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

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

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

Living jellyfish =/= earliest stage in metazoan evolution…

So, admittedly, I wasn’t interested enough in Bielecki et al. (2013) to read the whole thing. But if the abstract is an accurate reflection of their reasoning, then “WTF” is an accurate reflection of my reaction.

The reason I went to have a look at this shiny new PLoS paper is that it was titled “Fixational Eye Movements in the Earliest Stage of Metazoan Evolution”. Anything to do with early metazoan evolution automatically interests me, plus my immediate reaction was to ask how the hell they discovered any kind of eye movement in the earliest animals (which have been, you know, dead for like 600 million years).

Turns out they didn’t. Turns out all they found was that the rhythmic contraction of a box jelly‘s bell keeps the image in its eyes changing so they don’t go blind from photoreceptor fatigue. We accomplish the same effect by constantly moving our eyes (though apparently that’s more for the brain getting bored than photoreceptors burning out?), but the jellies supposedly don’t have the same level of nervous and muscular control over their eyeballs.

Yes, box jellies have frickin’ amazing eyes, complete with lenses. In fact, they have 4 sets of 6 eyes, two of the six being proper camera eyes and the other four much simpler. They can use their eyes to navigate around obstacles and stuff. They are pretty cool creatures. Here’s a box jelly eye cluster (rhopalium) in its full glory from the UCMP:

(Was that just a little bit unsettling? :D)

But these complex, image-forming eyes are an innovation of box jellies. No other cnidarian – in fact, no other animal outside the Bilateria – has them. So complex eyes and good vision are examples of convergent (or should I say parallel?*) evolution, not inheritance from a common ancestor. Conversely, bilaterians don’t have bells like jellyfish, so anything they do to move their eyes has to be an independent invention from the get-go.

So, while box jellies are awesome and it’s always cool to learn more about them, I’m not sure what profound insight about animal evolution we are supposed to find here. That animals with eyes have ways of avoiding visual fatigue? Well, duh. Of course they would, it’s really useful. But I’m not even sure the pulsation of a jellyfish should be regarded as a vision-enhancing adaptation, never mind an adaptation with any relation to what we do. To me it seems like the default way a jelly moves just happens to be good at keeping its eyes entertained. Evolution doesn’t have to do anything special about it.

Of course, the whole thing is soaked with that grandmother of evolutionary misconceptions, exemplified by this quote from the introduction:

Cnidarians were the first of the extant metazoan phyla to develop a nervous system which is therefore considered close to the evolutionary origin of all nervous systems [9].

Nooooooo, for the love of hungry anomalocaridids, don’t do this to me.

Cnidarians and bilaterians shared a common ancestor with a nervous system. Never mind “phyla” – phyla are arbitrary lines humans drew around the branches of the phylogenetic tree. Our ancestors and theirs had nervous systems for the exact same length of time. Neither of us was “first”. Life is a tree, not a goddamned ladder.

Well, at least we got to look at some disembodied jellyfish eyes. Yay!

*goes away to growl quietly*

***

*The difference being that parallel evolution is convergence  from a common starting point. While complex eyes are clearly later inventions, the common ancestor of cnidarians and bilaterians might well have possessed simple eyespots of some sort, providing said common starting point. But we’re getting pedantic here.

***

Reference:

Bielecki J et al. (2013) Fixational eye movements in the earliest stage of metazoan evolution. PLoS ONE 8:e66442

Jelly babies, dead and pretty

Is it really, really wrong to find pictures of dead baby animals adorable?

OK, the animals in question are sea anemones and jellyfish, but I still feel kind of perverted for the sentiment. But seriously, look at this young polyp of a starlet sea anemone (stained blue because the point of this image was the expression of the muscleLIM2 gene, not the cuteness of the creature ;)):

It looks like a little slug! D’awwww!

(I think I may be reading too much Featured Creature… ^.^;)

And then there’s this baby jellyfish, with fluorescent stains for actin protein and cell nuclei…

… or a field full of poppies, depending on your point of view! 😀

[Both images are from the supplementary figures of Steinmetz et al. (2012), Nature 487:231-234.]

Thornbushes

When I discussed sponge microRNAs last week, I said deep animal phylogeny was difficult. Quite fortuitously, another paper went online recently that explores exactly this difficulty (Nosenko et al., 2013). Following on from the microRNA post, I’ll use this paper as an excuse/guide to discuss the tangled relationships of animals.

First of all, let’s recap the problem. My trusty old family tree of animals just so happens to be an excellent illustration:

When I first made this tree to explain what the hell I was talking about re: the Cambrian creature Nectocaris, I put in some question marks mostly out of laziness. To illustrate why the “old” Nectocaris didn’t make sense, I only needed the relationships of bilaterians among themselves. Everything outside the Bilateria was irrelevant to the little creature’s mystery, so I decided to forgo reading up on them and stay on an uninformed fence.

But, in fact, said fence is not just my half-arsed perch. I appear to share it with an entire, very much whole-arsed field. While now there’s a reasonable agreement over ecdysozoans and deuterostomes and all that jazz, the non-bilaterians still wander all over the place depending on how you do your analysis. Nosenko et al. cite a number of recent large-scale studies, and point out that they totally fail to agree where to put poor Trichoplax and jellies of various kinds. The other thing they fail at is deciding how many branches sponges actually represent (the problem the microRNA study I discussed tried to tackle). To illustrate the extent of the chaos, I sketched the phylogenies six recent studies cited by Nosenko and colleagues came up with (sponge lineages are marked by dots):

Remarkably, all six studies agree on the basic deuterostome-ecdysozoan-lophotrochozoan arrangement inside Bilateria in spite of using different sets of bilaterian species. In contrast, the non-bilaterian animals – sponges of all kinds, cnidarians, ctenophores and Trichoplax – appear in pretty much every conceivable configuration.

A plethora of pitfalls

Why? What makes these questions so difficult that datasets made of 100+ genes from dozens of species representing all major animal groups and using the best available methods have this much trouble answering them?

Time is probably not the issue, or at least not in the simple sense of “it all happened too long ago”. The Nosenko paper brings up the example of fungi, which are roughly as ancient (or, in the context of all living things, as young) as animals. Studies that tried to use the exact same set of genes to analyse the relationships within each group could apparently produce a nice clear tree for fungi. Animals? A whole lot of noise.

Perhaps the “tree” of animals is really more like Rokas and Carroll’s (2006) evolutionary bushes, with its base branching so quickly that genes didn’t have time to accumulate many informative changes between one split and the next. Perhaps it even happened so fast that ancient within-species sequence variation was carried through several such events, resulting in what population geneticists call incomplete lineage sorting, a situation where the history of genes is not the same as the history of species.

Perhaps we haven’t got a good enough sample of genes, animals, or both.

If early animal evolution was bush-like, only a large amount of good data has any hope of accurately resolving how it went. But finding suitable genes for phylogenetic analysis is not easy. They have to be known in all of our species. They should have unambiguous identities so we know we’re actually comparing the same gene across species. They should evolve slowly enough that chance hasn’t had time to wash away their records of relatedness.

Likewise, picking suitable species can be difficult. Aside from the availability of sequences, the two greatest problems are taxon sampling and long branches. Good taxon sampling means covering the diversity of a group. So for example, if you have to pick three vertebrates, you don’t want them all to be mammals. A mammal, a shark and, say, a bony fish would be a much more representative sample.

Long branches are the bogeyman of phylogenetics. “Long” here means many evolutionary changes compared to other lineages in your sample. Similarities in gene/protein sequences are not always due to shared ancestry: because there’s a limited number of letters in the DNA and protein alphabets, sometimes they happen just by chance. If you have two unusually long branches, they might have a lot of these chance similarities, many more than either of them shares with its true relatives by common ancestry. Some of the newer changes might also have overwritten the older similarities linking them with their real families, a problem known as saturation. The overall outcome is that long branches attract each other.

Last but not least, perhaps the assumptions we put into our analyses don’t actually fit the data. All phylogenetic analyses are based on a model of evolution. For molecular data, these models specify, for example, how likely different sequence changes are, and which bases or amino acids are commonest and rarest. All analyses also need a way of picking the best tree, which range from simply choosing the one with the fewest changes to choices based on complicated probability theory. Sometimes, models and methods still work reasonably well when their assumptions are violated, but, as you might expect, counting on that is generally a stupid idea.

Nosenko et al. (2013) come to the conclusion that the issue of non-bilaterian animal phylogeny is plagued by pretty much the whole package.

Dissecting the Problem

First, studies may have increased the size of their datasets by incorporating less than ideal genes. To test the effect of gene sampling, Nosenko et al. (2013) divided their collection of 122 genes into two parts. One consisted of genes involved in protein synthesis, mostly genes encoding ribosomal proteins, which all evolve very slowly. The other was a mixed bag of non-ribosomal genes with all sorts of functions and evolutionary rates.

Perhaps not surprisingly, the latter set displayed a much higher level of saturation. Accordingly, when they analysed the ribosomal dataset with models of evolution that are more prone to errors due to saturation, they got the same trees they’d seen using more accurate models on the non-ribosomal data. Clearly, saturation, gene and model choice are affecting the answers they’re getting, and they are all problems that would affect your average phylogenomic study.

Second, the authors found every indication of a serious long-branch problem. In most phylogenetic trees, the longest branch is the outgroup. Outgroups are organisms outside your group of interest (the ingroup). Similarities between the outgroup and members of the ingroup are likely to have evolved before the origin of the ingroup, therefore they can be used to locate the root of the ingroup tree. However, outgroups are rarely sampled as well as ingroups, hence they tend to form long branches, making them a liability.

In the case of animals, removing the outgroup cleared the disagreements between the different gene sets, demonstrating that some of them had been due to long-branch artefacts. (Of course, without an outgroup you don’t know which animal lineages split first, which makes this solution not much use at all for important evolutionary questions like what the common ancestor of all animals looked like.)

Likewise, using a more distant outgroup changed the trees considerably. Ctenophores are worth special mention here. When Dunn et al. (2008) placed these jellyfish-like creatures as the sister group to all other animals, it was an odd, unexpected result. Well, ctenophore genomes evolve ridiculously fast, and there’s a good chance that their position “way out there” is an artefact of that. In Nosenko et al.‘s analyses, they ended up in the Dunn position when the more saturated non-ribosomal data were used – or when the ribosomal dataset was analysed with a more distant outgroup. When everything possible was done to reduce long-branch issues, they stayed deep in the crown of the tree next to cnidarians.

Fourth, the assumptions of even the best evolutionary model don’t take into account an annoying property of protein sequences: their overall amino acid compositions can differ across lineages. Changing the entire makeup of an organism’s protein complement involves changes in evolutionary patterns that none of the models account for. Once again, those damned ctenophores are one of the problem taxa with “deviant” sequence compositions. (The even worse news is that the closest available outgroups also differ from typical animals in this respect.)

Fifth, taxon sampling is influencing what you get. For example, the more sponges Nosenko et al. included, the more support they got for sponges being a single lineage. Ctenophores probably also suffer from this problem. For one thing, they’re very poorly known in almost every way that is relevant to picking species for phylogenetic analysis.

For another, they may actually have an additional problem that is literally impossible to crack – phylogenetic analysis of ctenophores themselves and a look at their fossil record hint that most ctenophore lineages have died out, with existing species all coming from a relatively recent common ancestor. That would make the entire phylum incurably long-branched no matter how many living species you throw at your datasets!

And finally, the ribosomal dataset that was the least prone to long-branch artefacts and the most informative about the deepest branches in animal phylogeny comes with a big caveat: it’s not a random selection of genes. In fact, all of these genes are interacting parts of a single system, which means they might not evolve independently (in the statistical sense). Are they all affected by a common set of biases, and does it render them unsuitable for recovering the true history of animals? We don’t yet know.

Hope dies last…

Being the phylogeny nut that I am, I really enjoyed this dissection of a thorny problem. At the same time, the results are kind of depressing. (Especially if, like me, you’re interested in early animal evolution.) No matter how carefully you set up your analysis, biases lurk around the corner waiting to jump on you and destroy your conclusions. You have a choice between not knowing where to root the tree of animals and being screwed by the outgroup. Well-worn measures of statistical confidence can support contradictory hypotheses. Ctenophores are fucking hopeless.

Is there anything we can do about this conundrum? Nosenko et al. conclude their paper on a somewhat hopeful note. There are other methods in molecular phylogenetics than simple sequence comparison. Although they’ve been no more helpful so far than traditional sequence analysis, we’re getting more and more full genome sequences from all over the animal kingdom. There’s more to look at than ever. Perhaps, one day, we’ll find a tool that can trim this thorny beast of a bush (or bush of beasts?) into shape.

Meanwhile, the quandary of deep animal phylogeny stands as a reminder that science is not all-powerful. The universe is a puzzle, but we have no reason to assume that nature left us enough information to solve it all. Which, as far as I’m concerned, shouldn’t stop us from trying. 😉

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References:

Dunn CW et al. (2008) Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452:745-749

Erwin DH et al. (2011) The Cambrian conundrum: early divergence and later ecological success in the early history of animals. Science 334:1091-1097

Nosenko T et al. (2013) Deep metazoan phylogeny: when different genes tell different stories. Molecular Phylogenetics and Evolution (in press), doi: 10.1016/j.ympev.2013.01.010

Philippe H et al. (2009) Phylogenomics revivew traditional views on deep animal relationships. Current Biology 19:706-712

Pick KS et al. (2010) Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships. Molecular Biology and Evolution 27:1983-1987

Rokas A & Carroll SB (2006) Bushes in the tree of life. PLoS Biology 4:e352

Schierwater B et al. (2009) Concatenated analysis sheds light on early metazoan evolution and fuels a modern “urmetazoon” hypothesis. PloS Biology 7:e20

Sperling EA et al. (2009) Phylogenetic-signal dissection of nuclear housekeeping genes supports the paraphyly of sponges and the monophyly of Eumetazoa. Molecular Biology and Evolution 26:2261-2274

Another man after my own heart

It’s not terribly hard to turn me into a squealing fangirl. One of the ways is to agree with me eloquently and/or share my pet peeves. Another is to give me lightbulb moments. A third is to disagree with me in a well-reasoned, intelligent way. And finally, if I see you thoughtfully examining your own thinking, you are awesome by definition. Michaël Manuel’s monster review of body symmetry and polarity in animals (Manuel, 2009) did all of the above.

(In case you wondered, that means a long, squeeful meandering >.>)

Manuel writes about the evolution of two fundamental properties of animal body plans [1]: symmetry and polarity. You probably have a good intuitive understanding of symmetry, but here’s a definition anyway. An object is symmetrical if you can perform some transformation (rotation, reflection, shifting etc.) on it and get the same shape. Polarity is a different but equally simple concept – it basically means that one end of an object is different from the other, like the head and tail of a cat or the inner and outer arcs of a rainbow.

I can’t say that I’d thought an awful lot about either before I came across this review, so it’s not really surprising that I had lightbulbs going off in my head left and right while I was reading it. Because I didn’t think deeply about symmetry and polarity and complexity, I basically held the mainstream view I – and, I suspect, most of the mainstream – mostly picked up by osmosis.

That meant I fell victim to my own biggest pet peeve big time – I believed, without good reason and without even realising, that the body plan symmetries of major lineages of living animals represented successive increases in complexity. Sponges are kind of asymmetrical, cnidarians and ctenophores are radially symmetrical, and bilaterians such as ourselves have (more or less) mirror image symmetry, and these kinds of symmetry increase in complexity in this order. Only… they aren’t, and they don’t.

It turns out that this guy not only shares my pet peeve but uses it to demolish my long-held hidden assumptions. Double fangirl points!

Let there be light(bulbs)!

Problem number one with the traditional view – aside from ignoring that evolution ain’t a ladder – is that the distribution of symmetry types among animals is a little more complicated. Most importantly, most kinds of sponges are not asymmetrical. Most species may be, but that’s not the same thing. You see, most sponge species are demosponges, which make up only one of the four great divisions among sponges. Demosponges do have a tendency towards looking a bit amorphous, but the other three – calcareous sponges, glass sponges and homoscleromorphs – usually are some kind of symmetrical. All in all, the evidence points away from an asymmetrical animal ancestor. (Below: calcareous sponges being blatantly symmetrical, from Haeckel’s Kunstformen der Natur.)

The second problem is that my old view ignores at least one important kind of symmetry. Some “radially” symmetrical animals are actually closer to cylindrical symmetry. To understand the difference, imagine rotating a brick and a straight piece of pipe around their respective long axes. You can rotate the pipe as much or as little as you like, it’ll look exactly the same. In contrast, the only rotation that brings the brick back onto itself is turning it by 180° or multiples thereof. A pipe, with its infinitely many rotational symmetries, is cylindrically symmetrical, while the brick has a finite number of rotational symmetries [2], making it radially symmetrical.

Problem number three is that bilateral symmetry is actually no more complex than radial symmetry! What does “complexity” mean in this context? Manuel defines it as the number of coordinates required to specify any point in the animal’s body. In an animal with cylindrical symmetry, you only need a maximum of two: where along the main body axis and how far from the main body axis you are. Everything else is irrelevant, since these are the only axes along which the animal may be polarised. (Add any other polarity axis, and you’ve lost the cylindrical symmetry.)

Take a radially symmetrical creature, like a jellyfish. These also have a main rotational axis and an inside-outside axis of polarity. However, now the animal’s circumference is also divided up into regions, like slices in a cake. How does a skin cell around a baby jelly’s mouth know whether it’s to grow out into a tentacle or contribute to the space between tentacles? That is an extra instruction, an extra layer of complexity. We’re up to three. (Incidentally, here’s some jellyfish symmetry from Haeckel’s Kunstformen. [Here‘s photos of the real animal] A big cheat he may have been, but ol’ Ernst Haeckel certainly had an eye for beauty!)

And with that, jellies and their kin essentially catch up to the basic bilaterian plan. Because what do you need to specify a worm? You need a head-to-tail coordinate, you need a top-to-bottom one, and you need to say how far from the plane of symmetry you are. Still only three! Many bilaterians, including us, added a fourth coordinate by having different left and right sides, but that’s almost certainly not how we started when we split from the cnidarian lineage. (Below: radial symmetry doesn’t hold a monopoly on beauty! Three-striped flatworm [Pseudoceros tristriatus] by wildsingapore.)

Not only that, but Manuel argues that there’s very little evidence bilateral symmetry evolved from radial symmetry. By his reckoning, the most likely symmetry of the cnidarian-bilaterian common ancestor was cylindrical and not radial (more on this later, though). Thus the (mostly) radial cnidarians and the (mostly) bilateral bilaterians represent separate elaborations of a cylinder rather than stages in the same process.

There were a bunch more smaller lightbulb moments, but I’m already running long, so let’s get on to other things.

Respectful disagreement

I think my disagreements with Manuel’s review are more of degree than of kind. Our fundamental difference of opinion comes back to the symmetries of various ancestors and the evidence for them. He argues that key ancestors in animal phylogeny – that of cnidarians + bilaterians, that of cnidarians + bilaterians + ctenophores, and that of all animals – were cylindrical. (Below is the reference tree Manuel uses for his discussion, with symmetry types indicated by the little icons.)

I think he may well be correct in his conclusions, but I’m not entirely comfortable with his reasons. For example, he infers that the last common ancestor of cnidarians and ctenophores was cylindrical. One of his main arguments is that the repeated structures that “break up the cylinder” to confer radial symmetry are not the same in these two phyla. I think this is an intelligent point a smart guy who knows his zoology would make, so disagreement with it becomes debate as opposed to steamrolling [3].

Why I still disagree? As I said, it comes down to degrees and not kinds. Manuel considers the above evidence against a radially symmetrical common ancestor. I consider it lack of evidence for same. The situation reminds me of Erwin and Davidson (2002), which is also one of my favourite papers ever. They raise perhaps the most important point one could make about comparative developmental genetics: homologous pathways could have been present in common ancestors without the complex structures now generated by those pathways being there. Likewise, I think, radial symmetry could have been there in the common ancestor of cnidarians and ctenophores while none of the complex radially symmetrical structures (tentacles, stomach pouches, comb rows etc.) in the living animals were. Perhaps there were simpler divisions of cell types or whatnot that gave rise to the more overt radial symmetry of jellyfish, sea anemones and comb jellies.

In a related argument, Manuel discusses the homology (or lack thereof) of the dorsoventral axis in bilaterians and the so-called directive axis in sea anemones. Sea anemones actually show hints of bilateral symmetry, which prompted some authors (e.g. Baguñà et al., 2008) to argue that this bilateral symmetry and ours was inherited from a common ancestor (i.e. the cnidarian-bilaterian ancestor was bilateral).

I agree with Manuel that the developmental genetic evidence for this is equivocal at best. I even agree with him that developmental genetics isn’t decisive evidence for homology even if it matches better than it actually does in this case. But again, once the genetic evidence is dismissed as inconclusive, he relies on the non-homology of bilaterally symmetrical structures to conclude non-homology of bilateral symmetry. Again, I think this is a plausible but premature inference. Since I’m not sure whether homology or independent origin of bilateral symmetry is the better default hypothesis in this case, and I don’t think the evidence for/against either is convincing, I actually wouldn’t come down on either side as of yet.

But I can see his point, and that’s really cool.

Why else you’re awesome, Michaël Manuel…

Because you have a whole rant about “basal lineages”. I grinned like a maniac throughout your penultimate paragraph. Incidentally, you might have given me another favourite paper – anything with “basal baloney” in its title sounds like it’s worth a few squees of its own!

Because you apply critical thinking to your own thinking. See where we disagreed, non-homology of structures vs. symmetries, evidence against vs no evidence for, and all that? After you made the argument from non-homology of structures, I expected you to leave it at that. And you didn’t. You went and acknowledged its limitations, even though you stood by your original conclusions in the end.

Because you reminded me that radial symmetry is similar to metamerism/segmentation. I’d thought of that before, but it sort of went on holiday for a long time. Connections, yay!

Because you were suspicious about sponges’ lack of Hox/ParaHox genes. And how right you were!

*

Phew, that turned out rather longer and less coherent than I intended. And I didn’t even cover half of the stuff in my notes. I obviously really, really loved this paper…

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[1] Or any body plan, really…

[2] Astute readers might have noticed that a brick has more than one axis of symmetry, plus several planes of symmetry as well. So it’s not only radially but also bilaterally symmetrical. The one thing it certainly isn’t is cylindrical 😉

[3] Not to say I don’t enjoy steamrolling obvious nonsense, but I also like growing intellectually, and steamrolling obvious nonsense rarely stretches the mind muscles…

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References:

Baguñà J et al. (2008) Back in time: a new systematic proposal for the Bilateria. Philosophical Transactions of the Royal Society B 363:1481-1491

Erwin DH & Davidson EH (2002) The last common bilaterian ancestor. Development 129:3021-3032

Manuel M (2009) Early evolution of symmetry and polarity in metazoan body plans. Comptes Rendus Biologies 332:184-209