Category: paleobiology

Readers’ wildlife photos

November 10, 2025 • 9:12 am

Today we have a contribution of miscellaneous flora and fauna from reader David Riddell, a Kiwi.  His descriptions and IDs are indented, and you can enlarge the photos by clicking on them.

Recently I sent in some pictures of seabirds to be posted here, several of them taken on a trip to New Zealand’s Chatham Islands. I thought I’d add a few more images from that trip, starting with this group of Pitt Island shags (Phalacrocorax featherstoni).  These are endemic to the Chathams – one of two species found only there, and one of 13 New Zealand cormorant species, which are generally all referred to as shags in this country.  There are fewer than 500 pairs of both Chatham species, and their numbers appear to be declining.  Unfortunately these are not in breeding plumage, when they look a lot more handsome:

Shore plovers (Charadrius novaeseelandiae) were wiped off the New Zealand mainland by exotic mammalian predators by the 1870s, and for more than a century existed only on Rangatira Island, which lies just off Pitt Island in the Chathams. Small populations have now been re-established on a couple of predator-free islands off the New Zealand mainland, as well as another island in the Chathams group, but the global population is still below 200.  Intensive predator control on Pitt (where a few feral cats persist) has recently allowed the odd pair to breed there, which is where we saw this one, along with a recently fledged juvenile:

In the 1970s there were only about 50 Chatham Island oystercatchers (Haematopus chathamensis). With management there are now over 300, but they are still the world’s rarest oystercatcher.  These were on Pitt, very close to the shore plover above:

Back on main Chatham, the parea, or Chatham Island pigeon (Hemiphaga chathamensis) has benefited from predator control which has seen its numbers rise from a low of about 45 birds in 1989 to an estimated population of more than 600. They are larger and greyer than the New Zealand pigeon, or kereru (Hemiphaga novaeseelandiae), with a stouter, more brightly coloured bill:

For comparison, this is a kereru, which are reasonably common and widespread on the New Zealand mainland:

Not the most photogenic of creatures perhaps, but this is a chick of one of the world’s rarest seabirds, the Chatham Island taiko, or Magenta petrel (Pterodroma magentae). First described from a bird collected in 1867 by the Italian research vessel Magenta it was tentatively identified in the 20th century with the taiko, which was believed to be extinct.  The identity was confirmed in 1978 when ornithologist David Crockett found live birds in the southwest of Chatham Island.  About 20 breeding burrows are currently known, many with observation hatches like this one, and mostly within a predator-fenced reserve.  The total population is probably fewer than 200, though slowly increasing:

The Chathams only have one lizard species, the Chatham Island skink (Oligosoma nigriplantare). It’s extinct on the main island, but is still common on Pitt and the outlying islands:

The Chatham Island red admiral (Vanessa gonerilla ida) is an endemic subspecies which is notably common throughout the islands:

The Chatham Islands’ plants also show a high degree of endemism. This is a rautini (Brachyglottis huntii), sometimes called the Chatham Island Christmas tree as it flowers conspicuously in the height of the southern hemisphere summer.  This one is a bit past its best in March:

The Chatham Island geranium (Geranium traversii) is a pretty little flower sometimes grown in rock gardens on the mainland:

There was an attempt to establish a business farming emus (Dromaius novaehollandiae) in New Zealand late last century, but it never became a significant industry, though a few of the big birds remain here and there, mostly in small flocks (herds?) on lifestyle blocks. They’ve gone feral in a few areas, although they are still not officially recognised as part of the local avifauna.  Chatham Island now has dozens roaming wild through central parts of the island; there’s talk of trying to eradicate them, but for now they’re an unexpected addition to the landscape:

Much of Chatham Island is occupied by a huge brackish lagoon, along the shores of which, at a spot called Blind Jim’s Creek, you can find fossilised shark teeth. These are between 30 and 60 million years old; most are mako (Isurus oxyrhynchus, or perhaps an ancestor), but other species, including Otodus megalodon, also occur.  In the background of the picture below there are also some fossilised urchin spines, which are present along with the teeth.  Three of us found this collection in about an hour of searching:

It’s a bit hard to make out, but this is a dendroglyph, markings carved into the bark of a kopi (Corynocarpus laevigatus) tree by the Moriori, who were the original inhabitants of the Chathams. They had one of the world’s only true pacifist societies, and when Maori from New Zealand invaded in 1835 they put up no resistance.  Consequently they were massacred, many of them were eaten (Maori were cannibals), and the rest enslaved.  Within a century the last full-blooded Moriori was dead, though a few people today still claim Moriori ancestry, descended from slaves and their Maori masters.  The dendroglyphs are now at least 190 years old, and very few are left.  We found this one, not signposted and not visible from the track, entirely by chance, in a patch of forest where their presence was not known, or at least not publicised:

A Denisovan skull–at last!

June 24, 2025 • 9:00 am

JAC: Greg sent me some thoughts on the new hominin finds involving what used to be known as Denisovans. I suggested he put up his own post on these thoughts, and he kindly agreed. The result is below.

Greg has asked me to weigh in at the end, and I will, under the JAC initials. Except for that, credit for this post goes to Greg.

by Greg Mayer

In a recent pair of papers, Qiaomei Fu and colleagues show, via both DNA and protein analyses, that the skull known as “Dragon Man” from Harbin, China, is a Denisovan. The Denisovans, first identified in 2010 by DNA from a single finger bone from a cave in Siberia, are a long-separated (several 100 kya) lineage of humans that has interbred with anatomically modern humans and Neanderthals, leaving a fairly strong signature (ca. 6%) in the ancestry of modern humans from East Asia and the Pacific. Although several more Denisovans were identified by DNA after the first one, all were from very incomplete remains– until now.

The Harbin skull. CCA 4.0 https://doi.org/10.1016/j.cell.2025.05.040

The Harbin skull was first made known to science in 2018, and was named Homo longi in 2021. I have been able to access only the DNA paper, not the protein one, but Carl Zimmer gives a fine summary in the NY Times.

Zimmer notes that some scientists, including Chris Stringer of the British Museum (Natural History), are now using the name Homo longi, based on the Harbin skull, as the name for the Denisovans. John Hawks of the University of Wisconsin, pushed back on this, telling Zimmer “I’m pretty confident saying these are all Homo sapiens.”

Jerry, Matthew, and myself have discussed Neanderthals (or Neandertals) and Denisovans several times here at WEIT.

About 10 years ago, Jerry, I, and Hawks all agreed on all three forms (Neanderthal, Denisovan, anatomically moderns) being members of one interbreeding species. But when I read David Reich’s book and other papers about five years ago, I was impressed by the paucity of Neanderthal DNA on the X chromosome of moderns, suggesting that Haldane’s Rule had kicked in, and there was partial intrinsic isolation (probably sterility) of hybrids between Neanderthals and moderns. (Haldane’s Rule states that if there is partial reproductive isolation due to infertility or sterility of hybrids, it is the heterogametic sex—XY males in Homo— that is most affected.) So, my view now is that a few hundred thousand years of isolation had moved the Neanderthals and moderns measurably down the road to speciation, though obviously not completely.

My earlier view had been that the low percentage of Neanderthal DNA in moderns was due to social/historical factors, analogous to how there is little European/American Indian admixture in North America, even though there is no intrinsic isolation between these two groups. There’s probably still some social/historical factors involved in the Neanderthal/modern encounter, but part of the disparity in genetic contribution is due to some infertility in male hybrids. [JAC: This infertility is suggested by the observation that introgression of Neanderthal DNA into modern humans is less pronounced on the X chromosome than on the other chromosomes, or autosomes.]

As far as nomenclature goes, I’d be happy with them all being sapiens, but we should recognize that the differences between Neanderthals/Denisovans and moderns are greater, and of a different sort, than differences between the obvious geographic races that exist within modern humans today.

Hawks has a piece on his website, “The humanity of a new Denisovan“, in which he expands on his comments to Zimmer and goes much deeper into the issues of the history of Homo in the last million years; I heartily recommend it. His fourth figure (the second phylogeny) in particular provides a nice summary of his view of that history, including various episodes of interbreeding. He does not mention the distribution of Neanderthal DNA within the moderns’ genome (i.e., the paucity of it on the X), so I’m not sure if this has affected his thinking in any way. I’m hoping that Jerry will weigh in with his current thoughts on the significance, if any, of the distribution of Neanderthal DNA across the moderns’ genome.

JAC:  I’m in agreement with Greg (and Matthew, who I hope will also weigh in here) that “modern” sapiens, Denisovans, and Neanderthals should be considered members of the same biological species, Homo sapiens.  I don’t know how big the disparity between introgression of X-linked vs. autosomal DNA is with respect to modern human genomes, so I cannot judge if it is substantive evidence for some sterility (or inviability) of the hybrids between modern sapiens and Neanderthals. Since the sterility would have to be strong to even consider these two as different biological species, and because there is a sizable aliquot of Neanderthal DNA in many modern humans, the sterility could not have been nearly complete. (I don’t know if Denisovan DNA in modern humans show the same disparity between that from the X chromosome versus the autosomes. If it doesn’t show that, there’s no reason to split Denisovans off as a new species.).

At any rate, the biological species concept (BSC) regards two populations as members of the same species if they can hybridize when they encounter each other in nature and some of the hybrids are viable and fertile. To the extent that Neanderthals meet that requirement, I would say that they, too, are members of H. sapiens.  This kind of “splitting” of groups into different named species is pervasive in human paleobiology, as it is in some other groups, like giraffes, but to me rests on shaky grounds. People like to split human groups into new species, for you get a lot more attention if you can say you found a new species than if you say you simply found a new subspecies or population.

Matthew: The identification of the extraordinary ‘Dragon man’ skull with the Denisovan lineage is probably what most people expected, but is nonetheless an astonishing development, using protein profiles to establish evolutionary relationships (first suggested by Francis Crick in his 1957 ‘central dogma’ lecture, but he never imagined this could be done on a sample over 140,000 years old!). The issue is what we call the Denisovans – the skull was described as Homo longi, and paleoanthropologists, such as the Natural History Museum’s Chris Stringer, accept this, just as they accept Homo neanderthalensis for the Neanderthals. I agree with Jerry that from a biological point of view, these are all members of the same species, because of the existence of fertile hybrids (us!).

This was Chris’s reply to me on Bsky:

This is a link to the article he refers to.

There are two points that make me pause. First, the taxonomic powers that be are unlikely to change their collective minds on this (they haven’t shifted over H. neanderthalensis in the last decade or more, since the first Neanderthal genome was sequenced and the existence of introgression was established. It’s mildly irritating, but that’s the way it will be. Secondly, the points raised by Greg are interesting – we were separated from these lineages for hundreds of thousands of years, and during this time some striking morphological adaptations occurred. They clearly did not lead to the establish of biological species, although we have little grasp of morphological or genetic variation in these groups (all of which were composed of very small (tens of thousands at most), dispersed populations). The role of the X chromosome, as highlighted by Greg, suggests that all three lineages may have been on the way to speciation, although that process was stopped by the demise of the Denisovans and Neanderthals (whether it would have continued in the presence of introgression is another thing to consider).

Finally, our understanding of human evolutionary history is perpetually changing. Stephen Jay Gould used to rewrite his slides each year; I did the same, pretty much, until I found this on Twitter, back when it was good, and now use it in all my human evolution lectures (along with more serious stuff).

 

Fu, Q., P. Cao, Q. Dai, E. A. Bennett, X. Feng, M. A. Yang, W. Ping, S. Pääbo, and Q. Ji. 2025. Denisovan mitochondrial DNA from dental calculus of the >146,000-year-old Harbin cranium. Cell 188:1-8. pdf

Fu, Q., F. Bai, H. Rao, S. Chen, Y. Ji, E. A. Bennett, F. Liu, and Q. Ji. 2025. The proteome of the late Middle Pleistocene Harbin individual. Science in press. locked

Reich, D. 2018. Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past. Pantheon, New York

ABC News (and me) on the Dire Wolf “de-extinction”

April 11, 2025 • 9:45 am

A reporter from ABC News interviewed me yesterday about the Dire Wolf, and her piece appears on their website today (see below). I had to find it myself because, as is usual, when I ask reporters to send me the link to a story for which I was interviewed, they all say “yes”, but only about 10% ever do.  Frankly, I think it’s kind of selfish to exploit scientists for their expertise and not even send them a lousy link.

Well, I digress, but this is in line with the kind of science journalism that has often accompanied the Dire Wolf story. Fortunately, the ABC article is pretty good.

First I’ll add a few comments.  My own view is that Colossal has behaved in a sleazy and overly secretive way with respect to their “de-extinction” and “we-are-big-conservationists” claims.  Some of the secrecy seems unwarranted. For example, they told the New Yorker reporter who wrote about the “Dire Wolf” what genes they had edited, but did not permit him to publish their identity.  Since the faux Dire Wolves are now romping around a secret pasture monitored by drones, there’s no chance that anybody else is going to do what Colossal did, so no need to hide the genes.

The paper about the “woolly mouse” is on bioRχiv, but is still not accepted for publication. (The accompanying note says “This article is a preprint and has not been certified by peer review.”)

And Colossal Bioscience is getting considerable flak from the better science journalists, and is getting peevish about it. They issued a press release yesterday that was defensive, clearly a response to the pushback they’re getting and heavily concerned with species definitions, trying to argue that the dire wolf is a “new species” even though it’s just a gray wolf with 20 DNA letters changed.  Here’s short excerpt of the two-page release:

We invested over a year collaborating with academic colleagues to improve the dire wolf paleogenome and decode the dire wolf’s evolutionary history. Our scientific manuscript has been submitted for peer review and posted to the preprint server–please go check it out.

I cannot find the preprint of the Dire Wolf paper anywhere on the web. If you can find it, let us all know. It would of course list the genes that had been changed.

You can read the ABC article by clicking below; it’s free. The article includes a ten-minute video of the project showing the “Dire Wolves” (I have to admit that they’re cute).  Note that Colossal decline to let the reporter see the faux Dire Wolves “up close,” though they showed her the videos.  And Colossal co-founder Ben Lamm asserts that they are on target to produce woolly mammoths by 2028! I’m ready to bet a thousand dollars that that won’t happen—especially if you define “de-exincted woolly mammoth” as being something with at least 50 gene edits that’s ready to release on the tundra.

Three quotes from Beth Shapiro, the chief scientific officer of Colossal Biosciences, from the video in the article:

“. . . that animal looks like a dire wolf, it will behave like a dire wolf, and it is a dire wolf.”

“When I saw them born, and they were white, I was like: ‘we’ve done it–those are dire wolves.'”

“I think that the best definition of a species is if it looks like that species, if it is acting like that species, if it is filling the role of that species, then you’ve done it.”

They are heavily invested in the claim that this really IS a dire wolf.  The press release makes that clear, as they’re trying to revise species definitions so that the Dire Wolf qualifies as a new species. From Colossal’s press release:

So many experts out there are demanding that species are defined solely by their DNA. That’s some version of “insane”. Even evolutionary biologists can’t agree on species definitions. Mammoth species? Defined by teeth ridges. Ancient bison? Horn shapes. And so arbitrarily that someone accidentally mixing up length and width measurements had zero impact on species classification. Brown bears and polar bears, humans and Neanderthals, wolves and coyotes are all different species unless you apply the most commonly taught species concept, which would classify them as the same species because they can interbreed and produce healthy, fertile offspring.

Getting dragged into arguments about species definitions is a distraction from the real achievement. This is the most significant advancement in gene-editing in history. Even our harshest critics admit it. As one of our founders stated, “this is the moon landing of synthetic biology.”

. . .We get it. We totally understand that some scientists are not comfortable calling these dire wolves because they feel like the wolves are not sufficiently genetically similar to a particular extinct individual to merit that name. That’s ok with us.  This is not a fight that we care about. We’re calling them dire wolves, and if you prefer something else (how about “Colossal’s dire wolves”?) that works too. And maybe also take a breath and think about what the birth of these technologies means to the future of our planet instead of nitpicking terminology.

This is a fight they don’t care about? I think they should care, at least a bit. They are calling these tweaked canids members of a new species, the “Dire Wolf”.  I prefer “gray wolves with fifteen DNA letters from dire wolves” or, better, “genetic variants of the gray wolf.” The whole hype around this animal is that it is a new species that existed in the past, not simply a minor variant of the gray wolf that is nowhere near being genetically similar to the extinct gray wolf.

Quotes from the ABC piece, including what I said:

Colossal Laboratories & Biosciences, the company behind the revived dire wolf and based in Dallas, said it is “a scientific breakthrough for global conservation efforts” and is even trying to bring back the extinct woolly mammoth by 2028.

However, bioethicists and ecologists say they are skeptical that the animals created are actually dire wolves and said there are ethical concerns including where the animals would be kept and if they could ever survive in the wild.

“All claims of de-extinction are the invocation of a metaphor, and what they have produced and what they will at some point produce, may be technologically impressive, but they are not and never can be the actual previously extinct creatures,” Samuel Gorovitz, professor of philosophy at Syracuse University and a leader in the development of the medical ethics field, told ABC News.

“Only adult dire wolves can raise a dire wolf and there aren’t any. … One thing that we know for sure, that they are not, is dire wolves.”

. . . Stuart Pimm, Doris Duke professor of conservation ecology at Duke University’s Nicholas School of the Environment, called the news of the resurrected dire wolf a “colossal fabrication” and referred to the species created as a “designer dog.”

“This is just a big dog with a few genes inserted from a once extinct wolf,” Pimm told ABC News. “Incidentally, a dire wolf is not really closely related to a regular wolf.”

He went on, “It’s about as different to a regular wolf as we are from chimpanzees and if you inserted a chimpanzee gene into a human, I think that will be a horribly unethical thing to do.”

One of my beefs is that none of Colossal’s projects involve changing the behavior of the “de-extincted” organism, even though behavior is absolutely critical not only in bringing back a species as it really was, but allowing it to survive in nature.  Remember, wolves and mammoths are social animals, programmed to learn many things from their parents. And they have genetically coded behavioral repertoires whose genetic basis we do not understand. For example, maybe lichens tasted good to a Woolly Mammoth but wouldn’t to a replica tweaked by Colossal. Such a difference, if it existed, would likely be genetic.

A few more criticisms from the ABC piece:

However, today’s environment does not resemble the environment in which historic dire wolves lived and releasing them into the wild could harm the ecosystem.

“It has to live somewhere, and it isn’t clear what the environment was that the dire wolf lived in, or what it ate, or sort of its behavior, and so you kind of face a possibility you won’t know where to keep this animal that you made healthy,” Arthur Caplan, a professor of bioethics at the NYU Grossman School of Medicine, told ABC News.

He added that the behavior of dire wolves was likely shaped by the packs they roamed in or packs that they may have competed against. However, those groups also don’t exist anymore.

“If you bring back something that’s been dead 10,000 or 40,000 or 100,000 years, you need to bring back its environment, not just the animal,” Caplan continued. “Otherwise, you potentially are going to have issues.”

Jerry Coyne, professor emeritus in the department of ecology and evolution at the University of Chicago, said there is no way to release the “de-extincted” dire wolves back into the wild because they wouldn’t know how to survive.

Coyne told ABC News that if the revived dire wolves are let loose into the wild “without the social group that they’re evolved to be in” it would be hard to expect them to “behave properly” around other animals because they’ve never been exposed to other species.

“So that’s also unethical, because those animals are kind of separate. They’re not going to have the right thing to eat, it’s not going to know what to eat, how to eat, probably got the wrong digestive system. … So that’s one of the ethical considerations.”

Colossal Laboratories did not reply to ABC News’ request for comment on these concerns.

Of course they wouldn’t!

Again, I think there is a destructive and perhaps unwitting collusion between Colossal and much of the press. Now the ABC piece by Mary Kakatos is fine, and gives the proper caveats and room for critics, but a lot of pieces don’t (see the New Yorker piece, for instance).  But the press isn’t going to get clicks by saying that “this is not a real Dire Wolf,” so they amp up the gee-whiz factor and dial down the critics. And, as you see above, Colossal is perfectly happy with the rah-rah press coverage. The real losers in all this are the public, who miss the chance to learn something about genetics and conservation.

And, by the way, Colossal should stop spreading the view that de-extinction is one way to keep us from worrying about endangered species, implying that we can always bring them back again with cloning, Crispr and surrogate mothers!

UPDATE: Beth Shapiro defends the criticisms leveled against the Dire Wolf project. Many of her points was in the press release. Click to hear (h/t Matthew Cobb). She is quite defensive.

An analysis of this statement followed by a thread. I can’t embed the Bluesky post, but click on it to go to the thread:

Frozen mummy of a sabre-toothed juvenile gives clues about what the species looked like

November 18, 2024 • 9:30 am

Nature Scientific Reports has an open-access article reporting a rare find: a mummy of a kitten (“juvenile”) of a sabre-toothed cat, found frozen in the Russian Republic of Sakha, in Siberia. You can read the report by clicking below, or download the pdf here.

Mummies are rare because an animal has to die and then be permanently frozen in ice, and then later discovered. This is, as far as I know, the first mummy of a sabre-toothed cat, though skeletal remains are known. (These skeletal remains were used to identify the species of cat; see below)  It appears to be a young kitten, judging from comparison with a living relative, a three-week-old African lion (Panthera leo). The mummy’s remains were carbon dated to 31,808 ± 367 years ago, so it could have been contemporaneous with humans, who were probably in Siberia about that time.

Here’s a description of the specimen and then some photos:

The Badyarikha mummy (specimen DMF AS RS, no. Met-20-1) contains the head and the anterior part of the body preserved approximately to the caudal edge of the chest (Fig. 1). There are also incomplete pelvic bones articulated with the femur and shin bones. They were found encased in a piece of ice along with the front part of the cub corpse. The specimen is stored at DMF AS RS in Yakutsk.

Figure and caption from the paper (click figures to enlarge them):

The frozen mummy of Homotherium latidens (Owen, 1846), specimen DMF AS RS, no. Met-20-1, Russia, Republic of Sakha (Yakutia), Indigirka River basin, Badyarikha River; Upper Pleistocene: (A) external appearance; (B) skeleton, CT-scan, dorsal view.

And here’s a comparison of the heads of the specimen (top) with a preserved three-week old lion cub. The face of the sabre-tooth is flatter than that of the lion, but this is probably due to deformation of the specimen (see skulls below). But the mummified cats’ external ears (auricles) are not as prominent as those of the lion. (Smaller ears are a characteristic adaptation to cold climate, as protruding ears are a source of heat loss.) The mummy’s fur color was dark brown, with the paws and chin being lighter brown:

‘The authors make a big deal about the thickness of the neck, which shows that this was a muscular cat (compare with the lion cub below):

(From the paper): External appearance of three-week-old heads of large felid cubs, right lateral view: (A) Homotherium latidens (Owen, 1846), specimen DMF AS RS, no. Met-20-1, frozen mummy, Russia, Republic of Sakha (Yakutia), Indigirka River basin, Badyarikha River; Upper Pleistocene; (B) Panthera leo (Linnaeus, 1758), specimen ZMMU, no. S-210286; Recent.

From the paper:

The mummy neck is longer and more than twice as thick as that of P. leo, ZMMU S-210286 (80.0 vs. 74.0, 52.0 vs. 32.0, respectively). The difference in thickness is explained by the large volume of muscles, which is visually observed at the site of separation of the skin from the mummified flesh.

Based on comparison of the skull with known fossil skeletons, they identified this cub tentatively as a juvenile Homotherium latidens.

Here’s an 8-minute movie about the genus Homotherium, showing a reconstruction of the animal and a lot of useful information:

And a photo of skulls of the sabre-tooth cub specimen (top row) and a 3-week old lion cub (bottom row).   The enlarged arches, where chewing muscles are attached, suggest that the species was adapted to inflict a strong bite (perhaps to use its serrated incisor teeth), though I’m not a paleontologist and am just guessing.

(from paper): Skulls of three-week-old large felid cubs, left lateral view (A, C) and dorsal view (B, D): A, B, Homotherium latidens (Owen, 1846), specimen DMF AS RS, no. Met-20-1, frozen mummy, 3D computer models (image is reconstructed based on the undeformed right half of the skull, mirrored); Russia, Republic of Sakha (Yakutia), Indigirka River basin, Badyarikha River; Upper Pleistocene; C, D, Panthera leo (Linnaeus, 1758), specimen ZMMU, no. S-3034, photographs; Recent.

The authors say this:

One of the striking features of the morphology of Homotherium, both in adults and in the studied cub, is the presence of an enlarged premaxillary bone, containing a lateromedially expanded row of large cone-shaped incisors that form a convex arch. Among all the unerupted teeth of the Homotherium cub mummy, only the upper and lower deciduous incisors protrude with their tops from the alveoli.

Here’s where the premaxillary bone is: the orange one in front. You can see that this bone is larger in the mummy than in the lion cub.

 

Finally, the configuration of the paws, which are far more rounded in the mummy than in a lion cub, support the suggestions from the cub’s ears that this was a cat adapted to the cold. Forepaw photos, with A-C being the mummy and D being a lion cub. Rounded paws, also seen in lynxes and other cold-weather cats, are better for walking on snow, as they act as “snowshoes” that give a greater area of contact with the snow:

(from Fig. 7 of paper): Forepaws of three-week-old large felid cubs: A, B, С, Homotherium latidens (Owen, 1846), specimen DMF AS RS, no. Met-20-1, frozen mummy, right forepaw; Russia, Republic of Sakha (Yakutia), Indigirka River basin, Badyarikha River; Upper Pleistocene: A thumb claw; B second digit claw; С plantar view; (D) Panthera leo (Linnaeus, 1758), specimen ZMMU, no. S-210286, right forepaw, plantar view; Recent. Designations: 1, first digital pad; 2, carpal pad (absent in H. latidens).

And the authors’ interpretation:

The front paw of the juvenile Homotherium latidens has a rounded shape. Its width is almost equal to its length, in contrast to lion cubs with their elongated and relatively narrow front paw (Fig. 7). The wide paw, the subsquare shape of its pads, and the absence of a carpal pad are adaptations to walking in snow and low temperatures. The small, low auricles and absence of the carpal pad in Badyarikha Homotherium contrast with the taller auricles and normally developed pads in the lion cub. All these features can be interpreted as adaptations to living in cold climate.

The carpal pad (“2” in the lion photo) is apparently missing in the sabre-tooth, and this is said to be an adaptation to walking in snow, though I’m not sure why.  But all the data indicate that this species of cat was muscular (the forepaws also suggest more muscles than the lion) and, as suggested from its Siberian habitat, adapted to a cold climate. You can learn more about the lifestyle of this genus of cat from the movie above.

h/t: Erik

New paper puts the “last universal common ancestor”: the creature that gave rise to all living things, much earlier than previously thought: 4.2 billion years.

July 17, 2024 • 9:30 am

A brand-new paper from Nature Ecology & Evolution used a clever technique to estimate the age of “LUCA”,. the “last universal common ancestor” of all living things. What that means is LUCA is the last creature whose descendants include every species alive: the ancestor of all of us.  And it dates LUCA to about 4.2 billion years ago! That is far older than people thought. Previous estimates were in the 3.5-3.8 billion-year range, after the famous “Late Heavy Bombardment” (LHB), during which the Earth was continually battered with asteroids and comets. It was assumed that nothing alive on Earth could have survived those impacts. But if the authors are right, LUCA’s ancestors did survive this, for 4.2 billion years is probably a big underestimate of of when life on earth began.

The earliest generally accepted fossil evidence for life is about 3.7 billion years, which is based on isotopes that, scientists think, could have been produced only by living creatures. But the earliest genuine fossilized organisms occur a bit later than that: fossilized blue-green algae (“stromatolites”), whose fossils go back 3.5 billion years ago.

The new paper by Moody et al., which has an accompanying research brief (click screenshots below to access, or find the pdf here) pushes the age of LUCA back to 4.2 billion years ago, which actually precedes the LHB. And the new LUCA date comes soon after the Earth actually formed (about 4.54 billion years ago) and after the Moon was created, probably by a huge, Mars-size planet striking Earth and throwing off debris that consolidated to create our Moon. (That occurred soon after the Earth formed.)  Surely no life could have survived that collision, so if the authors are right, it took only about  0.3 billion years, or 300 million years after the Earth was formed, before life existed.

But LUCA wasn’t the first life on Earth: it is simply the bacteria-like species of organism that gave rise to all living creatures. Surely life originated before that, and the new paper suggests that the 4.2 billion year old (byo) LUCA was only one of a number of life forms existing back then, with the rest going extinct without leaving descendants. The authors think this because LUCA probably needed complex carbon compounds to live, and is also likely to have provided niches for other creatures.  That means that life itself began well before LUCA, especially because, based on its genome, the authors conclude that LUCA was quite complex— about as complex as modern bacteria. Surely it would take millions of years of evolution to get to the point where a LUCA-like creature could have existed.  See below for the diagram of what LUCA was like.

The main lesson from the paper is that life began very, very soon after the Earth had cooled off and the dust had settled from the LHB and carving out of the Moon. If that’s the case, then perhaps life on other planets could evolve more easily than we thought.

But on to the paper. If you want the whole megillah, click on the first link, while the second gives a two-page précis.  It’s a very complicated and long paper, so give me kudos for reading it twice to distill it here. But I can’t claim to have understood everything, as the analyses of the data, or even the methodology, is quite arcane and sophisticated.

A two -age summary from the same journal:

Why do we think that all life descended from a single species rather than having multiple origins? Because all living creatures have some similarities that probably reflect the workings of chance: whatever mutations happened to give rise to our ancestor. The paper explains:

The common ancestry of all extant cellular life is evidenced by the universal genetic code, machinery for protein synthesis, shared chirality of the almost-universal set of 20 amino acids [JAC: all amino acids used in modern creatures are the L rather than the D form] and use of ATP as a common energy currency. The last universal common ancestor (LUCA) is the node on the tree of life from which the fundamental prokaryotic domains (Archaea and Bacteria) diverge. As such, our understanding of LUCA impacts our understanding of the early evolution of life on Earth.

The way scientists usually estimate LUCA is using molecular dating based on DNA divergence among living organisms. Because there is a “molecular clock”, with the DNA changing roughly in a linear fashion with time, you can back-calculate from living creatures to estimate when their DNA sequences would have converged on a single sequence, which would be the DNA sequence of LUCA.  But there are formidable problems with this, making DNA-based estimates  contentious. But the authors found a way around this.

What they did is to estimate divergence times of all living creatures (for practicality, they used bacteria [prokaryotes] and Archaea, bacteria-like organisms that form their own kingdom) using DUPLICATED GENES.  These are genes that, tracing the sequences of living organisms back, had already been duplicated in LUCA.  As you may know, genes often get duplicated during cell division or (in sexual organisms) meiosis, so a single gene can now occur in two copies. Those two copies will initially be identical, but then, being genetically independent, will begin to diverge via mutation and then selection or drift. (Examples of duplicated genes are are different forms of globins in humans, two of which, alpha and beta, produce products that combine to make adult hemoglobin.  But many, many genes have duplicated over the history of life.)

A gene that is duplicated (based on sequence similarity) in LUCA must have been present in the ancestor of LUCA, and have duplicated before LUCA existed. Thus an estimate of the age of a duplicated gene in LUCA gives us a lower-bound on the age of LUCA itself. And since some genes are already duplicated in LUCA, we can use them, combined with a molecular clock (and other statistics) to estimate how long it took for each copy to give rise to the diversity of DNA-sequences in descendant copies in modern microbes.  The advantage comes because we have two estimated DNA sequences in LUCA that began identically but then diverged over evolutionary time. This gives us two chances to estimate the age of the creature. Using other methods, we can estimate how many genes there were in LUCA, the size of its genome, and what kind of genes it had.  The latter can then give us an idea of what kind of creature it was and how it lived.

Here are the results, in short:

a.) LUCA lived about 4.2 billion years ago. Here’s the reconstructed phylogeny (note that there are two estimates of its age since they use two copies of each of the five genes they chose for age estimation). Click to enlarge. On the right are all the kingdoms of living organisms, traced back to LUCA.  The use of two gene copies give similar estimates, about 4.2 billion years ago. I’ve circled the two LUCA estimates, which work out to a similar age (see age scale at top for divergence times):

(From paper): Our results suggest that LUCA lived around 4.2 Ga, with a 95% confidence interval spanning 4.09–4.33 Ga under the ILN relaxed-clock model (orange) and 4.18–4.33 Ga under the GBM relaxed-clock model (teal). Under a cross-bracing approach, nodes corresponding to the same species divergences (that is, mirrored nodes) have the same posterior time densities. This figure shows the corresponding posterior time densities of the mirrored nodes for the last universal, archaeal, bacterial and eukaryotic common ancestors (LUCA, LACA, LBCA and LECA, respectively); the last common ancestor of the mitochondrial lineage (Mito-LECA); and the last plastid-bearing common ancestor (LPCA). Purple stars indicate nodes calibrated with fossils. Arc, Archaea; Bac, Bacteria; Euk, Eukarya.

b.) LUCA had a big genome and many genes. The authors estimate that LUCA’s genome had 2.75 million DNA base pairs, capable of making 2,657 proteins (an underestimate of gene number). That is a big and complex organism, comparable to existing bacteria. (Modern E. coli produce about 4288 proteins from 4.6 million base pairs.) This complexity shows that even LUCA was preceded by a long period of evolution.

c.) LUCA was probably an anaerobic and autotrophic creature, which means that it didn’t need oxygen to grow and flourish, and also that it produced its own “food”, getting energy from substances like hydrogen and carbon dioxide.  The authors suggest two places where such a creature could have lived: in warm hydrothermal vents in the ocean, or on the ocean surface, where it would have ample access to the gases that constitute its food.  There was no evidence that the organism was photosynthestic, as it lacked genes involved in modern photosynthesis.

Here’s a sketchy diagram of what kind of genes LUCA had (note the “immune” system, based on CRISPR-like genes that are used to destroy viruses. LUCA probably had a virus problem, too! Figure b) show us how LUCA fit into the tree of life:

(From paper): a, A representation of LUCA based on our ancestral gene content reconstruction. Gene names in black have been inferred to be present in LUCA under the most-stringent threshold (PP = 0.75, sampled in both domains); those in grey are present at the least-stringent threshold (PP = 0.50, without a requirement for presence in both domains). b, LUCA in the context of the tree of life. Branches on the tree of life that have left sampled descendants today are coloured black, those that have left no sampled descendants are in grey. As the common ancestor of extant cellular life, LUCA is the oldest node that can be reconstructed using phylogenetic methods. It would have shared the early Earth with other lineages (highlighted in teal) that have left no descendants among sampled cellular life today. However, these lineages may have left a trace in modern organisms by transferring genes into the sampled tree of life (red lines) before their extinction. c, LUCA’s chemoautotrophic metabolism probably relied on gas exchange with the immediate environment to achieve organic carbon (Corg) fixation via acetogenesis and it may also have run the metabolism in reverse.

d.) LUCA was part of a community of other organisms.  It’s inconceivable that LUCA. which was a sophisticated organism, could live without a source of organic compounds (like amino acids) to use for constructing its body (remember, these organic compounds were not a “food,” but a construction material). Further, LUCA would itself provide organic compounds that would create niches for other species. (It’s likely that viruses, which aren’t good candidates for a LUCA-like creature, already existed.) The phylogeny in figure (b) just above shows how LUCA would fit into the tree of life, giving rise to all modern creatures via speciation  events, but would itself also be part of an earlier family tree, all of whose members save LUCA went extinct without leaving descendants.

These are the four big conclusions of the paper, with the most interesting to me being how short the time was after Earth’s formation for complex life to have evolved.  And the age of LUCA, remember, is an UNDERESTIMATE of how long it took complex life to evolve after the Earth’s conditions were suitable for such evolution.

I’ll end with the authors’ own conclusions, which are lucid enough for the layperson (bolding is mine)

Conclusions:

By treating gene presence probabilistically, our reconstruction maps many more genes (2,657) to LUCA than previous analyses and results in an estimate of LUCA’s genome size (2.75 Mb) that is within the range of modern prokaryotes. The result is a picture of a cellular organism that was prokaryote grade rather than progenotic  [JAC: not having the characteristic of a prokaryote, which LUCA did] and that probably existed as a component of an ecosystem, using the WLP [JAC: the Wood-Ljungdahl pathway for producing energy, based on hydrogen and carbon dioxide] for acetogenic [JAC: producing acetate as a product of anaerobic metabolism] growth and carbon fixation. We cannot use phylogenetics to reconstruct other members of this early ecosystem but we can infer their physiologies based on the metabolic inputs and outputs of LUCA. How evolution proceeded from the origin of life to early communities at the time of LUCA remains an open question, but the inferred age of LUCA (~4.2 Ga) compared with the origin of the Earth and Moon suggests that the process required a surprisingly short interval of geologic time.

Oh, and the authors suggest the intriguing possibility that if we could reconstruct the DNA sequence of LUCA—something that is not beyond the realm of possibility—then perhaps we could perhaps make in the lab a LUCA-like organism, and actually see what our ancestor looked like!

Fossil of giant fanged salamander found in Namibia

July 7, 2024 • 9:30 am

A giant salamander—and by “giant” I mean about 2.5-4 meters long—equipped with teeth and wicked fangs was found in Namibia, dated at about 270 million years ago, and just reported in Nature.  Its significance is that it is early, but is considered a “stem” tetrapod, meaning that it has some of the characteristics of modern amphibians, which are tetrapods (four-legged animals that could move around on land).  The authors, according to this CBS News story, suremise that it “was considerably longer than a person, and it probably hung out near the bottom of swamps and lakes”.  It was also an apex predator, meaning that it ate other animals, but there was nothing around that could eat it.

Its was found in an area that, 270 million years ago, was at high latitude, ergo cold and partly glaciated. This beast is the first suggestion that there was a tetrapod fauna in cold-ish climates at that time.

Click below to see the article, or download the pdf here:

The researchers recovered a skull that was about 60 cm (2 feet long), as well as the front part of the postcranial skeleton. The authors don’t give a size estimate, but with a two-foot head it was probably large, and could have been 12 feet long: the longest salamander known yet. (The largest living salamander, the Japanese giant salamander (Andrias japonicus), can attain a length of about 5 feet.  This puppy could have been twice as long.

Two skull fragments were known of this animal before, but it hadn’t been named and there were no remains of the skeleton. The authors named this one Gaiasia jennyae, after the Gai-As formation in which it was found, and also after Jenny Clack (1947-2020), who studied early tetrapods. (This, of course, will anger the pecksniffs who think that animals shouldn’t be named after people, but they can jump in the lake.) It is the only species in the genus Gaiasia.

The sample in the field (from the Supplementary information):

(From paper): B. Reassembling the ex situ type specimen of Gaiasia jennyae (F 1528)– a dorsal up skull with lower jaw and most of the articulated axial skeleton. C. In situ dorsal-up Gaiasia jennyae skull (F 1522) at locality shown in A. panorama. D. Type specimen of Gaiasia jennyae (F 1528) shown in B. after preparation. Note the differential compression of the skull roof. There is no evidence of pre-burial breakage or subaerial weathering. Scale bar =10cm.

Here’s the skull in dorsal (a,b) and ventral (c,d) views, and reconstructions.

From the paper: a,b, Skull in dorsal view. a, Photograph. b, Interpretative drawing. c,d, Skull in ventral view. c, Photograph. d, Interpretative drawing. e, Reconstruction of the articulated specimen in lateral view showing preserved elements of the skeleton. adsym, adsymphysial bone; an, angular; anf, angular fenestra; c1, anterior coronoid; c2, middle coronoid; caf, carotid artery foramen; chf, chordatympanic foramen; d, dentary; ept, ectopterygoid; exo, exoccipital; f, frontal; it, intertemporal; j, jugal; l, lacrimal; mx, maxilla; n, nasal; p, parietal; par, prearticular; pfr, prefrontal; pl, palatine; po, postorbital; pof, postfrontal; pp, postparietal; pospl, postsplenial; psph, parasphenoid; pt, pterygoid; qj, quadratojugal; sa, surangular; spl, splenial; sq, squamosal; st, supratemporal; t, tabular; v, vomer. Scale bars, 50 mm (a,c).

And a reconstruction of the skull and postcranial skeleton they found. Because we don’t have the posterior skeleton, length estimates are guesses.

Here are photos and a reconstruction of the lower jaw. The white circles show the fangs, which are indicated in the upper drawing. There were three on each side, and interlocking fangs on the top mandible as well. It ate by both suction and biting:

(From the paper): e, f. Photographs of the right hemimandible. e, Ventral view of the posterior half. f, Dorsal view of the symphyseal area. adsym, adsymphysial plate; an, angular; anf, angular fenestra; c1, anterior coronoid; c2, middle coronoid; chf, chordatympanic foramen; d, dentary; par, prearticular; pospl, postsplenial; sa, surangular; spl, splenial. Dotted white circles show the position of the symphysial fangs. Scale bar, 50 mm.

. . . and a reconstruction of the front of the animal from the paper. Remember, that fearsome head was about two feet long!

(From the paper): c, Artistic reconstruction of Gaiasia in lateral view; artwork by Gabriel Lio.

Now this is unlikely to be any kind of ancestor of reptiles, but it’s likely that this is one of several species occurring when tetrapods had already evolved from fish and one of its relatives probably gave rise to modern amphibians, while another gave rise to all modern reptiles (and after followed the evolution of birds and mammals). Its importance is not only the “gee whiz” factor, but also the indication that there was a thriving ecosystem at high latitudes about 270 myr ago. After all, this is an apex predator, and it had to eat something aquatic (fish or, perhaps, other early amphibians).  So if these creatures existed, there must also have been many other animals living at high latitudes at that time.

New findings about the Denisovans

July 5, 2024 • 11:45 am

We’ve known about the Denisovans for about 15 years, since part of a finger was found in a Russian cave (the “Denisova Cave“) in 2008 and wasw published two years later.  They were a hominin subspecies like Neanderthals. I consider these groups subspecies of H.sapiens because they both interbred with H. sapiens and left fertile offspring. Denisovans lived in Asia from about 300,000 to 25,000 years ago. (They may also have bred with Neanderthals.)  They are considered a sister taxon to Neanderthals, which means that these two groups shared a common ancestor that had already branched off from the ancestor of “modern” H. sapiens.

Wikipedia gives a useful table of all the known remains of Denisovans, which are judged as a distinct group from DNA sequencing. We have small bits of bone, including teeth, parietal bones, mandibles, and limb bones (and now, according to the Nature article below, a rib bone) from the three locations—all caves—shown below from the Wikipedia map shown below:

And here’s a picture of the Denisova Cave in Russia where it all started:

Xenochka, CC BY-SA 4.0, via Wikimedia Commons

Here’s a diagram of the route the Denisovans took as they colonized Siberia and SE Asia from the Middle East, as well as a “family tree” on the right showing the sister-group relationship of Neanderthals and Denisovans (the figure presumes that the common ancestor of the two was a different species, Homo heidelbergensis, which, confusingly. has been considered a subspecies of H. erectus or even H. sapiens.

John D. Croft at English Wikipedia, CC BY-SA 3.0, via Wikimedia Commons

Just as many Westerners have some Neanderthal DNA (I have a bit among my Ashkenazi genes), so some Asians and people from Oceania have Denisovan DNA.  This shows the hybridization I talked about above. And if two groups meet, mate, and produce fertile hybrids, they’re considered by evolutionary biologists to be subspecies, not species. Unless, that is, they’re hominins, for paleobiologists love to split names and create new species, a practice that produces more excitement and fame than simply saying “we found a new subspecies of Homo sapiens.”

Well, we’ve known about the Denisovans for a while, so what’s new? This news report from Nature (click to read) gives us a bit more information, like what kind of food they ate, as well as reporting on a new Denisovan rib bone found this year.

The results aren’t that thrilling to me, but many people thrive on human paleobiology, and so here are some extracts from the news:

When life got tough, the Denisovans got tougher. The enigmatic ancient humans hunted birds, rodents, even hyenas, helping them to thrive high on the Tibetan plateau for well over 100,000 years.

Those conclusions emerge from a study of thousands of mostly tiny animal bones that provide an insight into life at Baishiya Karst Cave in China1 — only the second archaeological site known to host Denisovans, after the Siberian cave that gave the group its name. Denisovans are a sister group to Neanderthals, and might have once lived across Asia.

Many of the cave remains could be identified only by their protein signatures. This included a rib bone that represents a new Denisovan individual, one of just a handful known.

“Denisovans are dealing with the full suite of animals they’re surrounded with in order to survive in this quite harsh landscape,” says Frido Welker, an archaeological scientist at the University of Copenhagen who co-led the study, published in Nature on 3 July. “It’s at high altitude. It’s cold. It’s not a nice place to be as a hominin.”

The article they’re discussing, a new one also in Nature, is below: click on the screenshot to read it:

And here’s the paper’s abstract, which discusses not only the discovery of a new rib bone from the cave in Tibet, but also some scratches on associated animal bones, indicating that they’d been processed for food, presumably by Denisovans:

Using zooarchaeology by mass spectrometry, we identify a new hominin rib specimen that dates to approximately 48–32 thousand years ago (layer 3). Shotgun proteomic analysis taxonomically assigns this specimen to the Denisovan lineage, extending their presence at Baishiya Karst Cave well into the Late Pleistocene. Throughout the stratigraphic sequence, the faunal assemblage is dominated by Caprinae, together with megaherbivores, carnivores, small mammals and birds. The high proportion of anthropogenic modifications on the bone surfaces suggests that Denisovans were the primary agent of faunal accumulation. The chaîne opératoire of carcass processing indicates that animal taxa were exploited for their meat, marrow and hides, while bone was also used as raw material for the production of tools. Our results shed light on the behaviour of Denisovans and their adaptations to the diverse and fluctuating environments of the late Middle and Late Pleistocene of eastern Eurasia.

Here, from the paper, is a human-cut bird wing bone showing the scratches, probably made when feathers were removed. This happens to be a golden eagle. How did they catch it?

(from the paper): Aquila chrysaetos right humerus (layer 4) with superficial and straight cut mark clusters, associated with the removal of feathers

And here from the paper is a photo of the rib bone from a Denisovan also found in the Tibetan cave, along with a phylogeny showing that the rib is closely related to a Denisovan mandible found in the same cave.  It’s not really earth-shaking that a Denisovan rib would be genetically similar to a Denisovan mandible found in a different level of the same cave, but it does add to the specimens we have. Note as well that Denisovans and Neanderthals are, again, placed by DNA analysis as sister groups: each other’s closest relatives.

(From paper): a, Photograph of the Xiahe 2 specimen. Scale bar, 1 cm. b, Phylogenetic tree for the Xiahe 2 specimen and reference proteomes. Support values at nodes are shown for the maximum likelihood and Bayesian analysis, respectively.

A summary from the News & Views piece of how scientists decided which species the animal bones came from (they used protein sequences from collagen rather than DNA to do this), and which animals they ate:

Proper excavations of the cave revealed more signs of occupation: dirt from the site dating to between 100,000 and 45,000 years ago contained DNA sequences from maternally inherited cell structures called mitochondria, matching those of the Denisova Cave remains. The dig, led by archaeologist Dongju Zhang at Lanzhou University in China, also uncovered thousands of mostly fragmentary animal bones.

To identify more than 2,000 of these remains, Zhang, Welker and their colleagues chemically analysed collagen protein signatures, which vary between animals. Especially common were caprines (the subfamily that includes goat and sheep) as well as wild yak, horses and gazelle. Carnivores, including wolves and foxes, also turned up in the mix.

Many of the bones from the cave, including those of hyena, caprines and golden eagles (Aquila chrysaetos), contained cut-marks and other signs of human predation. Even rodents and hare were probably hunted: a marmot (Marmota) leg bone was split open, potentially to harvest its marrow. Such small, speedy animals wouldn’t have been easy to catch, says Zhang, and bringing down carnivores such as hyenas would have taken moxie.

And here’s the Tibetan cave, Baishiya Karst Cave.  It’s no wonder they call these hominins “cavemen”. Where else could you get shelter from the rain and wind and a place to process your catch? And cook it, too, for there’s evidence that both the Denisovans and the Neanderthals could probably make fires.

What more do we know now? Well, we know what the Denisovans ate, which is really no surprise. Callaway tries to give his piece more oomph by saying that we now know the Denisovans’ “survival secrets”, but of course they had to eat something. But knowing what they ate is better than nothing. And we also have more bones, though as yet they haven’t yielded much new information. There’s more to come as excavations proceed, but the N&V ends rather lamely:

. . . . scientists’ picture of Denisovans is becoming less opaque thanks to information gleaned from dirt and shards of bone subjected to cutting-edge DNA and protein analysis, says Brown. “Denisovans are essentially, at the moment, a biomolecular population.”

The remains Zhang and her colleagues analysed are from pre-pandemic excavations of Baishiya Karst Cave. But the researchers are now back excavating the enormous cavern, hoping to find more insights into Denisovan life. “We haven’t reached the bottom,” says Zhang.

Perhaps I’ve gotten jaded, for the discovery of a new subspecies of humans in Eastern Asia, one that probably went extinct like the Neanderthals, truly is a surprise.