To dump a chunk of trunk

The Mammal has deemed that Hox genes and good old-fashioned feel-good evo-devo are a good way to blink back to life*. Also, tardigrades. Tardigrades are awesome. Here is one viewed from above, from the Goldstein lab via Encyclopedia of Life:

hypsibius_dujardini_eol

Tardigrades or water bears are also a bit unusual. Their closest living relatives are velvet worms (Onychophora) and arthropods. Exactly who’s closest to whom in that trio of phyla collectively known as the Panarthropoda is not clear, and I don’t have the energy to wade into the debate – besides, it’s not really important for the purposes of this post. What Smith et al. (2016) concluded about these adorably indestructible little creatures holds irrespective of their precise phylogenetic position.

Anyway. I said tardigrades were unusual, and I don’t mean their uncanny ability to survive the apocalypse¬†and pick up random genes in the process (Boothby et al., 2015). (ETA: so apparently there may not be nearly as much foreign gene hoarding as the genome paper suggests – see Sujai Kumar’s comment below! Doesn’t change the fact that tardigrades are tough little buggers, though ūüôā ) The oddity we’re interested in today¬†lies in the fact that all known species are built to the exact same compact body plan.¬†Onychophorans and many arthropods are elongated animals with lots of segments, lots of legs, and often lots of variation in the number and type of such body parts. Tardigrades? A wee head, four chubby pairs of legs, and that’s it.

How does a tardigrade body relate to that of a velvet worm, or a centipede, or a spider? Based solely on anatomy, that’s a hell of a question to answer; even the homology¬†of body parts between different kinds of arthropods can be difficult to determine. I have so far remained stubbornly uneducated on the minutiae of (pan)arthropod segment homologies, although I do see papers purporting to match brain parts, appendages¬†and suchlike between different kinds of creepy-crawlies¬†on a fairly regular basis. Shame on me for not being able to care about the details, I guess – but¬†the frequency with which the subject comes up suggests that the debate is far from over.

Now, when I was first drawn¬†to the evo-devo field, one of the biggest attractions was the notion that the expression of genes as a body part forms¬†can tell us what that body part really is even when anatomical clues are less than clear. That, of course, is too good to be simply true, but sometimes the lure of genes and neat¬†homology stories is just too hard to resist. Smith et al.‘s investigation of¬†tardigrade Hox genes is definitely that kind of story.

Hox genes are generally a good place to look if you’re trying to decipher¬†body regions, since their more or less neat, orderly expression patterns are remarkably conserved between very distantly related animals (they are¬†probably as old as the Bilateria, to be precise). A polychaete worm, a vertebrate and an arthropod show the same general pattern – there is no active Hox gene at the very front of the embryo, then Hoxes 1, 2, 3 and so on appear in roughly that order,¬†all the way to the rear end. There are variations in the pattern – e.g. the expression of a gene¬†can have sharp boundaries or fade in and out gradually; different genes can overlap to different extents, the order isn’t always perfect, etc. – but staggered Hox gene expression domains, with the same genes starting up in the same general area along the main body axis, can be found all across the Bilateria.

Tardigrades are no exception, in a sense – but they are also quite exceptional. First, their complement of Hox genes is a bit of a mess. At long last, we have a tardigrade genome to hand, in which Smith et al. (2016) found good honest¬†Hox genes. What they didn’t find was a Hox cluster, an orderly series of Hox genes sitting like beads on a DNA string. Instead, the Hox genes in Hypsibius dujardini, the sequenced species,¬†are all over the genome, associating with all kinds of dubious fellows¬†who aren’t Hoxes.

What Smith et al.¬†also didn’t find was half of the Hox genes¬†they expected. A typical arthropod has ten or so Hox genes, a pretty standard ballpark for an animal that isn’t a vertebrate. H. dujardini has only seven, three of which are triplicates of Abdominal-B, a gene that normally exists in a single copy in arthropods. So basically, only five kinds of Hox gene – number two and most of the “middle” ones are missing. What’s more, two more tardigrades that aren’t closely related to H. dujardini also appear to have the same five Hox gene types (though¬†only one Abd-B each), so this massive loss is probably a common feature of Tardigrada. (No word on whether the scattering of the Hox ¬†cluster¬†is also shared by the¬†other two species.)

We know that the genes are scattered and decimated, but are their expression patterns similarly disrupted? You don’t actually need an intact Hox cluster for orderly Hox expression, and indeed, tardigrade Hox genes are activated in a perfectly neat and perfectly usual pattern that resembles what you see in their panarthropod cousins. Except for the bit where half the pattern is missing!

Here’s¬†part of Figure 4 from the paper, a schematic comparison of tardigrade Hox expression to that of other panarthropods – a generic arachnid, a millipede and a velvet worm. (otd is a “head” gene that¬†lives in the Hox-free anterior region;¬†lab is the arthropod equivalent of¬†Hox1, Dfd is Hox4, and I’m not sure which of Hox6-8 ftz is currently supposed to be.) The interesting thing about this is that according to Hox genes, the entire body of the tardigrade corresponds to just the front end of arthropods and velvet worms.

Smith_etal2016-hox_tardigrade_fig4A

In addition, one thing that is not shown on this diagram is that Abdominal-B, which normally marks the butt¬†end of the animal, is still active in the tardigrade, predictably in the last segment (L4, that is). So if you take the Hox data at face value, a tardigrade is the arse end of an arthropod tacked straight onto its head. Weird. It’s like evolution took a perfectly ordinary velvet worm-like creature and chopped out most of its trunk.

The tardigrade data suggest¬†that the original panarthropod was probably more like arthropods and velvet worms than tardigrades – an elongated animal with many segments.¬†The strange tardigrade situation can’t be the ancestral one, since the Hox genes that tardigrades lack long predate the panarthropod ancestor. Now, it¬†might be¬†possible to lose half your Hox genes while keeping your¬†ancestral body plan, but an unusual body plan and an unusual set of Hox genes is a bit of a big coincidence, innit?

Smith et al. point out that the loss of the Hox genes was unlikely to be the cause of the loss of the trunk region¬†– Hox genes only specify what grows on a segment, they don’t have much say in how many segments develop in the first place. Instead, the authors reason, the loss of the trunk in the tardigrade ancestor probably made the relevant¬†Hox genes dispensable.

Damn, this story makes me want to see the Hox genes of all those oddball lobopodians from the Cambrian. Some of them are bound to be tardigrade relatives, right?

***

References:

Boothby TC et al. (2015) Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. PNAS 112:15976-15981

Smith FW et al. (2016) The compact body plan of tardigrades evolved by the loss of a large body region. Current Biology 26:224-229

***

*The Mammal has been pretty depressed lately. As in mired up to her head in weird energy-sucking flu. Unfortunately, writing is one of those things that the damn brain monster has eaten most of the fun out of. Also, I have a shitty normal person job at the moment, and shitty job taking up time + barely enough motivation to crawl out of bed and pretend to be human¬†means I have, at best, one afternoon per week that I actually spend on catching up with science. That is just enough to scroll through my feeds and file away the interesting stuff, but woefully insufficient for the writing of posts, not to mention that my ability to concentrate is, to be terribly technical, absolutely fucked. It’s not an ideal state of affairs by any stretch, and I’m pretty sure that if I made more of an effort to read and write about cool things, it would pay off in the mental health department, but‚Ķ well. That sort of reasonable advice is hard to hear with the oozing fog-grey suckers of that thing clamped onto my brain.

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In which a “living fossil’s” genome delights me

I promised myself I wouldn’t go on for thousands and thousands of words about the Lingula genome paper (I’ve got things to do, and there is a LOT of stuff in there), but I¬†had¬†to indulge myself a little bit. Four or five years ago when I was a final year undergrad trying to figure out things about Hox gene evolution, I would have killed for a complete brachiopod genome. Or even a complete brachiopod Hox cluster. A year or two ago, when I was trying to sweat out something resembling a PhD thesis, I would have killed for some information about the genetics of brachiopod shells that amounted to more than tables of amino acid abundances. Too late for my poor dissertations, but a brachiopod genome is finally sequenced! The paper is right here, completely free (Luo et al., 2015). Yay for labs who can afford open-access publishing!

In case you’re not familiar with Lingula, it’s this guy (image from Wikipedia):

In a classic case of looks being deceiving, it’s not a mollusc, although it does look a bit like one except for the weird white stalk sticking out of the back of its shell. Brachiopods, the phylum to which Lingula belongs, are one of those strange groups no one really knows where to place, although nowadays¬†we are pretty sure they are somewhere in the general vicinity of molluscs, annelid worms and their ilk.¬†Unlike bivalve molluscs, whose shell valves are on the left and right sides of the animal, the shells of brachiopods like Lingula have top and bottom¬†valves. Lingula‘s shell is also made of different materials: while bivalve¬†shells contain¬†calcium carbonate deposited into a mesh of chitin and silk-like proteins,* the subgroup of brachiopods Lingula belongs to uses calcium phosphate, the same mineral that dominates our bones, and a lot of collagen (again like bone). But we’ll come back to that in a moment…

One of the reasons the Lingula genome is particularly interesting is that Lingula is a classic “living fossil”. In the Paleobiology Database, there’s even an entry for a Cambrian fossil classified as Lingula, and there are plenty of entries from the next geological period. If the database is to be believed, the genus¬†Lingula has existed for something like 500 million years, which must be some kind of record for an animal.** Is its genome similarly conservative? Or did the DNA hiding under a deceptively conservative shell design evolve as quickly as anyone’s?

In a heroic feat of self-control, I’m not spending all night¬†poring over the paper, but I did give a couple of interesting sections a look. Naturally, the first thing I dug out was the Hox cluster hiding in the rather large supplement. This was the first clue that Lingula‘s genome¬†is definitely “living”¬†and not at all a fossil in any sense of the word. If it were, we’d expect one neat string of Hox genes, all in the order we’re used to from other animals. Instead, what we find is two missing genes, one plucked¬†from the middle of the cluster and tacked onto its “front” end, and two genes totally detached from the rest. It’s not too bad as Hox cluster disintegration goes – six out of nine genes are still neatly ordered – but it certainly doesn’t look like something left over from the dawn of animals.

The bigger clue that caught my eye, though, was this little family tree in Figure 2:

Luo_etal2015-fig2

The red numbers on each branch indicate the number of gene families that expanded or first appeared in that lineage, and the green numbers are the families shrunk or lost. Note that our “living fossil” takes the lead in both. What I find funny is that it’s miles ahead of not only the animals generally considered “conservative” in terms of genome evolution, like the limpet Lottia and the lancelet Branchiostoma, but also the sea squirt (Ciona). Squirts are notorious for having incredibly fast-evolving genomes; then again, most of that notoriety was based on the crazily divergent sequences and often wildly scrambled order of its genes. A genome can be conservative in some ways and highly innovative in others. In fact, many of the genes involved in basic cellular functions are very slow-evolving in Lingula. (Note also: humans are pretty slow-evolving as far as gene content goes. This is not the first study to find that.)

So, Lingula, living fossil? Not so much.

The last bit I looked at was the section about shell genetics. Although it’s generally foolish to expect the shell-forming gene sets of two animals from different phyla to be similar (see my first footnote), if there are similarities, they could potentially go at least two different ways. First, brachiopods might be quite close to molluscs, which is the hypothesis Luo et al.‘s own treebuilding efforts support. Like molluscs, brachiopods also have a specialised mantle that secretes shell material, though having the same name doesn’t mean¬†the two “mantles” actually share a common origin. So who knows, some molluscan shell proteins, or shell regulatory genes, might show up in Lingula, too.

On the other hand, the composition of Lingula’s shell is more similar to our skeletons’. So, since they have to capture the same mineral, could the brachiopods share some of our skeletal proteins? The answer to both questions seems to be “mostly no”.

Molluscan shell matrix proteins, those that are actually built into the structure of the shell, are quite variable even within Mollusca. It’s probably not surprising, then, that most of the relevant genes¬†that are even present in Lingula are not specific to the mantle, and those that are are the kinds of genes that are generally involved in the handling of calcium or the building of the stuff around cells¬†in all kinds of contexts. Some of the regulatory mechanisms might be shared – Luo et al. report that BMP signalling seems to be going on around the edge of the mantle in baby Lingula, and this cellular signalling system is also involved in molluscan shell formation. Then again, a handful of similar signalling systems “are involved” in bloody everything in animal development, so how much we can deduce from this similarity is anyone’s guess.

As for “bone genes” – the ones that are most characteristically¬†tied to bone are missing (disappointingly or reassuringly, take your pick). The SCPP protein¬†family is so far known only from vertebrates, and its various members are involved in the mineralisation of bones and teeth. SCPPs originate from an ancient protein called SPARC, which seems to be generally present wherever collagen is (IIRC, it’s thought¬†to help collagen fibres arrange themselves correctly). Lingula has a gene for SPARC all right, but nothing remotely resembling an SCPP gene.

I mentioned that the shell of Lingula is built largely on collagen, but it turns out that it¬†isn’t “our” kind of collagen. “Collagen”¬†is just a protein¬†with a particular kind of repetitive sequence. Three amino acids (glycine-proline-something else, in case you’re interested) are¬†repeated¬†ad nauseam in the collagen chain,¬†and these repetitive regions let¬†the protein twist into characteristic rope-like fibres¬†that make collagen such a wonderfully tough basis for connective tissue. Aside from the repeats they all share, collagens are¬†a large and diverse bunch. The ones that form most of the organic matrix in bone¬†contain a non-repetitive and rather easily recognised domain at one end, but when Luo et al. analysed the genome and the proteins extracted from the Lingula shell, they found that none of the shell collagens possessed this domain. Instead, most of them had EGF domains, which are pretty widespread in all kinds of extracellular proteins. Based on the genome sequence, Lingula has a whole little cluster of these collagens-with-EGF-domains that probably originated from¬†brachiopod-specific gene duplications.

So, to recap: Lingula is not as conservative as its looks would suggest (never judge a living fossil by its cover, right?) We also finally¬†have actual sequences for lots of its shell proteins, which reveal that when it comes to building shells, Lingula does its own thing. Not much of a surprise, but still, knowing is a damn sight better than thinkin’ it’s probably so. We are scientists here, or what.

I am Very Pleased with this genome. (I just wish it was published five years ago ūüėõ )

***

Notes:

*This, interestingly, doesn’t seem to be the general case for all molluscs. Jackson et al. (2010) compared the genes building the pearly layer of snail (abalone, to be precise) and bivalve (pearl oyster) shells, and found that the snail¬†showed no sign of the chitin-making enzymes and silk type proteins that were so abundant in its bivalved cousins. It appears that even within molluscs, different groups have found different ways to make often very similar shell structures. However, all molluscs shells regardless of the underlying genetics are predominantly composed of calcium carbonate.

**You often hear about sharks, or crocodiles, or coelacanths, existing “unchanged” for 100 or 200 or whatever million years, but in reality, 200-million-year-old crocodiles aren’t even classified in the same families, let alone the same genera, as any of the living species. Again, the living coelacanth is distinct enough from its relatives in the Cretaceous, when they were last seen, to warrant its own genus in the eyes of taxonomists. I’ve no time to check up on¬†sharks, but I’m willing to bet the situation is similar. Whether Lingula‘s jaw-dropping 500-million-year tenure on earth is a result of taxonomic lumping or the shells genuinely looking that similar, I don’t know.¬†Anyway, rant over.

***

References:

Jackson DJ et al. (2010) Parallel evolution of nacre building gene sets in molluscs. Molecular Biology and Evolution 27:591-608

Luo Y-J et al. (2015) The Lingula genome provides insights into brachiopod evolution and the origin of phosphate biomineralization. Nature Communications 6:8301

The things you can tell from a pile of corpses…

I’m really late to this party, but I never claimed to be timely, and the thing about the reproductive habits of Fractofusus is too interesting¬†not to cover.* Rangeomorphs ¬†like Fractofusus are really odd creatures. They lived in that Ediacaran twilight zone between older Precambrian seas devoid of macroscopic animals and younger Cambrian seas teeming with recognisable members of modern groups.¬†Rangeomorphs such as Rangea,¬†Charnia¬†and Fractofusus itself¬†have such a unique fractal body plan (Narbonne, 2004)¬†that no one really knows what they are. Although they were probably not photosynthetic¬†like plants or algae (they are abundant¬†in deep sea sediments where there wouldn’t have been enough light), their odd body¬†architectures are equally¬†difficult¬†to compare to any animal that we know.

Mitchell et al. (2015) don’t bring us any closer to the solution of that mystery; they do, however, use the ultimate power of Maths to deduce how the enigmatic creatures might have reproduced. Fractofusus is an oval-shaped thingy that could be anywhere from 1 cm to over 40 cm in length. Unlike some other rangeomorphs, it lay flat on the seafloor with no holdfasts or stalks to be seen.¬†Fractofusus fossils are very common¬†in the Ediacaran deposits of Newfoundland.¬†Since there are so many of them, and there is no evidence that they were capable of movement in life, the researchers figured their spatial distribution might offer some clues as to their reproductive habits.¬†A¬†bit of seafloor covered in Fractofusus might look something like this (drawing from the paper):

clusters within clusters

(The lines between individuals don’t actually come from the fossils, they just represent the putative connection between a parent¬†and its babies.)

Statistical models suggest that the fossils are not randomly distributed but clearly clustered: small specimens around medium-sized ones, which are in turn gathered around the big guys. Two out of three populations examined show these clusters-within-clusters; the third has only one layer of clustering, but it’s still far from random. As the authors note, the real populations they studied involve a lot more specimens than shown in the diagram, but they “rarefied” them a bit for clarity of illustration while keeping their general arrangement.

The study looked not only at the distances between small, medium and large specimens, but also directions – both of where the specimens were and which way they pointed.¬†If young Fractofusus¬†spread by floating on the waves, they’d be influenced by currents in the area. It seems the largest specimens were – they are unevenly distributed in different directions. In contrast, smaller individuals were clustered around the bigger ones without regard to direction. Small and¬†large specimens alike pointed randomly every which way.

What does this tell us about reproduction? The authors conclude that the big specimens probably arrived on the current as waterborne¬†youngsters, hence their arrangement along particular lines . However, once there, they must have colonised their new home¬†in a way that doesn’t involve currents. Mitchell et al. think that way¬†was probably stolons – tendrils¬†that grew out from the parent and sprouted¬†a new individual at the end. This idea is further strengthened by the fact that among thousands¬†of specimens, not a single one shows evidence for other types of clonal reproduction – no fragments, and no budding¬†individuals, are known. (Plus if a completely sessile organism fragments, surely the¬†only way the pieces could spread¬†anywhere would be by riding currents, and that would show up in their distribution.)

Naturally, none of this tells us whether Fractofusus was an animal, a fungus or something else entirely. Sending out runners is not a privilege of a particular group, and while there is evidence that the original founders of the studied populations came from far away on the waves, we have no idea what it was that floated in to take root in those pieces¬†of ancient seafloor. Was it a larva? A spore? A small piece of adult tissue? Damned if we know. Despite what Wikipedia and¬†news headlines would have you believe, there is nothing to suggest¬†that¬†sex was involved. It may have been, but the evidence is silent on that count. (Annoyingly, the news¬†articles themselves acknowledge that. Fuck headlines is all I’m saying…)

While sometimes we gain insights into ancient reproductive habits via spectacular fossils like brooding dinosaurs or pregnant ichthyosaurs, this study is a nice reminder that in some cases, a lot can be deduced even in the absence of¬†such blatant evidence.¬†This was an interesting little piece of Precambrian ecology, and a few¬†remarks in the paper suggest¬†more to come: “Other taxa exhibit an intriguing range of non-random habits,” the penultimate paragraph says, “and our preliminary analyses indicate that Primocandelabrum and Charniodiscus may have also reproduced using stolons.”

An intriguing range of non-random habits? No citations? I wanna know what’s brewing!

***

*Also, I’ve got to write¬†something so I can pat myself on the back for actually achieving something beyond getting out of bed. Let’s just say Real Life sucks, depression sucks worse, and leave it at that.

***

References:

Mitchell EG et al. (2015) Reconstructing the reproductive mode of an Ediacaran macro-organism. Nature 524:343-346

Narbonne GM (2004) Modular construction of Early Ediacaran complex life forms. Science 305:1141-1144

Putting the cart before the… snake?

Time to reexamine some assumptions (again)! And also, talk about Hox genes, because do I even need a reason?

Hox genes often come up when we look for explanations for various innovations in animal body plans ‚Äď the digits of land vertebrates, the limbless abdomens of insects, the various feeding and walking and swimming appendages of crustaceans, the strongly differentiated vertebral columns of mammals, and so on.

Speaking of differentiated vertebral columns, here’s one group I’d always thought of as having pretty much the exact opposite of them: snakes. Vertebral columns are patterned, among other things, by Hox genes. Boundaries between different types of vertebrae such as cervical (neck) and thoracic (the ones bearing the ribcage) correspond to boundaries of Hox gene expression in the embryo ‚Äď e.g. the thoracic region in mammals begins where HoxC6 starts being expressed.

In mammals like us, and also in archosaurs (dinosaurs/birds, crocodiles and extinct relatives thereof), these boundaries can be really obvious and sharply defined ‚Äď here’s Wikipedia’s crocodile skeleton for an example:

In contrast, the spine of a snake (example from Wikipedia below) just looks like a very long ribcage with a wee tail:

Snakes, of course, are rather weird vertebrates, and weird things make us sciencey types dig for an explanation.

Since Hox genes appear to be responsible for the regionalisation of vertebral columns in mammals and archosaurs, it stands to reason that they’d also have something to do with the comparative lack of regionalisation (and the disappearance of limbs) seen in snakes and similar creatures. In a now classic paper, Cohn and Tickle (1999) observed that unlike in chicks, the Hox genes that normally define the neck and thoracic regions are kind of mashed together in embryonic pythons. Below is a simple schematic from the paper showing where three Hox genes are expressed along the body axis in these two animals. (Green is HoxB5, blue is C8, red is C6.)

Cohn_Tickle1999_hoxRegions

As more studies examined snake embryos, others came up with different ideas about the patterning of serpentine spines. Woltering et al. (2009) had a more in-depth look at Hox gene expression in both snakes and caecilians (limbless amphibians) and saw that there are in fact regions ruled by different Hoxes in these animals, if a little fuzzier than you’d expect in a mammal or bird ‚Äď but they don’t appear to translate to different anatomical regions. Here’s their summary of their findings, showing the anteriormost limit of the activity of various Hox genes in a corn snake compared to a mouse:

Woltering_etal2009-mouse_vs_snake

Such differences aside, both of the above studies operated on the assumption that the vertebral column of snakes is ‚Äúderegionalised‚ÄĚ – i.e. that it evolved by losing well-defined anatomical regions present in its ancestors. But is that actually correct? Did snakes evolve from more regionalised ancestors, and did they then lose this regionalisation?

Head and Polly (2015) argue that the assumption of deregionalisation is a bit stinky. First, that super-long ribcage of snakes does in fact divide into several regions, and these regions respect the usual boundaries of Hox expression. Second, ordinary lizard-shaped lizards (from which snakes descended back in the days of the dinosaurs) are no more regionalised than snakes.

The study is mostly a statistical analysis of the shapes of vertebrae. Using an approach called geometric morphometrics, it turned these shapes from dozens of squamate (snake and lizard) species into sets of coordinates, which could then be compared to see how much they vary along the spine and whether the variation is smooth and continuous or clustered into different regions. The authors evaluated hypotheses regarding the number of distinct regions to see which one(s) best explained the observed variation. They also compared the squamates to alligators (representing archosaurs).

The results were partly what you’d expect. First, alligators showed much more overall variation in vertebral shape than squamates. Note that that’s all squamates ‚Äď leggy lizards are nearly (though not quite) as uniform as their snake-like relatives. However, in all squamates, the best-fitting model of regionalisation was still one with either three or four distinct regions in front of the hips/cloaca, and in the majority, it was four, the same number as the alligator had.

Moreover, there appeared to be no strong support for an evolutionary pattern to the number of regions ‚Äď specifically, none of the scenarios in which the origin of snake-like body plans involved the loss of one or more regions were particularly favoured by the data. There was also no systematic variation in the relative lengths of various regions; the idea that snakes in general have ridiculously long thoraxes is not supported by this analysis.

In summary, snakes might show a little less variation in vertebral shape than their closest relatives, but they certainly didn’t descend from alligator-style sharply regionalised ancestors, and they do still have regionalised spines.

Hox gene expression is not known for most of the creatures for which vertebral shapes were analysed, but such data do exist for mammals (mice, here), alligators, and corn snakes. What is known about different domains of Hox gene activation in these three animals turns out to match the anatomical boundaries defined by the models pretty well. In the mouse and alligator, Hox expression boundaries are sharp, and the borders of regions fall within one vertebra of them.

In the snake, the genetic and morphological boundaries are both gradual, but the boundaries estimated by the best model are always within the fuzzy boundary region of an appropriate Hox gene expression domain. Overall, the relationship between Hox genes and regions of the spine is pretty consistent in all three species.

To finish off, the authors make the important point that once you start turning to the fossil record and examining extinct relatives of mammals, or archosaurs, or squamates, or beasties close to the common ancestor of all three groups (collectively known as amniotes), you tend to find something less obviously regionalised than living mammals or archosaurs ‚Äď check out this little figure from Head and Polly (2015) to see what they’re talking about:

Head_Polly2015-phylogeny_of_spines

(Moving across the tree, Seymouria is an early relative of amniotes but not quite an amniote; Captorhinus is similarly related to archosaurs and squamates, Uromastyx is the spiny-tailed lizard, Lichanura is a boa, Thrinaxodon is a close relative of mammals from the Triassic, and Mus, of course, is everyone’s favourite rodent. Note how alligators and mice really stand out with their ribless lower backs and suchlike.)

Although they don’t show stats for extinct creatures, Head and Polly argue that mammals and archosaurs, not snakes, are the weird ones when it comes to vertebral regionalisation. For most of amniote evolution, the norm was the more subtle version seen in living squamates. It was only during the origin of mammals and archosaurs that boundaries were sharpened and differences between regions magnified. Nice bit of convergent/parallel evolution there!

***

References:

Cohn MJ & Tickle C (1999) Developmental basis of limblessness and axial patterning in snakes. Nature 399:474-479

Head JJ & Polly PD (2015) Evolution of the snake body form reveals homoplasy in amniote Hox gene function. Nature 520:86-89

Woltering JM et al. (2009) Axial patterning in snakes and caecilians: evidence for an alternative interpretation of the Hox code. Developmental Biology 332:82-89

Finally, that sponge ParaHox gene

ParaHox genes are a bit like the underappreciated sidekicks of Hox genes. Or little sisters, as the case may be, since the two families are closely related. Hox genes are probably as famous as anything in evo-devo. Being among the first genes controlling embryonic development to be (a) discovered, (b) found to be conserved between very distantly related animals, they are symbolic of the late 20th century evo-devo revolution.

ParaHoxes get much less attention despite sharing some of the most exciting properties of Hox genes. Like those, they are involved in anteroposterior patterning ‚Äď that is, partitioning an embryo along its head to tail axis. Also like Hox genes, they are often neatly clustered in the genome, and when they are, they tend to be expressed in the same order (both in space and time) in which they sit in the cluster*. Their main ancestral roles for bilaterian animals seem to be in patterning the gut and the central nervous system (Garstang and Ferrier, 2013).

There are three known types of ParaHox gene, which are generally thought to be homologous to specific Hox subsets of Hox genes ‚Äď by the most accepted scheme, Gsx is the closest sister of Hox1 and Hox2, Xlox is closest to Hox3, and Cdx to Hox9 and above. It is abundantly clear that Hoxes and ParaHoxes are closely related, but there has been a bit of debate concerning the number of genes in the ancestral gene cluster that gave rise to both ‚Äď usually called ‚ÄúProtoHox‚ÄĚ (Garcia-Fern√†ndez, 2005).

Another big question about these genes is precisely when they originated, and in this regard, ParaHox genes are proving much more interesting than Hoxes. You see, there are plenty of animals with both Hox and ParaHox genes, which is what you’d expect given the ProtoHox hypothesis, but there are also animals with only ParaHoxes. If there really was a ProtoHox gene/cluster that then duplicated to give rise to Hoxes and ParaHoxes, then lone ParaHoxes (or Hoxes for that matter) shouldn’t happen ‚Äď unless the other cluster was lost along the way.

So a suspiciously Gsx-like gene in the weird little blob-creature Trichoplax, which has nothing remotely resembling a Hox gene, was a big clue that (a) Hox/ParaHox genes might go back further in animal evolution than we thought, (b) the loss of the entire Hox or ParaHox cluster is totally possible**, despite how fundamental these genes appear to be for correctly building an animal.

I wrote (at length) about a study by Mendivil Ramos et al. (2012), which revealed that while Trichoplax had no Hox genes and only one of the three types of ParaHox gene, it preserved the more or less intact genomic neighbourhoods in which Hox and ParaHox clusters are normally situated. One of the more interesting results of that paper was that the one sponge genome available at the time ‚Äď that of Amphimedon queenslandica, which had no trace of either Hox or ParaHox genes ‚Äď also contained statistically significant groupings of Hox and ParaHox neighbour genes, as if it had a Hox neighbourhood and a ParaHox neighbourhood, but the Hoxes and ParaHoxes themselves had moved out.

That study thus pointed towards an intriguing hypothesis, previously championed by Peterson and Sperling (2007) based solely on gene phylogenies: sponges once did have Hox and ParaHox genes/clusters, which at least some of them later lost. This would essentially mean that the two gene clusters go straight back to the origin of animals if not further***, and we may never find any surviving remnant of the ancestral ProtoHox cluster, since the closest living relatives of animals have neither the genes nor their neighbourhoods (that we know of).

Hypotheses are nice, but as we know, they do have a tendency to be tragically slain by ugly facts. Can we further test this particular hypothesis about sponges? Are there facts that could say yay or nay? (Of course there are. I wouldn’t be writing this otherwise ūüėČ )

I keep saying that we should always be careful when generalising from one or a few model organisms, that we ignore diversity in the animal kingdom at our own peril, and that ‚Äúdistantly related to us‚ÄĚ = ‚Äúlooks like our distant ancestors‚ÄĚ is an extremely dodgy assumption. Well, here’s another lesson in that general vein: unlike Amphimedon, some sponges have not just the ghosts of vanished ParaHox clusters, but intact, honest to god ParaHox genes!

It’s calcareous sponges again. Sycon ciliatum and Leucosolenia complicata, two charming little calcisponges, recently had their genomes sequenced (alas, they weren’t yet public last time I checked), and since then, there’s been a steady stream of ‚Äúcool stuff we found in calcisponge genomes‚ÄĚ papers from Maja Adamska’s lab and their collaborators. I’ve discussed one of them (Robinson et al., 2013), in which the sponges revealed their rather unhelpful microRNAs, and back in October (when I was slowly self-destructing from thesis stress), another study announced a couple of delicious ParaHoxes (Fortunato et al., 2014).

(Exciting as it is, the paper starts by tickling my pet peeves right off the bat by calling sponges ‚Äústrong candidates for being the earliest extant lineage(s) of animals‚ÄĚ… I suppose nothing can be perfect… *sigh*)

The study actually covers more than just (Para)Hox genes; it looks at an entire gene class called Antennapedia (ANTP), which includes Hoxes and ParaHoxes plus a handful of related families I’m far less interested in. Sycon and Leucosolenia don’t have a lot of ANTP genes ‚Äď only ten in the former and twelve in the latter, whereas a typical bilaterian like a fruit fly or a lancelet has several times that number ‚Äď but from phylogenetic analyses, these appear to be a slightly different assortment of genes from those present in Amphimedon, the owner of the first sequenced sponge genome. This picture is most consistent with a scenario in which all of the ANTP genes in question were present in our common ancestor with sponges, and each sponge lineage lost some of them independently. (You may not realise this until you start delving into the history of various gene families, but genes come and go a LOT in evolution.)

Sadly, many of the branches on these gene trees are quite wonky, including the one linking a gene from each calcisponge to the ParaHox gene Cdx. However, somewhat fuzzy trees are not the only evidence the study presents. First, the putative sponge Cdxes possess a little motif in their protein sequences that is only present in a handful of gene families within the ANTP class. If you take only these families rather than everything ANTP and make trees with them, the two genes come out as Cdx in every single tree, and with more statistical support than the global ANTP trees gave them. Another motif they share with all Hoxes, ParaHoxes and a few of their closest relatives, but not with other ANTP class families.

Second, at least the gene in Sycon appears to have the right neighbours (Leucosolenia was not analysed for this). Since the Sycon genome sequence is currently in pieces much smaller than whole chromosomes, only four or so of the genes flanking ParaHox clusters in other animals are clearly linked to the putative Cdx in the sponge. However, when the researchers did the same sort of simulation Mendivil Ramos et al. (2012) did for Amphimedon, testing whether Hox neighbours and ParaHox neighbours found across all fragments of the genome are (a) close to other Hox/ParaHox neighbours or randomly scattered (b) mixed or segregated, they once again found cliques of genes with little overlap, indicating the once-existence of separate Hox and ParaHox clusters.

Fortunato et al. (2014) also examined the expression of their newfound Cdx gene, and found it no less intriguing than its sequence or location in the genome, although their description in the paper is very limited (no doubt because they’re trying to cram results on ten genes into a four-page Nature paper). The really interesting activity they mention and picture is in the inner cell mass of the young sponge in its post-larval stages ‚Äď the bit that develops into the lining of its feeding chambers. Which, Adamska’s team contend, may well be homologous to our gut lining. In bilaterians, developing guts are one of the major domains of Cdx and ParaHox genes in general!

So at least three different lines of evidence ‚Äď sequence, neighbours and expression ‚Äď make this picture hang together quite prettily. It’s incredibly cool ‚Äď the turning on their heads of long-held assumptions is definitely the most exciting part of science, I say! On the other hand, it’s also a little disheartening, because now that everyone in the animal kingdom except ctenophores has definitive ParaHox genes and at least the empty seats once occupied by Hox genes, are we ever going to find a ProtoHox thingy? May it be that it’ll turn up in one of the single-celled beasties people like I√Īaki Ruiz-Trillo are sequencing? That would be cool and weird.

The coolest twist on this story, though, would be to discover traces of ProtoHoxes in a ctenophore, since solid evidence for ProtoHox-wielding ctenophores would (a) confirm the strange and frankly quite dubious-sounding idea that ctenophores, not sponges, are the animal lineage farthest removed from ourselves, (b) SHOW US A FREAKING PROTOHOX CLUSTER. (*bounces* >_> Umm, * cough* OK, maturity can suck it ūüėÄ ) However, given how horribly scrambled at least one ctenophore genome is (Ryan et al., 2013), that’s probably a bit too much to ask…

***

Notes

*Weirdly, the order of expression in time is the opposite of that of the Hox cluster. In both clusters, the ‚Äúanterior‚ÄĚ gene(s), i.e. Hox1-2 or Gsx, are active nearest the front of the embryo, but while anterior Hox genes are also the earliest to turn on, in the ParaHox cluster the posterior gene (Cdx) wakes up first. /end random trivia

**Of course we’ve long known that losing a Hox cluster is not that big a deal, but previously, all confirmed losses occurred in animals with more than one Hox cluster to begin with ‚Äď a fish has plenty of Hox genes left even after chucking an entire set of them.

***With the obligatory ctenophore caveat

***

References

Fortunato SAV et al. (2014) Calcisponges have a ParaHox gene and dynamic expression of dispersed NK homeobox genes. Nature 514:620-623

Garcia-Fernàndez J (2005) The genesis and evolution of homeobox gene clusters. Nature Reviews Genetics 6:881-892

Garstang M & Ferrier DEK (2013) Time is of the essence for ParaHox homeobox gene clustering. BMC Biology 11:72

Mendivil Ramos O et al. (2012) Ghost loci imply Hox and ParaHox existence in the last common ancestor of animals. Current Biology 22:1951-1956

Peterson KJ & Sperling EA (2007) Poriferan ANTP genes: primitively simple or secondarily reduced? Evolution and Development 9:405-408

Robinson JM et al. (2013) The identification of microRNAs in calcisponges: independent evolution of microRNAs in basal metazoans. Journal of Experimental Zoology B 320:84-93

Ryan JF et al. (2013) The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science 342:1242592

Hi, real world, again!

The Mammal has emerged from a thesis-induced supermassive black hole and a Christmas-induced food coma, only to find that in the month or so that she spent barely functional and buried in chapters covered in the supervisor’s dreaded Red Pen, things actually happened in the world outside. This, naturally, manifested in thousands of items feeling thoroughly neglected in RSS readers and email inboxes. (Jesus. How many times have I vowed never to neglect my RSS feed again? Oh well, it’s not like unemployment is such a busy occupation that I can’t deal with a measly two and a half thousand articles ūüėõ )

… earlier tonight, the paragraph here said I wasn’t doing a proper post yet, “just pointing out” a couple of the cooler things I’ve missed. Then somehow this thing morphed into a 1000+ word post that goes way beyond “pointing things out”. It’s almost like I’ve been itching to write something that isn’t my thesis. >_>

So the first cool thing I wanted to “point out” is the genome paper of the centipede Strigamia maritima, which is a rather nondescript little beast hiding under rocks on the coasts of Northwest Europe. This is the first sequenced genome of a myriapod – the last great class of arthropods to remain untouched by the genome sequencing craze after many genomes from insects, crustaceans and chelicerates (spiders, mites and co.).¬† The genome sequence itself has been available for years (yay!), but its “official” paper (Chipman et al., 2014) is just recently out.

Part of the appeal of Strigamia – and myriapods in general – is that they are considered evolutionarily conservative for an arthropod. In some respects, the genome analysis confirms this. Compared to its inferred common ancestor with us, Strigamia has lost fewer genes than insects, for example. Quite a lot of its genes are also linked together similarly to their equivalents in distantly related animals, indicating relatively little rearrangement in the last 600 million years or so. But this otherwise conservative genome also has at least one really unique feature.

Specifically, this centipede – which is blind – has not only lost every bit of DNA coding for known light-sensing proteins, but also all known genes specific to the circadian clock. In other animals, genes like clock and period mutually regulate one another in a way that makes the abundance of each gene product oscillate in a regular manner (this is about the simplest graphical representation I could find…). The clock runs on a roughly daily cycle all by itself, but it’s also connected to external light via the aforementioned light-sensing proteins, so we can constantly adjust our internal rhythms according to real day-night cycles.

There are many blind animals, and many that live underground or otherwise find day and night kind of irrelevant, but even these are often found to have a functioning circadian clock or keep some photoreceptor genes around. However, based on the genome data, our favourite centipede may be the first to have completely lost both. The authors of the genome paper hypothesise that this may be related to the length of evolutionary time the animals have spent without light. Things like mole rats are relatively recent “inventions”. However, the geophilomorph order of centipedes, to which Strigamia belongs, is quite old (its most likely sister group is known from the Carboniferous, so they’re probably at least that ancient). Living geophilomorphs are all blind, so chances are they’ve been that way for the last 300+ million years.

Nonetheless, the authors also note that geophilomorphs are still known to avoid light – the question now is how the hell they do it… And, of course, whether Strigamia has a clock is not known – only that it doesn’t have the clock we’re used to. We also have no idea at this point how old the gene losses actually are, since all the authors know is that one other centipede from a different group has perfectly good clock genes and opsins.

In comparison with fruit flies and other insects, the Strigamia genome also reveals some of the ways in which evolutionary cats can be skinned in multiple ways. There is an immune-related gene family we share with arthropods and other animals, called Dscam. The product of this gene is involved in pathogen recognition among other things, and in flies, Dscam genes are divided into roughly 100 chunks or exons, most of which are are found in clusters of variant copies. When the gene is transcribed, only one of these copies is used from each such cluster, so in practical terms the handful of fruit fly Dscam genes can encode tens of thousands of different proteins, enough to adapt to a lot of different pathogens.

A similar arrangement is seen in the closely related crustaceans, although with fewer potential alternative products. In other groups – the paper uses vertebrates, echinoderms, nematodes and molluscs for comparison – the Dscam family is pretty boring with at most one or two members and none of these duplicated exons and alternative splicing business. However, it looks like insects+crustaceans are not the only arthropods to come up with a lot of DSCAM proteins. Strigamia might also make lots of different ones¬†(“only” hundreds in this case), but it achieved this by having dozens of copies of the whole gene instead of performing crazy editing feats on a small number of genes. Convergent evolution FTW!

Before I paraphrase the entire paper in my squeeful enthusiasm (no, seriously, I’ve not even mentioned the Hox genes, and the convergent evolution of chemoreceptors, and I think it’s best if I shut up now), let’s get to something else that I can’t not “point out” at length: a shiny new vetulicolian, and they say it’s related to sea squirts!

Vetulicolians really deserve a proper discussion, but in lieu of a spare week to read up on their messiness, for now, it’s enough to say that these early Cambrian animals have baffled palaeontologists since day one. Reconstructions of various types look like… a balloon with a fin? Inflated grubs without faces? I don’t know. Drawings below (Stanton F. Fink, Wikipedia) show an assortment of the beasts, plus Yunnanozoon, which may or may not have something to do with them. Here are some photos of their fossils, in case you wondered.

Vetulicolians from Wiki

They’re certainly difficult creatures to make sense of. Since their discovery, they’ve been called both arthropods and chordates, and you can’t get much farther than that with bilaterian animals (they’re kind of like the Nectocaris of old, come to think of it…).

The latest one was dug up from the Emu Bay Shale of Australia, the same place that yielded our first good look at anomalocaridid eyes. Its newest treasure has been named Nesonektris aldridgei by its taxonomic parents (Garc√≠a-Bellido et al., 2014), and it looks something like this (Diego Garc√≠a-Bellido’s reconstruction from the paper):

Garcia-Bellido_etal2014-nesonektris_recon

In other words, pretty typical vetulicolian “life but not as we know it”, at first glance. Its main interest lies in the bit labelled “nc” in the specimens shown below (from the same figure):

García-Bellido_etal2014-nesonektris_notochords

This chunky structure in the animal’s… tail or whatever is a notochord, the authors contend. Now, only one kind of animal has a notochord: a chordate. (Suspicious annelid muscle bundles notwithstanding. Oh yeah, I also wanted to post on Lauri et al. 2014. Oops?) So if this thing in the middle of Nesonektris’s tail is a notochord, then at the very least it is more closely related to chordates than anything else.

Why do they think it is one? Well, there are several long paragraphs devoted to just that, so here goes a summary:

1. It’s probably not the gut. A gut would be the other obvious ID, but it doesn’t fit very well in this case. Structures interpreted as guts in other vetulicolians – which sometimes contain stuff that may be half-digested food – (a) start in the front half of the body, where the mouth is, (b) constrict and expand and coil and generally look much floppier than this, (c) don’t look segmented, (d) sometimes occur alongside these tail rod-like thingies, so probably aren’t the same structure.

2. It positively resembles modern half-decayed notochords. The notochords of living chordates are long stacks of (muscular or fluid-filled) discs, which fall apart into big blocks as the animal decomposes after death. Here’s what remains of the notochord of a lamprey after two months for comparison (from Sansom et al. (2013)):

Sansom_etal2013-adult_lamprey_notochord_d63

This one isn’t as regular as the blockiness in the fossils, I think, but that could just be the vetulicolians not being quite as rotten.

There is, of course, a but(t). To be precise, there are also long paragraphs discussing why the structure might not be a notochord after all. It’s much thicker than anything currently interpreted as such in reasonably clear Cambrian chordates, for one thing. Moreover, it ends right where the animal does, in a little notch that looks like a good old-fashioned arsehole. By the way, the paper notes, vetulicolian tails in general don’t go beyond their anuses by any reasonable interpretation of the anus, and a tail behind the anus is kind of a defining feature of chordates, though this study cites a book from the 1970s claiming that sea squirt larvae have a vestigial bit of proto-gut going all the way to the tip of the tail. (I suspect that claim could use the application of some modern cell labelling techniques, but I’ve not actually seen the book…)

… and there is a phylogenetic analysis, in which, if you interpret vetulicolians as deuterostomes (which impacts how you score their various features), they come out specifically as squirt relatives whether or not you count the notochord. I’m never sure how much stock to put in a phylogenetic analysis based on a few bits of anatomy gleaned from highly contentious fossils, but at least we can say that there are other things – like a hefty cuticle – beyond that notochord-or-not linking vetulicolians to a specific group of chordates.

Having reached the end, I don’t feel like this paper solved anything. Nice fossils either way ūüôā

And with that, I’m off. Maybe next time I’ll write something that manages to be about the same thing throughout. I’ve been thinking that I should try to do more posts about broader topics rather than one or two papers (like the ones I wrote about ocean acidification or homology versus developmental genetics), but I’ve yet to see whether I’ll have the willpower to handle the necessary reading. I’m remarkably lazy for someone who wants to know everything ūüėÄ

(Aside: holy crap, did I ALSO miss a fucking Nature paper about calcisponges’ honest to god ParaHox genes? Oh my god, oh my GOD!!! *sigh* This is also a piece of incredibly exciting information I’ve known for years, and I miss it when it actually comes out in a journal bloody everyone reads. You can tell I’ve been off-planet!)

References:

Chipman AD et al. (2014) The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima. PLoS Biology 12:e1002005

García-Bellido DC et al. (2014) A new vetulicolian from Australia and its bearing on the chordate affinities of an enigmatic Cambrian group. BMC Evolutionary Biology 14:214

Lauri A et al. (2014) Development of the annelid axochord: insights into notochord evolution. Science 345:1365-1368

Sansom RS et al. (2013) Atlas of vertebrate decay: a visual and taphonomic guide to fossil interpretation. Palaeontology 56:457-474

Because I couldn’t not post about Dendrogramma

And the deep sea surprises us yet again (photos of the type specimen of Dendrogramma enigmatica from Just et al. [2014]).

I totally ignored the original hype about these beasties. I saw them pop up on I Fucking Love Science the other day, read the headline, decided it was probably another annoyingly sensationalised news story about a moderately strange new species and went on with my life. (The fact that they kinda look like weird flatworms didn’t help) Well, now that I’ve seen the paper, I… nah, I don’t regret the decision to ignore the news story, because hyperbole like that headline about rewriting the tree of life drives me up the wall, but I am glad that I finally checked what the hype was all about.

It’s really cool, after all these years of humanity cataloguing the living world, to find something so weird that basically all we can say about it is that it’s an animal. At this point it’s not clear to me how much of that is genuine weirdness and how much is simply down to the lack of data. The organisms were found in bulk seafloor samples brought up from depths of 400 and 1000 m somewhere off Tasmania nearly thirty years ago, and they are apparently quite poorly preserved. There’s no DNA, though commenters on the PLoS article seem to think it might be possible to get some out of the specimens. (That would be nice!)

According to the authors’ description, the general organisation of Dendrogramma species can be discerned and is much like a cnidarian or a ctenophore – two basic germ layers with thick jelly in between, and a blind gut – but they appear to lack anything that would clearly identify them as a member of either group, such as comb rows or stinging cells. Because they appear to have only two germ layers, the authors conclude they are probably not bilaterians, but because they don’t have diagnostic features of any other kind of animal, and because there’s so much more we don’t know about them, they don’t feel brave enough to place them beyond that.

The beasties are made of a stalk and a flat disc; the mouth opens at the tip of the stalk and the gut extends into the disc, where it bifurcates repeatedly to form dozens of branches. Two comments on the PLoS website point out that this arrangement is a bit like a flatworm – many of which have a long pharynx that they can poke out to feed, and a highly branched intestine occupying most of the body (a lovely diagram and photo can be found in the bottom half of this page).

Superficially at least, it sounds possible that Dendrogramma‘s “stalk” is an extended pharynx. However, flatworms are bilaterians, and between their skin and their gut wall they are full of the tissues of the mesoderm, the third germ layer – muscles, simple kidneys, reproductive organs and quite a lot of cell-rich connective tissue. Just et al.‘s description of Dendrogramma states that the equivalent space in these creatures is filled with mesogloea, i.e. jelly with few or no cells. If Dendrogramma really lacks mesodermal tissues, then it wouldn’t make a very good flatworm! (The paper itself doesn’t discuss the flatworm option at all, presumably for similar reasons.)

Of course, the thing that piqued my interest in Dendrogramma is its supposed resemblance to certain Ediacaran fossils, specifically these ones. It would be awesome if we could demonstrate that the living and the fossil weirdos are related, since then determining what Dendrogramma is would also classify the extinct forms, but I’m not holding my breath on this count. The branching… whatevers in the fossils in question may look vaguely like the branching gut of Dendrogramma, but, as discussed above, so do flatworm guts. The similarity to the fossils may well have nothing to do with actual phylogenetic relatedness, which the authors sound well aware of.

Nature, helpful as always. >_>

It seems all we can do for the moment is wait for more material to come along, hopefully in a good enough state to make detailed investigations including genetic studies. My inner developmental biologist is also praying for embryos, but the gods aren’t generally kind enough to grant me these sorts of wishes ūüėõ

I do quite like the name, though. Mmmmm, Dendrogramma. ūüôā

***

Reference:

Just J et al. (2014) Dendrogramma, new genus, with two new non-bilaterian species from the marine bathyal of southeastern Australia (Animalia, Metazoa incertae sedis) ‚Äď with similarities to some medusoids from the Precambrian Ediacara. PLoS ONE 9:e102976

Precambrian muscles??? Oooooh!

Okay, consider this a cautious squee. I wish at least some of those Ediacaran fossils were a little more obvious. I mean, I might love fossils, but I’m trained to squirt nasty chemicals on bits of dead worm and play with protein sequences, not to look at faint impressions in rock and see an animal.

Most putative animals from the Ediacaran period, the “dark age” that preceded the Cambrian explosion, are confusing to the actual experts, not just to a lab/computer biologist with a¬†fondness for¬†long-dead things. The new paper by Liu et al. (2014)¬†this post is about lists a “but see” for pretty much every interpretation they cite. The problem is twofold: one, as far as I can tell, most¬†Ediacaran fossils¬†don’t actually preserve that much interpretable detail. Two, Ediacaran organisms¬†lived at a time when the kinds of animal body plans we’re familiar with today were just taking shape. The Ediacaran is the age of ancestors, and it would be more surprising to find a creature we can easily categorise¬†(e.g. a snail) than a¬†weird beastie¬†that isn’t quite anything we know.

Having said that, Liu et al. think they are able to identify the new fossil they named Haootia quadriformis. Haootia comes from the well-known Fermeuse Formation of¬†New Foundland, and is estimated to be about 560 million years old. The¬†authors¬†say its body plan – insofar as it can be made out on a flat image pressed into the rock – looks quite a lot like living¬†staurozoan¬†jellyfish, with a four-part symmetry and what appear to be branching arms or tentacles coming off the corners of its body. The most obvious difference is that Haootia seems to show the outline of a huge circular holdfast that’s much wider than usual¬†for living staurozoans.

However, the most exciting thing about this fossil is not its shape, but the fact that most of it is made up of fine, highly organised parallelish lines Рwhat the authors interpret as the impressions of muscle fibres. The fibres run in different directions according to their position in the body; for example, they seem to follow the long axes of the arms.

(Below: the type specimen of Haootia with some of the fibres visible, and various interpretive drawings of the same fossil. Liu et al. is a free paper, so anyone can go and look at the other pictures, which include close-ups of the fibres and an artistic reconstruction of the living animal.)

If the lines do indeed come from muscle fibres, then regardless of its precise¬†affinities,¬†Haootia is certainly an animal, and it is probably¬†at least related to the group called eumetazoans, which includes cnidarians like jellyfish and bilaterians like ourselves (and maybe comb jellies, but let’s not open that can of jellies¬†just now). Non-eumetazoans – sponges and Trichoplax – do not have muscles, and unless comb jellies¬†really are what some people think they are, we can be almost certain that the earliest animals didn’t either.

Finding Ediacaran muscles is also interesting because it gives us further evidence that things capable of the kinds of movement attributed to some Ediacaran fossils really existed back then. Of course, it would have been nicer to find evidence of muscle and evidence of movement in the same fossils, but hey, this is the Precambrian. You take what you get.

(P.S.: Alex Liu is cool and I heart him. OK, I saw him give one¬†short talk, interviewing for a job at my department that he didn’t get *sniffles*, so maybe I shouldn’t be pronouncing such fangirlish judgements, but that¬†talk was awesome. As I’ve said before, my fangirlish affections are not very hard to win ūüôā )

***

Reference:

Liu AG et al. (2014) Haootia quadriformis n. gen., n. sp., interpreted as a muscular cnidarian impression from the Late Ediacaran period (approx. 560 Ma). Proceedings of the Royal Society B 281:20141202

Ctenophore nervous systems redux

… and reasons I suddenly find myself liking Joseph Ryan.

Ryan was the first author on the first ctenophore genome paper, published last December, though I’d known his name long before that thanks to his¬†developmental genetic work on jelly creatures of various kinds. As is clear from the genome study, he leans quite strongly towards the controversial idea that ctenophores represent¬†the sister lineage to all other animals.

And here’s¬†reason one that my eyes suddenly have little cartoon hearts pulsing in their irises upon reading his short perspective paper in Zoology (Ryan, 2014). Throughout the paper, not once does he refer to ctenophores as “the” basal animal lineage. Instead, he uses phrases like “most distant relative to all other animals” or “the sister group to the rest of the animals”.

In other words, he’s scrupulously¬†avoiding my giantest pet peeve, and I’m sure he doesn’t do it to please an obscure blogger, but gods, that’s even better. I don’t want to be pleased, I want evolutionary biology¬†to get rid of stupid anthropocentric ladder-thinking nonsense.

Anyway, the little paper isn’t actually about animal phylogeny, it’s about nervous systems.

Both ctenophore genome papers argued that the ancestors of these pretty beasties might have¬†evolved nervous systems independently of ours. The second one¬†seemed positively convinced of this, but, as Ryan’s review¬†points out, there are other possibilities even assuming that the placement of ctenophores outside the rest of the animals is correct.

While it’s possible that nerve cells and nervous systems evolved twice among the animals – it is equally¬†possible that they have been lost twice (i.e. in sponges and blobby little placozoans). Full-fledged nerve cells wouldn’t be the first things that sponges and blobs have lost.

And Ryan¬†basically wrote this short piece just to point that out. The argument that ctenophore nervous systems are their own invention is based on the absence or strange behaviour of many “conserved” nervous system-related genes. Ctenophores appear to completely lack some common neurotransmitters such as dopamine, as well as a lot of genes/proteins that are necessary for nerve synapses to work in us. Other genes that are “neural” in other animals are present but not associated with the nervous system in ctenophores.

BUT, Ryan cautions, there are also commonalities that shouldn’t be dismissed. While ctenophores can’t make dopamine, they do possess several¬†other¬†messenger molecules common in animal nervous systems. Same goes for the proteins involved in making synapses. Likewise, while they completely lack some of the genes responsible for defining various types of nerve cells (see: Hox genes), other genes involved in the same kind of stuff are definitely¬†there.

The key thing, he says, is to take a closer look at more of these genes and find out what they do by manipulating them. Since there are clearly both similarities and differences, we must assess their extent.

And that, my friends, is the question¬†at the heart of every homology argument ever. How similar is similar enough? Greater minds than mine have struggled with the answer, and I imagine they’ll continue to struggle until we invent time machines or find fossils of every single stage in the evolution of everything.

Until then, I’ll leave you with the closing lines of Ryan’s paper.¬†I may not agree that we’ve “revealed” the position of ctenophores, but I’m absolutely on board with the excitement ūüôā

One thing is quite clear: something remarkable happened regarding the evolution of the nervous system very early in animal evolution. Either a nervous system existed in the ancestor and was lost in certain lineages, or ctenophores invented their own nervous system independently (Fig. 1). Either possibility is quite extraordinary. The revelation that ctenophores are the sister group to the rest of animals has sparked a truly exciting debate regarding the evolutionary origins of the nervous system, one that will continue as additional genomic and functional data come to the fore.

Reference:

Ryan JF (2014) Did the ctenophore nervous system evolve independently? Zoology in press, available online 11/06/2014, doi: 10.1016/j.zool.2014.06.001

About X-frogs and failing at regeneration

Not the usual mad squee, but here’s a neat little system for studying regeneration that I quite liked today. I normally think about regeneration in terms of amputated limbs, mutilated hearts, decapitated¬†flatworms. But you can induce a kind of “regeneration” in a less drastic and rather more tricksy way, at least in some animals. In newts and salamanders, you can create a small, superficial wound on the side of a limb, then manipulate¬†a nearby nerve into it and add some skin from the other side of the limb.

The poor hurt limb¬†then decides you’ve actually cut something off and tells the wound to grow a new limb. If you don’t add skin, regeneration begins but doesn’t progress very far; if you don’t add a nerve, nothing happens. IIRC you can also make extra heads in some worms in a similar¬†way, but I digress.¬†The figure below from Endo et al. (2004) illustrates just how well the procedure¬†can work. The top row shows stages in the development of the extra limb, while¬†D¬†shows the stained skeletons of the original and new limbs. I’d say that’s a pretty good looking forearm and hand!

Endo_etal2004-ectopicLimb

 

That this trick works is in itself a very interesting insight into the nature of regeneration, as it helps us figure out exactly what it is that triggers various steps of regeneration as opposed to a simple healing process (Endo et al., 2004).

Clawed frogs (Xenopus) have been staples of embryology for a long time, but they are also quite fascinating from a regeneration point of view. One, they can regrow their limbs¬†while they are tadpoles, but mostly lose the ability as they mature. They also have a really weird thing going on with their tadpole¬†tails, which they can regenerate early on, then can’t, then can again¬†(Slack et al., 2004). Huh? O.o

Two, their adult limb regeneration ability is not totally absent: it’s somewhere between salamanders’ (oh, whatever, fine, I can do that!) and ours (uh… as long as I’m a baby and it’s just a fingertip?). In a frog, an amputated arm or leg doesn’t simply¬†heal over, but the… thing that grows out of¬†the stump¬†is just a simple cartilaginous spike with no joints or muscles. It’s as if the system was trying very hard to remember how to form a limb¬†but kind of got distracted.

We are obviously interested in creating superhumans with mad regeneration skillz, which also makes us interested in how and why animals lose this seemingly very useful ability*. (Bely (2010) wrote a lovely piece on this not at all simple question.) So: Xenopus yay!

Now, Mitogawa et al. (2014) have devised a skin wound + nerve deviation system to grow little extra limb buds in adult frogs. As you might expect, it doesn’t work nearly as well as it does in axolotls: you need three nerves rather than one, and it only induces a bud about half the time, but it¬†works well enough for research purposes.

The bud (technically, a blastema when you’re talking about regeneration) looks like a good regeneration blastema: it’s got the seemingly undifferentiated cells inside, it’s got the thickened epidermis at the tip that teams up with the nerves to give developmental instructions to the rest of the thing, and it expresses a whole bunch of genes that are turned on in normal limb blastemas.

(Totally random aside: thanks to Chrome’s spell checker, I have discovered¬†that “blastema” is an anagram for “lambaste”.)

One area where this blastema-by-trickery fails is making cartilage, which is one of the few proper limb things the defective spike regenerates in frogs do contain. There’s no simple way of coaxing a complete spike out of these blastemas. The researchers tried the skin graft thing from axolotls (which can already form cartilage without the skin graft), but they still only got a little blastema with no cartilage. To get a skeleton, however crappy,¬†¬†you¬†need to cut out muscles and crack the underlying bone, which kind of defeats the purpose of the whole exercise¬†IMO. At that point, you might as well just chop off the arm.

Below: the best a frog can do. Development of blastema-like bumps and “spike limbs” on the upper arm from Mitogawa et al. (2014). Compared to the fully formed accessory limbs of axolotls, the things you can see in B-D here are¬†not terribly impressive, but they may be just the “transitional form” we need!

The failure of skin grafts alone at inducing cartilage, however, does hint at the things that go wrong with regeneration in frogs. Mitogawa et al. speculate that newt and axolotl limbs produce factors that frogs can only get from damaged bone. Broken bones even in us form a cartilaginous callus as they begin to heal, and unlike the cartilage in the extra limbs of axolotls, the cartilage in frog spikes is directly attached to the underlying bone.

They also point out that if you add proteins called BMPs¬†to amputated mouse arms, which are otherwise even shitter at regeneration than frog arms, a surprising¬†amount of bone formation¬†occurs. (“BMP” stands for bone morphogenetic protein, which is a big clue to their function.) So it looks like there may be a kind of regeneration gradient from mammals (need bone damage AND extra BMP), through frogs (need bone damage, take care of BMPs themselves) to salamanders (don’t need either).

I should¬†point out that salamanders and frogs are equally closely related to us, so this isn’t a proper evolutionary gradient, but given all the ways in which¬†we and amphibians¬†are fundamentally similar, our loss of regenerative ability may well have evolved¬†through a similar stage¬†to where frogs are now. Neat!

(I just wish they stopped calling us “higher vertebrates”. That phrase annoys me right up the fucking wall, because, and I may have said this before, EVOLUTION IS NOT A GODDAMNED LADDER. The group they are referring to has a perfectly good name that doesn’t imply ladder thinking. Amniotes, people. Or mammals, if you mean mammals, but I think if they’d¬†meant mammals they¬†would have said mammals. End grump.)

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*I mean “us” in a very general sense. I think regenerative medicine is the coolest thing in medicine¬†since vaccines and antibiotics, but I personally don’t think that the evolution of regenerative ability needs medical considerations to make it interesting. Whatever. I’m not exactly a practically minded person ūüėõ

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References:

Bely AE (2010) Evolutionary loss of animal regeneration: pattern and process. Integrative and Comparative Biology 50:515-527

Endo T et al. (2004) A stepwise model system for limb regeneration. Development 270:135-145

Mitogawa K et al. (2014) Ectopic blastema induction by nerve deviation and skin wounding: a new regeneration model in Xenopus laevis. Regeneration 2:11

Slack JMW et al. (2004) Cellular and molecular mechanisms of regeneration in Xenopus. Philosophical Transactions of the Royal Society B 359:745-751