Finally, that sponge ParaHox gene

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

***

Notes

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

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

***With the obligatory ctenophore caveat

***

References

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

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

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

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

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

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

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

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

A bit of Hox gene nostalgia

I had the most random epiphany over my morning tea today. I don’t even know what got me thinking about the Cambrian explosion (as if I needed a reason…). Might have been remembering something from the Euro Evo Devo conference I recently went to. (I kind of wanted to post about that, because I saw some awesome things, but too much effort. My brain isn’t very cooperative these days.)

Anyway.

I was thinking about explanations of the Cambrian explosion and remembering how the relevant chapter in The Book of Life (otherwise known as the book that made me an evolutionary biologist)  tried to make it all about Hox genes. It’s an incredibly simplistic idea, and almost certainly wrong given what we now know about the history of Hox genes (and animals)*. At the time, and for a long time afterwards, I really wanted it to be true because it appeals to my particular biases. But I digress.

Then it dawned on me just how new and shiny Hox genes were when this book was written. I thought, holy shit, TBoL is old. And how far evo-devo as a field has come since!

The Book of Life was first published in 1993. That is less than a decade after the discovery of the homeobox in fruit fly genes that controlled the identity of segments (McGinnis et al., 1984; Scott and Weiner, 1984), and the finding that homeoboxes were shared by very distantly related animals (Carrasco et al., 1984). It was only four years after the recognition that fly and vertebrate Hox genes are activated in the same order along the body axis (Graham et al., 1989; Duboule and Dollé, 1989).

This was a HUGE discovery. Nowadays, we’re used to the idea that many if not most of the genes and gene networks animals use to direct embryonic development are very ancient, but before the discovery of Hox genes and their clusters and their neatly ordered expression patterns, this was not at all obvious. What were the implications of these amazing, deep connections for the evolution of animal form? It’s not surprising that Hox genes would be co-opted to explain animal evolution’s greatest mysteries.

It also occurred to me that 1993 is the year of the zootype paper (Slack et al., 1993). Slack et al. reads like a first peek into a brave new world with limitless possibilities. They first note the similarity of Hox gene expression throughout much of the animal kingdom, then propose that this expression pattern (their “zootype”) should be the definition of an animal. After that, they speculate that just as the pattern of Hox genes could define animals, the patterns of genes controlled by Hoxes could define subgroups within animals. Imagine, they say, if we could solve all those tough questions in animal phylogeny by looking at gene expression.

As always, things turned out More Complicated, what with broken and lost Hox clusters and all the other weird shit developmental “master” genes get up to… but it was nice to look back at the bright and simple childhood of my field.

(And my bright and simple childhood. I read The Book of Life in 1998 or 1999, not entirely sure, and in between Backstreet Boys fandom, exchanging several bookfuls of letters with my BFF and making heart-shaped eyes at long-haired guitar-playing teenage boys, I somehow found true, eternal, nerdy love. *nostalgic sigh*)

***

*Caveat: it’s been years since I last re-read the book, and my copy is currently about 2500 km from me, so the discussion of the Cambrian explosion might be more nuanced than I remember. Also, my copy is the second edition, so I’m only assuming that the Hox gene thing is there in the original.

***

References:

Carrasco AE et al. (1984) Cloning of an X. laevis gene expressed during early embryogenesis coding for a peptide region homologous to Drosophila homeotic genes. Cell 37:409-414

Duboule D & Dollé P (1989) The structural and functional organization of the murine HOX gene family resembles that of Drosophila homeotic genes. The EMBO Journal 8:1497-1505

Graham A et al. (1989) The murine and Drosophila homeobox gene complexes have common features of organization and expression. Cell 57:367-378

McGinnis W et al. (1984) A conserved DNA sequence in homoeotic genes of the Drosophila Antennapedia and bithorax complexes. Nature 308:428-433

Scott MP & Weiner AJ (1984) Structural relationships among genes that control development: sequence homology between the Antennapedia, Ultrabithorax, and fushi tarazu loci of Drosophila. PNAS 81:4115-4119

Slack JMW et al. (1993) The zootype and the phylotypic stage. Nature 361:490-492

Ctenophore nervous systems redux

… and reasons I suddenly find myself liking Joseph Ryan.

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

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

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

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

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

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

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

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

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

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

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

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

Reference:

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

The ctenophore conundrum, by popular demand

So, a new ctenophore genome has just been published in Nature (Moroz et al., 2014), it makes some extraordinary claims, and my resident palaeontologist/web-buddy Dave Bapst wants my opinion 😉

Given that I already planned to have an opinion about the first ctenophore genome back in December (Ryan et al., 2013) and miserably failed to finish the post… the temptation is just too strong. (That thesis chapter draft in the other window of MS Word wasn’t going to be finished today anyway  >_>)

Whatever I might seem from words on the internet, I’m not some kind of expert on phylogenetics, so I’m going to use a crutch. I had this idea back when I first read Ryan et al. (2013), because I remember thinking that it was written almost as if Nosenko et al. (2013) had never happened, and I’d really liked Nosenko et al. (as you can guess from the word count of this post), so I was mildly indignant about that. The Nosenko paper is going to be my crutch. (No offence to Hervé Philippe and friends, but there are only so many papers I’m going to reread for an out of the blue blog post 😉 )

Although I’m obviously not writing a public post specifically for a phylogeny nut, I may get somewhat technical, and I’m definitely going to get verbose.

***

Ctenophores. Comb jellies, sea gooseberries, Venus girdles. They are floaty, ethereal, mesmerizingly beautiful creatures, and I have it on good authority that they are also complete pains in the arse.

Here’s some pretty pictures before it gets too painful 😉 Left: Mnemiopsis leidyi from Ryan et al. (2013); right: Pleurobrachia bachei from Moroz et al. (2014). And a bonus video of a Venus girdle making like an ancient nature spirit. I could watch these beasties all day.

mnemi_pleuro

Venus from Sandrine Ruitton on Vimeo.

The problem(s)

And now, the pain. Let’s pull out my trusty old animal phylogeny, because the question marks are once again highly appropriate. (Also, I’m hell-bent on breaking your bandwidth with PICTURES.)

animalPhylogeny

Ryan et al. (2013) helpfully have a figure distilling the ideas people have had about those question marks so far:

ryan_etal2013-ctenophoreHypotheses

Bi = bilaterians, Cn = cnidarians, Ct = ctenophores, Tr = Trichoplax, and Po = sponges (Porifera).

I say “helpfully,” but it’s not all that helpful after all, since pretty much every possible configuration has been proposed. Why is this such a difficult question? Here’s a quick rundown of the problems Nosenko et al.’s study found to affect the question marks:

  1. Fast-evolving protein sequences – these can cause artefacts because too much change overwrites informative changes and creates chance similarities. Excluding faster-evolving sequences from the analysis changes the tree.
  2. Sequence data that don’t conform to the simplifying assumptions of popular evolutionary models – again, this can result in chance similarities and artefacts, and using a poorer model replicates the effects of using less ideal sequences.
  3. Long-branched outgroups – these are the non-animal groups used to place the root of animals. The more distant from animals and less well-sampled the outgroup, the longer the branches it forms, which can attract fast-evolving animal lineages towards the root. In Nosenko et al.’s analyses, even the closest outgroup seemed to cause problems, and removing the outgroup altogether made the conflicts between different models and datasets disappear completely – but this isn’t exactly helpful when you’re looking for the root of the animal tree!

The problem with ctenophores in particular is illustrated by this one of Nosenko et al.’s trees, made from one of their less error-prone datasets:

Nosenko_etal2013-ribosomalCATtree

The ctenophore branch is not only longer overall than pretty much any other in the tree; its length is also very unevenly distributed between the loooong history common to all species and the short unique lineage of each individual species. That is bad news. And it may stay that way forever, because the last common ancestor of living ctenophores may genuinely be very recent, so there’s no way to divide up that long-ass internal branch without a time machine.

Round 1: Nosenko vs. Ryan

In fairness, the Mnemiopsis genome team probably didn’t have a whole lot of time to specifically deal with Nosenko et al.’s points (OTOH, none of those individual points were truly new). The Nosenko paper came out in January 2013, and the Mnemiopsis genome paper was received by Science in July of the same year – I imagine most of the data had been generated way before then, and you can’t just redo all your data analysis and rewrite a paper on short notice.

I’m still going to view Ryan et al. (2013) in the light of Nosenko, because regardless of the genome team’s ability to answer them, some of Nosenko et al.’s points are very relevant to the claims they make. Their biggest claim, of course, being that ctenophores are the sister group to all other animals.

In Nosenko et al.’s experiments, this placement showed up in trees where faster-evolving genes, poorer models or more distant outgroups were used, but not when the slowest-evolving gene set was analysed with the best models and the closest outgroup.

Ryan et al. acknowledge that “supermatrix analyses of the publicly available data are sensitive to gene selection, taxon sampling, model selection, and other factors [cite Nosenko].” Their data are obviously sensitive to such factors. In fact, they behave rather similarly to what I saw in the Nosenko study.

Ryan et al. used two method/model combinations – one of the models was the preferred CAT model of Nosenko et al., and the other was the OK but not great GTR model that CAT beat by miles in terms of actually fitting Nosenko et al.’s data. (Caveat: in the genome paper, the CAT and GTR models were used with different treebuilding methods, so we can’t blame the models for different results with any certainty.) Also, they analysed the data with three different outgroups.

And guess what – the ctenophores-outside-everything tree was best supported with (1) the GTR model, (2) the more distant outgroups. There is not much testing of the effect of gene choice – there were two different data sets, but they were both these massive amalgamations of everything useable, and they also included totally different samples of species.

However, here comes another nod to Nosenko et al. and all the other people who advocated trying things other than “conventional” sequence comparisons through the years. Provided you can securely identify genes across different organisms, you can also try to deduce evolutionary history based on their presences and absences rather than their precise sequences. This is not a foolproof approach because genes can be (commonly) lost or (occasionally) picked up from other organisms, but it is often regarded as less artefact-prone than sequence-based trees.

But does it help with ctenophores? Like the GTR model-based sequence trees, the tree based on gene presence/absence (you obviously need complete genomes for this!) supports ctenophores being the outsider among animals:

Ryan_etal2014-RGCtree

My problem with this? Note what else it supports. The white circles indicate groupings that this method had absolutely no doubt about. And these groupings include things that frankly sound like abject nonsense. Here’s one annelid worm (the leech Helobdella) sitting next to a flatworm, while another annelid worm (Capitella) teams up with a limpet right next to a chordate. If anything, that is more controversial than the placement of ctenophores, because we thought we had it settled!

So if we’re concluding that ctenophores are basal to all other animals, why aren’t we also making a fuss about the explosion of phylum Annelida? Surely, if this method gives us strong enough conclusions to arbitrate between different sequence-based hypotheses about ctenophores, it’s strong enough to make those claims too. The cake can’t quite decide if it’s being eaten, I think.

I’m not sure what to think about the sequence trees. I’m far more confident about the presence/absence one. Maybe I’m just demonstrating the Dunning-Kruger effect here, but I’m not buying that tree for a second.

Overall verdict?

Not convinced. Not by a long shot.

Round 2: Nosenko vs. Moroz

The Pleurobrachia genome took me completely by surprise. I’d known Mnemiopsis was sequenced since Ryan et al. (2010). (Three years. Can you imagine the twitching?) I had no idea this other project was happening, so I nearly fell off my chair when Nature dropped it into my RSS reader yesterday. Another ctenophore genome – and another one that supports ctenophore separatism? (This hypothesis is becoming strangely popular…)

Bonus: it’s not just a genome paper, it also describes the transcriptomes of ten different ctenophores. Transcriptomes, the set of all active genes, are a little bit easier to sequence and assemble than genomes, and if you’re thorough they’ll catch most of the genes the organism has, so they can be almost as good for the analysis of gene content.

Which they kind of don’t do properly. There is a discussion of specific gene families that ctenophores lack – including many immune- and nervous system-related genes – but that’s not exactly saying much given that we know even “important” genes can be lost (case in point: the disappearing (Para)Hox genes of Trichoplax). The fact that ctenophores seem to completely lack microRNAs is interesting, but again, it doesn’t mean they never had them. Sponges do have microRNAs but don’t seem to be nearly as big on them as other animals.

As for the global analysis of gene content – I had to chase down a reference (Ptitsyn and Moroz, 2012) to understand what they actually did. As far as I can tell, there is no phylogenetic analysis involved – they just took a tree they already had, and used this method to map gene gains and losses onto that tree. Which is cool if you’re fairly sure about your tree, but pretty much meaningless when the tree is precisely the question. The Mammal is disappointed.

One of the problems with listing genes that aren’t there or don’t work in the “expected” way in ctenophores is that even if they’re not outside everything else, it’s still a distinct possibility that these guys branched off from our lineage before cnidarians did. For example, the Pleurobrachia paper spends a lot of time on “nervous system-specific” genes like elav missing or not being expressed in neurons, and common neurotransmitters like serotonin not being used by ctenophores.

But, assuming that the tree of animals looks something like (sponges + (ctenophores + (cnidarians + bilaterians))), we wouldn’t expect ctenophore nervous systems to share every property that cnidarians and bilaterians share. Remember: (1) sponges don’t have nervous systems, so they’re not much use as a comparison, (2) cnidarians + bilaterians had a longer common ancestry than either did with ctenophores. Genes possessed by sponges PLUS cnidarians and/or bilaterians but missing from ctenophores are more suggestive, but only if you can demonstrate that they weren’t lost. (We’re kind of going in circles here…)

The other problem is that pesky last common ctenophore ancestor. If it really is very recent, then taking even all living ctenophores to represent ctenophore diversity is like taking my close family to represent human diversity. Just like my family contains pale-skinned, lactose tolerant people, it is entirely possible that this lone surviving ctenophore lineage possesses (or lacks) important traits that aren’t at all typical of ctenophores as a whole. Ryan et al.’s supplementary data are clear that at least the Mnemiopsis genome is horribly scrambled, all trace of conserved gene neighbourhoods erased from it. That’s not exactly promising if you’re hoping for “trustworthy” animals.

The actual phylogenetic trees in Moroz et al. (2014) seem to follow an approach of throwing AAAALLL the genes at the problem. The biggest dataset contains 586 genes, compared to 122 in Nosenko et al.’s largest collection, and there is not much filtering by gene properties other than “we can tell what it is”. I have no idea how the CAT + WAG model they used compares to CAT or WAG or GTR on their own; unfortunately, the Nosenko paper doesn’t test that particular setup and this one doesn’t do any model testing. Moroz et al.’s supplementary methods claim it’s pretty good, cite something, and I’m not gonna chase down that reference. (Sorry, I’ve been poring over this for four hours at this point).

Interestingly, the support for ctenophores being apart from other animals increases when they start excluding distant outgroups. The only time it’s low is when they add all ten ctenophores and use fewer genes. Hmm. This is where I would like to hear some real experts’ opinions, because on the face of it, I can’t pinpoint anything obviously wrong. (Other than saying that chucking more genes at a problem tree is perfectly capable of making the problem worse)

TL;DR version: While I’m generally underwhelmed by the gene content stuff, I literally have no idea what to think about the trees.

I’m banking on the hope that someone will do.

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And… I think that is all the opinion I’m going to have about ctenophores for a long time. Lunch was a long time ago, my brain is completely fried, and I’m not sure how much of the above actually makes sense. To be clear, I don’t really have a horse in this race, though I’d really like to know the truth. (Fat chance of that, by the looks of it…) I think I’m going to need a bit more convincing before I stop looking sideways at this idea that ctenophores are further from us than sponges. If anything is clear from recent phylogenomics papers, it’s that what data you analyse and how you analyse them makes a huge difference to the result you get, and this is happening with data and methods where it’s not necessarily easy to dismiss an approach as clearly inferior.

It’s a mess, damn it, and I’m not qualified to untangle it. Urgh.

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References

Moroz LL et al. (2014) The ctenophore genome and the evolutionary origin of neural systems. Nature advance online publication, 21/05/2014; doi: 10.1038/nature13400

Nosenko T et al. (2013) Deep metazoan phylogeny: When different genes tell different stories. Molecular Phylogenetics and Evolution 67:223-233

Ptitsyn A & Moroz LL (2012) Computational workflow for analysis of gain and loss of genes in distantly related genomes. BMC Bioinformatics 13:S5

Ryan JF et al. (2010) The homeodomain complement of the ctenophore Mnemiopsis leidyi suggests that Ctenophora and Porifera diverged prior to the ParaHoxozoa. EvoDevo 1:9

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

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.

Vinther_etal2014-sf3_crop

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.

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*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.

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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

Catching up

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

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

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

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

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

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

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2. Similar cells repair muscles in crustaceans and vertebrates

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

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

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

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

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

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3. Convergent evolution is a poor explanation of rhodopsins

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

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

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

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

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4. Starfish can see their way back home

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

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

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

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

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

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5. What makes wormies settle

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

Shikuma_etal2014-hydroidesBabies

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

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

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

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

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6. Relative of animals does strange multicellularity with familiar genetics

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

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

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

Sebé-Pedros_etal2013-F4.capsasporaClump

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

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

References:

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

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

A bunch of cool things

From the weeks during which I failed to check my RSS reader…

1. The coolest ribozyme ever. (In more than one sense.)

I’ve made no secret of my fandom of the RNA world hypothesis, according to which early life forms used RNA both as genetic material and as enzymes, before DNA took over the former role and proteins (mostly) took over the latter. RNA is truly an amazing molecule, capable of doing all kinds of stuff that we traditionally imagined as the job of proteins. However, coaxing it into carrying out the most important function of a primordial RNA genome – copying itself – has proven pretty difficult.

To my knowledge, the previous record holder in the field of RNA copying ribozymes (Wochner et al., 2011) ran out of steam after making RNA strands only half of its own length. (Which is still really impressive compared to its predecessors!) In a recent study, the same team turned to an alternative RNA world hypothesis for inspiration. According to the “icy RNA world” scenario, pockets of cold liquid in ice could have helped stabilise the otherwise pretty easily degraded RNA as well as concentrate and isolate it in a weird inorganic precursor to cells.

Using experimental evolution in an icy setting, they found a variation related to the aforementioned ribozyme that was much quicker and generally much better at copying RNA than its ancestors. Engineering a few previously known performance-enhancing mutations into this molecule finally gave a ribozyme that could copy an RNA molecule longer than itself! It still wouldn’t be able to self-replicate, since this particular guy can only copy sequences with certain properties it doesn’t have itself, but we’ve got the necessary endurance now. Only two words can properly describe how amazing that is. Holy. Shit. :-O

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Attwater J et al. (2013) In-ice evolution of RNA polymerase ribozyme activity. Nature Chemistry, published online 20/10/2013, doi: 10.1038/nchem.1781

Wochner A et al. (2011) Ribozyme-catalyzed transcription of an active ribozyme. Science 332:209-212

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2. Cambrian explosion: evolution on steroids.

This one’s for those people who say there is nothing special about evolution during the Cambrian – and also for those who say it was too special. (Creationists, I’m looking at you.) It is also very much for me, because Cambrian! (How did I not spot this paper before? Theoretically, it came out before I stopped checking RSS…)

Lee et al. (2013) used phylogenetic trees of living arthropods to estimate how fast they evolved at different points in their history. They looked at both morphology and genomes, because the two can behave very differently. It’s basically a molecular clock study, and I’m still not sure I trust molecular clocks, but let’s just see what it says and leave lengthy ruminations about its validity to my dark and lonely hours 🙂

They used living arthropods because, obviously, you can’t look at genome evolution in fossils, but the timing of branching events in the tree was calibrated with fossils. With several different methods, they inferred evolutionary trees telling them how much change probably happened during different periods in arthropod history. They tweaked things like the estimated time of origin of arthropods, or details of the phylogeny, but always got similar results.

On average, arthropod genomes, development and anatomy evolved several times faster during the Cambrian than at any later point in time. Including the aftermath of the biggest mass extinctions. Mind you, not faster than modern animals can evolve under strong selection – they just kept up those rates for longer, and everyone did it.

(I’m jumping up and down a little, and at the same time I feel like there must be something wrong with this study, the damned thing is too good to be true. And I’d still prefer to see evolutionary rates measured on actual fossils, but there’s no way on earth the fossil record of any animal group is going to be good enough for that sort of thing. Conflicted much?)

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Lee MSY et al. (2013) Rates of phenotypic and genomic evolution during the Cambrian explosion. Current Biology 23:1889-1895

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3. Chitons to sausages

Aplacophorans are probably not what you think of when someone mentions molluscs. They are worm-like and shell-less, although they do have tiny mineralised scales or spines. Although they look like one might imagine an ancestral mollusc before the invention of shells, transitional fossils and molecular phylogenies have linked them to chitons, which have a more conventional “sluggy” body plan with a wide foot suitable for crawling and an armoured back with seven shell plates.

Scherholz et al. (2013) compared the musculature of a living aplacophoran to that of a chiton and found it to support the idea that aplacophorans are simplified from a chiton-like ancestor rather than simple from the start. As adults, aplacophorans and chitons are very different – chitons have a much more complex set of muscles that includes muscles associated with their shell plates. However, the missing muscles appear to be present in baby aplacophorans, who only lose them when they metamorphose. (As a caveat, this study only focused on one group of aplacophorans, and it’s not entirely certain whether the two main groups of these creatures should even be together.)

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Scherholz M et al. (2013) Aplacophoran molluscs evolved from ancestors with polyplacophoran-like features. Current Biology in press, available online 17/10/2013, doi: 10.1016/j.cub.2013.08.056

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4. Does adaptation constrain mammalian spines?

Mammals are pretty rigid when it comes to the differentiation of the vertebral column. We nearly all have seven neck vertebrae, for example. This kind of conservatism is surprising when you look at other vertebrates – which include not only fairly moderate groups like birds with their variable necks, but also extremists like snakes with their lack of legs and practically body-long ribcages. Mammalian necks are evolutionarily constrained, and have been that way for a long time.

Emily Buchholz proposes an interesting explanation with links to previous hypotheses. Mammals not only differ from other vertebrates in the less variable numbers of vertebrae in various body regions; these regions are also more differentiated. For example, mammals are the only vertebrates that lack ribs in the lower back. In Buchholz’s view, this kind of increased differentiation contributes to adaptation but costs flexibility.

Her favourite example is the muscular diaphragm unique to mammals. This helps mammals breathe while they move, and also makes breathing more powerful, which is nice for active, warm-blooded creatures that use a lot of oxygen. However, it also puts constraints on further changes. Importantly, Buccholz argues that these constraints don’t all have to work in the same way.

For example, the constraint on the neck may arise because muscle cells in the diaphragm come from the same place as muscle cells associated with specific neck vertebrae. Moving the forelimbs relative to the spine, i.e. changing the number of neck vertebrae, would mess up their migration to the right place, and we’d end up with equally messed up diaphragms.

A second possible constraint has less to do with developmental mishaps and more to do with plain old functionality. If you moved the pelvis forward, you may not screw with the development of other bits, but you’d squeeze the space behind the diaphragm, which you kind of need for your guts, especially when you’re breathing in using your lovely diaphragm.

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Buccholz E (2013) Crossing the frontier: a hypothesis for the origins of meristic constraint in mammalian axial patterning. Zoology in press, available online 28/10/2013, doi: 10.1016/j.zool.2013.09.001

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And… I think that approximately covers today’s squee moments 🙂

Oxygen and predators and Cambrian awesomeness (with worms!)

I didn’t plan to write anything today, but damn, Cambrian explosion. And polychaetes. I can’t not. Plus I’m going on holiday soon, so I might as well get something in before I potentially disappear off the internet. (Below: a Cambrian polychaete, Canadia spinosa, via the Smithsonian’s Burgess Shale pages.)

First, a confession.

I’m a bit of a coward about the Cambrian explosion.

Make no mistake, I love it. It’s fascinated me ever since I came across the heavily Stephen Jay Gould-flavoured account in The Book of Life. It’s an event that made the world into what it is today, with its complex ecosystems full of animals eating, cooperating or competing with each other. And it’s one of the great mysteries of palaeontology. What actually happened? What caused it? Why did it happen when it did? Why didn’t it happen again when animal life was nearly wiped out at the end of the Permian?

The problem is, I love it so much that I’m afraid to have an opinion about it. You have no idea how many times I wanted to discuss the big questions, only to shy away for fear of getting it wrong. Which is really kinda stupid, because no one has the one and only correct answer. Whether I’m qualified to comment on it is a different issue, but it wouldn’t be the first subject I comment on that I don’t fully understand.

So, here I take a deep breath and plunge into Sperling et al. (2013).

The abstract started by scaring me. It begins, “The Proterozoic-Cambrian transition records the appearance of essentially all animal body plans (phyla), yet to date no single hypothesis adequately explains both the timing of the event…” To which my immediate reaction was “why the fuck would you want a single hypothesis to explain it?” But luckily, they don’t. They actually argue for a combination of two hypotheses, which they think are more connected than we thought.

But let’s just briefly establish what the Cambrian explosion is.

I want to make this absolutely clear: it’s not the sudden appearance of modern animals out ot nowhere. It could be more accurately described as the appearance of basic body plans we traditionally classify as phyla, such as echinoderms, molluscs, or arthropods, in a relatively short geological period.

Doug Erwin (2011) trawled databases and literature to draw up a timeline of first appearances for animal phyla, and he found that they increase in number gradually over a period of 80 million years (see Erwin’s plot below).

Erwin2011-cumulativePhyla

Appearance of “phyla” also doesn’t equal appearance of modern animals, as Graham Budd has been known to emphasise (e.g. Budd and Jensen, 2000). For example, I already mentioned how none of the mid-Cambrian echinoderms recently described by Smith et al. (2013) would look familiar today. In fact, the modern classes of echinoderms, which include sea urchins, starfish and sea lilies, didn’t appear until after the Cambrian. Likewise, while there were chordates (our own phylum), and probably even vertebrates, in the Cambrian, such important vertebrate features as jaws or paired appendages were yet to be invented. (If memory serves, both of those inventions date to the Silurian.)

There is also a discussion to be had about the meaning and validity of concepts like a phylum or a body plan, but let’s not complicate things here. I have a paper to get to! 🙂

With that out of the way…

There is no doubt that something significant happened shortly before and during the Cambrian. Before the very latest Precambrian, fossils show little evidence of movement, of predation, or of the diverse hard parts that animals use to protect themselves or eat others today. All of these become commonplace during the Cambrian, establishing essentially modern ecosystems (Dunne et al., 2008).

There are many explanations proposed to account for the revolution. I’ve not the space (or the courage) to discuss them in any detail. If you’re interested, IIRC Marshall (2006) is a very nice and balanced review. (Link leads to a free copy.) However, we can discuss what Sperling et al. have to say about two of them.

The first hypothesis is oxygen, which likely became more abundant in the ocean towards the end of the Precambrian. That  could explain the timing, but maybe not the nature of the explosion. Oxygen levels impose a limit on the maximum size of animals, but what compels larger animals to “invent” more disparate body plans? (Also, on a side note, many Ediacaran organisms weren’t exactly tiny, so I’m not sure how much of a size limit there is in the first place.)

The second one is animal-on-animal predation (Sperling et al. prefer the term “carnivory”), which can lead to predator-prey arms races and therefore encourage the evolution of innovations like shells or burrowing or jaws that give one party an edge. This is a decent enough basis for body plan innovation, but it applies for any time and place with animals. So if carnivory is the explanation, why did the explosion happen when it did?

Because, Sperling et al. argue, carnivory and oxygen are linked.

I’m intrigued by their approach. They’re not looking at fossils in this study at all. (I always like it when palaeontology and the biology of the living join forces!) They are looking at oxygen-poor habitats in modern oceans. Specifically, they asked how low oxygen levels affect polychaete worm communities.

Why polychaetes? The authors give a list of reasons. One, polychaetes are really, really abundant on the seafloor, and particularly so in low-oxygen settings. Two, different species feed in almost every conceivable way from filtering plankton through chewing through sediment to flat out devouring other animals, and their feeding mode can usually be guessed even if you haven’t seen that particular species eat. Three, they are actually quite good at handling oxygen limitation. This is important because back in the Precambrian, all animals would have been well adapted to a low-oxygen environment, so a group that can tolerate the same may be the best comparison. (They do note that  a previous study of a single low-oxygen site that took other animals into account came up with similar results to theirs.)

They worked partly with pre-existing datasets that met a set of criteria designed to get a complete and unbiased view of local polychaete diversity. In total, they analysed data from 68 sites together featuring nearly a thousand species of worms. They also had some of their own data.

They categorised their study sites into four levels of oxygen deprivation, and counted numbers of carnivorous individuals and species at each site. They came to the conclusion that lack of oxygen basically makes carnivores disappear. The lowest-oxygen samples contained fewer carnivores on both the individual and species levels, and they were more likely to be devoid of predators altogether (# species plot from the paper below):

sperling_etal2013-fig2c

There are a couple of different ways in which lack of oxygen could limit predators. For example, the aforementioned size limit is one, because it’s good for a predator to be larger and stronger than its prey. But the biggest factor according to the authors is the energy required for an active predatory lifestyle. While a suspension feeder can sit in one place all day and only move to stuff a food-laden tentacle into its mouth, a predator has to find, subdue and eat its prey, which are all pretty expensive activities. Then it also has to digest a sudden, large meal, whereas the suspension feeder’s digestion works at a low and steady rate. Animals can get energy from a variety of metabolic processes, but by far the most efficient route requires oxygen. And that really sucks when you are a hunter who might need large amounts of energy at short notice.

Hmm…

Although I’m quite intrigued by the study, there are a couple of issues that bother me. For example, as far as I could tell, all of the study sites included in the analyses were low on oxygen. I would have liked to see them compared to “normal” sites, in particular because the trend in predator abundance wasn’t a neat straight upwards line. In fact, the least oxygen-deprived habitats appeared less predator-infested than slightly more oxygen-poor ones. What’s going on there?

In terms of interpretation in relation to the Cambrian, I also would have liked to see a comparison of the oxygen levels at their study sites to what’s estimated for the geological periods in question. I take it they just didn’t have precise enough estimates, because one of the things they discuss in the closing paragraph is the need to measure just how much oxygen went into the oceans during this late Precambrian oxygen increase.

And my semi-silly question is, how does this apply to “predators” who don’t run around chasing after and wrestling with prey? For example, sea anemones might be perfectly happy to eat large creatures. But they don’t really do much. They just sit and wait, and if a poor fish stumbles onto their sticky venomous tentacles, tough luck for it. Or there’s the unknown predator that drilled holes in late Precambrian Cloudina specimens (Bengtson and Zhao, 1992). Cloudina was sessile, the creature didn’t have to chase it… Predators such as these still have to cope with the energy demands of digesting sudden large meals, I suppose, so maybe the energetics idea still applies. And of course, if there’s no oxygen, large prey is less likely to be swimming around bumping into your tentacles.

Is this “the” explanation of the Cambrian explosion? Probably not, says the cynic in me. I highly doubt we’re done with that question. Is it a good explanation? Well, it is certainly evidence-based, and I like it that it tries to take different factors together and in context. What I don’t think it does is explain the uniqueness of the Cambrian. A thousand words or so ago, I mentioned the Permian extinction. That cataclysm very nearly left the earth devoid of animals. Afterwards, there was certainly enough oxygen for predators to thrive in the sea, and indeed they did, from sea urchins to ichthyosaurs. So why didn’t the first 40 million years of the Mesozoic era beget many new phyla the way the first 40 million years of the Palaeozoic did? Is that just an artefact of our classifications or was something really fundamentally different going on?

I ain’t Jon Snow, but when it comes to the Cambrian, I still feel like I know nothing…

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References:

Bengtson S & Zhao Y (1992) Predatorial borings in Late Precambrian mineralized exoskeletons. Science 257:367-369

Budd GE & Jensen S (2000) A critical reappraisal of the fossil record of the bilaterian phyla. Biological Reviews 75:253-295

Dunne JA et al. (2008) Compilation and network analyses of cambrian food webs. PLoS Biology 6:e102

Erwin DH (2011) Evolutionary uniformitarianism. Developmental Biology 357:27-34

Marshall CR (2006) Explaining the Cambrian “explosion” of animals. Annual Review of Earth and Planetary Sciences 34:355-384

Smith AB et al. (2013) The oldest echinoderm faunas from Gondwana show that echinoderm body plan diversification was rapid. Nature Communications 4:1385

Sperling EA et al. (2013) Oxygen, ecology, and the Cambrian radiation of animals. PNAS 110:13446-13451