My synapsid family

Nice image to illustrate a basic cladistic principle. I still get whines from creationists complaining that I said we humans are fish — but that’s just a bigger circle enclosing everyone in this image.

I have no illusions that this will ever sink into the brains of the people who deny it.

…cut off their tails with a CRISPR knife…

Brachyury (Greek for “short tail”) is an important protein in animal development — it’s found in all chordates and is expressed along the midline, and sets up the anterior-posterior axis. It seems to play an essential role in defining tissues along the length of the animal, and many mutations have been found in the gene TBXT for it that cause defects in the spinal cord. In addition to the short tail phenotype it’s named for, different variants affect other regions as well. For instance, you probably know that almost all mammals have precisely 7 cervical vertebrae, but there is a mutation in TBXT that reduces that number to 6.

So, basically, if you want to profoundly muck up the developing vertebrae and spinal cord, mutating TBXT is a way to do it, as long as you don’t mind inducing neural tube defects, like say, spina bifida. It’s a dangerously significant gene to tinker with, and most of the outcomes would not be good. But note — humans and other hominoids have an inherited, ubiquitous spinal cord defect. We don’t have tails, unlike other mammals. Could we be carrying a mutation in our TBXT gene? Could that be what caused all us apes to lose our tails? Maybe we should look and compare our TBXT to that of other animals. Huh, what do you know…we do have a curiously broken TBXT.

A little background first. Eukaryotic genes are broken up into segments called exons alternating with other segments called introns. To make a functional gene product, like Brachyury, the cell has enzymes that cut out the introns from the RNA and splice together the exons. The intronic RNA is then generally allowed to be broken down and recycled. So TBXT has 7 exons, E1, E2, E3, E4, E5, E6, and E7, with intervening introns which must be snipped out and the exons spliced together to make a final, complete RNA, E1-E2-E3-E4-E5-E6-E7, which will be translated to make the Brachyury protein.

Another complication: there are these short bits of selfish DNA called Alus which are scattered throughout the genome. We have over a million Alu elements sprinkled throughout, and usually they do nothing, although if an Alu gets inserted into an exon of a gene, it can disrupt the function of that gene. The good news: there is no Alu stuck in the exons of TBXT. There are a couple of them in the introns of TBXT, but remember, the introns get chopped out and thrown away, so they shouldn’t matter. Except that in this case, they do.

In us hominoids, there is one Alu, AluSx1, in intron 5. There is another Alu, AluY, in intron 6. They happen to complement each other in reverse, so in the TBXT RNA, before the introns are edited out, the RNA folds over to make a loop that allows the two Alus to bind to each other. This messes up the editing, because the cell then snips out the introns and the loop, throwing away exon 6. Uh-oh. That means that instead of producing the full length TBXT, we make a shortened version lacking exon 6, called TBXT-Δexon6.

This observation was tested with a couple of nifty experiments. First question: is it really the Alus that are causing this error in splicing? Yes. Doing a little gene editing and knocking out either Alu in human embryonic stem cells causes them to generate full length TBXT transcripts. These are just single cells in a dish, and while you might be curious to know if deleting those specific Alus in a human embryo would lead to it developing a tail, that would be unethical. In a sense, you’d be generating a neural tube defect, never a desired outcome, and we don’t know what other compensatory or cooperative genes to our, for us, normal TBXT-Δexon6 exist.

But hey, good news, we don’t have the same ethical restrictions when working with mouse embryos! Let’s dive into the mouse genome and insert Alus, just like ours, into the introns of the mouse TBXT gene! And so it was done, producing mice that made TBXT-Δexon6, and lo, they had little stumpy tails, or no tails at all.

There are a few complications. Mice that were homozygous for TBXT-Δexon6 died embryonically with substantial neural tube defects. Heterozygotes for TBXT-Δexon6 survived, and exhibited the tailless phenotype with variable penetrance, that is some mice were lacking the whole shebang, missing sacral vertebrae (sv) and all caudal vertebrae (cv), and others lost variable numbers of caudal vertebrae.

It’s lovely work, but I still have to disagree a little bit with their interpretation. Their model of hominoid evolution puts the tail-loss mutation right at the base of the progression.

That’s too simple. The lethality of the homozygous mutant in mice, while we homozygous mutants are fine, tells me that there are a lot of other genes that work together with TBXT to make a viable embryo — that we have a suite of supporting genes that can compensate for the lethal effects of TBXT-Δexon6. This model assumes that all those supporting roles evolved after the TBXT-Δexon6 mutation occurred. There is no reason to think that. Why not consider that our ancestral hominoid had a few exaptations that made it slightly more fault-tolerant in axis formation? Put those additional mutations ahead of the AluY insertion. Then have additional mutations afterwards. Our ancestors were not mice, so there’s no reason to think they’d have had the same response (that is, the lethality) to TBXT-Δexon6 as do modern mice.

Also, now I’m really interested in those additional mutations. TBXT isn’t the whole story.


Xia, b, Zhang W, Wudzinska A, Huang E, Brosh R, Pour M, Miller A, Dasen JS, Maurano MT, Kim SY, Boeke JD, Yanai I (2021) The genetic basis of tail-loss evolution in humans and apes. https://www.biorxiv.org/content/10.1101/2021.09.14.460388v1

We’re in this business for the unanswered questions

What I like about this episode of Crash Course Zoology is that it shows that it shows how scientists aren’t at all afraid of evolutionary mysteries, or of being wrong about something. Take that, creationists! That seems to be their primary line of attack, and all they’ll get out of me when they point out how our knowledge is incomplete is bafflement. Yeah, we know. That’s why we’re scientists.

Also, it’s got spiders in it.

The next episode is going to be about the species concept. Gosh, it’ll be nice when that one is finally explained!

Bring back the weird

The paleontological literature is a showcase for tragedy — it’s a graveyard of long-dead species, all snuffed out millions and millions of years before any human was around to appreciate them, and all we can do is look in awe at their fossilized corpses. In particular, fans of the Cambrian fauna can only pine for magnificently weird creatures that have been extinct for hundreds of millions of years, and represent entire exotic lineages that have left no descendants today. Two of the strangest are Anomalocaris and Opabinia.

Two of the most peculiar Burgess Shale animals, Anomalocaris and Opabinia, illustrate the complicated history of research of many Cambrian soft-bodied taxa – a result of their unfamiliar morphologies compared to the occupants of modern oceans. Both Anomalocaris and Opabinia possess compound eyes, lateral swimming flaps, filamentous setal structures, and a tail fan. Recent work has revealed that Anomalocaris and its relatives, the radiodonts, are united by the presence of paired sclerotized protocerebral frontal appendages and mouthparts composed of plates of multiple sizes, forming a diverse group containing over 20 taxa. Radiodonts range in age from the early Cambrian to at least the Devonian, and have been recovered from numerous palaeocontinents. Meanwhile, the most celebrated animal from the Burgess Shale, Opabinia regalis, with its head bearing five stalked eyes and a proboscis, remains the only opabiniid species confidently identified and is only known from a single quarry in the Burgess Shale. Myoscolex ateles from the Emu Bay Shale was proposed as a possible close relative, though this interpretation was hotly contested, and other authors have proposed a polychaete affinity.

The radiodonts (arthropods with mouths containing plates arranged in a wheel, that irised open and closed) are diverse and notorious. For a time, they were the largest predators on the planet, with their paired long spiky Great Appendages extending from the front of their head. Like the quote says, the opabiniiids are known from one location and one species, but they are weird. A similar array of swimming flaps like Anomalocaris, but then having 5 eyes on stalks and a long snout with a mouth on the end of it…it’s heartbreaking that they no longer exist. Spiders are cool and all, but I’d love to have schools of anomalocariids or opabiniids swarming in our local lakes.

At least one new opabiniid species has been identified, though. This cutie:

For perspective, here’s where they fall on the phylogenetic tree.

Tardigrades and velvet worms and mantis shrimp are certainly wonderful and interesting animals, but I have to yearn to see more of that glorious radiation of interesting forms in between. All gone, though. If gods were real, they’d never have let them die off.

I am inclined to like this hypothesis

I’m still going to criticize it, though.

For years, anthropologists and evolutionary biologists have struggled to explain the existence of menopause, a life stage that humans do not share with our primate relatives. Why would it be beneficial for females to stop being able to have children with decades still left to live?

According to a study published today in the journal Proceedings of the Royal Society B, the answer is grandmothers. “Grandmothering was the initial step toward making us who we are,” says senior author Kristen Hawkes, an anthropologist at the University of Utah. In 1997 Hawkes proposed the “grandmother hypothesis,” a theory that explains menopause by citing the under-appreciated evolutionary value of grandmothering. Hawkes says that grandmothering helped us to develop “a whole array of social capacities that are then the foundation for the evolution of other distinctly human traits, including pair bonding, bigger brains, learning new skills and our tendency for cooperation.”

I guess I’m personally inclined to appreciate the importance of grandmothers, having had a pair of good ones myself, and seeing how much time my wife invests in our granddaughter, but I’m less impressed with the study, which is based entirely on a computer simulation. I don’t trust simulations of complex phenomenon that necessarily have to simplify all the parameters. What about aunts and sisters? What about uncles?

What about the grandfathers?

None of those individuals are of interest, because this version of the hypothesis is structured around explaining menopause as the product of selection. Nope, I don’t buy it.

But why would females evolve to only ovulate for 40 or so years into these longer lives? Hawkes and other advocates of the hypothesis note that, without menopause, older women would simply continue to mother children, instead of acting as grandmothers. All children would still be entirely dependent on their mothers for survival, so once older mothers died, many young offspring would likely die too. From an evolutionary perspective, it makes more sense for older females to increase the group’s overall offspring survival rate instead of spending more energy on producing their own.

I’m willing to accept the benefit of an extended family and social cooperation, but the effort to justify menopause seems misplaced. There are many grandmothers who are not menopausal, and there would have been even more in ancient populations, where pregnancy shortly after the onset of menstruation would have been common. It also doesn’t explain the contributions of sisters and aunts to childrearing, or that brothers and sisters, who are also “distractions” from the business of raising a single delicate child. Why couldn’t it benefit a woman to raise her own child born late and also contribute to the well-being of grandchildren born to previous offspring? I suspect the simulation has assumptions built into the code about how much grandparental investment can be offered if they also have a child.

But, yeah, what about the grandfathers?

We help, too. So why isn’t there a male menopause where our testicles shrivel up and make us more willing to contribute to child-rearing? A man has a certain number of progeny, then boom, the reproductive urge goes away and he has to sit down and focus on taking care of the kids he’s got. Or his grandchildren. Or his nieces and nephews. That would be the logical endpoint of this arch-selectionist model, after all, and what’s good for the goose is good for the gander.

Yet somehow people feel compelled to come up with adaptationist explanations for accidents of evolutionary history.

Did native Americans have more equality 9000 years ago than we do now?

A pretty picture of a Peruvian hunter from 9000 years ago, bringing down vicuna with her atlatl and spear:

The image is based on the remains of the dead hunter, and an analysis of grave goods.

At Wilamaya Patjxa, an archaeological site in southern Peru, archaeologists unearthed the skeleton of a young woman whose people buried her with a hunters’ toolkit, including projectile points. The find prompted University of California Davis archaeologist Randall Haas and his colleagues to take a closer look at other Pleistocene and early Holocene hunters from around the Americas.

Their results may suggest that female hunters weren’t as rare as we thought. And that, in turn, reminds us that gender roles haven’t always been the same in every culture.

“The objects that accompany [people] in death tend to be those that accompanied them in life,” Haas and his colleagues wrote. And when one young woman died 9,000 years ago in what is now southern Peru, her people buried her with at least six stone spear tips of a type used in hunting large prey like deer and vicuña (a relative of the alpaca). The points seem to have been bundled along with a stone knife, sharp stone flakes, scraping tools, and ocher for tanning hides.

I also learned a new genetics fact! The bones were fragmentary, and the bits that you use for a morphological assessment of sex had crumbled to dust. But you can sex a skeleton by looking at the proteins that make up tooth enamel.

Tooth enamel contains proteins called amelogenins, which play a role in forming the enamel in the first place. The genes that produce these proteins are located on the X and Y chromosomes, and each version is slightly different. As a result, people who are genetically female have slightly different amelogenins than people who are genetically male. The proteins in the ancient hunter’s tooth enamel had a distinctly female signature, with no trace of the Y chromosome version.

The hunter from Wilamaya Patjxa is a young woman with the tools of an activity usually associated with men. If the objects people are buried with are the objects they used in life, then that raises some questions.

Maybe she was some weird outlier, I hear you ask. So they surveyed what was found at other grave sites, and it looks like a significant fraction of ancient hunters in the Western hemisphere happened to be women.

The hunter from Wilamaya Patjxa raises a similar question: was she the exception that proved the rule, or does her burial suggest that (in at least some ancient cultures) women were sometimes hunters? To help answer that question, Haas and his colleagues looked for other ancient people who had been buried with hunting tools. In published papers from archaeological sites across the Americas, they found 27 people at 18 different sites: 16 men and 11 women.

…the fact that so many apparent women turned up on that list is surprising. “Female participation in early big-game hunting was likely nontrivial,” wrote Haas and his colleagues. They suggest that as many as a third to half of women across the ancient Americas may have been actively involved in hunting.

The final line in this article is perfect.

Based on animal bones at Wilamaya Patjxa, large game like vicuña and taruca (a relative of deer) were extremely important to the community’s survival. In that case, hunting may have been an all-hands-on-deck activity. Haas and his colleagues also suggest that letting other members of a community keep an eye on the kids while the parents hunted might have freed more women up to bring home the bacon—or venison, in this case.

In other words, whether women hunted or fought probably depended on social factors, not biological ones.

I thought I ought to let David Futrelle know about this, since it makes the title of his blog even more ironic, but he beat me to it and has already posted about how She Hunted the Mammoth.

Crunchies vs. Squishies: ask the pterosaurs

I’m not a taxonomist; early in my career I settled on the model systems approach, which meant all the nuances of systematics disappeared for me. “That’s a zebrafish” and “that’s not a zebrafish” were all the distinctions I had to make, and zebrafish were non-native and highly inbred so I didn’t have to think much about subtle variations. There was one taxonomic boundary one of my instructors forced me to recognize: Graham Hoyle had nothing but contempt for “squishies”, as he called vertebrates like fish or mice or people, and was much more focused on the “crunchies”, insects and crustaceans and molluscs. These seemed like odd ad hoc taxonomic categories to me, I and could think of lots of exceptions where “crunchies” were pretty squishy (see witchetty grubs or slugs), and “squishies” were armored and crunchy (armadillos, any one?), and besides, as a developmental biologist, they were all squishy if you caught them young enough. But OK, if you like dividing everything into two and only two categories, go ahead.

Then today I read this paper, “Dietary diversity and evolution of the earliest flying vertebrates revealed by dental microwear texture analysis”, and saw that there was at least one practical use for the distinction. What you eat affects wear patterns on your teeth, that if you eat lots of crunchy things vs. lots of squishy gooey things, you’ll have a different pattern of dental scratches, and since teeth fossilize — unlike guts — you can get an idea of what long dead animals had for dinner. Furthermore, you can compare fossil microwear textures to the textures in extant animals, where you do know what kinds of things they eat.

This is cool — so you can estimate the range of things ancient pterosaurs ate from how their teeth were worn, whether they ate lots of soft-bodied bugs like flies, or hard-shelled crustaceans, or soft-fleshed fish, by making a fine-grained inspection of their fossilized teeth and comparing them to modern reptiles.

a–c Reptile dietary guilds; a piscivore (Gavialis gangeticus; gharial), b ‘harder’ invertebrate consumer (Crocodylus acutus; American crocodile) and c omnivore (Varanus olivaceus; Grey’s monitor lizard). d–f Pterosaurs; d Istiodactylus, e Coloborhynchus (PCA number 5) and f Austriadactylus (PCA number 2). Measured areas 146 × 110 µm in size. Topographic scale in micrometres. Skull diagrams of extant reptiles and pterosaurs not to scale.

But they’re not done! Knowing the phylogenetic relationships of those pterosaurs, you can then infer evolutionary trajectories, getting an idea of how dietary preferences in species of pterosaurs shifted over time.

a Phylo-texture-dietary space of pterosaur microwear from projecting a time-calibrated, pruned tree from Lü et al.33 onto the first two PC axes of the extant reptile texture-dietary space. b Ancestral character-state reconstruction of pterosaur dietary evolution from mapping pterosaur PC 1 values onto a time-calibrated, pruned tree from Lü et al.33. To account for ontogenetic changes in diet, only the largest specimen of respective pterosaur taxa, identified by lower jaw length, were included. Pterosaur symbols same as Fig. 2. Skull diagrams of well-preserved pterosaurs not to scale (see ‘Methods’ for sources).

These results provide quantitative evidence that pterosaurs initially evolved as invertebrate consumers before expanding into piscivorous and carnivorous niches. The causes of this shift towards vertebrate-dominated diets require further investigation, but might reflect ecological interactions with other taxa that radiated through the Mesozoic. Specifically, competition with birds, which first appeared in the Upper Jurassic and diversified in the Lower Cretaceous, has been invoked to explain the decline of small-bodied pterosaurs, but this hypothesis is controversial. DMTA provides an opportunity for testing hypotheses of competitive interaction upon which resolution of this ongoing debate will depend.

In summary, our analyses provide quantitative evidence of pterosaur diets, revealing that dietary preferences ranged across consumption of invertebrates, carnivory and piscivory. This has allowed us to explicitly constrain diets for some pterosaurs, enabling more precise characterisations of pterosaurs’ roles within Mesozoic food webs and providing insight into pterosaur niche partitioning and life-histories. Our study sets a benchmark for robust interpretation of extinct reptile diets through DMTA of non-occlusal tooth surfaces and highlights the potential of the approach to enhance our understanding of ancient ecosystems.

So pterosaurs started as small bug-eaters and diversified into niches where they were consuming bigger, more diverse prey over time, which certainly sounds like a reasonable path. I don’t know that you can really assume this was a product of competition with birds — I’d want to see more info about the distribution of pterosaur species’ sizes, because expanding the morphological range doesn’t necessarily mean that you’re losing at one end of that range, but I’ll always welcome more ideas about how Mesozoic animals interacted.

Tell me again how evolutionary psychology is not a con game

This is how evo psych works: state your hypothesis about past human societies with absolute confidence in the absence of any evidence, and then follow up with how The Lord of the Rings supports your model of a transition from a brutish form to a more gracile, effeminate form. Geoffrey Miller demonstrates:

So, the kill count competition between Legolas and Gimli is easily understood evidence of the evolution of warfare. Does that make Aragorn a transitional form?

When will the criticisms of evolutionary psychology sink in?

I’ve been complaining for years, as have others. The defenders of evolutionary psychology just carry on, doing more and more garbage science built on ignorance of evolutionary biology, publishing the same ol’ crap to pollute the scientific literature. It’s embarrassing.

Now Subrena Smith tries valiantly to penetrate their crania. It’s a familiar explanation. She sees it as a matching problem between their claims about the structure of the brain and behavioral history.

The architecture of the modern mind might resemble that of early humans without this architecture having being selected for and genetically transmitted through the generations. Evolutionary psychological claims, therefore, fail unless practitioners can show that mental structures underpinning present-day behaviors are structures that evolved in prehistory for the performance of adaptive tasks that it is still their function to perform. This is the matching problem.

In a little more detail…

Ancestral and present-day psychological structures have to match in the way that is needed for evolutionary psychological inferences to succeed. For this, three conditions must be met. First, determine that the function of some contemporary mechanism is the one that an ancestral mechanism was selected for performing. Next, determine that the contemporary mechanism has the same function as the ancestral one because of its being descended from the ancestral mechanism. Finally, determine which ancestral mechanisms are related to which contemporary ones in this way.

It’s not sufficient to assume that the required identities are obvious. They need to be demonstrated. Solving the matching problem requires knowing about the psychological architecture of our prehistoric ancestors. But it is difficult to see how this knowledge can possibly be acquired. We do not, and very probably cannot, know much about the prehistoric human mind. Some evolutionary psychologists dispute this. They argue that although we do not have access to these individuals’ minds, we can “read off” ancestral mechanisms from the adaptive challenges that they faced. For example, because predator-evasion was an adaptive challenge, natural selection must have installed a predator-evasion mechanism. This inferential strategy works only if all mental structures are adaptations, if adaptationist explanations are difficult to come by, and if adaptations are easily characterized. There is no reason to assume that all mental structures are adaptations, just as there is no reason to assume that all traits are adaptations. We also know that adaptationist hypotheses are easy to come by. And finally, there is the problem of how to characterize traits. Any adaptive problem characterized in a coarse-grained way (for example, “predator evasion”) can equally be characterized as an aggregate of finer-grained problems. And these can, in turn, be characterized as an aggregate for even finer-grained problems. This introduces indeterminacy and arbitrariness into how adaptive challenges are to be characterized, and therefore, what mental structures are hypothesized to be responses to those challenges. This difficulty raises an additional obstacle for resolving the matching problem. If there is no fact of the matter about how psychological mechanisms are to be individuated, then there is no fact of the matter about how they are to be matched.

One problem is that evolutionary psychologists all seem to think that their assumptions are obvious — and if you don’t agree, why, you must truly hate Charles Darwin and be little better than a creationist. Man, it’s weird when the intelligent design creationists are all calling you a dogmatic Darwinist, and the evolutionary psychologists are accusing you of being an intelligent design creationist. They’re both wrong.

Everyone likes cute furries more than spiders, I’ve noticed

I can’t be the only one who reads outside my discipline to get material to help me cover all those evolutionary phenomena I know little about. I know a bit about fish and arthropods, but my understanding of the details of mammalian evolution is a bit thin — yet for some reason, students are more interested in the history of mammals than of spiders. I really appreciate it when I stumble across information that fills in the gaps in my knowledge in presentable ways, and Nature has done just that with a graphically rich article on How the earliest mammals thrived alongside dinosaurs. There is lots of good stuff here, and I particularly like the emphasis on the importance of fossilized infants. Development matters!

Sometimes it goes a little too far, though — for example, this illustration is way too dense to be useful, but it it interesting.