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 😛

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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

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Catching up

So I felt like I couldn’t put off the sixteen hundred articles twiddling their thumbs and tapping their feet in my RSS reader any longer. This is the first part of the crop that has accumulated since late December (yikes!). Legless axolotls, homing starfish, secretly related proteins, and more!

1. Axolotls are good at regenerating – until you make them grow up.

(Portrait of a pale lab/aquarium variety axolotl by Orizatriz, Wiki Commons.)

It’s probably not exactly obvious from my posting record, but a large part of my PhD work is about regeneration. It’s something we humans are pretty shit at, but many other vertebrates aren’t. Axolotls, these adorably dumb-faced salamanders, can easily regrow their legs. However, lab axolotls are kind of permanent babies. Although they can grow up in the sense that they are able to breed, they normally keep larval characteristics like gills throughout their lives. It’s reasonable to suspect that this influences their regenerative ability – after all, tadpoles lose their ability to regrow limbs the moment they turn into frogs.

It’s possible to make axolotls metamorphose, too, if you treat them with thyroxine (the same hormone that induces metamorphosis in “normal” amphibians). And when they turn into proper adult salamanders, they suddenly become much poorer regenerators. They can still replace a limb – kind of. But they take twice as long as non-metamorphosed axolotls of the same age and size, and they invariably wind up with small, malformed limbs, often missing bones. After amputation, new skin is slower to grow over their wounds, and the cells that gather under the new skin are sluggish to divide. Something about metamorphosis – that isn’t simply age – dramatically changes how they respond to amputation.

Reference: Monaghan JR et al. (2014) Experimentally induced metamorphosis in axolotls reduces regeneration rate and fidelity. Regeneration advance online publication, doi: 10.1002/reg2.8

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2. Similar cells repair muscles in crustaceans and vertebrates

“Regeneration” can cover a lot of different processes. For example, depending on the creature and the organ you’ve damaged, regenerated body parts can come from totally different kinds of cells. In planarian flatworms, a single kind of stem cell can replace anything else in the body. In the eyes of newts, mature cells of the iris transform into lens cells to replace a missing lens. In our muscles, there are special cells called satellite cells that are held in reserve specifically to make new muscle cells when needed.

This recent study of a little crustacean called Parhyale hawaiensis suggests that muscle regeneration in the fingernail-sized arthropod works in much the same way. Konstantinidis and Averof shot early embryos of Parhyale with DNA encoding a fluorescent marker, which randomly integrated into the genomes of some of the cells it hit. In a few “lucky” individuals, the marker ended up labelling just one cell lineage, and the pair used these animals to figure out which cells made which tissues in a regenerated limb.

It turned out that cells in Parhyale are limited in their potential. Descendants of the ectodermal lineage could make skin and nerves but not muscle, and the mesodermal lineage built muscle but not skin or nerves. Moreover, labelled cells only contributed to regeneration near their original location – animals with their left sides labelled never regrew glowing limbs on the right side. This is starting to sound a lot like vertebrates, but it’s still a very general observation. However, the similarities don’t end there.

Like vertebrate muscles, the muscles of the little crustaceans contain satellite-like cells derived from the mesodermal lineage that sit beside mature muscle cells and express the Pax3/7 gene. When the researchers transplanted some of these cells from animals with the glowy label into leg stumps of non-glowy animals, there were glowing muscle cells in some of the regenerated limbs. So like satellite cells, these cells can turn into muscle during regeneration. There’s little question that muscle cells have a common origin in vertebrates and arthropods like Parhyale, but it’s really cool to see that their mechanisms of regeneration also might.

Reference: Konstantinidis N & Averof M (2014) A common cellular basis for muscle regeneration in arthropods and vertebrates. Science, published online 02/01/2014, doi: 10.1126/science.1243529

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3. Convergent evolution is a poor explanation of rhodopsins

Proteins can be difficult. I mean, sometimes they do their darnedest to hide their family ties. A protein is a chain of amino acids (on average about 300 of them) often folded into a complex shape. Closely related proteins have obviously similar amino acid sequences. However, more distant relatives can be harder to identify. There are about 20 different kinds of amino acids in proteins, so the number of possible sequences is unimaginably vast. The same function can be carried out by very different sequences, and therefore enough evolution can completely erase sequence similarity.

Protein structures are generally thought to be more conserved than sequences. Like function, structure allows for a huge amount of sequence variation without significantly changing. However, theoretically, it’s possible that two unrelated proteins have similar structures because of their similar functions, not because of common ancestry. Apparently, this has been argued for the two types of rhodopsins – proteins that harvest light in systems as different as a the “solar generator” of a salt-loving microbe and the photoreceptors of our own eyes.

If Type I and Type II rhodopsins are similar despite being unrelated, one would assume that this is because they need to be that way to capture light. There are, after all, astronomical numbers of possible protein structures, and the chances of two protein families accidentally stumbling onto the same one without selection steering are slim to say the least. But, in fact, you can rearrange the structure of a rhodopsin in all kinds of cunning ways without destroying its function. This rather weakens the case for convergent evolution, and suggests that similarity of structure does indicate common ancestry here.

Reference: Mackin KA et al. (2014) An empirical test of convergent evolution in rhodopsins. Molecular Biology and Evolution 31:85-95

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4. Starfish can see their way back home

(Blue starfish, the beast featured in the paper, in its natural habitat. Richard Ling, Wiki Commons.)

Starfish aren’t widely known as visual creatures, but they do have eyes at the tips of their arms. The eyes are a bit… basic – no lenses, just a hundred or two little units filled with photoreceptors. Garm and Nilsson set out to find out how the starfish used their eyes. They measured or calculated the eyes’ visual fields (five arm-eyes together can see pretty much everywhere around the animal), resolution (very coarse), reaction speed (slow), and their sensitivity to various wavelengths (they are colour-blind, most sensitive to ocean blue).

Then they took some poor starfish and dumped them a little way off the coral reefs they like staying on. The creatures could walk home from short distances (about 2 m or less), but if you take them too far away, they just wander around in random directions. Likewise if you take off their eyes (don’t worry, they regenerate) or do the experiment in the dark. In conclusion: starfish eyes aren’t exactly top-end cameras, but they are definitely useful to the animals. And what would a slow, brainless mopper-up of coral reef rubbish do with eagle eyes anyway?

(The paper states the walking speed of these starfish as about 4-5 cm per minute. I have a feeling this wasn’t the most exciting fieldwork these guys have done…)

Reference: Garm A & Nilsson D-E (2014) Visual navigation in starfish: first evidence for the use of vision and eyes in starfish. Proceedings of the Royal Society B 281:20133011

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5. What makes wormies settle

OK, Shikuma et al. (2014) one isn’t so much for its own news value, but I hadn’t known that my favourite worms need bacteria to settle until I saw this paper, so I think it deserves a mention. (Besides, it has beautiful pictures of baby Hydroides in it, which I couldn’t resist posting below. They are So. Cute. Yes, I’m weird.)

Shikuma_etal2014-hydroidesBabies

Tubeworms of the serpulid family have swimming larvae which are in many ways like the acorn worm larvae mentioned in my previous post (except cuter). They are tiny, look nothing like an adult worm, have bands of cilia for swimming and feeding, and live in the plankton until they’re ready to metamorphose. When they find a place they like, they settle and turn into adult worms. And apparently, this particular species (Hydroides elegans) not only needs a specific bacterium to like a place, it needs specific proteins produced by that bacterium.

The proteins in question are the components of a nasty device bacteria probably stole from viruses and then used to poke holes in one another. But to Hydroides larvae, they appear to be necessary for metamorphosis. Put healthy bacteria together with worm babies in a dish, and you’ll get happily settled little worms. Do the same with bacteria with damage to the relevant genes, and nothing happens. Use an extract containing the proteins but not the bacteria, and you still get metamorphosing worms. Use too much, though, and they start dying. Everything in moderation…

(Maybe my dismal failure at raising happy young worms years ago could have been remedied with the right bacteria?)

Reference: Shikuma NJ et al. (2014) Marine tubeworm metamorphosis induced by arrays of bacterial phage tail-like structures. Science 343:529-533

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6. Relative of animals does strange multicellularity with familiar genetics

Although this idea probably hasn’t reached popular perception, animals are surrounded by other multicellular lineages in the tree of life. Sure, most of them are only part-time multicellular, but that’s beside the point. What’s clear is that multicellularity, at least in its simpler forms, is rampant in our extended family. Slime moulds do it, fungi do it, our closest relatives choanoflagellates do it, and our next closest relatives, filastereans and ichthyosporeans also do it.

These latter two groups are really poorly known (the fact that only a taxonomist could like the latter’s name probably doesn’t help), but the situation is getting better with the attention they are receiving as relatives of animals. There are now genome sequences out, and some people are looking at the life cycles of the little creatures to search for clues to our own origins.

Iñaki Ruiz-Trillo recently published a paper describing an ichthyosporean that can form a weird kind of colony with many nuclei in the same membrane starting from a single cell (Suga and Ruiz-Trillo, 2013). Now his team describe a different kind of multicellularity in a filasterean, Capsaspora owczarzaki. Rather than developing from a single cell, this guy does something more akin to the slime mould way: take a load of individual cells and bring them together. (Below: a clump of Capsaspora cells from Sebé-Pedros et al. [2013]. On the right is a regular photograph of the colony. The two-coloured fluorescence on the left indicates that the colony formed by different cells coming together rather than a single cell dividing.)

Sebé-Pedros_etal2013-F4.capsasporaClump

But, interestingly, some of the genetics involved is similar to what animals use, despite the different ways in which the two groups achieve multicellularity. For example, we’ve known since all those genomes came out that the proteins animals use to glue cells together and make them talk to each other are often older than animals. Well, Ruiz-Trillo’s filasterean appears to ramp up the production of some of these when it goes multicellular. It also uses a gene regulation strategy that animals are really big on: it edits the RNA transcribed from many genes in different ways depending on cell type/life stage before it’s translated into protein.

A lot of the details are going to need further investigation, since this was a global RNA-sequencing study with a bird’s-eye view of what genes are doing. It’s still a nice reminder that, like most other innovations in evolutionary history, the multicellularity of animals didn’t spring fully formed out of nowhere.

References:

Suga H & Ruiz-Trillo I (2013) Development of ichthyosporeans sheds light on the origin of metazoan multicellularity. Development 377:284-292

Sebé-Pedros A et al. (2013) Regulated aggregative multicellularity in a close unicellular relative of metazoa. eLife 2:e01287

The use of a larva?

Hi! Long time no see!

(I think we’ve reached the point where it’s weird to say happy new year. I could swear xkcd had a pertinent chart of funny, but I couldn’t find it.)

Once upon a time, I briefly mentioned the problematic relationships of hemichordates. Since a short paper bearing on the subject came out relatively recently (i.e. in December, yes, I’m far behind the times ;)), I thought I’d revisit it.

To begin, let’s orient ourselves on my trusty old animal phylogeny.

animalPhylogeny

Hemichordates are a phylum of deuterostomes, and their closest relatives appear to be echinoderms like starfish. The inside of Deuterostomia looks something like this:

deuterostomes

Hemichordates come in two flavours: the butt-ugly (but nevertheless intriguing) acorn worm, which even the artistic eye of 19th century zoologists couldn’t make appealing (a selection of them from Johann Wilhelm Spengel’s work below):

… and the slightly nicer-looking pterobranch. Well. They’re kind of fluffy. That counts as “nicer,” right? (A couple of Cephalodiscus from the Halanych lab below):

Acorn worms and pterobranchs have different bodies adapted to very different lifestyles. Pterobranchs are stalked, tentacled filter-feeders that often clone themselves into colonies that live together in a branching tube system. Acorn worms are solitary burrowers without tentacles, tubes or shells. Hemichordates possess features in common with vertebrates, such as gill slits, and they seem a lot less freakish than their sister phylum Echinodermata. So hemichordates are kind of the natural go-to group to look for properties of the deuterostome common ancestor.

The only problem is, to do that, you need a solid understanding of hemichordate phylogeny itself. Because there are two very different kinds of hemichordates, you have to first figure out which of those best represents their common ancestor: the sit-at-home plankton sifter or the roaming mud-eating worm. (Maybe neither. Wouldn’t that be funny.) And, as it happens, there’s some disagreement about that.

One view, espoused by the mighty zoological tome of Brusca and Brusca (2002) among others, puts acorn worms and pterobranchs as separate sister groups, and considers pterobranchs the more conservative of the two. The Bruscas write, on page 869, that “the enteropneusts [= acorn worms] have lost [their tentacles], no doubt in connection with their development of an infaunal lifestyle.” In this view, the deuterostome ancestor was a sessile filter feeder, and the long worm-like body and general moving-aboutiness of other deuterostomes is a new feature.

The other hypothesis, backed by DNA sequence data (Cannon et al., 2009)* and more recently the discovery of a tube-dwelling acorn worm from the Cambrian (Caron et al., 2013), is that pterobranchs are a weird subgroup of acorn worms and therefore unlikely to say much about our own distant ancestors.

One thing that AFAIK both camps agree on is that the ancestral acorn worm had a larva that looked nothing like an acorn worm. That’s something pretty common for marine invertebrates. Creatures as different as sea urchins and ragworms explore the seas by way of tiny, planktonic larvae that later metamorphose into a completely different animal**. (Tornaria larva of an unidentified hemichordate below by Alvaro E Migotto from the Cifonauta image database.)

However, the specific family of acorn worms that pterobranchs supposedly come from does not have such a larval stage. They develop more or less directly from fertilised eggs into mini-acorn worms.

Pterobranchs are poorly studied, so not much is known about their babies. Are they like the conventional acorn worm larva, with its distinctive body plan and curly rows of cilia? Or are they more straightforward precursors of the adult, like their presumed closest cousins? Stach (2013) describes a larva of the pterobranch Cephalodiscus gracilis that looks more like the latter. He found the minuscule creature crawling around in a colony of adult Cephalodiscus, and used thin sections and transmission electron microscopy to make a 3D reconstruction of it.

(His account of finding the baby makes me wonder how the hell he knew it did belong to Cephalodiscus. If my experience with tube-dwelling marine invertebrates is anything to go by, being found in a certain animal’s home is no guarantee that you’re related to said animal. I suppose, incomplete though they may be, older descriptions of pterobranch babies were good enough to identify the little guy?)

The image that emerges is of a rather featureless little sausage. According to Stach, it has a through gut, one full-fledged and one partially formed gill opening (asymmetry like that is not unheard of in deuterostome embryos/larvae), as well as a body cavity and a bunch of muscle cells. What it doesn’t have is any trace of the bands of cilia that “typical” acorn worm larvae use to swim and feed, nor some other structures (e.g. nerve centres) that characterise such larvae.

Taken at face value, this would suggest (assuming this is a typical pterobranch larva) that the pterobranchs-are-acorn worms people are right. I have my reservations, and not just because a sample size of one makes me statistically nervous. Using this description as evidence for evolutionary relationships assumes that traditional larvae with ciliary bands are hard to lose. But that’s quite possibly not the case.

Echinoderm larvae, for example, have changed a lot even in the last few million years. The changes occurred many times independently, and often involved a return from a full-fledged larval stage to more direct development (Raff and Byrne, 2006). I don’t know whether acorn worms display a similar sort of flexibility. How many have even been studied in terms of development?

So: detailed internal structure of a pterobranch larva? Cool. As to the worms first hypothesis… “consistent with” would be a better description than “supports”, I think.

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Notes:

*Although microRNAs beg to differ (Peterson et al., 2013).

**The history of these larvae is a mighty can of worms, or trochophores and tornariae as the case may be. I shall say no more on the matter here. 🙂

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References:

Brusca RC & Brusca GJ (2002) Invertebrates (second edition). Sinauer Associates.

Cannon JT et al. (2009) Molecular phylogeny of hemichordata, with updated status of deep-sea enteropneusts. Molecular Phylogenetics and Evolution 52:17-24

Caron J-B et al. (2013) Tubicolous enteropneusts from the Cambrian period. Nature 495:503-506

Peterson KJ et al. (2013) MicroRNAs support the monophyly of enteropneust hemichordates. Journal of Experimental Zoology B 320:368-374

Raff RA & Byrne M (2006) The active evolutionary lives of echinoderm larvae. Heredity 97:244-252

Stach T (2013) Larval anatomy of the pterobranch Cephalodiscus gracilis supports secondarily derived sessility concordant with molecular phylogenies. Naturwissenschaften 100:1187-1191

Thumbs down, what?

Bird fingers confuse me, but the explanations confuse me more, it seems.

I didn’t mean to post today, but I’ve just read a new review/hypothesis paper about the identities of the stunted little things that pass for fingers in the wings of modern birds. The review part is fine, but I’m not sure I get the difference between the hypothesis Čapek et al. (2013) are proposing and the hypothesis they are trying to replace/improve.

To recap: the basic problem with bird fingers is that fossil, genetic and developmental evidence seem to say different things about them.

1. Fossils: birds pretty clearly come from dinosaurs, and the early dinosaurs we have fossils of have five fingers on their hands with the last two being reduced. Somewhat closer to birds, you get four fingers with #4 vestigial. And the most bird-like theropods have only three fingers, which look most like digits 1, 2 and 3 of your ordinary archosaur. (Although Limusaurus messes with this scheme a bit.)

2. Embryology: in developing limb buds, digits start out as little condensations of tissue, which develop into bits of cartilage and then finger bones. Wing buds develop a short-lived condensation in front of the first digit that actually forms, and another one behind the last “surviving” digit. Taking this at face value, then, the fingers are equivalent to digits 2, 3 and 4.

3. Genetics: In five-fingered limbs, each digit has a characteristic identity in terms of the genes expressed during its formation. The first finger of birds is most like an ordinary thumb, both when you focus on individual genes like members of the HoxD cluster and when you take the entire transcriptome. However, the other two digits have ambiguous transcriptomic identities. That is, bird wings have digit 1 and two weirdos.

Add to this the fact that in other cases of digit loss, number one is normally the first to go and number four stubbornly sticks around to the end, and you can see the headache birds have caused.

So those are the basic facts. The “old” hypothesis that causes the first part of my confusion is called the frame shift hypothesis, which suggests that the ancestors of birds did indeed lose digit 1, as in the digit that came from condensation 1 – but the next three digits adopted the identities of 1-2-3 rather than 2-3-4. (This idea, IMO, can easily leave room for mixed identities – just make it a partial frame shift.)

Čapek et al.’s new one, which they call the thumbs down hypothesis, is supposedly different from this. This is how the paper states the difference:

The FSH postulates an evolutionary event in which a dissociation occurs between the developmental formation of repeated elements (digits) and their subsequent individualization.

versus

According to the TDH no change of identity of a homeotic nature occurs, but only the phenotypic realization of the developmental process is altered due to redirected growth induced by altered tissue topology. Digit identity stays the same. Also the TDH assumes that the patterning of the limb bud, by which the digit primordia are laid down, and their developmental realization, are different developmental modules in the first place.

(Before this, they spent quite a lot of words explaining how the loss of the original thumb could trigger developmental changes that make digit 2 more thumb-like.)

I…. struggle to see the difference. If you’ve (1) moved a structure to a different position, (2) subjected it to the influence of different genes, (3) and turned its morphology into that of another structure, how exactly is that not a change in identity?

Maybe you could say that “an evolutionary event” dissociating digit formation and identity is different from formation and identity being kind of independent from the start, but I checked Wagner and Gauthier’s (1999) original frame shift paper, and I think what they propose is closer to the second idea than the first:

Building on Tabin’s (43) insight, we suggest causal independence between the morphogenetic processes that create successive condensations in the limb bud and the ensuing developmental individualization of those repeated elements as they become the functional fingers in the mature hand, thus permitting an opportunity for some degree of independent evolutionary change.

Am I missing something? I feel a little bit stupid now.

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References:

Čapek D et al. (2013) Thumbs down: a molecular-morphogenetic approach to avian digit homology. Journal of Experimental Zoology B, published online 29/10/2013, doi: 10.1002/jez.b.22545

Wagner GP and Gauthier JA (1999) 1,2,3 = 2,3,4: A solution to the problem of the homology of the digits in the avian hand. PNAS 96:5111-5116

Heads are rolling in Nature

The Nature website has been overrun with headless flatworms, my RSS feed tells me! These adorable guys called planarians are known for their ability to regenerate from almost any little scrap of their squishy bodies. (And yes, I find lots of things adorable.) More than a century ago, TH Morgan, who invented like half of modern biology, observed that a whole planarian complete with a head, tail, eyes, brain, and digestive system can regrow itself from a fragment as tiny as 1/279th of the original animal*.

If you’re not familiar with these neat creatures, here’s one of regeneration expert Alejandro Sánchez Alvarado’s pet planarians from Wikipedia:

(OK, “pet” is probably the wrong word. Unless your concept of pets involves frequent mutilation and poisoning.)

Of course, once humanity discovered that planarians can do that, we just had to try and figure out how. Solana_etal2012-ctrlheadWho knows, one day the knowledge might even help us boost our own pathetic regeneration abilities. (Well, aside from the fact that planarian regeneration is pretty weird compared to what vertebrates do. But they are dead easy to keep and you can do lots of fancy things with them.) I felt like I should include some pictures of head regeneration in action, so here’s a few shots from Solana et al. (2012). Watch the eyes!

When you chop bits off a planarian, the remainder of the body has to know a couple of things to repair itself correctly. First, of course, it has to recognise that something is missing. This happens when tissues that don’t normally meet come into contact as the wound closes. The system can be fooled – if you cut off a piece of worm, turn it upside down, and stick it back on, things start growing out even though technically nothing is missing (Kato et al., 1999). The next step is to recognise precisely what needs to be replaced. An example of failing at this step is this two-headed flatworm obtained from a chemical treatment (from Nogi et al. [2012] via Wikipedia):

Making heads or tails

So how does a headless planarian know whether it needs a new head or tail? There’s a venerable theory (apparently also TH Morgan’s) according to which the body of the animal has a sort of built-in molecular coordinate system. Some molecules are more abundant at one end of the beast, while different molecules mark the other end. The anterior (head) and posterior (tail) signals would interact negatively, banishing each other from their respective head(or tail)quarters and resulting in opposing gradients. So any particular point along the head to tail axis would have a precise level of “headness” and “tailness”, and a wounded worm would “know” exactly where it was cut based on this information.

The tail end has long been known to be a seat of an ancient signalling pathway. Wnt (pronounced “wint”) genes are really, really important in a variety of developmental processes; in fact, it’s been proposed that they were involved in defining the head to tail axes of animals long before the more famous Hox genes (Guder et al., 2006). (The merits of that proposition are a discussion for another day. :)) Similar to their axis-defining developmental role, they – or rather, one of the several pathways they act through – also signal “tail” in adult planarians (Gurley et al., 2008).

Butts rule?

In one of the three new planarian studies, Umesono et al. (2013) set out mainly to figure out how the less well-understood head signal worked, but they managed to chuck in something vastly more interesting (to me, evolution nerd that I am) in an almost throwaway paragraph towards the end of the paper. Not all planarians have awesome regeneration superpowers. In particular, many species have difficulty regrowing heads while they can still regenerate tails just fine. Umesono et al. found out why.

Knowing how important Wnt signalling is in making tails, they wondered if an over-enthusiastic Wnt system might be behind some species’ head regeneration defects. They took members of such a species, demolished their Wnt pathway by hijacking their own gene regulatory mechanisms, and proceeded to hack off their heads. A couple of weeks later, shiny new heads started appearing!

It’s not just that one species, either. The other two new headless worm studies (Sikes and Newmark, 2013; Liu et al., 2013) basically did the exact same thing with two other kinds of regeneration-deficient planarian, and got the exact same result. So it looks like the same failure to overcome tailness underlies head regeneration failure in these three species.

The latter two papers examined worms from the same family, and the two animals proved to fail at regeneration in eerily similar ways. Everything up to a point goes correctly: the wound heals properly, stem cells across the body start dividing and gather at the amputation site… and then it stops. Wnts run rampant, heady genes remain silent, and nothing regenerates.

What I’d like to know is why it’s nothing rather than a second tail. After all, the molecular makeup of their wounded parts is screaming “tail!”, and they can regenerate missing tail ends. If you overactivate Wnt signalling in better regenerators among planarians, you still get something growing out at the front, it’s just not a very good head. (Umesono et al., in fact, did a couple of experiments like that in the process of figuring out heads.)

I thought the key was in the Umesono paper, because their prime suspect for “head stuff” as they call it is actually briefly needed in tail regeneration as well, so if it’s not activated at all due to too much Wntiness, then nothing will happen. But if you can turn that on in the middle of a tail in one species, why can’t the same thing happen in the others, which are also perfectly capable of regenerating their tails? Does tail regeneration work differently in them?

Did I mention that living things are complicated?

(And this is the part where I don’t start discussing the whole issue of how and why regeneration is lost in evolution. ‘Tis beautiful, but the night’s getting old ;))

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*I can’t for the life of me find the original source, even though I distinctly remember having read Morgan’s account. The 1/279th figure is cited, among others, by Newmark and Sánchez Alvarado (2001).

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References:

Guder C et al. (2006) The Wnt code: cnidarians signal the way. Oncogene 25:7450-7460

Gurley KA et al. (2008) β-catenin defines head versus tail identity during planarian regeneration and homeostasis. Science 319:323-327

Kato K et al. (1999) The role of dorsoventral interaction in the onset of planarian regeneration. Development 126:1031-1040

Liu SY et al. (2013) Reactivating head regrowth in a regeneration-deficient planarian species. Nature advance online publication 24/07/2013, doi: 10.1038/nature12414

Newmark PA and Sánchez Alvarado A (2001) Regeneration in Planaria. In: Encyclopedia of Life Sciences. John Wiley & Sons Ltd, Chichester. http://www.els.net; doi: 10.1038/npg.els.0001097

Nogi T et al. (2009) A novel biological activity of praziquantel requiring voltage-operated Ca2+ channel β subunits: subversion of flatworm regenerative polarity. PLoS Neglected Tropical Diseases 3:e464

Sikes JM & Newmark PA (2013) Restoration of anterior regeneration in a planarian with limited regenerative ability. Nature advance online publication, 24/07/2013, doi: 10.1038/nature12403

Solana J et al. (2012) Defining the molecular profile of planarian pluripotent stem cells using a combinatorial RNA-seq, RNA interference and irradiation approach. Genome Biology 13:R19

Umesono Y et al. (2013) The molecular logic for planarian regeneration along the anterior-posterior axis. Nature advance online publication, 24/07/2013, doi: 10.1038/nature12359

I couldn’t resist

Damn, I said I wasn’t going to talk about the Moroccan helicoplacoid-on-stalk, but it’s just so. Bloody. Amazing.

Here it is in its full glory, from the supplementary figures of Smith and Zamora (2013). Left is a cast of a young specimen, right is the authors’ reconstruction of the adult creature:

helicocystis_casthelicocystis_recon

So… the thing is a transitional form all right. It’s got a little stalk and cup like eocrinoids, built with a rather irregular arrangement of mineralised plates. On top of that it has a spiral body like helicoplacoids. It has ambulacra, the “rays” with porous plates where the tube feet that characterise living echinoderms can come out. This photo of the underside of a starfish is a pretty nice illustration of ambulacra (the white regions with little holes) and tube feet:

Even more interestingly, the new beastie (christened Helicocystis moroccoensis by the authors) seems to have five of them, like modern echinoderms (and a lot of extinct types, including eocrinoids). Helicoplacoids do have ambulacra, but only three or a single Y-shaped one, depending on interpetation.

Again unlike (one interpretation of) helicoplacoids but like modern echinoderms, the mouth of Helicocystis is right at the stalkless end. It’s also surrounded by an arrangement of skeletal plates that resembles more “conventional” echinoderms and has no equivalent in helicoplacoids proper. It’s about as neat a transitional form as you could hope for.

The question is which way the transition goes. It could be that the familiar five-rayed echinoderms are derived from a helicoplacoid-like ancestor, going through something like this guy. Or it could be that helicoplacoids are actually weird even for echinoderms, and their ancestors were more conventional stalked, five-armed beasties that lost their proper echinoderm shapes via something like Helicocystis.

Smith and Zamora actually did a phylogenetic analysis, but it’s not that helpful IMO. The tree in the paper is very pretty, and it says Helicocystis is the next branch after helicoplacoids on the path leading to “proper” echinoderms. The tree in the supplementary figures actually has measures of statistical support on it – which pretty confidently put Helicoplacus, Helicocystis, and a bunch of less weird echinoderms, together.

However, the relationships within that group are, shall we say, a little bit fluid. Granted, I come from a more sequency background and don’t often have to deal with morphology-based trees or parsimony as the method of analysis – but I’d definitely view a 56% bootstrap support with a big dose of scepticism, and this is the number they got for the hypothesis that Helicocystis is more closely related to “proper” echinoderms than to Helicoplacus. The other measure they display doesn’t make me any more confident about the relationship.

(I find it kind of amazing they got any resolution at all in that tree – with only 17 characters, some of which aren’t applicable to all species, and only nine species to begin with… yeah. The whole phylogenetic analysis is far from ideal even if it’s the best they could think of.)

So, based on that tree, the phylogenetic hypothesis they present is, at this point, just a plausible hypothesis. That doesn’t lessen the value of Helicocystis, though. The creature is still a damn neat transitional form – we just can’t be terribly sure which way the transition went.

There’s some interesting speculation in the paper about developmental evolution (yay!). Smith and Zamora point out that the spirally bit in Helicocystis looks like a complete helicoplacoid; the stalk and cup are kind of tacked onto that. The tissues of most modern echinoderm adults come from two different places: regular old tissues of the larva, and a special set of cells set aside for adult-making purposes*. So Smith and Zamora hypothesise that the two-part body of Helicocystis marks the point where this dual origin appeared. (Or, if they’re wrong about the phylogeny, the point where proto-helicoplacoids lost it?)

There’s also another interesting bit of evo-devo speculation (mixed with a bit of “eco”) about the stalk. Full-grown Helicocystis have pretty small stalks compared both to their own young and more typical stalked echinoderms. The authors wonder if this is because stalks for attachment originally functioned to help young echinoderms settle in a comfortable place, and only later became important for adults. I’m not sure how much sense that actually makes, and of course we only have a single species of Helicocystis to go by, but hey, ideas are fun.

Helicocystis has a random weird quirk as well, in that its spirals curl the opposite way to every proper helicoplacoid. That sort of variation happens even within species (e.g. in snail shells), but isn’t it a weird coincidence that such a unique creature should also twist the wrong way?

One thing is for sure: this beast is made of pure, distilled awesome. I think we should make a new Archaeopteryx out of it. Invertebrates need their evolutionary icons, too!

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*And that’s a nice reminder for me, because I thought they basically threw away the larva. Apparently I need a refresher on echinoderm development. Or just a reminder that not all echinoderms are sea urchins. The funny thing is a couple of years ago I actually specifically read and puzzled over literature discussing what comes from where in various echinderms…

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Reference:

Smith AB, Zamora S (2013) Cambrian spiral-plated echinoderms from Gondwana reveal the earliest pentaradial body plan. Proceedings of the Royal Society B advance online publication 26/06/2013, doi:10.1098/rspb.2013.1197

Phantom hourglasses

Holy ribosome, I’ve just written close to two thousand words about a paper. I… think I may have got a bit too excited. Or too bogged down in little technical details. Either way, you got lucky. The two-thousand word monster is not what you’re getting.

The reason I got excited about Piasecka et al. (2013) is that it, er, qualifies some other things I’d previously got excited about. And by “qualifies”, I mean turns inside out and performs a thorough autopsy on.

I previously touched upon the idea of the developmental hourglass – meaning that the embryos of related creatures are most similar to each other somewhere in the middle of development. The great rival of this hypothesis is that of early conservation (or the “funnel”), where embryos diverge from a similar starting point. The latter has been around as long as comparative embryology itself. The hourglass is a pretty intriguing pattern and raises all kinds of questions about what causes it – but of course, to have a cause, it has to exist in the first place.

So my previous excitement had been partly about the observation that the hourglass – originally noted in visible traits of embryos – also exists in the changing sets of genes activated throughout development (the transcriptome). According to various papers, genes expressed in mid-embryogenesis are on average older, slower-evolving and behave more similarly across species than genes active at other stages. If such observations are correct, that would certainly indicate that the hourglass is a real thing and something strange is going on with constraints and evolvability.

But, and here comes the Piasecka paper – is it?

This study is huge. There is (to use a highly technical phrase) a fucking shitload of stuff in it. Instead of looking at some big global property of the transcriptome, these authors went into all kinds of detail about various properties of specific sets of genes. They looked at – well, they say they looked at five different measures of evolutionary constraint, but actually some of those are made up of more than one thing, so really it’s quite a bit more than five.

And when they go down to that level of detail, they find that the hourglass is not a universal property of the developmental genetics of zebrafish embryos (unlike Domazet-Lošo and Tautz [2010] reported). Different measures of evolutionary constraint such as the strength of selection against protein-changing mutations, the age of the genes (which is what the original study focused on), or the conservation of their regulatory elements, show different patterns. There are hourglasses, there are a couple of funnels, and then there are parameters that just don’t exhibit much systematic change at all.

(There’s also a couple of points about potentially dodgy statistical approaches in some of these papers, which may make all the difference between an hourglass and a funnel. That’s a bit scary.)

I can’t say I’ve properly digested this paper. There’s an awful lot in it, and, my head was spinning non-stop when I finished reading. It’s definitely fascinating stuff, though, and once again, the conclusion is that things are More Complicated. (I’m kind of getting used to that at this point…) Before, you could look at a group of creatures, compare their development and ask, funnel or hourglass? Then you could ask why. Now, you can’t just make grand generalisations about anything. Taking Piasecka et al. at face value, “funnel or hourglass” is not even a valid question – it depends on exactly what you’re measuring. So much for “laws” of developmental evolution…

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References:

Domazet-Lošo T & Tautz D (2010) A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns. Nature 468:815-818

Piasecka B et al. (2013) The hourglass and the early conservation models—co-existing patterns of developmental constraints in vertebrates. PLoS Genetics 9: e1003476

A small planet hidden in plain sight, and a must-read book

Random squeey post!

Squee number one: Dumusque et al. (2012) found a probably earth-sized planet literally next door to the solar system. The newly announced rockball orbits α Centauri B, one of the three(?)* stars making up the star system closest to the sun. Alas, it’s unlikely to harbour life of any kind given its very close orbit – it goes around a star not much cooler than our sun in slightly over 3 days. However, the authors point out that small planets are most likely to be found in multiplanet systems, and given the difficulty of finding this one, the star may well have even harder to detect, more distant companions. I think this is a nice reminder of how much more we need to learn about other solar systems – this little guy has been circling there, a mere four point something light years from us, and we only found it now. Keep it up, planet hunters, you’re doing amazing stuff!

Reference: Dumusque X et al. (2012) An Earth-mass planet orbiting α Centauri B. Nature advance online publication available online 17/10/2012, doi: 10.1038/nature11572

*I’ll let the real astronomers argue whether Proxima Centauri is part of the α Centauri system…

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Squee number two: I totally must read this book. It’s the ultimate evo-devo book: it’s about fossilised development, basically. It seems overwhelmingly vertebrate-centred based on the review in Developmental Dynamics, but hey, there is an invertebrate chapter and I take what I can get 😀

And wow, it’s not even that expensive as far as university-published hardcover sciencey books go! Hmm. Shall we give in to temptation right now or save it for a Christmas present?

 

Birds are baby dinosaurs

Just a quick squee over something from the recent crop 😀

Paper: Bhullar BAS et al. (2012) Birds have paedomorphic dinosaur skulls. Nature advance online publication 27/05/2012, doi:10.1038/nature11146

New body forms often seem to evolve by tweaking the timing of developmental events. For example, axolotls are salamanders that become mature without ever losing larval traits such as gills, and many things about adult humans can be interpreted as retentions of baby ape characteristics. Now a new study in Nature argues that birds’ characteristic skull shape – big-brained, big-eyed, and usually small-snouted compared to their dinosaurian relatives – are similarly leftovers from dinosaur childhood. The team collected various skull measurements from young and adults of birds, non-avian dinosaurs, alligators and the early Triassic reptile Euparkeria, a distant cousin of both alligators and dinosaurs. When they analysed the variation in the data, they found that the skull of all of these animals changes in similar ways as they mature. However, adult dinosaurs more closely related to birds grouped with embryos and youngsters of more distant bird relatives, and modern birds were even further on the “baby” side of the diagram. Thus, it seems that the origin of birds was marked by the adoption of increasingly babylike faces. No wonder some of these feathery bastards are so disarmingly cute! (Blue tit above by Maximilian Dorsch, Wikimedia Commons)