Snake segmentation

Blogging on Peer-Reviewed Research

Life has two contradictory properties that any theory explaining its origin must encompass: similarities everywhere, and differences separating species. So far, the only theory that covers both beautifully and explains how one is the consequence of the other is evolution. Common descent unites all life on earth, while evolution itself is about constant change; similarities are rooted in our shared ancestry, while differences arise as lineages diverge.

Now here's a new example of both phenomena: the development of segmentation in snakes. We humans have 33 vertebrae, zebrafish have 30-33, chickens have 55, mice have 65, and snakes have up to 300 — there's about a ten-fold range right there. There are big obvious morphological and functional differences, too: snakes are sinuous slitherers notable for their flexibility, fish use their spines as springs for side-to-side motion, chickens fuse the skeleton into a bony box, and humans are upright bipeds with backaches. Yet underlying all that diversity is a common thread, that segmented vertebral column.

(Click for larger image)

Vertebral formula and somitogenesis in the corn snake.
a, Alizarin staining of a corn snake showing 296 vertebrae, including 3
cervical, 219 thoracic, 4 cloacal (distinguishable by their forked
lymphapophyses) and 70 caudal. b, Time course of corn snake development
after egg laying (118-somite embryo on the far left) until the end of
somitogenesis (~315 somites).

The similarities are a result of common descent. The differences, it turns out, arise from subtle changes in developmental timing.


Let's consider the similarities first. We know how segments form in many vertebrates: it's a process of progressive partitioning of an unsegmented, relatively undifferentiated mass of cells called the presomitic mesoderm. This mass extends the length of the body and tail of the early embryo. If you just watch the developing embryo, you can actually see the cells self-organize serially, from front to back, with little knots of cells pinching off to form each segment. It's very cool to see, and I've often witnessed it in my zebrafish embryos.

Looking deeper at the molecules involved, there is an elegant clockwork mechanism ticking away. There is a slowly receding gradient of Wnt/FGF molecules that travels down the presomitic mesoderm, and at the same time, there is a faster oscillation of Notch-related molecules that has the same cycle as the timing of segment formation. Each tick of the Notch clock sets aside the most anterior cells expressing Wnt/FGF, and the go on to form a segment. Wnt/FGF recedes back a little further, and at the next cycle of Notch, the next segment is pinched off, and so on, until the gradient runs out of presomitic mesoderm, and the array of segments is complete.

This latest work is an extensive analysis of the molecular basis of segment formation in the zebrafish (Danio rerio), chicken (Gallus gallus), mouse (Mus musculus), and the new player in this game, the corn snake (Pantherophis guttatus), with its impressive roster of 315 total segments. They examined many genes, including FGF and Wnt3a of course, but also many of their downstream targets, as well as components of the retinoic acid counter gradient, and molecules involved in the oscillator, like Lunatic fringe.

No one should be surprised to learn that snakes have the very same segmental clock that fish and mammals and birds have already been shown to have — the same molecules are observed, operating in the same compartments, with roughly the same relationships. They all use a conserved developmental mechanism.


So what causes the obvious difference of 300 segments vs. 30? There are two simple hypotheses that would fit within the clock and wavefront model. One would be that the wavefront recedes more slowly, or at the same speed but over a longer mass of presomitic mesoderm, allowing more ticks of the oscillator to occur before the wavefront ends at the tailtip. The other is that the wavefront is operating at roughly the same rate, but the oscillator is operating at a much faster rate, partitioning off many more smaller segments.

The answer is the latter. The snake clock is running at a much higher speed than the clock in a chicken or mouse, so that over the same relative span of time for segment formation, it counts off many more pulses and triggers many more segments to assemble. The estimates are a little bit complex, because these species all have very different overall times of development, with the snake being slowest overall, so rates had to be normalized to specific developmental events. Among the standard metrics was the number of cell generations during the period of segment formation; about 21 cell generations to make 300 segments in the snake, about 17 generations to make 65 segments in the mouse.

There were other subtle differences that hint at some changes in gene regulation, for instance, in that Lunatic fringe expression shows more simultaneous stripes in the corn snake than in other species, but this may also simply be a side effect of the more rapid cycling of the somitic clock.

This is a demonstration of the real power of evo-devo. When we talk about major evolutionary changes in phenotype, like the increase in segment numbers in snakes, the way to track down and figure out the specific molecular details is to study the developmental processes behind the morphology, and look for the small differences that lead to the differing outcomes. In this case, we see a direction for further research: it looks like a quantitative change in the regulation of a developmental regulator, the somitic clock, is responsible for the variation. Now the next big question is to identify the specific adjustments to the clock — what small shifts in the sequence of various genes lead to the clock running faster or slower?

At any rate, it's another case where we don't need a watchmaker, just blind, tiny, incremental changes to the machinery of development.

Gomez C, Ozbudak EM, Wunderlich J, Baumann D, Lewis J, Pourquie O (2008) Control of segment number in vertebrate embryos. Nature 454:335-339.

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that photo sequence is freaking amazing, zebedee lives!!

By extatyzoma (not verified) on 23 Jul 2008 #permalink

At any rate, it's another case where we don't need a watchmaker, just blind, tiny, incremental changes to the machinery of development.

And thank (so to speak) God, because ID is simply a statement that we'll never know anything about these matters.

While life's complexity is stunning, the simplicity of the changes in so much of that complexity is almost as amazing. It seems to be the story of life, that the very complexity that would make radical change in human machines difficult, makes radical change in organisms (relatively) simple.

Anyhow, I do appreciate these explanatory posts (the epigenetics post was a great explanation for those who didn't understand it).

Glen D

These are the kinds of posts that really got me hooked on Pharyngula way back when. Shit-stirring atheism is just a side benefit! :-)


By minusRusty (not verified) on 23 Jul 2008 #permalink

Agreeing with minusRusty - I'm another of those oddballs who looks forward to science posts on Pharyngula. :-)

PZ, do you seriously think you can fool us with this patently obvious attempt at disguising your festering cracker obsession with some serious and fascinating science blogging? You're not fooling anyone, you know! ;)

There is nothing I've ever seen, experienced or read about in any faith practiced now or ever before that comes close the awe and inspiration I derive from understanding the pure beauty of the natural world... the real beauty... it's enthralling.

By Celtic_Evolution (not verified) on 23 Jul 2008 #permalink

So when are you going to do the cracker? Huh, when? Can I watch?

By Blind Squirrel FCD (not verified) on 23 Jul 2008 #permalink

Now the next big question is to identify the specific adjustments to the clock -- what small shifts in the sequence of various genes lead to the clock running faster or slower?

Uh-oh, I foresee a future in which someone's lab is populated by long slinky mice or eely zebrafish as the tinkering proceeds. Though the change could easily compromise something else in development along the way.

It's a brilliant strategy to follow up the crackergate traffic spike with some real and interesting science posts. Lure them in with a blood-boiling controversy and smack them in the face with some rational thought. I applaud your (not-so) secret plan.

Re: the post, did the authors of the snake paper touch on the role of Hairy1? IIRC, Hairy1's expression domain oscillates at the same rate as the Notch patterning, though last I heard, no-one had figured out exactly what it does or what its downstream targets are. Any news on that front?

By leukocyte (not verified) on 23 Jul 2008 #permalink

That is simply amazing! Do all snakes have around 300 vertebrae? Because I'm wondering if there is even more subtle changes in the clock rate between species of snakes.

finally another good and interesting science blog entry on Pharyngula.

I foresee a future in which someone's lab is populated by long slinky mice

The future sounds very entertaining. :D

Thanks for this! Informative and easy-to-read, just as I've come to expect.

How many segments does a crocoduck have?

long slinky mice

The living Mink Stole of Tomorrow!

...I foresee a future in which someone's lab is populated by long slinky mice...

"What walks down stairs,
gene expressions impaired,
and makes a squeekeity sound?"

I love the writing in this, so clear and lucid. Keeps me entertained between issues of SEED.

The part about the clock and the wave was vividly clear. Thank you for the metaphor, PZ.

(where's my sketchbook...?)

Fascinating article.

I remain unconvinced of this "evolution" thing though. It's just a "theory", right? ;)

Now, about that cracker...

Wow! Those are such beautiful images! Life is so amazing...

It's like easy listening (but not irritating) for science. The reason I came here in the first place, for the science references and a break from the tedium of the classroom and lab. It makes life so much more meaningful and if the IDiots would just take up reason and science I feel they would come away with the awe that I have for life and our magnificent Planet and Universe. Geez you don't even need a god to feel it, right?

By Barklikeadog (not verified) on 23 Jul 2008 #permalink


Thanks for the informative article. Every little bit of this information is a potential answer to someone's talking point or sincere question.

Studying embryos? You mean you're a *gasp* fish abortionist? Quick, I need some pearls to clutch! (mental image of PZ sneaking up on a aquarium wit an evil leer and a rusty coat hanger clutched in a tentacle)

Another complex subject explained with clarity. Your students are lucky.

It looks like all that "junk" DNA in the human genome may not be so junky after all. It may be the real engine behind evolution. (Oh no, the theory of evolution is evolving.):)

By Nerd of Redhead (not verified) on 23 Jul 2008 #permalink

Thanks for summarizing an interesting article that I would not have gotten through myself!

Mildly related question: Has anyone done a similar sort of survey but focusing on brain gyrations? How much is known about the molecular signaling involved in creating various levels of 'in-folding' in the brain?

In the somite development photographs, can we see limb buds that are eventually reabsorbed? Also, it seems that we can predict that snakes with legs should have them adjacent to those cloacal vertebrae, and not elsewhere. What would ID predict about snakes with legs? A tempting question...

It's interesting to wonder if other very long+skinny (and often limbless) organisms (slow worms (genus Anguis), caecilians, eels ... and I think a few others that I forget) have the same general altered timing developmental process as snakes.

Hm. Among mammals, would ferrets and weasels and such count?

By Owlmirror (not verified) on 23 Jul 2008 #permalink

Well there it is! Most of chickens energies went into forming vertebrae. No wonder they have no brains.
Seriously PZ, I'm starting to like this stuff more all the time. I understand about half of it. :)

Scary - that article is not only in my field, not only is the final author my bosses' ex boss, but one of the students in my lab presented it as a Journal club two days ago! (I missed it because I was on holiday, so it's good to find out what it was about). I'm amazed by how similar the snake embryos look to chicken embryos - mice at the equivalent stage look very different.

And never turning down the opportunity to shoot my mouth off on a topic I know something about...

Answers to those who are interested in messing with the timing of segmentation (#3 and #20) - almost everyone is trying to do this (my lab included). The problem is that the clock cycle is actually horribly complicated; there are dozens of genes from different pathways that cycle in time with the segmentation clock, and any one (or combination) of them could be the crucial element in setting clock periodicity. There are already a couple of mutant mice that have disrupted somites (and therefore vertebrae); such as Hes7 and Lfng (Notch components). I suspect the Vestigial Tail Wnt hypomorph phenotype is also a defect in segmentation, but I could be wrong about that.

#31 Sulci and gyri are pretty specific to primates, I think - certainly, rodents don't have them, so any study would be limited to looking at monkeys, with all the ethical issues involved. Iirc, their depth and prevalence is to do with the number of cells in the cortex. The brain forms as a sheet (specifically, the wall of a tube), so if you increase the number of neurons in the sheet, it will naturally form creases and folds. There are a range of adaptations that control this and make it easier for cells to survive and find where they should be, but my impression is that the driving factor is cell number.

#33 - I forget the details, but I'm fairly sure the clock and wavefront model of somitogenesis is fairly unique to vertebrates; invertebrates tend to form segments in completely different ways. It doesn't even need to be one-at-a-time (although it sometimes is) - insects like drosophila divide themselves into segments all in one go using Pair-rule genes (wouldn't surprise me if PZ hasn't written about this in the past).

Also, just because something is longer and "slinkier" does not mean it has more segments. Compared to a human, chickens are shorter and more stiff, but they have more segments. This variation is probably differences in how flexible the vertebrae an organism has are, rather than the number. A good example is the giraffe - it doesn't have more bones in it's neck than the average mammal, they're just bigger.

By Confuseddave (not verified) on 23 Jul 2008 #permalink

Why does the snake illustration have a fish hook coming out the back of it?

(for any of you Harun Yahya fans out there!)

By Fred Mounts (not verified) on 23 Jul 2008 #permalink

It's true that rodents have smooth brains, but various degrees of gyration are found among mammals - cats, dogs, cows, etc.
And there's something more to it than simply cell number - gray matter at the base of deep sulci is of different thickness (and I suspect slightly different composition) than that at the top of gryi.
I was actually asking if anyone knew about the molecular signaling because my lab had done some microarrays on polymicrogyria patients ('too many, small folds'), and I think it would be an interesting study to compare genes implicated by the microarrays with, say, their rates of evolution in species developing more gyri.

Addendum: Those snake embryo pictures are awesome. Haven't seen a snake embryo before!

#31 Holometabolous insects (those that have larval and pupal stages) patterns of segmentation are quite different from this clock and wavefront type of development, which is specific for vertebrate somitogenesis.

#37 Without looking anything up, I recall VLDLR/ApoER2 dKO having a large effect on folding.

#13 - The number of vertebrae in snakes varies considerably, both with behavior and with phylogeny. Most boas and pythons have huge numbers, usually over 300, sometimes as many as 500. Within "advanced" (caenophidian or colubroid) snakes, that number can vary a lot, with short, chunky species who don't constrict such as water snakes (of several convergent lineages) having less and flexible constrictors (and some arboreal species) having more. There's also plenty of variation within genera, species, populations, even individuals of the same clutch/litter.

Other elongate species have a mix of more vertebrae vs. elongate vertebrae, as well as the locations of elongation. Legless anguid lizards have increased numbers of vertebrae, but most of them are in the tail, not the body. Amphisbaenians ("worm lizards") have a pattern like snakes. Mustelids have longer vertebrae than other mammals, but not many more.

Oh, and a general note: the change from Elaphe to Pantherophis has been rejected as based on insufficient evidence.

The Fringe gene was first found as part of the Notch-signalling pathway in flies (google and Wikipedia tell me).

When homologous genes were found in vertebrates, the variants were given distinguishingly mnemonic adjectives, like Manic Fringe, Radical Fringe, and Lunatic Fringe.

I suspect "fringe" was at least a little more pedestrian, describing some actual phenotypic trait, but let me see if I can find out...

Heh! I was right (I think; since I'm still in the process of scanning this article ( ) about Fringe) -- apparently variations in the expression of fringe in flies can affect the smoothness or serratedness of the edge of the wing. It's a lot more complicated than that, and involves the interesting interaction of multiple other genes, and the differentiation of segments, but my quick'n'dirty impression is that the name relates to the variants in phenotypic expression that are seen when you mess with the gene.

By Steviepinhead (not verified) on 23 Jul 2008 #permalink

Thanks, PZ! Excellent article. After reading your posts on Pharyngula, I wish I had majored in science.

Thanks for an interesting article and explanation. As someone whose last formal biology schooling was in 10th Grade ever so many years ago, I appreciate the opportunity to learn something about a topic I know almost nothing about.

Thanks again PZ, that was great! I am actually studying FGF/Wnt and Notch genes in neural stem cells... so thank you for doing my homework for me :)

Seriously though, that was a great post. You really have a great talent for putting these sorts of papers into perspective for us and letting us know why they are so important.

I loved the figure you included as well. It's so incredible to see how at such an early stage of development, all embryos look so much alike - humans, mice, snakes, etc. So cool!

Those snake embryo pictures are totally sweet. For anyone who doesn't know, they look pretty much like mouse embryos, but with a swirly little thing where the body and tail "ought" to be.

Dan B., you should check out some of Chris Walsh's work (if you don't know it intimately already) -- his lab is looking at just that. To some degree, gyri and sulci are created by cell number, specifically by regulating the timing/proportion of progenitors (especially in the upper layers) which leave the cell cycle vs. stay in. I feel like I know more about the molecular regulation of gyrus/sulcus development somewhere in my head, but I can't find it at the moment.

By molliebatmit (not verified) on 23 Jul 2008 #permalink

If I had to guess, I'd say Lunatic Fringe must have been first isolated or sequenced in a creationist, and named after them, accordingly.

"In this case, we see a direction for further research"

And that's the most important thing of all. That's what ID simply can't do, and why it fails so miserably. (Well, one of the reasons, anyways.)

By (not verified) on 23 Jul 2008 #permalink

Very interesting. It sort of reminded me of how different species of zebra get different numbers of sstripes. I may be totally wrong though. What i've always wondered about is what happens during the pupa stage in an insect. I know, at least as far as D. melanogaster goes, how the HOX genes form the different segments, but i can only think about a blender mixing cells when i try to think of what happens during metamorphoses. Can you comment on that, or point me to a possible explanation.

By astrobiologiste (not verified) on 23 Jul 2008 #permalink

It sort of reminded me of how different species of zebra get different numbers of stripes.

It struck me when encountering mention of zebra stripes in Sean Carroll's Endless Forms Most Beautiful that this is an idea that has not actually been tested, and may never be -- not because of impossibility in principle, but simply because zebra embryos are in short supply. It was first suggested in the early 80s and was popularized, as a speculative possibility, by S. J. Gould at that time; Carroll's discussion 20 years later is almost identical to Gould's, and still speculative.

PZ wrote:

No one should be surprised to learn that snakes have the very same segmental clock that fish and mammals and birds have already been shown to have

But shouldn't Creationists be surprised, if there's no natural common cause of developmental mechanisms in different 'kinds'? An omnipotent Creator would have an infinite range of mechanisms to choose from, why would he be so unCreative as to do it the same way twice?

By John Scanlon FCD (not verified) on 23 Jul 2008 #permalink

The bit of the paper I was most interested in (along with the lovely curly snake embryos) was this on p.336:

the somite size as a fraction of the PSM size directly reflects the duration of the clock cycle as a fraction of the average PSM cell generation time (that is, average cell-cycle time; Supplementary Box 1). In snake, this fraction is approximately one-quarter of the value observed in other species (Fig. 4c). Thus, the snake segmentation clock runs approximately four times faster relative to the average PSM cell generation time than in the other species.

I had previously speculated (aloud, though not in print) that the evolution of the snake body form involved two discrete doublings of presacral segment number from the lizard ancestor, so that number 'four' got my attention. Lizards mostly have around 26 presacrals, a couple of long-bodied burrowing lizards (not closely related to snakes) and apparently the Cretaceous Dolichosaurus (probable close relative or 'stem-snake') have about 50-70, and the most complete Cretaceous snake fossils have about 120. Suggestive, anyhow. I couldn't see anything in the Gomez et al. paper to suggest a mechanism for discrete rate-doublings (except for the hyper-variable patterns of LFNG expression suggesting possible chaotic dynamics, where period-doubling bifurcations could be expected).
In the modern fauna, the highest total vertebra numbers may be in the Oenpelli Python (Morelia oenpelliensis) - but that's an inference from the number of ventral and subcaudal scales, which are mostly in 1:1 correspondence to vertebrae and rib pairs (V 429-445, Sc 155-163), giving it a total (but not presacral) number higher than the maximum usually cited for the Eocene fossil Archaeophis proavus, with approximately 452 presacral and 565 total.
Sexual dimorphism, geographic and individual variation (including effects of incubation temperature) in segment number are common in snakes, so there are certainly mechanisms for continuous evolutionary tweaking, not just evo-devo 'macromutations'.

The existence of a common pharyngula stage for vertebrates was first proposed by German biologist Ernst Haeckel (1834-1919) in 1874. However, more recent work has cast doubt on the validity of this proposed common stage. A detailed analysis of Haeckel's drawings and of variations in timing of appearance of various structures common to vertebrate embryos (analysis of sequential heterochrony) suggests that it may not be possible to find a single set of criteria that define a common pharyngula stage after all.

Uh-oh, I foresee a future in which someone's lab is populated by long slinky mice or eely zebrafish as the tinkering proceeds. Though the change could easily compromise something else in development along the way.

Indeed, like the spinal cord patterning and the issue of what vertebra will get made (thoracic, lumbar, what?) and snakes don't have to worry about limb nerves finding their way either which all points to the clock changing rate gradually which would allow the other things to catch up. Mind you there is some evidence for the somites patterning the neural tube (nascent spinal cord) so maybe not.

By Peter Ashby (not verified) on 23 Jul 2008 #permalink

Lovely post. Almost makes me miss the work I did on skeletal segmentation in my old lab! Hundreds of millions of years of conserved gene networks - very cool stuff. Pretty happy in a clinical lab now, but I do love stopping by to read PZ's latest . . . .

By ctenotrish (not verified) on 24 Jul 2008 #permalink

Let's get the number of comments over 1,000! Lovely post, as all science posts are. Too bad "Fr. J" can't leave the fray and actually learn something.

Uh-oh, I foresee a future in which someone's lab is populated by long slinky mice or eely zebrafish as the tinkering proceeds.

I see stumpy snakes, plump as knockwursts.

By Longtime Lurker (not verified) on 24 Jul 2008 #permalink

The existence of a common pharyngula stage for vertebrates was first proposed by German biologist Ernst Haeckel (1834-1919) in 1874. However, more recent work has cast doubt on the validity of this proposed common stage. A detailed analysis of Haeckel's drawings and of variations in timing of appearance of various structures common to vertebrate embryos (analysis of sequential heterochrony) suggests that it may not be possible to find a single set of criteria that define a common pharyngula stage after all.

This seems very odd to me. Why would anyone suggest that analyzing Haeckel's drawings as having anything to do with modern developmental biology? Embryology has advanced more than a little since the late 1800s, and dev bio's now use stainings of the embryos themselves.

Like in the image above...

Didn't PZ address all this already in painstaking detail?…

By Owlmirror (not verified) on 24 Jul 2008 #permalink

#58 - For 'stumpy snakes', just do a google image search for "Kenyan sand boa" - they're about as stumpy as it gets.

Celtic_evolution #9, your post just about sums it up beautifully. How can any religion ever dream of comparing to the wonders of the universe for anyone who has their eyes and mind truly open.

By John Phillips, FCD (not verified) on 24 Jul 2008 #permalink

Ah cool, I'm a postdoc at the same institute as Dr. Pourquie's lab... their work (especially on how the segmentation clock works) is really elegant. I'll let him know you posted this.

As already mentioned many times, those corkscrew embryos are ridiculously adorable.

(Could someone possibly point out those limb buds to me? I wouldn't say no to a link about how the snake lost its legs either.)