Return to Origin part 2

In which Darwin’s Introduction sends me off on tangents about academic writing, gender and the nature of explanations.

The Origin of Species reread returns! Eventually! So much for increasing my productivity, but hey, at least I didn’t give up after the first one! (For the record, this post has been 99% written for the past month. It only took me that long to convince myself that hitting the “publish” button won’t turn me into the laughing stock of the universe.)

This won’t be as long as Part One, since the Introduction isn’t as long as the Historical Sketch either. In comparison with modern scientific works, the Intro is basically the abstract of Origin, mixed with a few acknowledgements. It covers pp. 65-69 of my copy.

It’s amusing and endearing how much of the first couple of pages is spent swearing up and down that Darwin didn’t pull his theory out of his backside. Also, the “sorry I couldn’t give you all the facts, I had to be brief” apology always cracks me up – if 400 pages full of facts is your idea of brevity, man, you should be writing epic fantasy, not science 😛 (Also: perfectionist much?)

I have written my own handful of scientific articles in my time as a PhD student, which definitely gives one a different perspective on some of the writing conventions in such works. (It should go without saying, but this is my individual perspective; I certainly don’t claim to represent all writers of scientific articles.) When authors talk about caution and caveats and more data being needed, I think most of the time they are both sincere and not. Scientists – the ones I’ve met, at least – generally seem like decent people who honestly worry about getting stuff right and not letting wishful thinking get in the way of good science.

However, when you’re preparing a manuscript for a peer-reviewed academic journal, there is always an element of satisfying reviewers, and if you sound more confident than the reviewers think your data warrant, they will comment on that. Adding caveats is not just a sign that you understand the limitations of your work, it is also insurance against being hassled by editors and reviewers. (And then there’s always throwing a bone to your worst enemies just in case they try to sabotage your paper, because scientists can be just as petty and occasionally awful as humanity at large, and often, anonymity doesn’t actually make it that much harder to figure out whose paper you’re reviewing.)

With all that said, it never occurred to me that Darwin wasn’t perfectly sincere in his numerous apologies for not providing even more evidence. He just doesn’t seem like that kind of guy. Please don’t disillusion me. I’m a giant ol’ sap at heart, okay?

P65 has another shoutout to Wallace, and p66 a huge acknowledgement to Hooker (an eminent scientist in his own right). This Darwin-Hooker bromance is making me all mushy inside! (See above: giant, sappy)

Pp66-7 contain, aside from another little dig at the Vestiges of Creation, some first-class philosophy fodder. Here, Darwin emphasises the importance of providing mechanisms when positing a new phenomenon. Lots of people, he says, might look at the similarities among species and conclude that different species have descended from common ancestors. “Nevertheless,” he continues, “such a conclusion, even if well founded, would be unsatisfactory, until it could be shown how the innumerable species inhabiting this world have been modified, so as to acquire that perfection of structure and coadaptation which most justly excites our admiration.”

Do we agree with this assessment? How much is suggesting a “what” worth without an accompanying “how”? And how necessary is a mechanism for the acceptance of a new scientific idea? The simple, distilled high-school science class version of the story of continental drift, for example, tells you that Alfred Wegener was laughed out of the room because he couldn’t say what force might make continents waltz across the surface of the planet. Then someone came up with mantle convection, and Wegener’s idea finally triumphed. The actual story, as is usually the case, seems a bit more complicated than that, but it does sound like the general acceptance of the idea needed that mechanistic underpinning that its proponents couldn’t quite provide at first.

While looking for scientific ideas that might have been widely accepted without that underpinning, I found myself getting really philosophical and wondering what counts as a mechanism. Perhaps this is easier to answer in biology, where most explanations can at least be conceptualised. One doesn’t have much difficulty imagining some individuals being better at procreation than others, and babies resembling their parents (the very dumbed-down essence of natural selection). What about physics, where shit gets really weird and soon leaves the realm of human experience when you start digging deep enough? Did physicists accept concepts like gravity, dark matter and dark energy because the maths worked out, because the observations were so bloody obvious that something had to be going on, or because “attractive force”, “weakly interacting massive particle” or “vacuum energy” make sense to human brains? (Of course, I wouldn’t expect a physicist to accept anything based solely on the third, but where the maths could go multiple ways, as – so far as I understand – on the boundaries of modern cosmology, is it easier to lean towards the equations that correspond to concepts that make the most sense?)

… I guess what I’m saying is that this stuff is fascinating to ponder, and if anyone points me to a readable discussion of the subject by someone who actually knows what they’re talking about, I might well put it on my ever-expanding reading list…

P67 then reminded me how times have changed since Darwin’s day. Here, he discusses “man” and his “great power” in “accumulating slight variations”. Every time he talks about something humans did, it’s always a “he” (well, at least up to the end of the next chapter 😛 ). We’ve certainly come a long way when it comes to recognising the rest of humanity’s role in history…

This is where I decided that I needed to keep an eye out for any mention of female scientists (or just women in general) – women of science have existed for as long as science itself, but I’m curious whether Darwin drew on the work of any. It’s always satisfying to see women’s achievements recognised by their male contemporaries, especially in times when it wasn’t fashionable to do so. It would be extra satisfying to see it from a man I like and admire in his own right.

There is not much to say about the rest of the Introduction, except to note that it’s a decent summary of Darwin’s evolutionary theory. He lists the basic elements of the theory (variation + competition = natural selection + extinction), the main categories of evidence he used to come to his conclusions (artificial selection, embryology, ecology, biogeography, fossils) and the main questions that the theory must answer (novelties of morphology and behaviour, the sterility of hybrids, and the gaps in the fossil record). All of these will make extended appearances in the course of the book.

The last paragraph of the Intro is such a typical conclusion to a scientific abstract that I had to smile when reading it. There is still much to be learned, but the author is convinced that he is right about X, Y and Z. Not saying this is a bad way to conclude an introduction – all I’m saying is that for me, it’s a well-worn trope of academic writing that echoes with the voices of a thousand other works.

Next time, we’ll get into the meat of Origin proper. It turns out that the meat in Origin is often pigeon. (Seriously. Darwin was obsessed with pigeons.)

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Return to Origin part 1

Introducing my new pet project

The Mammal has had an idea to boost her productivity! (OK, I’ve actually had this idea pretty much since I started CM. Speed has never been among my selling points 😛 ) Since most of the posts I start writing about current science seem to die in their cradles these days, I have decided to go back to Ye Olde Science and try my hands at an Origin of Species re-read. Because Origin is one of the foundational works of my discipline, and it proved to be a lot more interesting than a callow undergraduate student of evolutionary biology had expected. Also, there is a lot of material in it, and on previous reads I’ve had no shortage of thoughts about it. There is a faint chance it can sustain a few months of blog posts 🙂

I’ve never been too bothered about reading “the classics”. The classics of literature that school forced me to read often turned out to be terribly written, boring tomes whose “profound” meanings held little interest for a young person. Much of my higher education gave me the feeling that biology is such a fast-moving field that anything older than a decade or so is probably of little value except as a historical curiosity. I was, it turns out, very wrong about that for more than one reason. First, you don’t really start appreciating the value of older literature until decades-old, obscure zoological papers are the only place you can find any information at all about the question you are researching. Biology may move fast when it comes to the genetics of well-known model organisms, but it sure as hell takes its time in investigating the development and regeneration of serpulid opercula.

Second, history can be interesting in itself. Science is not a series of independent discoveries; it is a complex, organic growth cultivated by interconnected minds embedded deep in their respective societies. Which ideas get picked up and which ones are forgotten doesn’t just depend on the quality of the evidence but also on the zeitgeist. (The first example I thought of was, disturbingly, the triumph of Lysenkoism over real genetics under Stalin. I guess straight-up imprisoning or executing anyone who doesn’t like your pet advisor’s pet theory kind of counts as an effect of the zeitgeist?)

I first decided to read Darwin’s Origin a number of years ago out of curiosity. I was, after all, studying for an evolutionary biology degree, and Origin was kind of the book that kicked it all off. (I think it might have been on offer at the university bookstore when I went to buy some textbooks, too.) To be honest, I fully expected a boring, painfully outdated, horribly convoluted book. I expected reading it to be a chore. I certainly didn’t expect to find beauty – never mind revelations – in it.

Suffice to say I was pleasantly surprised. While Darwin’s writing style can be a drag for a modern reader with an attention span trained on Facebook posts and cat memes (he’s waaaaaay more fond of run-on sentences than I am, and I have to actively restrain myself from letting them grow out of control), it is quite beautiful at times. What’s more interesting from the scientist’s perspective – while a lot of Origin is indeed outdated, there are some surprisingly “modern” ideas that I never would have expected to find in a 19th century book. The third major surprise of my first read was the sheer amount of data involved. I suppose I’d always known that Darwin didn’t pull his theory out of thin air, but I hadn’t realised just how much careful observation went into his best-known work. No wonder it took him decades to finish [1].

And so, from the vantage of a few more years of learning, I decided to give Origin of Species another read and document my thoughts along the way. I have no idea if this is going to work out, but hopefully publishing the first part will give me the incentive to carry on.

Origin saw six editions altogether. The version I have, the 1985 Penguin Classics edition, contains the text of the first edition, but also includes the Historical Sketch that Darwin added later. The Sketch itself went through a number of revisions; I’m not entirely sure which version my copy has. (Origin can be read free of charge in several places online, including TalkOrigins and Darwin Online. TalkOrigins’s version is also a first edition text with the Sketch added.) It is with this Sketch that I’m going to kick off the re-read.

I won’t even attempt to summarise chapters, and I might have to split most of them into multiple posts for sheer length. Comments might be a bit disjointed, since they reflect thoughts that came into my head as I was reading – sometimes connected, but often quite scattered and tangential. Any page numbers refer to my Penguin edition, but I’ll try to remember to give some pointers (paragraph descriptions, section headings, quotes) for anyone reading a different version.

Darwin on the shoulders of giants – the Historical Sketch (pp53-63)

I find the Historical Sketch (hereafter: HS) tremendously interesting. I’m not entirely sure why it appeared in later editions of Origin; I had assumed that it was a response to claims that he was ripping people off, but googling the subject yielded surprisingly little information. Johnson (2007) calls its origin “somewhat obscure,” and Darwin’s own statements on the matter contradictory. Darwin’s correspondence doesn’t even clarify when the HS was written, let alone why. Similar historical introductions, Johnson notes, are not uncommon in scientific writings of the era, and it is quite possible that Darwin was already drafting one for his “big species book” (of which Origin was the abridged version) years before the publication of Origin, but not much evidence remains to fill in the details.

General observations

Regardless of where it comes from, the HS is an intriguing little run-down of the history of evolutionary ideas as Darwin saw it. If there is one take-home message from this brief preface to Origin, it is that no scientific advance is a lightbulb suddenly blinking on in the dark. Ideas have roots, and complicated ideas come together from many different roots, some of them, in this case, going right back to antiquity.

Any good biology curriculum includes some of the researchers and thinkers featured in the HS – who hasn’t heard of Lamarck and his silly-silly inheritance of acquired characteristics, for example?[2] However, schools tend to gloss over the sheer quantity of evolutionary thinking going on in late 18th and early- to mid-19th century biology. Well, in his ten-and-a-half-page summary, Darwin discusses 34 authors, all of whom entertained the idea that species might change over time, and many of whom considered possible mechanisms for such change. Most of these guys I’d either never heard of at the time I first read Origin, or I’d never known they had a connection to evolution. All in all, the HS definitely gives the impression of a biological community ripe for an evolutionary revolution.

Finally: oh GODS, some of this is so funny. The HS exhibits some prime examples of the kind of borderline impolite academic snark that you can also find in today’s scientific debates. Having done research and written a few papers myself, I find academic snark doubly entertaining; just how many ways can you call someone an idiot while maintaining that essential veneer of professionalism?

A page-by-page trip through Tangentia

A.k.a. any old silliness that popped into my head along the way.

Victorian titling conventions: clearly long before the invention of clickbait! The full title of Origin is the unwieldy The Origin of Species by Means of Natural Selection, or The Preservation of Favoured Races in the Struggle for Life. [3] The HS is technically called An Historical Sketch of the Progress of Opinion on the Origin of Species Previously to the Publication of the First Edition of This Work. Quite a mouthful, but at least it tells you exactly what to expect. None of this “You Won’t Believe What This Man Found in His Soup!” nonsense!

Right off the bat, on p53: giant footnote that takes up half the page AND some of the next page. The HS has several of those, and I’m not entirely sure why they aren’t simply part of the main text. Luckily, the rest of the book is blissfully devoid of them.

By the way, this first footnote is pretty interesting. To me, anyway, since I spent a lot of time interacting with creationists, and by the quotes Darwin gives here, Aristotle (!) got something right that most creationists (or most people?) struggle with to this day. That being the idea that the traits of organisms do not arise in order to fulfil some goal – they just are, and if organisms seem well-adapted to their circumstances, that is because any that weren’t were exterminated by said circumstances.

P55, the discussion of Étienne Geoffroy Saint-Hilaire (the guy who sort-of invented dorsoventral inversion) and his ideas about the descent of species from original “types”: I love how Darwin just assumes that his readership knows French. This isn’t the last untranslated French quote in this book by a long shot. (This particular one, Google Translate tells me, basically boils down to “we need more research”.)

Also on the same page, in the next paragraph about WC Wells’s views – I honestly hadn’t known that “negroes and mulattoes [enjoying] immunity from certain tropical diseases” was already established in the early 19th century. Darwin doesn’t detail which diseases – wonder if malaria is among them? Seeing as sickle cell trait and malaria immunity is one of the textbook examples of heterozygote advantage in modern courses on evolution. I’m quite impressed (though maybe I shouldn’t be) that not only were scientists aware of differences in disease susceptibility, but also attributed these to something akin to natural selection. (Although I’m pretty certain that an understanding of the genetics was far out of reach for the naturalists of the time.)

On the next couple of pages, there are at least three allusions to archetypes that related species are thought to have diverged from. There seems to be a theme running through all of these “type” concepts, although Darwin doesn’t always give direct quotes, so I don’t know how accurate his descriptions of his colleagues’ views are. In connection with Geoffroy Saint-Hilaire, he mentions related species being “degenerations of the same type”; W. Herbert supposedly suggested “highly plastic” original forms to be the ancestor of each plant genus, and Rafinesque (this is a direct quote) wrote that “varieties are gradually becoming species by assuming constant and peculiar characters”, that is, “except the original types or ancestors of a genus”.

So the general thrust of this seemingly fashionable idea is that the ancestors of living species were more variable and less specialised than their descendants. Does anyone hear definite SJ Gouldian undertones here? Isn’t this basically the late great Gould’s view of the Cambrian Explosion in a nutshell? I guess I should have expected this idea to go very far back, what with Platonic ideals and all that, but it still took me by surprise to find it in this context.

… also, it took me until this point, nearly halfway through the HS, to realise that Darwin was going in chronological order. I blame sleep deprivation.

P57 is where I had a sudden “I really should know this” moment. I’m reading this bit and thinking, who the fuck wrote the Vestiges of Creation? I distinctly remembered hearing about it in class years ago, but I couldn’t for the life of me attach a name to it. For the record, Vestiges, a pop-sci book about the evolution of everything (written by a Scotsman named Robert Chambers) was originally published anonymously, so I’m not going to feel too bad about not remembering the author.

Here comes our first example of wonderful academic snark. Vestiges, by Darwin’s account, sounds like a big heap of vitalistic mumbo-jumbo, complete with ladder-thinking and generally likely to make me tear my hear out should I ever be brave enough to read it. I get the distinct impression that I share this opinion with one Mr Darwin – heck, I’m just going to quote his description of Vestiges in its full glory:

“But I cannot see how the two supposed ‘impulses’ account in a scientific sense for the numerous and beautiful co-adaptations which we see throughout nature; I cannot see that we thus gain any insight how, for instance, a woodpecker has become adapted to its peculiar habits of Life. The work, from its powerful and brilliant style, though displaying in the earlier editions little accurate knowledge and a great want of scientific caution, immediately had a very wide circulation. In my opinion it has done excellent service in this country in calling attention to the subject, in removing prejudice, and in thus preparing the ground for the reception of analogous views.”

So: it’s an overenthusiastic pile of pseudoscience that fails to actually explain anything, but I guess it’s… well-written? Oh, ol’ Chuck, you’re such a diplomat.

(Totally random aside: despite leaning towards biology and occasionally astronomy from an early age – so, definitely NOT chemistry – my first real encounter with vitalism, the belief that living things run on some kind of special life force, was in a book about the history of chemistry. Specifically, I learned how the first synthesis of an organic compound – urea – from completely inorganic sources dealt a great blow to the whole life force thing. The book in question was written in 1960s socialist Hungary and was, if memory serves, quite ideologically charged in places. That book would make for another interesting re-read, though probably not for anyone besides myself…)

Immediately after delivering third-degree burns to Vestiges, Darwin unleashes his diplomatic snark on Richard Owen, who was a bit of a… character. He has a reputation for trying to pass other people’s discoveries off as his own, and apparently Darwin’s natural selection was one of his targets. In the HS (p59 of my copy), Darwin summarises his take on Owen thusly:

“It is consolatory to me that others find Professor Owen’s controversial writings as difficult to understand and to reconcile with each other, as I do. As far as the mere enunciation of the principle of natural selection is concerned, it is quite immaterial whether or not Professor Owen preceded me, for both of us, as shown in this historical sketch, were long ago preceded by Dr Wells and Mr Matthews.”

Or: Owen, WTF are you on about?

P60 – It appears that Herbert Spencer was the granddaddy of evolutionary psychology, in that he was the first to propose that mental capacities could evolve gradually in the same way physical characteristics can. Cool.

(Also in this general area: more untranslated French quotes. From Geoffroy Saint-Hilaire, not Spencer.)

P61: Add Naudin to the “plastic archetypes” fan club. And have YET MORE French.

There is an interesting, if only tangentially related, footnote here. All through my reread of the HS I was waiting for Darwin to explain why his take on evolution was special and important, and contrary to my hazy recollection, he never does. (Not in the HS, anyway; my memory of Origin proper is not good enough to recall whether he does it later.) The closest he gets is in the p61 footnote, where he notes that 27 of the 34 authors he discusses “have written on special branches of natural history or geology”, which I interpret to mean that a general discussion of evolutionary theory had been lacking up to that point. So Origin’s perk is the breadth of its coverage? I’m not going to disagree with that…

(Our regular scheduling is interrupted for more French quotes. *le sigh*)

On p62, we finally get to the “other guy”, Alfred Russel Wallace, whom everyone always forgets about. Darwin doesn’t go into great detail; I suppose he figured the fact that they kind of published their theories of natural selection together sufficed. However, he does praise Wallace’s 1858 essay that made its way into the Journal of the Linnean Society for its “admirable force and clearness”. Darwin does seem like a guy who gives credit where credit is due.

Something I found interesting a few paragraphs from the end of the HS: how the same “Great Man” can mean totally different things to different people. I know Karl von Baer as one of the founding fathers of evo-devo, with his famous laws of embryology. However, when Darwin mentions von Baer’s belief in common descent, he only says that it was based mainly on biogeography. Are we even talking about the same von Baer??

Finally, the HS concludes with a little hat-tip to Darwin’s long-time friend, correspondent and fellow nerd, Joseph Hooker. Hooker will make many more appearances in Origin if memory serves – he was the source of many of the observations on which Darwin built his mighty edifice. Those two: geeky bromance of the (19th) century.

Concluding thoughts

Reading this Historical Sketch again made me wonder why it is Darwin that we remember today as “the” father of evolution. Origin may not be a totally academic work, but it sure as hell isn’t light reading. Yet it was immensely popular – the first edition sold out as soon as it was published, and the book saw six editions during Darwin’s lifetime. Was it the completeness of his treatment? His excellent social network? Was it simply a case of right place, right time? I should probably let historians of science ruminate on that. Instead, I shall move on to the Introduction. But not today. Definitely enough meandering for today!

***

(Small) footnotes:

[1] Which, by the way, he still considered unfinished at the time of publication, but I’m jumping ahead of myself here. [Back to post]

[2] As we’ll (hopefully) see later in the re-read, this idea didn’t seem quite so silly at the time – Darwin himself didn’t fully discount it. He did scoff at other components of Lamarck’s theory of evolution, however. [Back to post]

[3] No, he does not use “race” in that sense. [Back to post]

***

Reference:

Johnson CN (2007) The preface to Darwin’s Origin of Species: the curious history of the “Historical Sketch”. Journal of the History of Biology 40:529-556.

To dump a chunk of trunk

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

hypsibius_dujardini_eol

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

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

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

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

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

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

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

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

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

Smith_etal2016-hox_tardigrade_fig4A

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

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

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

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

***

References:

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

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

***

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

Worldbuilding. With SCIENCE!

Today, I felt like meandering around a random piece of my mind that is a bit outside my usual blogging territory. Most of my academic reading (and consequently, most of my stuff here) is in the general areas of evolutionary biology, developmental biology, palaeontology and intersections thereof. Occasionally I’ll see something about abiogenesis or exoplanets or animal cognition and read it for the coolness. However, besides being a scientist, I also happen to be an avid reader and occasional writer of fantasy fiction, and one of the most appealing aspects of that genre for me is worldbuilding.

I am fascinated by the diversity of human cultures; the myriad different ways of seeing the world and constructing identities for ourselves. I love reading novels with interesting, well thought-out cultures, and tinkering with my own world is one of my favourite pastimes. If I had unlimited money and weren’t the lazy sod I am, I’d probably be thinking about getting a cultural anthropology degree on top of my first one in evolutionary biology*. Since I have very limited money and motivation, I content myself with watching out for interesting titles in the generalist journals I read. Even as a worldbuilder, I can’t stop being a scientist, so I love seeing scientific takes on what makes cultures the way they are.

Music, the many ways thereof

The other day, for example, I bumped into an analysis of music from around the world in PNAS (PNAS is a pretty good general journal for the occasional worldbuilding fodder.) Savage et al. (2015) searched for universal features of human music in about 300 recordings from around the world. It was particularly interesting to me because I have a culture with what I always suspected was a really weird religious prohibition relating to music. From what I can gather from this paper, my suspicion was correct: my little religious gimmick would be very unusual in the real world.

One of the main points of the study, however, is that there aren’t really any truly universal properties of music. There are exceptions even to “self-evident” rules that stem from the way our brains work, like having a regular beat or (if the music isn’t purely percussion) a scale made of discrete pitches. (So: I can do what I want with the music of my imaginary cultures, as long as I don’t make them all weird in the same way. Science says so. *smug face*)

There’s also the fact that most of the music recorded in the database is performed by men despite the fact that women are just as capable of making music. This is a valuable piece of information for a worldbuilder, one I wasn’t (consciously) aware of before I read this paper, and also one that highlights the importance of context. Me being a girl and rather acutely aware of the curses of patriarchy from a young age, I have thought up several societies that are either gender-equal or matriarchal (most of these societies are not human). How would that change the balance? If the hypothesis that male-dominated music has something to do with sexual selection is correct, should we see pretty much equal participation in cultures where both men and women are promiscuous and participate in literal mating displays? (Playing with sexuality in a fantasy world is even more fun than playing with religion! Also, an evolutionary biology degree can give you some really funky worldbuilding ideas…)

(Incidentally, Savage et al. draw a parallel between male-dominated music in humans and male-dominated vocalisations in, among other groups, songbirds. I find it curious that they didn’t mention a recent study that suggested that actually, females probably also sang in the ancestral songbird, and pointed out that this state of affairs is still the norm rather than the exception when you look at the whole group [Odom et al., 2014].)

Religions evolving

Today, I found a paper introducing a really shiny new database in PLoS ONE (which is why I decided to ramble about worldbuilding). “Pulotu” (Watts et al., 2015a) is a free database of supernatural beliefs and practices from 100+ Austronesian cultures, designed to study the cultural evolution of religion. Austronesian peoples originated from Taiwan many thousands of years ago. Today, they inhabit a huge area including Indonesia, Papua New Guinea, New Zealand, zillions of Pacific islands (Polynesians!) and Madagascar. They are a very diverse bunch in every respect, and their family tree is pretty well understood from linguistics and genetics. A decent database of those diverse cultural traits combined with the understanding of history is truly an amazing resource for those interested in how said cultural traits evolve. (Seriously, this thing looks like a goddamned gold mine.)

The authors have clearly done thorough work, using multiple sources, ethnographies written by scholars who actually met the people in question where possible, to characterise each culture. The database has three separate time focuses to distinguish the “pristine” state of a culture from what happened after contact with major religions like Hinduism or Christianity. They recorded both characteristics of religion like the types of supernatural beings worshipped and the types of rituals practiced, and characteristics of the societies themselves such as how they get most of their food, and how many layers of political hierarchy they have. You can visualise these features on a map with a couple of clicks, so you can immediately see if they are randomly distributed or found in particular places.

So what can you learn about cultural evolution from this treasure trove? One example the paper gives concerns something I came across years ago when I was researching theories about the evolution of religion for an undergrad assignment. The idea is that fear of supernatural punishment, particularly the belief in “high gods” who punish immoral acts, fosters cooperation and promotes the formation of large and politically complex societies. The supernatural punishment hypothesis has been around for a while, but I think I first encountered it in Johnson (2005).

Johnson tried to test the idea by looking at correlations between belief in moralising high gods and various proxies of cooperation (e.g. size of the society, presence of money lending, centralised authorities) in a cross-cultural sample. However, correlation does not equal causation, so that kind of study leaves it unclear whether moralising gods lead to complex societies or the other way round. However, with a solid family tree of cultures, you can add a historical dimension to a cross-cultural comparison, which allows you to infer causality.

When the Pulotu authors did this (Watts et al., 2015b), they found that Johnson probably got his causal arrow pointing the wrong way. If moralising gods do indeed lead to complex societies, then societies with moralising gods should increase in complexity more often than societies without. What actually seems to be happening in Austronesia is that complex societies came first, and they were more likely to develop beliefs in moralising gods. Nonetheless, a more general version of the supernatural punishment hypothesis, in which agents that aren’t high gods (e.g. karma, ancestors) may do the punishing, is supported by the analysis.

That’s mostly irrelevant for worldbuilding, where the correlation alone is enough to work out what’s “realistic”, but I also find the science fascinating in its own right. And while I’ve not tried downloading the Pulotu dataset (as I said, I only found out about it today, and I’ve been writing this post since), from a brief look it’s a handy text file that appears to be useable by anyone who knows the first thing about spreadsheets. I might have to go and play with it. Just have to think of some interesting questions…

So, now you know. I’m a hopeless geek even when I’m not officially being a scientist. (Does this surprise anyone?)

Notes:

*If I had unlimited money, I’d probably spend my entire life at university…

References:

Johnson DDP (2005) God’s punishment and public goods. A test of the supernatural punishment hypothesis in 186 world cultures. Human Nature 16:410-446

Odom KJ et al. (2014) Female song is widespread and ancestral in songbirds. Nature Communications 5:3379

Savage PE et al. (2015) Statistical universals reveal the structures and functions of human music. PNAS 112:8987-8992

Watts J et al. (2015a) Pulotu: database of Austronesian supernatural beliefs and practices. PLoS ONE 10:e0136783

Watts J et al. (2015b) Broad supernatural punishment but not moralizing high gods precede the evolution of political complexity in Austronesia. Proceedings of the Royal Society B 282:20142556

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

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

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

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

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

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

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

Luo_etal2015-fig2

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

So, Lingula, living fossil? Not so much.

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

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

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

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

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

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

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

***

Notes:

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

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

***

References:

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

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

The things you can tell from a pile of corpses…

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

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

clusters within clusters

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

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

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

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

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

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

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

***

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

***

References:

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

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

Putting the cart before the… snake?

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

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

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

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

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

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

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

Cohn_Tickle1999_hoxRegions

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

Woltering_etal2009-mouse_vs_snake

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

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

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

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

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

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

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

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

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

Head_Polly2015-phylogeny_of_spines

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

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

***

References:

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

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

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

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):

Liu_etal2014-haootia_recon

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:

Miranda_etal2015-haootia_alt_recon

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

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

Hi, real world, again!

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

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

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

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

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

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

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

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

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

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

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

Vetulicolians from Wiki

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

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

Garcia-Bellido_etal2014-nesonektris_recon

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

García-Bellido_etal2014-nesonektris_notochords

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

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

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

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

Sansom_etal2013-adult_lamprey_notochord_d63

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

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

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

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

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

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

References:

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

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

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

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