Oldest evidence for animals found? New sponge-like fossil is 890 million years old, several hundred million years older than next oldest animal

July 29, 2021 • 9:15 am

First, we have to know what biologists mean by “animals”. In brief, they are multicellular organisms comprising eukaryotic cells (“true cells” with a nucleus and nuclear membrane, as well as organelles like mitochondria). Or, to be more specific, I’ll give the Wikipedia definition:

Animals (also called Metazoa) are multicellular, eukaryotic organisms in the biological kingdom Animalia. With few exceptions, animals consume organic material, breathe oxygen, are able to move, can reproduce sexually, and go through an ontogenetic stage in which their body consists of a hollow sphere of cells, the blastula, during embryonic development.

Long before animals existed, living organisms existed, but these were cyanobacteria (“blue green algae”) and other microbes, not regarded as animals. The first cyanobacteria date back about 3.5 billion years, only a billion years after the Earth formed. The cyanobacteria are identified in fossil stromatoliteslayered reef-like structures formed by the accretion of bacteria. Stromatolites are still forming in some places on Earth, like Shark Bay, Australia.

But when did the first metazoan, or “animal” appear? For that you can use either fossil or molecular evidence.

The earliest fossil scientists regard as an animal is Dickinsonia from the Ediacara fauna, dated about 540 million years ago.  Scientists think it’s an animal because its lipid biomarkers, which you can extract from fossils and the sediments above and below them, include cholesteroids, compounds found exclusively in animals. Dickinsonia is known only from imprints, like the one below, and its affinities are a mystery.

Dickinsonia

Molecular data, from which you can construct a phylogenetic tree of living animal groups and then extrapolate backwards, have shown that animals probably originated between 650 and 850 million years ago, but we have no animal fossils from that period. Those trees also show that perhaps the earliest animal was similar to sponges, for sponges seem to be the most “basal” animals—those that branched off the animal tree before other groups. This makes sponges the “sister group” of all other animals.

Now a new paper in Nature by Elizabeth C. Turner of Laurentian University in Canada has pushed the oldest animal fossil back a long way: several hundred million years—to 890 million years ago! And, in fact, the fossil shows features of early sponges, verifying the molecular conclusions.

Now not all paleobiologists agree that what Turner found is an animal—some say the structures observed may have a microbial origin—but Turner herself is pretty confident, as are some other paleontologists. So let’s take this conclusion as “likely, but not certain”. Surely further work will either strengthen or weaken Turner’s evidence.

You can access Turner’s paper by clicking on the screenshot below, or downloading the pdf here. The reference is at the bottom of this post.

Investigating the Little Dal Reef Formation in Northwestern Canada, itself a kind of stromatolite, Turner collected rocks between 1992 and 2018, and, in thin sections of those rocks, observed “vermiform” (worm-shaped) microstructures filled with calcite “spar”, or calcium carbonate crystals. These tube-like structures join and divide in a branching network, just like the tubules of modern sponges, some of which have a calcite skeleton. (The tubules of modern sponges allow them to circulate water through their bodies, getting food and oxygen.) These wormlike structures are surrounded in the fossils by a calcite “groundmass”, which may be the external body of the sponge.

Here’s what Turner says about these interconnecting tubules and why she regards them as early sponges:

The shape, size, branching style and polygonal meshworks of the Little Dal vermiform tubules closely resemble both spongin fibre networks of modern keratosan sponges (Fig. 2a–c) and vermiform microstructure either demonstrated or interpreted to be sponge-derived in diverse Phanerozoic microbial, reefal and non-reefal carbonate rocks. The compositional and textural homogeneity of the microspar groundmass supports an origin through permineralization of a pre-existing biological substance, rather than incremental accumulation of detrital sediment or microbial carbonate that passively incorporated complexly anastomosing tubular microfossils. Variable preservation and association with geopetal peloid accumulations are familiar aspects of Phanerozoic sponge taphonomy In previous work, detailed comparison of the three-dimensional characteristics of vermiform microstructure with branching cylindrical organism types yielded no convincing alternative to the sponge interpretation

Here are subfigures (a)-(b) of her Figure 2 showing the fossil network compared to that of a modern sponge (c), with the captions below (click photo to enlarge).

(From Fig. 2 of the paper): a, Well-preserved vermiform microstructure exhibits a polygonal meshwork of anastomosing, slightly curved, approximately 30-μm-diameter tubules embedded in calcite microspar (KEC25). Scale bar, 500 μm. b, Enlarged rectangle from a, showing branching tubules forming three-dimensional polygons intersected at various angles by the thin section; clear calcite crystals, about 10–20 μm in width, fill tubules in groundmass of more finely crystalline calcite (dark grey). Scale bar, 50 μm. c, Three-dimensional fragment of spongin skeleton from a modern keratosan sponge, illustrating its branching and anastomosing network of fibres (incident light). Scale bars, 100 μm (main panel), 20 μm (inset).

There are other pictures as well, but the first two are the heart of the matter. You may not think they look like much, but they do show the interconnecting, ramifying tubules with the light-colored calcite crystals typical of some groups of sponges. The area where these putative fossils are found is 890 million years old.  And these fossils are older than the next oldest and indisputable sponge fossils by 350 million years!

Turner hypothesizes that these early organisms couldn’t compete with the reef-building cyanobacteria, but were able to find “oxygen oases” to use the oxygen produced by the cyanobacteria. The association of these putative sponges with oxygen-producing bacteria may be one piece of evidence that these are indeed metazoans, which of course require oxygen.

As I said, some paleobiologists disagree about whether these are animals. You can hear a ten-minute Nature-sponsored discussion with Turner, some supporters, and some doubters here. I highly recommend that you listen to this short but lucid discussion.

One other point: these organisms must have survived at least one of the periods of extensive glaciation and freezing known as “Snowball Earth“, when the entire planet was either completely frozen or almost covered with ice except for some open water. (The most extensive was between 700 and 600 million years ago.)  In the linked article, author Laura Poppick says this about that period:

What did life on Earth look like at the time, and how did it change as a consequence of these events?

There were certainly bacteria and there were also algae and unicellular primitive animals, or protists.

There is also evidence that the first multicellular animals originated at this time, probably something like sponges.

Well, according to Turner, the first multicellular animals, probably something like sponges, originated nearly 200 million years earlier than this.

Stay tuned to see how the dispute about the nature of these fossils progresses. Are they animals or simply remnants of bacterial activity? As Turner says in the interview, “We are quite confident” that these are spongelike animals. “It’s almost,” she adds, “a no-brainer.”

And here’s Turner in the field:

(From source): Elizabeth C. Turner, geology professor at Laurentian University, conducting geological fieldwork on northern Baffin Island in 2012. (Supplied photo/Laurentian University)

_______________

Turner, E.C. 2021. Possible poriferan body fossils in early Neoproterozoic microbial reefs. Nature (2021). https://doi.org/10.1038/s41586-021-03773-z

Neil Shubin to give prestigious lecture on “Your Inner Fish”

March 23, 2021 • 12:00 pm

The University has just announced that my colleague Neil Shubin, paleontologist, developmental biologist, and author, will be giving this year’s prestigious Ryerson Lecture. Click on the screenshot below for details:

You have to register in advance, and it’s online, but it’s free. Here are the details and the link:

A prestigious tradition celebrating the scholarly work of a UChicago faculty member, the Ryerson Lecture will take place virtually April 20 at 5 p.m CT. The lecture, entitled “Finding Your Inner Fish: Fossils, Genes and the History of Life,” is free and open to the public; registration is now open through this link.

The Robert R. Bensley Distinguished Service Professor of Organismal Biology and Anatomy, Shubin is known widely for his evolutionary work including the groundbreaking discovery of Tiktaalik roseae, the 375-million-year-old fossil considered a missing link between fish and all animals on land, including humans.

After you register (all that’s needed is your name, email address, and “do you plan to attend this lecture”—a weird question), you get a note that you’ll receive an email link to the talk on Monday, April 19—the day before.

Be there or be square!

Readers’ wildlife photos

January 21, 2021 • 8:00 am

These photos come from Robert Seidel, whose notes (and the Biblical quote) are indented. Click the photos to enlarge them.

“In my distress I called to the LORD; I called out to my God. From his temple he heard my voice, and my cry for help came to his ears. – 2 Samuel 22:7”

In that vein, allow me to offer you some wildlife images, mostly of fossilized wildlife. I saw your review of the movie Ammonite early last month [JAC: here], which by co-incidence was right before I spent a weekend at Lyme Regis on the Jurassic coast of South England, where Mary Anning used to live and work and the film is set. My photos and notes:

Sunset at Lyme Regis harbour. The breakwater you see features in several films, including I believe Ammonite, as well as Jane Austen’s Persuasion.

View from top of the breakwater out to sea. I like how the stones and waves blend together in this picture.

The cliffs to the East of Lyme Regis. These are not your perfect white chalk cliffs of the Dover type, but rather more messy, with alternating layers of tough limestone and soft siltstone.

The beach in front of the cliffs, looking quite prehistoric in my opinion. This is a tidal beach which is submerged under high water. If you go out towards the East, you should take to heart the frequently posted warnings about the danger of getting cut off by the tide!

A tidal pool on the beach. Sea snails like to burrow into the soft siltstone, making it look like swiss cheese.

To the West of Lyme Regis lies Monmouth Beach, named after the ill-fated Duke of Monmouth, who in 1685 landed at this point with an invasion force in an attempt to take the English throne (). Ammonites like this are ever present along that beach.

A very large ammonite, about a foot in diameter. Smaller ammonites got washed into the empty shell as it lay on the sea floor. At the nearby town of Charmouth, there is a small museum with some fantastic specimen of such “graveyards”.

The famous “ammonite pavement” of Monmouth Beach, just a few hundred meters walk from Lyme Regis. These should be Arietites bucklandii.

Bonus photo. There is an alternative feline theory about the origin of these structures. These are four out of five of my partner’s cats. From front to back: Simba, Bella, Tonto and Katie.

Readers’ wildlife photos

January 2, 2021 • 8:00 am

Send in your wildlife photos!

Today’s contribution comes from reader Gregory Zolnerowich, and it’s an unusual one: dinosaur footprints! His captions are indented; click on photos to enlarge them.

I’ve attached some scenic photos of the Picketwire Canyonlands south of La Junta, CO. This network of canyons is part of the Comanche National Grasslands, and a group of kayaking compadres and I camped and hiked Withers Canyon to see dinosaur footprints during the weekend of December 4-6, 2020. All the photos were taken with my iPhone.

The surrounding countryside is pretty flat shortgrass prairie and there was snow on the ground. Days were in the mid-50s and night temperatures fell into the upper 20s. This was my first time camping with snow on the ground and I was glad I’d invested in a good down sleeping bag.

The day of the hike was sunny with clear blue skies, perfect for hiking. The campground is at the rim of the canyon and the well-marked trail descends to the floor of the canyon. The round-trip hike to the dinosaur tracks and back is a little over 11 miles.

This cottonwood tree looks like it has had a tough life, and we wondered how old it was.

A petroglyph that looks like a hand, and something abstract. Petroglyphs in the canyon date from 375-4,500 years old. No one knows what they signify and I wonder if some of them were just teenage graffiti. One of the petroglyphs reminded me of the Trix rabbit that appears in television commercials.

The Dolores Mission and a small cemetery that served a group of Catholic families who lived in the canyon around 1900.

Cast of an Apatosaurus shoulder blade.

The Purgatoire River; the dinosaur tracks are along both banks.

Allosaurus and Apatosaurus tracks, which were pretty cool to see. Excavating for additional tracks is still taking place.

The most challenging part of the hike was the ascent back to the top of the canyon. Since we were in the Mountain Time Zone in December, it was totally dark at 4 pm and we wanted to be sure to be back before sundown. A hot meal and a warm campfire were a nice ending to the day.

Jennifer A. Clack, 1947-2020

December 22, 2020 • 9:30 am

by Greg Mayer

Jennifer A. “Jenny” Clack,  Emeritus Professor and Curator of Vertebrate Palaeontology in the University Museum of Zoology, Cambridge, died on 26 March of this year. Jenny, as she was universally known, was one of the leading paleontologists of the past half century, making fundamental discoveries about the origin of tetrapods, and training, through her students and postdocs, many of the current generation of leaders in the field. The cause of her death was cancer.

Jenny Clack in 2009, at her election to Fellow of the Royal Society. Photo by Angela Milner.

After completing her undergraduate work in zoology at the University of Newcastle in 1970, Jenny took a certificate in museum studies at the University of Leicester, and then worked for several years in local museums. It was during this time that she began studying the specimen of the Carboniferous amphibian Pholiderpeton, which led to the Ph.D. thesis for which she returned to the University of Newcastle, taking her degree in 1984 under the supervision of her old undergraduate teacher, Alec Panchen.

Even before finishing her degree, Jenny took a position in the University Museum of Zoology, Cambridge, where she remained until her death, eventually rising to Professor and Curator. At Cambridge, she found unstudied material of the ‘co-first’ tetrapod, Acanthostega, collected by a Cambridge expedition to Greenland in 1970. It was study of these important specimens that led to Jenny’s most important and influential work, on the origin of tetrapods from their piscine (fish) ancestors. Jenny led two expeditions to collect more material in Greenland, in 1987 and 1998, revisiting the sites at which earlier specimens had been collected, and gathering new material not just of Acanthostega, but of the other ‘co-first’ tetrapod, Ichthyostega, which prior to Jenny’s work had been the better known of the two. Jenny and her colleagues, in addition to the material at Cambridge or newly collected, were able to study Erik Jarvik‘s Ichthyostega material in Stockholm.

“Grace”, an Acanthostega specimen studied by Jenny Clack and her colleagues.

Along with work by others on other forms (such as Tiktaalik and Panderichthys), Jenny’s work on these earliest tetrapods has made the fish-amphibian transition one of the best understood of all transitions between higher taxa (although much is still to be learned!). Jenny summarized the work of her and her colleagues in Gaining Ground: the Origin and Evolution of Tetrapods (Indiana University Press, Bloomington, 2002; 2nd edition 2012). Jenny also worked on a number of other related issues in vertebrate evolution–including the evolution of the ear, faunistic works, and Carboniferous fishes, to name a few–but she will be best remembered for her work on the transition from water to land, and especially the transition from fin to limb.

In addition to her scientific work, Jenny was actively involved in outreach to the general public, in which she conveyed the wonder, interest, and importance of her discoveries. She appeared in numerous video and television programs, including Nova’s The Missing Link (2002), in which she was referred to as the “Diva of the Devonian”; was a featured scientist in the PBS program based on Neil Shubin’s work, Your Inner Fish (2014); and was the subject of an episode of Beautiful Minds (2012) on the BBC. Here’s a short video from Cambridge University (which I could embed; another nice, short, video, The First Vertebrate Walks on Land (2001), which I could not embed, can be seen on Shape of Life, an educational website).

Jenny received many honors in her lifetime, including being elected a Fellow of the Royal Society (2009), the Daniel Giraud Elliot Medal of the National Academy of Science (USA 2008), membership in the National Academy of Sciences (USA 2009) and the Royal Swedish Academy of Science (2014), honorary doctorates from the University of Chicago (2013) and the University of Leicester (2014), and an ScD from Cambridge (a “higher” doctorate, not an honorary degree).

Last year, Jenny was honored by her colleagues, students, and collaborators with a festschrift, “Fossils, Function and Phylogeny: Papers on Early Vertebrate Evolution in Honour of Professor Jennifer A. Clack”, published in the Earth and Environmental Science Transactions of The Royal Society of Edinburgh.

Memorial notices and recollections have appeared by Tim Smithson in the Guardian, Per Ahlberg in Nature, Darren Naish at Tetrapod Zoology, and from her colleagues in the Cambridge Department of Zoology. I have drawn from these sources, Jenny’s own website, and the paper by Marcello Ruta, Per Ahlberg, and Tim Smithson in the Edinburgh festschrift for many of the facts above.

I found out about her death only about a month ago (perhaps part of my pandemic disconnect from the wider world–I spent most of three months at a poorly lit table in my basement). While reading her latest paper (published in November), I was shocked to notice the notation “Deceased” among the authors’ addresses. I could not think of who it could be. Two of the other authors were known to me–Tim Smithson, Jenny’s long-time colleague, and Stephanie Pierce, curator of vertebrate paleontology at the Museum of Comparative Zoology; the senior author turned out to be a recently minted Ph.D. student of Pierce’s–and, looking more closely, I saw that it was Jenny. A Harvard Gazette article provides a layman’s account of that latest paper, a functional analysis of the humeri (upper arm bones) of early tetrapods and close relatives. (The tetrapods’ piscine ancestors already had humeri.)

Jerry and I both followed her work. I taught a special topics seminar on her book, Gaining Ground, when the second edition came out in 2012, and I attended a symposium on “The Origin and Diversification of Stem Tetrapods” she organized at the Society of Vertebrate Paleontology meetings hosted by the Field Museum in 1997. I don’t think we ever met, either then or at some other meeting we might both have attended, but she was such a lively personality on the Your Inner Fish documentary series on PBS that I feel that I know what it would have been like to meet her.


Clack, J. A. 1987. Pholiderpeton scutigerum, an amphibian from the Yorkshire Coal Measures. Philosophical Transaction of the Royal Society of London B 318:1–107. pdf (Her Ph.D. work.)

Clack, J.A. 2012. Gaining Ground: The Origin and Evolution of Tetrapods. 2nd ed. Indiana University Press, Bloomington. (First edition published in 2002.)

Dickson, B.V., J.A. Clack, T.R. Smithson, and S.E. Pierce. 2020. Functional adaptive landscapes predict terrestrial capacity at the origin of limbs. Nature in press. pdf

Royal Society of Edinburgh. 2019. Fossils, function and phylogeny: Papers on early vertebrate evolution in honour of Professor Jennifer A. Clack. Earth and Environmental Science Transactions of the Royal Society of Edinburgh 109(1-2):1–369.

Ruta, M., P.E. Ahlberg, and T.R. Smithson. 2019. Fossils, function and phylogeny: Papers on early vertebrate evolution in honour of Professor Jennifer A. Clack – Introduction. Earth and Environmental Science Transactions of the Royal Society of Edinburgh 109:1–14. pdf

Five movies about lesbians, with a brief review of “Ammonite”

December 6, 2020 • 10:00 am

Yesterday I watched the new movie Ammoniteloosely based on the life of Mary Anning (1799-1847), famous as one of the first women paleontologists and fossil collectors, as well as an influential scientist whose ambit was limited because of her sex. Anning found some of the best pterosaur and plesiosaur skeletons known, though details of her private life are sketchy. Ammonite attempts to fill in those details by confecting a romance between Anning and a rich London lady put out to apprentice with her, a completely made-up story for which there’s not a scintilla of evidence. But never mind—it’s fiction, Jake.

I realized, after I watched the movie, that it was one of five good movies I watched in the last year about lesbian relationships. All are worth watching, and in all of them (and I’ll try not to give spoilers), a married/betrothed woman falls in love with a lesbian, and lives get overturned.

Here are the movies in order of when they were made. After a brief review of Ammonite, I’ll rank them from best to worst and show the official trailers. But I think all are worth watching (except perhaps Ammonite, which, despite its star power, isn’t that great, but certainly better than the comic book/sci fi/chase movies that dominate the screen):

Carol (2015), starring Cate Blanchett and Rooney Mara
Disobedience
(2017), starring Rachel Weisz and Rachel McAdams
My Days of Mercy (2017) starring Ellen (now Elliot) Page and Kate Mara
Portrait of a Lady on Fire (2019), starring Noémie Merlant and Adèle Haenel
Ammonite (2020), starring Kate Winslet and Saoirse Ronan

I’m not a professional critic, so all I can do is give a layperson’s take on Ammonite. very brief plot summary, with a little bit of a spoiler: Mary Anning (played by Kate Winslet), who lives with her mother in Lyme Regis, is a solitary and dedicated woman, collecting and selling fossils on the Jurassic coast. A gentleman drops into her shop to buy a fossil and then asks to follow her around and watch her work, for a fee. Anning, unwilling to have her routine disrupted, refuses.

The man returns with his wife, Charlotte Murchison (played by Saoirse Ronan), asking Anning to help relieve her malaise (perhaps caused by a miscarriage) by letting Charlotte apprentice with her instead, for Charlotte has been prescribed quiet and sea air. After Charlotte collapses, Anning takes her in and, gradually, teaches her the way of fossil collecting. Slowly, the women fall in love and then have sex, depicted rather graphically. After a month or so, Charlotte’s “rest cure” is ended and her husband summons her back to London.

Charlotte, unable to live without Anning, asks her to London, intending Charlotte to live with her and her husband, something Charlotte doesn’t know when she visits. Dedicated to her work as always, Anning turns down the live-in offer, but the ending is ambiguous—and that’s all I’ll say. (I’ll add, though, that, save for one of the movies, the endings of all these films are ambiguous.)

Of all the movies in the list above, Ammonite is to me the least satisfying. For one thing, it gives short shrift to Anning’s paleontological work. Yes, it shows her striding the shores near Lyme Regis, and finding and preparing fossils, but says little else about her science save a few-seconds shot of one of her fossils being labeled with a credit to a man.  To a scientist, at least, the dearth of science in the movie is disturbing. And I’ll add that it should be disconcerting to others, too, for, after all, why should we care about Mary Anning?

For if she was not the famous paleontologist she was, this would be a rather slow-moving and unengaging story of a romance. Given the dour personality portrayed by Winslet, there are few sparks, and while the sex scenes are, let us say, “vigorous,” one doesn’t feel drawn into the romance. The passion between the women, aside from the sex, seems laid on rather than growing from the story itself. That the romance is a fictional one doesn’t help, either.

Granted, both Winslet and Ronan are superb actors (both are Oscar nominees, with Winslet winning one), and give creditable performances; but the almost psychotic nature of new love, evident in the other four films, is missing. That’s what I mean by lack of “spark”. Perhaps British lesbians in the early 19th century were, in private, subdued in this way, but I can’t bring myself to believe that. Love is love, and should be even more passionate when it’s forbidden.

So that’s my brief review. Yes, see the movie, but don’t expect to be blown away. I’d put it at the bottom of my ranking of the five movies above. Here’s my ranking of all five from best to worst.

Portrait of a Lady on Fire.  I may be the odd person out here, but I think this movie is a masterpiece—one of the best I’ve seen in quite a few years. I wrote a brief review here.

Carol

Disobedience (perhaps ranked too highly because it’s about Orthodox Judaism and thus has a special interest for me. It’s not far behind Carol.)

My Days of Mercy

Ammonite

And here are the trailers for all the movies, with two for Ammonite.  If you’ve seen any of these movies, please weigh in below.

Ammonite:

Disobedience:

Portrait of a Lady on Fire:

Carol:

My Days of Mercy:

 

A genomic and evolutionary analysis of an extinct saber-toothed cat

October 18, 2020 • 1:00 pm

A recent article in Current Biology, which you should be able get for free by clicking on the screenshot below, describes sequencing the entire genome of an extinct saber-toothed cat, thereby gaining some insight into its evolutionary history. (You can get the pdf here, and the full reference is at the bottom. If you can’t see the piece, make a judicious inquiry.)

The cat is Homotherium latidens, also known as the European saber-toothed cat (it’s also called a “scimitar-toothed cat” because its teeth were smaller than true sabertooths like Smilodon), and it probably lived from a few million years ago until fairly recently (the late Pleistocene, about 12,000 years ago). It may thus have encountered modern humans. It was about the size of a male African lion, and a reconstruction from Prehistoric Fauna looks like this (note the saber teeth and very short bobtail).

The species was also widespread: as the article below notes, “it once spanned from southern Africa, across Eurasia and North America, to South America, arguably the largest geographical range of all the saber-toothed cats.” Although it was clearly a hunter, like all sabertooths, we know nothing about its social life, or whether it was social—nor about whether it hunted by day, night, or twilight (“crepuscular”). Some of these issues were addressed by the authors using the DNA sequence.

Click to read:

The data come from a single specimen found in the Yukon and in the possession of the Yukon Government paleontology program. A section of humerus was used for dating (the fossil was about 47,000 years old), and then was crushed up to extract DNA. The authors were able to get a substantial amount of sequence from the bone, and they compared that sequence to DNA taken from living lions, sand cats, fishing cats, leopard cats, and caracals.

The conclusions about where this cat fits on the evolutionary tree of felids are pretty sound, based as they are on lots of DNA sequence. However, the conclusions about what genes may have propelled its evolution are a lot more speculative. Here are the main conclusions.

1.) The species was long diverged from the lineage that led to modern cats.  The lineage that led to this species diverged from that of all living cats a long time ago: about 22.5 million years. We knew of this substantial age from mitochondrial DNA sequencing in previous work, but it’s dicey to make conclusions about family trees from mitochondrial DNA alone. The date above is one that we can rely on, though, as it’s based on DNA divergence in the whole genome that’s been calibrated from the fossil record.

Here’s the deduced phylogeny, showing where H. latidens (in red) fits in with 17 cats and two hyenas. You can see that it diverged from living cats over 20 million years ago.

2.) There doesn’t seem to have been much hybridization between this species and the ancestors of living cats, which began diverging from each other about 14 million years ago (see phylogeny above). The authors could have detected such hybridization by finding sections of the genome that were discordant in divergence from living cats—perhaps sections of DNA that got into the saber-toothed tiger from species after the divergence of modern cats about 14 million years ago. That is, most genes would show similar amounts of divergence from the same genes in the modern-cat lineage, but a few would be much less diverged, suggesting that those genes got into the H. latidens genome after hybridization with cats that diverged much later.

They didn’t find any such discordance, suggesting that H. latidens simply didn’t hybridize with cats that evolved in the last 14 million years. For some reason this absence caused a lot of consternation for the authors.  I guess they expected to find some evidence of hybridization and “introgression” (transfer of genes between species after speciation had occurred), and they go on at great length to speculate about this absence. They mention things like low population density (so members of different species don’t meet), ecological or behavioral isolation, and so on. But the most obvious possibility, which they don’t mention, is simply that speciation between the scimitar cat and its relatives had been completed by the time they encountered each other, so that no gene flow was possible. Yes, sometimes reproductive barriers are complete, as they are now between our own species and every other species on the planet.  And this is true for lots of species. Just because hybridization is more common than we thought doesn’t mean that nearly every species occasionally exchanges genes with others.

3.) The authors found genes in the H. latidens genome that apparently underwent natural selection. The way geneticists judge this is to look for which regions of a gene have changed relative to the genes of its relatives. This is expressed in what’s called the dN/dS ratio. That ratio gives the frequency of evolutionary changes in “non-silent” parts of proteins (dN: those parts where a mutation changes the protein sequence of the gene) to the changes in “silent” parts of genes (dS: those parts where a mutation is in a noncoding part of the gene or in a third position of a “codon”, where a mutation doesn’t usually change the protein sequence).

If genes just change randomly, without selection, this ratio should be about one. If the ratio is higher than one, protein sequences are changing faster than they would under a “neutral” process in which no changes in the gene alter its effect on reproduction (“fitness”). The authors used a cutoff ratio of dN/dS of between 2 and 5 as a criterion for selection, and they found 31 genes in this range out of the 2,191 analyzed. Eighteen of these genes, potential targets for selection in this cat, are shown in the diagram below (They don’t mention what the other 13 genes do.)

You can see they fall into four general classes, and into subclasses as well, like genes affecting vision fitting into the the “diurnal” class. The authors note that while dN/dS ratios are only suggestions of what genes in the lineage of this species may have been subject to positive natural selection, they do speculate at length about the form of selection. The cats, for example, could have been selected to adapt to daylight hunting (as opposed to most cats), with consequently improved vision. Selection on “endurance” genes may have facilitated “cursorial” hunting (i.e., running down prey). And there may have been positive selection on genes known to involve social behavior—in mice. From that they speculate that this cat may have become more social and thus able to hunt down big prey in groups.

I call this kind of speculation “genomic sociobiology”, because it involves making up “just so” stories about how genetic change impacted an extinct creature. It’s fine to single out genes like this for further examination, but one has to realize that if you see selection acting on a gene affecting social behavior, for instance, it could be reducing social behavior instead of increasing it. How do we know that the ancestors of this cat weren’t social, but then there was selection on those genes to reduce sociality in favor of a more solitary lifestyle? Ditto for all the other genes. That is, showing selection itself, even if these ratios do show selection, doesn’t mean you know the direction of selection. In fact, some media outlets, like this one, have bought uncritically the notion that this study has revealed that the cat evolved to become more social.

4.) This individual, and thus its species, was very genetically diverse. That is, if you looked at the two copies of a gene in the H. latidens genome—remember, we all carry two copies of nearly all our genes except for those on mitochondria and sex chromosomes in the heterogametic sex—there was a high probability that they would be different. This “heterozygosity” would not be the case if the species were in small populations that would lose genetic variation, or in an inbred species. We can conclude that the species was genetically diverse—no surprise given how wide ranging it was.

As to why H. latidens went extinct, well, we just don’t know. Given its genetic diversity, it probably wasn’t inbreeding, and could have been stuff like competition with cats that were better hunters, a disease or parasite, climate change, or any number of things.

Overall, this is a decent paper, and a good one insofar as doing whole-genome sequencing and phylogenetic analysis of a long-extinct species. The conclusions about natural selection are speculative, and the authors realize that. If there’s a flaw in the paper, I think it’s that the authors do go on too long with the natural selection business, especially given that it’s purely guesswork based on ratios of substitutions in DNA, and because we’re totally ignorant about what these genetic changes really meant for the evolution of these cats.

Oh, and I’m disappointed that they didn’t see positive selection in “tooth genes”!

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Barnett, R., M. V. Westbury, M. Sandoval-Velasco, F. G. Vieira, S. Jeon, G. Zazula, M. D. Martin, S. Y. W. Ho, N. Mather, S. Gopalakrishnan, J. Ramos-Madrigal, M. de Manuel, M. L. Zepeda-Mendoza, A. Antunes, A. C. Baez, B. De Cahsan, G. Larson, S. J. O’Brien, E. Eizirik, W. E. Johnson, K.-P. Koepfli, A. Wilting, J. Fickel, L. Dalén, E. D. Lorenzen, T. Marques-Bonet, A. J. Hansen, G. Zhang, J. Bhak, N. Yamaguchi, and M. T. P. Gilbert. 2020. Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens. Current Biology.

New report: Bacteria can remain alive for over 100 million years!

July 30, 2020 • 10:00 am

Well cut off my legs and call me Shorty (is that ableist?). A new report in the journal Nature Communications shows that some bacteria can remain dormant for over 100 million years in marine sediments—an unbelievable amount of time for an organism to remain “alive”—if you call it “alive.” I do: after all, the bacteria collected and revived by the researchers retained their ability to metabolize, take up labeled organic substances, and reproduce.  Dormancy, to me, at least, is not the same thing as “death”.

Click the screenshot to read the paper (the pdf is here and the full reference is at the bottom).

The experiment was laborious yet the results are simple. If you want to know the gory details, the paper is there for your reading.

In short, the authors sampled clay sediments of different ages from the South Pacific Gyre, and did so in a way that, they aver, precluded contamination with modern bacteria. Supporting their claim that the bacteria they found in the inside of sea-floor cores were really bacteria in situ, they argue that the clays are almost impermeable to bacteria, with very low pore size, and there are thick impermeable layer above the sampled sediments. And there were strict precautions to prevent contamination.

To see if any bacteria in the sediments were capable of biological activity including reproduction, they tested for “anabolism” (the synthesis of molecules) by incubating the bacteria with oxygen (controls lacked oxygen) as well as radioactively labeled molecules that could be taken up and made into proteins and other molecules. The added molecules included 13C6-glucose, 13C2-acetate, 13C3-pyruvate, 13C-bicarbonate, 13C-15N-amino acids mix [mixture of 20 Amino Acids], and 15N-ammonium. Another control involved killing any bacteria with formaldehyde.  The researchers could then visualize the bacteria and see, through fluorescence microscopy and radioactive visualization, if the precursor molecules had been taken up by bacteria.

Finally, the researchers could isolate bacteria at various times (the samples for activity, growth, and bacterial presence were taken at 3 weeks, 6 weeks, and 18 months) to see if the bacterial titer was increasing, i.e., they were dividing. Finally the authors isolated RNA (16S rRNA) from individual bacteria, amplified it, sequenced slow-evolving RNA, and saw what groups of living bacteria the ancient bacteria belonged to. (This assumes that we can still recognize the groups from modern sequences, but these molecules evolve very slowly).

The upshot:

1.) The aerobic bacteria (bacteria that require oxygen) were still viable, initiating metabolism and reproduction even in sediments as old as 101.5 million years. Anaerobic bacteria, which don’t require oxygen, didn’t do nearly as well, and the authors suggest that even low oxygen concentrations in the sediments over geological time simply kills anaerobic bacteria.

Here’s a figure from the paper showing photos of the bacteria, with the same bacteria then examined for uptake of added molecules. The caption is complicated, but you can see that, especially with added amino acids (and oxygen), the cells glow furiously (d and h are electron-microscope images of the same bacteria shown fluorescing in the rows).

(from paper): Cells from incubations of U1365 9H-3 with 13C-bicarbonate and 15N ammonium (a–d) and 13C,15N-Amino acid mix (e–h). (a, e) SYBR Green I-stained cells under fluorescence microscopy. b, c, f, g Ratio images of 13C/12C (b, f) and 12C15N/12C14N ratios (c, g) of the same regions imaged in a, e, demonstrating locations of 13C and 15N incorporation. Color-scale ranges of the ratios are shown as numbers appearing at top and bottom of the color bar. The background membrane region, which is identified by fluorescence images, is excluded from the ratio calculation and shown as black background. d, h. Secondary electron (NanoSIMS) images of the same regions in a, e. Bars represent 5 µm. Similar images were processed for obtaining the dataset (Supplementary Data 1) of substrate incorporations for 6986 individual cells.

2.) The bacteria divided, as measured by the increase in numbers over time in the samples.

3.)  Anaerobic bacteria were much harder to find metabolizing than aerobic bacteria. The former were effectively defunct.

4.) The lineages of bacteria identified as persisting in the sediments, judged from sequencing them and comparing the 16S rRNA to modern samples, include ActinobacteriaBacteroidetesFirmicutesAlphaproteobacteriaBetaproteobacteriaGammaproteobacteria, and Deltaproteobacteria, and cyanobacteria (“blue-green algae”). It would be interesting to compare the sequences of these early species with their modern relatives to see exactly how much and what kind of evolution has gone on.

5.) How did they survive? One thought was that they formed dormant spores, which can last a long time in bacteria. But this suggestion is ruled out because none of the bacteria identified were from spore-forming lineages. It seems the bacteria simply became dormant, surviving without any—or hardly any—detectable metabolism, and without reproduction.

This raises the question: were these things really alive for 101.5 million years? I can’t see why not, unless you think that something that becomes dormant is dead, and then, Lazarus-like, revives when the dormancy is broken. If you take the authors’ word that sufficient precautions were taken to prevent contamination with modern bacteria, then what we have here are the oldest living organisms on Earth.

h/t: Jeremy

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Morono, Y., Ito, M., Hoshino, T. et al. Aerobic microbial life persists in oxic marine sediment as old as 101.5 million yearsNat Commun 11, 3626 (2020). https://doi.org/10.1038/s41467-020-17330-1

A tiny 10-cm dinosaur that ate bugs

July 29, 2020 • 9:00 am

Note: The classification of “dinosaur” above isn’t totally accurate, for the creature discussed below is an archosaur, a member of the group that gave rise to dinosaurs, pterosaurs, and crocodilians. But we might as well call it a dinosaur, as few people know what an “archosaur” is.

The ancestors of the dinosaurs could not have been big, for they evolved from amphibians, and amphibians, for a number of reasons, are limited in size.  But this new paper in PNAS shows that some of the earliest ancestors of dinos were very small—not just small, but tiny. The new species described below, which falls into a group that later diverged into pterosaurs (flying reptiles) and the dinosaurs, was only 10 cm tall, the distance between my index fingers in the photo below:

Click on screenshot to read the paper; the pdf is here, and reference at bottom of post.

The partial skeleton of this tiny creature, whose dentition suggests it ate insects, was discovered in 1998 in Southwestern Madagascar. Although the age of the specimen is a bit uncertain, a good estimate is about 237 million years.

Here are some drawings of the parts of the skeleton they recovered, including leg bones, a forearm bone, and the jaws (interpreted as coming from single individual), and a figure showing where they fit into the body (figure F). The size, estimated from the bones, which clearly put the species in the ancestral group Ornithodira (also known as Avemetatarsalia), show that the creature was only about 10 cm tall. It must have been really cute: a pet-sized reptile. Note that the length of the scale bar on the left, showing the femurs, is one centimeter (about 4/10 of an inch), while on the right the scale bar for the jaws is only about 40 mm (1.6 inches):

(from paper): Anatomy of the femur and maxilla of Kongonaphon kely gen. et sp. nov. (UA 10618). (A) Right femur in anterolateral, (B) posteromedial, and (C) proximal views. (D) Right maxilla in right lateral and (E) palatal views. (F) Preserved elements in the holotype, UA 10618, presented in a silhouette of Kongonaphon. aof, antorbital fenestra; at, anterior trochanter; fht, tip of femoral head; fp mx, facial process of maxilla; ft, fourth trochanter; mx f, maxillary foramen; pf, palatine fossa; pmt, posterior medial tubercle; t, maxillary tooth. Illustrations credit: American Museum of Natural History/Frank Ippolito.

The authors named the fossil Kongonaphon kely, meaning “tiny bug slayer”. They explain the etymology:

. . . derived from kongona (Malagasy, “bug”) and φον (variant of ancient Greek φονεύς, “slayer”), referring to the probable diet of this animal; kely (Malagasy, “small”), referring to the diminutive size of this specimen.

The teeth, as you can see in the drawing above, were simple ones: conical and without serrations. That suggests that the creature lived on insects (I used “bug” in the title as a generic word for insects, though technically, bugs are in the order Hemiptera). The estimated size of 10 cm comes from the size of the preserved femur, which is only about 1.6 inches long. The specimen wasn’t a juvenile, as the authors saw signs of arrested growth in the fossil bones. The bones also indicate strongly that K. kely was bipedal, like T. rex and the theropods.

To place this individual in the phylogeny of dinosaurs and their ancestors, the authors did a computer analysis of 422 characters derived from these bones, and K. kely fell out in group B of the phylogeny below, which includes the dinosaurs and the pterosaurs (the relative size of this tiny species is shown to the right). I’ve put a box around K. kely.

B is the base of the Ornithodira, the group that gave rise to all dinosaurs and pterosaurs, and you see that K. kely is an early (“basal”) member of this group

(from paper): Body size of early avemetatarsalian (bird line) archosaurs mapped onto a consensus supertree, based on the current phylogenetic analysis (SI Appendix) and recent analyses (22). Silhouettes are scaled to estimated femoral lengths for the labeled nodes (SI Appendix, Table S1): A, base of Avemetatarsalia (represented by Teleocrater); B, base of Ornithodira (represented by Ixalerpeton); C, base of Dracohors (Silesauridae + Dinosauria) (represented by Silesaurus); and D, base of Saurischia (represented by Herrerasaurus). Silhouettes credit: Phylopic/Scott Hartman/Mathew Wedel, which is licensed under CC BY 3.0. Silhouette of Kongonaphon to the right of the taxon label is to scale.

Here’s a reconstruction of K. kely, eyeing a beetle, from Science Alert;  (artist’s impression by Alex Boersma):

Now the diminutive size of this creature doesn’t mean that the common ancestor of all dinos and peterosaurs was this small. But it does imply that the ancestor of those groups, which falls out in a “reconstruct-the-size” analysis, was smaller than we thought. K. kely itself could have been the result of a “miniaturization event” in which a somewhat larger ancestor produced some tiny descendants. The estimated size of ancestral Ornithodiran  is estimated fo be about 13.3 cm, or about 5.3 inches tall, and the ancestral species of the Dinosauromorphs, which includes dinos and birds but not pterosaurs, is even smaller, about 6.5 cm (2.5 inches)!

What are the implications of this beyond showing that the ancestral dino and ancestral dino/pterosaur were likely a lot smaller than we thought? Well, first of all, we have no idea why these early creatures were so small. My own guess is that since insects had already evolved, there was an “open niche” to specialize in eating them, and if you want to make a living as a terrestrial reptile eating insects, you can’t be the size of a T. rex.

The authors note that the small size of this species (and probably its close relatives) accounts for the absence of ornithodirans in Early and Middle Triassic faunas, for small creatures have tiny, fragile bones that aren’t easily preserved. In fact, our best knowledge of early Ornithodirans previously came from sediments in Argentina whose nature allowed for the preservation of small animals.

Finally, the authors speculate that these small species would have a problem with heat retention, since they were ectothermic (“cold blooded”). Small creatures have a higher surface area/volume ratio than larger ones, which means more heat lost by radiation. Thus, suggest the authors, the filaments covering the bodies of some dinos and pterosaurs—which might have been homologous to feathers that eventually covered the theropods—would have been useful as insulation. This sounds good, but of course there are plenty of extant small insect-eating reptiles, like geckos and anoles, that make a fine living without feathers. But it would still be useful to look at these early, small species to see if there is any evidence for filamentous body cover.

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Kammerer, C. F., S. J. Nesbitt, J. J. Flynn, L. Ranivoharimanana, and A. R. Wyss. 2020. A tiny ornithodiran archosaur from the Triassic of Madagascar and the role of miniaturization in dinosaur and pterosaur ancestry. Proceedings of the National Academy of Sciences 117:17932-17936.

 

Photographs of readers

June 7, 2020 • 2:30 pm

Today’s reader photos come from Bruce Thiel, whom I met at a talk I gave in Portland, Oregon. And there he gave me one of his fantastic preparations of fossil crabs, which I cherish and keep on my mantelpiece. You can see his preparations in his “reader’s photos” here. They are fantastic.  Bruce’s words are indented.

Here I am removing matrix from a Cretaceous Avitelmessus crab from North Carolina, using a pneumatic air chisel.  After 120 hours of work, the crab is still unfinished –including 40 hours work by two previous owners.  The two crabs on the right (#13) were given to the Smithsonian Natural History Museum and on display in the “Deep Time” Exhibit which reopened last summer after a five-year remodel.  A third crab also on display is not pictured.

What started out as a retirement hobby turned into an obsession to search for crab-bearing concretions in the 30-50 million year old ocean sediments in the Pacific NW.  Refining my technique led to the challenge of seeing if I could free the claws from the rock to create more sculptural poses.  However crabs are prepared exactly as they fossilize with no “rearrangement” of claws for aesthetics.

The top second-to-the-left crab in the second picture is noteworthy in that it hosts several 33-35 MYO tube worms. Two other tube-worm infested crabs were sent to Kent State where they were studied, published and donated to the Rice NW Museum of Rocks & Minerals here in Oregon.

While hunting for fossil crabs, I stumbled upon three concretions containing bones of a large penguin-like flightless bird, a Plotopterid, that turned out to be a new genus and species, published and named Olympidytes thieli, given to the Senckenberg Museum, in Frankfort, Germany.
See more crabs and info about the prep process at: https://whyevolutionistrue.com/2014/09/21/readers-wildlife-photos-100/