 percent of the world’s palm oil.

Images of orangutan babies in wheelbarrows are common on social media, but usually stripped of context. Orphanages use the wheelbarrows to bring infants and toddlers to and from “school” every day. Credit: International Animal Rescue

Asoka was found crying in the jungle by a fisherman in Borneo. He was brought to an orphanage in Borneo. Credit: International Animal Rescue’s rehabilitation Centre in Ketapang, West Kalimantan

We share 97 percent of our DNA with orangutans, making the species our second-closest cousins from a genetic standpoint. Some studies claim orangutans are our closest relatives based on our phenotypical similarities.

Orphaned orangutans attending “school” to learn how to survive in the wild. Credit: Borneo Orangutan Survival Foundation

A baby at an orangutan orphanage is fed by a caretaker. Credit: Borneo Orangutan Survival Foundation

Want to read more and learn how to help?

Here are some links to get you started. PITB is a big fan of the Jakarta Animal Aid Network, which successfully pushed Jakarta’s municipal government to ban the incredibly cruel “topeng monyet” monkey street shows:

World Wildlife Fund: Orangutans
Jakarta Animal Aid Network
Borneo Orangutan Survival Foundation
The Orangutan Project
Rainforest Trust