…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


  1. euclide says

    I suppose the next step would be to try to “fix” the gene in some ape species ?
    By the way, what are the ethical restrictions to gene-editing primates ?

  2. blf says

    The mildly deranged penguin claims this explains why Danger Mouse has no tail, one eye, is nonetheless binocular, and speaks English & about a zillion other languages — an Alus in the introns of the mouse TBXT gene — or, as Penfold would put it, “a walrus in the Chief’s genie”. “Penfold, shush!”

    Returning to the real world… Neat (at least to the extent I follow it (I’m not a biologist)). From the Smithsonian, Why Humans Don’t Have Tails (Smithsonian edits in {curly braces}):

    The discovery suggests our ancestors lost their tails suddenly, rather than gradually, which aligns with what scientists have found in the fossil record. The study authors posit that the mutation randomly might have cropped up in a single ape around 20 million years ago, and was passed on to offspring. Perhaps being tailless was a boon to the apes, and the genetic mutation spread like wildfire.

    “For something to be lost in one big burst is really significant, because you don’t then have to posit millions of years of successive tiny changes accumulating gradually,” says Carol Ward, an anthropologist at the University of Missouri who wasn’t involved in the work, to the New Scientist’s Michael Le Page. “It may tell us why all of a sudden when we see the apes {emerge}, they have no tails.”

    That speculation — and the apparent fossil record — seems to concur with poopyhead’s speculation in the OP that supporting mutations quite possibly occurred before this critical one.

  3. says

    This is VERY well explained, PZ! I have been waiting for a science reporter to notice the prevalence of neural tube defects reported in the experiment. But all the popular media has been able to do it to claim that now we know why we don’t have tails. As usual, the important subtleties are overlooked. Nice Job!

  4. raven says

    Strangely enough, rarely, humans are born with tails.

    https://www. healthline.com/health/vestigial-tail

    What’s a vestigial tail made of?
    When a vestigial tail doesn’t fuse with the coccyx and remains after birth, what’s left is skin that contain no bones. Although the tail lacks bones, it does contain nerves, blood, adipose tissue, connective tissue, and muscles.

    Interestingly, the tail is also movable (in some people) like other parts of the body, although it doesn’t provide a useful function. Therefore, the tail isn’t used to grasp or grip objects.

    This always throws the creationists for a few minutes until they can think up a lie to explain it.

    This article calls human tails vestigial which isn’t wrong. They are also good examples of atavisms.

  5. raven says

    Barbary macaque – Wikipedia https://en.wikipedia.org › wiki › Barbary_macaque

    The boneless vestigial tail is greatly reduced compared with other macaque species and, if not absent, measures 4–22 mm (0.16–0.87 in).

    There is one monkey that doesn’t have a tail. The Barbary ape which isn’t an ape but a Macaque monkey.

    It would be interesting to see what their Brachyury TBXT gene looks like.

  6. jrkrideau says

    @ 5 raven
    As a boy, I remember reading that some of the royal Stuarts had vestigial tails. Could be true and not just a slander?

  7. PaulBC says

    So the 21st century “farmer’s wife” is now doing recombinant genetic engineering? So much for GMO-free food. I’m beginning to have my suspicions about why those mice were blind in the first place.

    As a boy, I remember reading that some of the royal Stuarts had vestigial tails. Could be true and not just a slander?

    No point, except that I read “slander” as “salamander.” Maybe the lizard people who rule us are really amphibians.

  8. bodach says

    I love these trips down the rabbit hole of biology. In my dotage, I fantasize about taking a biology class in my spare time, but when I read these explanations my brain locks up. Back to the couch for me.

  9. PaulBC says

    Despite my flippant comment @9, I concur that these are the kinds of posts I look forward to on this blog.

  10. Becca Stareyes says

    A brief Google told me that Manx tailless cats also have a mutated form of the gene… which is why ethical breeders never breed two tailless Manx together. (The same sort of behavior — heterozygous cats can have anything from no tail to ‘short, but functional tail’, and the less tail, the more likely there’s other developmental problems.)

  11. lumipuna says

    No point, except that I read “slander” as “salamander.” Maybe the lizard people who rule us are really amphibians.

    A witch once turned a Stuart ancestor into a newt, but he mostly recovered from it.

    (Also, the current Elizabeth II Salamander shouldn’t be mixed with Lisbeth Salander, fictional Swedish detective in a popular novel series.)

  12. blf says

    @14, And an alien werewolf infected athe Victorian, making them Salamander-Talbot…

    Speaking of Lawrence / Larry Talbot, it’s the time of year to re-re-re-re-…re-read A Night in the Lonesome October… however, this year, unlike last, the Moon will not be full on the critical day.

  13. birgerjohansson says

    Never mind the tails, can we chop out those genes that only allow us to use 10% of the brain? I know the 10% stuff is true, because it crops up in social media almost as often as chloroquinine…

  14. PaulBC says

    Never mind the tails, can we chop out those genes that only allow us to use 10% of the brain?

    But then we’d all spontaneously levitate and what a mess that would be trying to stay on the ground. In fact, I’ve recently been doing some research into human potential and I’m pretty sure we are better off having all those limiting genes that prevent us from exercising our superpowers.

  15. birgerjohansson says

    PaulBC @ 18.
    I have worked it out. Cats only land on their feet and sandwiches always land the buttered side down. If we attach a cat and a buttered sandwich to the hat, we could with a bit of training use their antigravity forces pushing upwards instead of downwards, thus remaining in contact with the ground.

  16. birgerjohansson says

    A story by the late Stanislaw Lem (the anthology Star Diaries) had the cosmonaut visit a world where extreme body modification had become the norm.
    The inhabitants were thus no longer confined to the humanoid morphology but could be quadropedal, wheel-shaped or not confined to just one head. As they made these modifications as adults, they were presumably not concerned with embryology
    (Lem liked spoofing the literary style of classic authors like Swift).

  17. birgerjohansson says

    …and if we were echinoderms, we could have radial symmetry. Imagine a sea star shaped office worker, working several keyboards and reading the screens with his eye stalks.
    Dr Davros really fucked up the final form of the Khaleds. A Dalek is useless for operating the screens watching Dow Jones.

  18. birgerjohansson says

    “…our ancestral hominoid had a few exaptations that made it slightly more fault-tolerant in axis formation?”
    How I wish Stephen Jay Gould had survived the cancer and been here to read this.

  19. says

    Domestic cats in SE Asia frequently have deformed or shortened tails and some have no tails. The mutation responsible can be lethal. as it can also affect the development of the bowel and urinary tract.

  20. drsteve says

    raven @6. Macaques in general I think would be the place to look for the precursor mutations that PZ is hypothesizing in the hominoid ancestor, which would have a high likelihood of also being present in the most recent common ancestor of apes and other Old World monkeys. The complementary experiment to looking at TBXT genetics in Barbary macaques would be to repeat this mouse experiment with embryos of any other macaque species and see if they have an easier time recreating the same tailless phenotype while minimizing neurological defects.

  21. birgerjohansson says

    drsteve@ 24
    A problem with apes is that they seem to be somewhat more vulnerable to extinction than monkeys- the number of species have decreased during the last few million years*.
    There is a big risk that one or several species that would exhibit “intermediate” forms have gone extinct, and the generally poor conditions for presentation of fossils make it harder to fill in the gaps (and I suspect the paleontholigists are more interested in the more recent australopictine and erectus relatives we had).
    *there is of course the possibility that apes and homomines more closely related to us have competed for the same resources. We have left a trail of exinctions that goes Zod knows how far back.

  22. davidc1 says

    @8 Are you sure it wasn’t the Habsburgs ,that family were so inbred ,anything was possible .

  23. lpetrich says

    https://www.nature.com/articles/srep31583 – “In addition, some of our sampled kinked-tailed cats could not be explained by either HES7 or the Manx-related T-box, suggesting at least three independent events in the evolution of domestic cats giving rise to short-tailed traits.”

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3848309/ Multiple mutant T alleles cause haploinsufficiency of Brachyury and short tails in Manx cats

    Bears also have short tails, as do wombats and koalas.

    Most mammalian tails are relatively thin, unlike the tails of most other vertebrates, and that makes them something of a vestigial feature. Tails can become thick again, as in cetaceans and kangaroos, and they can have functions like troublesome-insect deterrence (horse tails, for instance) and deceptive bulk (bushy tails).

    Thin tails go back at least as far as the placental-marsupial divergence, likely in the Jurassic, and likely further.

    Could it be that it is easier to grow a thin tail than to stop growing a tail?