Wherein scientists DON’T spill blood over a Precambrian animal

Having gone through much of my backlog, I was going to post about pretty blue limpet shells, then I saw that people have been arguing over Haootia. You remember Haootia? It’s that Precambrian fossil with probable muscle impressions that looks kind of like a modern-day staurozoan jellyfish (living staurozoan Haliclystus californiensis by Allen Collins, Encyclopedia of Life; Haootia quadriformis reconstruction from Liu et al., 2014):

It’s pretty much a law of Precambrian palaeontology that no interpretation of a fossil can ever remain uncontested, and Haootia is no exception. Nonetheless, this might be the tamest debate anyone ever had about a Precambrian fossil, and it gives me all kinds of warm feels.

Good news: Miranda et al. (2015) don’t dispute that the fossils show muscle impressions. They don’t even dispute that they belong to a cnidarian-grade creature. However, they question some of the details of the muscular arrangement, which could have implications for what this creature was and how it functioned.

They don’t have much of an issue with the muscles that run along the stalk and arms. The main point of contention, as far as I can tell, is that the muscles that run around the body (called coronal muscles in modern jellies) are not that big in living staurozoans. Those are the muscles that regular jellyfish use to contract their bells while swimming, but staurozoans don’t swim and therefore don’t need huge coronal muscles.

By Liu et al.‘s (2014) reconstruction (see above), Haootia has pretty massive coronal muscles. Miranda et al. (2015) wonder whether this was really the case, or the deformation of the fossils combined with the subconscious influence of regular jellyfish misled the original authors. They offer an alternative reconstruction, in which most of the body musculature runs up and down rather than around the body wall:

However, they also entertain the possibility that Liu et al.‘s reconstruction is correct – in which case, they note, Haootia must have done something with those muscles. Did jellyfish-like pulsations somehow form part of its feeding method? Could this even be a precursor to the jellyfish way of swimming? Who knows!

Liu et al. (2015) gave the most amazing response – much of their short reply to Miranda et al.‘s comments is basically thanking them for all the extra information and insight. They seem really pleased that biologists who study living cnidarians are taking an interest in their fossils, and enthusiastic about fruitful discussions in the future. (I concur. Biologists and palaeontologists need to talk to each other!)

They did take another, closer look at Haootia and maintain that they still see a large amount of musculature running around the body. So perhaps this peculiar Precambrian animal was doing something peculiarly Precambrian that has few or no parallels in modern seas. “We must keep in mind,” they write,  “that some, or maybe most, Ediacaran body plans and feeding strategies may have been specifically adapted to Ediacaran conditions.”

Either way, the whole exchange makes me very warm and fuzzy – I love to see scientists having constructive debates and learning from each other. (I also love that Miranda et al. thank Alex Liu in their acknowledgements; they were so obviously not out to tear one another down.) Plus both teams agree that we DO have a cnidarian-type creature from the Precambrian, and we DO have lovely lovely muscle impressions. Here’s to nice people, and to the slowly sizzling fuse of the Cambrian explosion! 🙂

***

References:

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

Liu AG et al. (2015) The arrangement of possible muscle fibres in the Ediacaran taxon Haootia  quadriformis. Proceedings of the Royal Society B 282:20142949

Miranda LS et al. (2015) Is Haootia quadriformis related to extant Staurozoa (Cnidaria)? Evidence from the muscular system reconsidered. Proceedings of the Royal Society B 282:20142396

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 😛 )

… 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.

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 (García-Bellido et al., 2014), and it looks something like this (Diego García-Bellido’s reconstruction from the paper):

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):

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)):

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 🙂

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 😀

(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 😛

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

***

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) – 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 – what 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 🙂 )

***

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

OH MY GOD A FILTER-FEEDING ANOMALOCARIDID!!!

ETA: OK, technically it should be “suspension-feeding”, because there’s a good chance that its feeding mechanics involved more than simple filtering (see comments). I hate retconning, so I’ll leave the post as it is aside from this addendum. Thanks for the heads-up, Dave Bapst 🙂

This is when I put everything resembling work aside to squee madly over a fossil.

(Imagine me grinning like crazy and probably bouncing up and down a bit in my seat)

Tamisiocaris is a newly “updated” beast from the Cambrian, and the coolest thing I’ve seen since that helicoplacoid on a stalk (most cool things come from the Cambrian, right?). It is the Cambrian equivalent of a baleen whale.

Anomalocaridids were close relatives of arthropods and are among the most iconic creatures of the Cambrian. Most anomalocaridids we know of were large, swimming predators with large head appendages bearing sturdy spines to grab prey and bring it to that trilobite-crunching pineapple slice mouth. Going with the whale analogy, they were more like the killer whales of their time (although they would be easy snacks for an actual killer whale). In fact, when the putative head appendage of Tamisiocaris was originally described by Daley and Peel (2010), the only odd thing they noted about it was that it was not hardened or obviously segmented the way those of Anomalocaris were.*

Tamisiocaris was already cool back then, because it was the first animal of its kind found at Sirius Passet in Northern Greenland, one of the lesser known treasure troves of fabulous Cambrian fossils. However, since then, more appendages have been found, and it turns out that those long spines had been hiding a fascinating secret.

They were… kind of hairy.

Closer examination of the appendages shows that their long, slender spines bore closely spaced bristles, making each spine look like a fine comb (whole appendage and close-up of a spine above from Vinther et al. [2014]). With all the spines next to each other, the bristles would have formed a fine mesh suitable for catching prey smaller than a millimetre. Compared with modern filter-feeding animals, Tamisiocaris fits right in – it would have “fished” in a similar size range as a greater flamingo. Vinther et al. (2014) suggest that Tamisiocaris would have brought its appendages to its mouth (which isn’t among the known fossils) one at a time to suck all the yummies off.

These guys are tremendously interesting for more than one reason, as the new study points out. First, HOLY SHIT FILTER FEEDING ANOMALOCARIDIDS! (Sorry. I’m kind of excited about this.) Second, the mere existence of large**  filter feeders implies a richness of plankton people hadn’t thought existed at the time. Third, there is some remarkable convergent evolution going on here.

Often, really big plankton eaters evolve from really big predators – see baleen whales, basking sharks, and these humongous fish for example. It’s not an already filter-feeding animal growing bigger and bigger, it’s an already big animal taking up filter-feeding. The interrelationships of anomalocaridids suggest the same story played out among them – ferocious hunters begetting “gentle giants” in a group with a totally different body plan from big vertebrates. For all the dazzling variety evolution can produce, sometimes, it really rhymes.

And finally, Vinther et al. did something really cool that tickles my geeky side in a most pleasant way. In their phylogenetic analysis that they did to find out where in anomalocaridid evolution this plankton-eating habit came along, they found that Tamisiocaris was closely related to another anomalocaridid with (on a second look) not dissimilar appendages. They named the group formed by the two the cetiocarids – after an imaginary filter-feeding anomalocaridid created by artist John Meszaros for the awesome All Your Yesterdays project.

Man. That’s definitely worth some squee.

***

*Disclaimer: I’m basing this on the abstract only, since palaeontological journals are one of the unfortunate holes in my university library’s otherwise extensive subscriptions.

**For Cambrian values of “large” – based on the size of the appendages, this creature would have been something like two feet long.

***

References:

Daley AC & Peel JS (2010) A possible anomalocaridid from the Cambrian Sirius Passet Lagerstätte, North Greenland. Journal of Palaeontology 84:352-355

Vinther J et al. (2014) A suspension-feeding anomalocarid from the Early Cambrian. Nature 507:496-499

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:

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!

***

*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…

***

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

Petrified strawberries and the cnidarian that isn’t

In the last few weeks, tons of squee-worthy stuff has accumulated on my backlog. The echinoderm transitional form from Cambrian Morocco I got so excited about is now officially described (Smith and Zamora, 2013), Dennis Duboule and his team put out some really cool findings about how vertebrate Hox clusters work that connect to my old fascination with limb evo-devo (Andrey et al., 2013), the developmental hourglass returned (Schep and Adryan, 2013)…

I kind of regret not gushing about all of them, but let’s face it, I’m not gonna ever do that. Looking over the things I bookmarked recently, I decided I’d rather not ignore Yasui et al. (2013), though. One, it’s about early animals, two, it exploits one of the greatest treasures the fossil record has to offer: the record of ancient development. I almost don’t care what the findings are, because the fact that we can follow a 530+-million-year-old creature from egg to adult is so staggeringly awesome in itself that everything else pales in comparison.

The paper looks at a tiny creature known from the earliest Cambrian of China. The beastie is called Punctatus and looks something like this (the authors’ interpretation of its development from fig. 4 of the paper):

The observations in this paper come from some 10 thousand specimens of various developmental stages from a couple of different Punctatus species. With such an abundance of fossils covering the animal’s life cycle, it is possible to connect the different stages and identify them as the same animal. So how did Punctatus develop and what kind of animal was it?

The earliest development took place inside a smooth egg membrane. Broken or CT-scanned embryos show that the creatures went through a nice blastula stage that looked like a simple, hollow ball of cells which were maybe a bit fatter on one side than the other (below, left). This type of blastula is quite common, found in animals as disparate as jellyfish (middle, from celldynamics.org) and sea urchins (right, from exploratorium). So the blastulae don’t tell you much about the affinities of the creature. In fact, while the authors use the leftmost embryo as a pretty illustration, they’re not even sure this particular specimen belongs to Punctatus. (Which is not really surprising.)

By the time young Punctatus hatch from their eggs, they are much more identifiable. The authors compare them to strawberries (awwww! ^.^). They are spiny all over, slightly pointy on one end and slightly flattened on the other, and the flattened end is divided into five parts by a star-like pattern of Y-shaped grooves. At the centre of the star, there is the blastopore, the opening of the embryonic gut, which seems to develop straight into the mouth in this creature. Punctatus never develops another gut opening. The simple blastopore = mouth equation again isn’t terribly informative, since a lot of animals follow it, and it’s the most straightforward way to make a mouth. The only thing the lack of a through gut tells us is something that was already fairly obvious – Punctatus is not a bilaterian.

The early stages also exclude another group from the list of possible identities, that is ctenophores. Early embryos of modern ctenophores (comb jellies/sea gooseberries) have very unequal-sized cells (see image at the top of this article), and no such embryos are known from the deposits preserving Punctatus specimens. (Although given what I recently learned about living ctenophores having a very recent common ancestor, I wouldn’t bet on what their Cambrian ancestors were up to…)

Thirdly, embryos that haven’t yet hatched also tell us something important about the adults. The prickly covering of these animals had apparently been interpreted as the remnants of a tube in which the animal proper lived – but this covering clearly appears before the baby even pops out of the egg, and the mouth forms right in the middle of it. All of that makes it more likely to be the animal’s skin. And that weakens a possible link to a group of extinct tube-dwelling animals that are much more plausibly related to jellyfish.

After hatching, development enters a new stage. In young and adult Punctatus specimens, the strawberry-like hatchling body remains in place, but a new body region appears at the mouth end, which has a ringed appearance and no spines. Presumably, individuals with more rings were older.

CT cross-sections of such specimens (C-E below) show a huge, empty body cavity, with a small sac-like gut attached to the mouth. There’s apparently no “stuff” between the gut and the body wall: no mesenteries anchoring the gut, no jelly or mass of cells filling in the body cavity, just big fat nothing. This is unlike not just bilaterians or ctenophores, but also cnidarians, in which the gut wall tends to be much closer to the body wall, and a jelly-like layer containing a varying amount of cells fills any gaps between the two.

From this point, the basic body plan doesn’t seem to change. Specimens with only a couple of rings and those with a dozen have the same small gut and large body cavity. There’s nothing we might call metamorphosis – unlike most cnidarians, Punctatus didn’t have a larval stage. (BTW, can someone tell me what the hell the lumpy bit on top of G above is? The paper doesn’t bother to explain as far as I could tell, and it bugs me.)

An intriguing (and rather pretty) part of the animal is the mouth end, what the authors call the “oral ruffle”. You’ll see why it’s called that if you look at figure 3:

This is an inferred developmental series of the mouth region. The five-pointed star of the hatchlings develops into ten finely striped folds emerging from the body surface, and as the animal grows, a new oral ruffle appears inside the previous one. The old ruffle then becomes part of the body wall, forming the next ring. Rinse and repeat. There are no tentacles at any point, although this might still turn out to be an artefact of preservation.

Tenfold symmetry, stacks old oral ruffles, no tentacles, building an adult body on top of an intact piece of embryo – the whole thing is quite unlike your typical cnidarian. Or, indeed, your typical anything else. The authors use the unusual developmental and body plan features of this creature to question its previous assignment to cnidarians, but beyond that, they are unsure what to make of it.

Well, this is the Early Cambrian, when a lot of now-extinct animal lineages were kicking around. Of course they would give us classification headaches! 😉 Which probably means that we know an awful lot about the development of a member of a long-extinct lineage. That’s a comparative embryology goldmine right there, folks!

***

References:

Andrey G et al. (2013) A switch between topological domains underlies HoxD genes colinearity in mouse limbs. Science 340:1234167, doi:10.1126/science.1234167

Schep AN, Adryan B (2013) A comparative analysis of transcription factor expression during metazoan embryonic development. PLoS ONE 8:e66826

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

Yasui K et al. (2013) A diploblastic radiate animal at the dawn of cambrian diversification with a simple body plan: distinct from Cnidaria? PLoS ONE 8: e65890

Aspidella on the move?

This is Aspidella:

(Peterson et al. [2003] via Palaeos)

The Internet tells me this is also Aspidella:

(Amy Campbell)

And so is this:

(Menon et al., 2013)

(How on earth did all of those things end up with the same name???)

Aspidella, you see, is one of those problematic Ediacaran fossils that may or may not belong to a single kind of organism, which may or may not be an animal. It’s an impression of something soft with a rather variable assortment of surface features, and hence it’s pretty hard to tell what made it, although the wide holdfast of some bottom-dwelling, filter-feeding animal is a popular opinion. This nice Charniodiscus specimen (Tina Negus via Wikipedia) explains why:

Seeing how fossils like these are one of our precious few sources of evidence on the early history of animals, any additional evidence to help us figure out what they were is awesome. It’s especially cool to find evidence of behaviour, because “behaviour” is something that only certain groups of organisms exhibit, and some of the candidates for Ediacaran thingies like this (e.g. fungi, lichens, microbial mats) specifically don’t.

In a short paper in Geology, Menon et al. (2013) argue that they have found such evidence in some Aspidella specimens from the mid-Ediacaran Fermeuse Formation of Newfoundland. There are two kinds of features they report on. First, there are shallow, short trails that look like whatever made the impressions slid or hopped along a soft sediment surface in short movements. Some of the trails show faint impressions of the radiating ridges some conventional Aspidella specimens possess (like the one below, taken from the paper):

They are fairly rare, the best bet for finding them being slabs of rock practically carpeted with Aspidellas. A couple of things indicate that they weren’t just made by some random current or mudslide sweeping hapless Aspidella creatures along. For one thing, even in a whole pile of Aspidella imprints, you’ll find only a few such trails. (Although that could be because most of the living creatures would have been firmly rooted to the sediment!) For another, neighbouring trails point in all kinds of random directions, so if it was a current, it must have been the most chaotic one in earth history.

The other kind of evidence is what looks like the “evolution” of vertical burrows, layers of sediment dipping downwards like there used to be something sitting on them that gradually relocated further up as more sand and mud accumulated around it. Of course, an animal sitting in the mud isn’t the only thing that can produce similar features, so the authors considered a few alternatives.

They didn’t find any signs of water or gas bubbles escaping. They also didn’t think the features looked like sediment slumping into a hole, which they actually experimented with by piling sand and mud on top of dissolving liquid capsules (laundry capsules?? :o). The dips produced by falling sediment get conspicuously shallower towards the top, which the fossil dips don’t seem to do, plus the latter also have round structures like small Aspidella on top. Personally, I find the photos of the fossil dips really hard to compare with the picture of the experimental dips, though. Here’s perhaps the best specimen they show alongside one of their experiments:

Yeah… I can kind of see where you’re coming from, but…

So the idea is that an animal lived with its rear end buried in the sediment and its feeding structures up in the water column. As the water brought in more sediment (the Fermeuse Formation is thought to be marine in origin), the unknown creature moved upwards to avoid complete burial. Eventually, it would die, leaving behind a stack of little dips indicating its previous seats, topped by a good old-fashioned Aspidella impression.

Interestingly, only small Aspidella are associated with these vertical traces. Did young and old Aspidella creatures live in different ways, or do larger specimens simply belong to a different organism?

The authors specifically think the Aspidella animal was cnidarian-like because other possible candidates such as sponges and giant moving protists haven’t been observed to move vertically through sediment. Only well-muscled creatures like sea anemones (and bilaterians, but there’s absolutely no reason to think this thing was a bilaterian) are known to do that.

Which is really pretty exciting – more Ediacarans directly associated with traces of movement! I maybe should have mentioned that the paper keeps going on about Retallack (2013), mainly to say that it was Wrong, but I thought it was interesting enough in its own right. The fact that it discusses signs of animal-like behaviour in a kind of fossil that’s also common in the Australian rocks reinterpreted by Retallack as terrestrial is kind of beside the point.

***

References:

Menon LR et al. (2013) Evidence of Cnidaria-like behavior in ca. 560 Ma Ediacaran Aspidella. Geology advance online publication 06/06/2013, doi: 10.1130/G34424.1

Peterson KJ et al. (2003) A fungal analog for Newfoundland Ediacaran fossils? Integrative and Comparative Biology 43:127-136

Retallack GJ (2013) Ediacaran life on land. Nature 493:89–92

Thornbushes – it’s not just molecular data.

While I love phylogenetics, I rarely venture into the land of morphology-based phylogenetic trees.

Molecular sequences make sense to me as data. In a protein sequence, a proline is a proline, and if two proteins can acquire a proline in the same place by convergent evolution, well, you can look at large-scale patterns of amino acid substitution and estimate the chance of that. Genomes contain exactly 4 kinds of bases, they encode exactly 20 kinds of amino acids, and that’s that at least as far as conventional molecular phylogenies are concerned. Sequences are exactly the sort of neat, discrete data that you can describe and explore and simulate the heck out of to make sure that the assumptions you are making when you use them to infer relationships between genes or organisms are realistic.

Morphology, my brain says, is fuzzy and difficult and full of human subjectivity. In the anatomy of two animals, a limb and a limb can be totally different things with totally different evolutionary origins, and there’s no guarantee that you can tell them apart. Something can be “sort of” a limb, and there’s no well-defined number of ways of “limbness”.

Truth be told, morphology as a way of figuring out relationships kind of scares me.

However, I do love phylogenies. I’m also interested in the relationships of extinct creatures (where, unless they are very recently extinct, you simply don’t have molecular data to play with). Plus limitations intrigue me, not to mention that the limitations of the methods we use to arrive at conclusions have a huge practical importance. (As in: they can lead to bullshit conclusions.) Hence I thought a paper titled “When can clades be potentially resolved with morphology?” would be an interesting read.

And it absolutely was, only in a totally different way than I expected. I thought it would be all about the limitations I was thinking of – convergent evolution, defining and interpreting traits, the statistical biases of treebuilding methods, that sort of stuff. Instead, it ignored those issues completely in favour of a much more fundamental limitation. Bapst (2013) doesn’t talk about information that you or your fancy algorithms misinterpret. He talks about information that, due to the very nature of evolution, just isn’t there.

A modern classification of organisms is built out of clades: groups including all descendants of a single common ancestor. Phylogenetic trees are clades within clades within clades – or branches splitting into smaller branches splitting into twigs. A fully resolved tree consists only of two-pronged branching points. That is, if you pick any three creatures, you can tell which two of them are closer to each other than the third. (Resolution is determined by statistical support from methods such as bootstrapping. Bootstrapping basically asks whether all your data agree on the same tree.)

Clades are recognised by what their members share with one another but no one else: for example, a subgroup of dinosaurs that includes birds has feathers, which they inherited from their common ancestor. Each clade can have many such shared derived traits or synapomorphies. However, sometimes there are no synapomorphies. Take, for instance, the case of a single ancestral species “budding off” a series of descendants without changing much itself, like so:

(You could say that three-spine sticklebacks are doing exactly this – the ancestral form that lives in the sea is largely similar all over the northern hemisphere, but it keeps getting stuck in rivers and lakes and sprouting a huge variety of descendants.)

In such a scenario, Descendant 1 is kind of closer to Ancestor than Descendant 2 is, since there’s been less time since they split. However, because Ancestor didn’t change in all that time, there are no synapomorphies that unite it with D1 to the exclusion of D2. A morphology-based phylogenetic tree of these three species would be intrinsically unresolvable – no matter how much data you collect and how well you analyse them, you’re not going to get the true tree, only a sad little bush. (A molecular phylogeny may be able to resolve a history like this, since genomes aren’t going to stop evolving just because the creatures that have them look the same.)

This is the sort of limitation Bapst explores through his simulations. The simulations don’t actually model the evolution of morphology itself. They compress all morphological change into “differentiation events”, i.e. the point at which two taxa become distinguishable. (He later makes the important point that “taxa” could be anything on the traditional Linnaean scale – species, families, classes, whatever -, and his conclusions would remain the same.)*

Differentiation events then might happen in a variety of ways, illustrated by Bapst’s Figure 2 below:

In other words, there can be branching without differentiation, differentiation without branching, and anywhere in between.

The simulations investigate how many intrinsically unresolvable clades we should expect under various mixtures of the four scenarios above, combined with more or less complete sampling of the fossil record. Some of the observations I found fascinating:

• More complete sampling actually decreases resolvability, since your dataset is then more likely to include both ancestors and their descendants.**
• Unresolvable clades are spread evenly throughout the whole model phylogeny – they aren’t disproportionately older or younger than their well-behaved counterparts. This is very important to me because it means that intrinsic unresolvability could also affect the levels I’m most interested in, i.e. the phylum-level relationships of animals.
• No realistic simulation – i.e. those whose parameters and results are compatible with the real fossil record – produces fully resolvable phylogenies!

It’s worth noting that it’s actually close to impossible to tell whether the lack of resolution in any given real dataset is due to this intrinsic effect or some other issue. However, the take home message of this study is that however well you’ve eliminated other sources of ambiguity, you should pretty much never expect a fully resolved phylogeny if you are working with the morphology of real creatures. If you got one, you probably did something wrong!

(Considering that molecular data can be just as incapable of correctly resolving relationships under certain circumstances, I dearly hope that the problem groups are at least going to be different for the two kinds of data… :D)

***

*This is a distinctly punk eek-flavoured model, BTW; if morphological change is evenly spread out through time, the whole thing falls apart. But, then, if change is evenly spread through time, you wouldn’t have scenarios with unchanged ancestors like the one above, and I gather that the existence of those is an established palaeontological reality.

**However, this doesn’t mean that trees obtained from patchy fossil records will be more accurate – having a poorer sample also means potentially overlooking misleading changes like reversals to an ancestral state.

***

Reference:

Bapst DW (2013) When can clades be potentially resolved with morphology? PLoS ONE 8:e62312

Lotsa news

Hah, I open my Google Reader (damn you, Google, why do you have to kill it??? >_<), expecting to find maybe a handful of new articles since my last login, and instead getting both Nature and Science in one big heap of awesome. The latest from the Big Two are quite a treat!

*

By now, of course, the internet is abuzz with the news of all those four-winged birdies from China (Zheng et al., 2013). I’m a sucker for anything with feathers anywhere, plus these guys are telling us in no uncertain terms that four-wingedness is not just some weird dromaeosaur/troodontid quirk but an important stage in bird evolution. Super-cool.

*

Then there is that Cambrian acorn worm from the good old Burgess Shale (Caron et al., 2013). It’s described to be like modern acorn worms in most respects, except it apparently lived in a tube. Living in tubes is something that pterobranchs, a poorly known group related to acorn worms do today. The Burgess Shale fossils (along with previous molecular data) suggest that pterobranchs, which are tiny, tentacled creatures living in colonies, are descendants rather than cousins of the larger, tentacle-less and solitary acorn worms. This has all kinds of implications for all kinds of common ancestors…

*

Third, a group used a protein from silica-based sponge skeletons to create unusually bendy calcareous rods (Natalio et al., 2013). Calcite, the mineral that makes up limestone, is not normally known for its flexibility, but the sponge protein helps tiny crystals of it assemble into a structure that bends rather than breaks. Biominerals would just be ordinary rocks without the organic stuff in them, and this is a beautiful demonstration of what those organic molecules are capable of!

*

And finally, Japanese biologists think they know where the extra wings of ancient insects went (Ohde et al., 2013). Today, most winged insects have two pairs of wings, one pair on the second thoracic segment and another on the third. But closer to their origin, they had wing-like outgrowths all the way down the thorax and abdomen. Ohde et al. propose that these wing homologues didn’t just disappear – they were instead modified into other structures. Their screwing with Hox gene activity in mealworm beetles transformed some of the parts on normally wingless segments into somewhat messed up wings. What’s more, the normal development of the same bits resembles that of wings and relies on some of the same master genes. It’s a lot like bithorax mutant flies with four wings (normal flies only have two, the hindwings being replaced by balancing organs), except no modern insect has wings where these victims of genetic wizardry grew them. The team encourage people to start looking for remnants of lost wings in other insects…

Lots of insteresting stuff today! And we got more Hox genes, yayyyy!

***

References:

Caron J-B et al. (2013) Tubicolous enteropneusts from the Cambrian period. Nature advance online publication 13/03/2013, doi: 10.1038/nature12017

Natalio F et al. (2013) Flexible minerals: self-assembled calcite spicules with extreme bending strength. Science 339:1298-1302

Ohde T et al. (2013) Insect morphological diversification through the modification of wing serial homologs. Science Express, published online 14/03/2013, doi: 10.1126/science.1234219

Zheng X et al. (2013) Hind wings in basal birds and the evolution of leg feathers. Science 339:1309-1312