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 (GarcĂ­a-Bellido et al., 2014), and it looks something like this (Diego GarcĂ­a-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):

GarcĂ­a-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

GarcĂ­a-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

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Two for Team Mollusc

Yay, more involved invertebrate anatomy I don’t really understand but can’t resist writing about!

In other words, Martin Smith, one of the guys who likes to argue that a number of Cambrian weirdos are actually molluscs, published new stuff about, guess what, Cambrian weirdos he considers molluscs.

Above: the delightfully odd Wiwaxia by Nobu Tamura, from Wikipedia.

I don’t think he and JB Caron had much luck with the Nectocaris-is-a-cephalopod idea, but maybe he’s on to something with Odontogriphus and Wiwaxia. I mean, one of the big complaints about Nectocaris being a proto-squid was that none of the 90-odd specimens preserve any mouthparts at all, and mouthparts are normally among the toughest and most recognisable features of cephalopods. This time in the Proceedings of the Royal Society (Smith, 2012), there are mouthparts galore. The paper is about mouthparts.

Above image from the paper features an electron micrograph, closeup and drawing of a specimen belonging to Odontogriphus, showing two kinky rows of hooked teeth that were probably all embedded in one chunk of tissue in life (they tend to stay together in the fossils). They look kinda freaky, but more importantly, Smith argues, they look remarkably like a simple version of a radula. Which is a very mollusc thing to have – nothing else alive today has one. Most living molluscs sport more complicated radulae than this, with many more than the two or three tooth rows found in the Cambrian creatures in question, but hey, no one said modern radulae suddenly popped into existence fully formed. If they are molluscs, the strange Odontogriphus and Wiwaxia are probably among the early branches within the phylum, which may well mean that their ancestors said bye to the rest of the molluscs before the first hopeful monster with more than three rows of teeth hatched from a slimy clutch of proto-mollusc eggs.

Another major interpretation of these creatures, especially Wiwaxia, is as something close to annelid worms (ragworms, earthworms etc.). Their mouthparts have previously been claimed to resemble dorvilleid annelid jaws, a lovely example of which is shown on the right of this image. (Warning: closeups of polychaete faces are not for the faint-hearted ;)) However, Smith argues that the structure of Odontogriphus and Wiwaxia tooth rows is nothing like that of worm jaws. For example, they consist of teeth that can rotate relative to one another whereas the worm jaws in question have teeth sitting in fixed rows, and the teeth are apparently shed and replaced in completely different ways. Not to mention that the living worms have paired jaws, whereas each tooth row of the Cambrian critters appears connected in the middle. Of course, Smith says they aren’t connected in the same way that some other annelid jaws they’ve also been compared to are.

So, Team Mollusc has delivered some toothy punches, but I’m sure this is not the final word on something as old and weird as Odontogriphus and Wiwaxia. Holding my breath for the responses of Team Worm and Team Grandaddy of Molluscs AND Worms…

(BTW, I recall that Wiwaxia, in addition to its mollusc mouth, also has scaly armour that looks suspiciously like a bunch of fused annelid bristles. Dunno how accurate that information is today, since IIRC I read it in a pretty old book that also had an agenda, but that just goes to show that so soon after all the Common Ancestors lived, family resemblances might get a bit muddled… And crazy thought, what if the common ancestor of annelids and molluscs – they are pretty close relatives, after all – had a radula? Annelids today don’t, but you never know. It wouldn’t be the first time an animal lost something complex in the history of evolution.)

***

Reference

Smith MR (2012) Mouthparts of the Burgess Shale fossils Odontogriphus and Wiwaxia: implications for the ancestral molluscan radula. Proceedings of the Royal Society B, advance online publication, doi: 10.1098/rspb.2012.1577

It’s life, Jim, but not as we know it!

A bit belatedly, but as the Cambrian mammal, I feel it’s my duty to jump on the Siphusauctum bandwagon. I was actually a bit surprised by how much news and blog coverage the creature got. I didn’t expect something with no clear affinities to anything and no particularly “cool” features of its own to make many headlines. It’s just a peaceful filter-feeder that looks like a mutant tulip, FFS.

Guess I fail the internet?

Below is a nice bouquet of tul… I mean, Siphusauctum fossils on their slab of rock, from O’Brien and Caron, 2012. They are completely soft-bodied creatures that range from under 2 cm to more than 20 in total height. Presumably, the live animals stood upright on their thin stalks and filtered food particles from the water. The authors speculate that they may have been able to move from one spot to the other, because the small holdfasts at the end of the stalk don’t seem like strong, permanent anchors.

I don’t particularly want to dwell on the details of the paper. It’s the dry and tedious sort of thing descriptions of new taxa usually are, and all those news and blog articles probably beat me to all the basics as far as explaining the animal to a lay audience goes. I just want to make a couple of totally random observations.

One – how the hell do they know that the creature had a mouth? The authors seem quite certain that the digestive tract of Siphusauctum had both a mouth and an anus, but as far as I can tell, they only actually found one hole (which they interpreted as the anus). The mouth is only mentioned a few times, and the most information you get about it is this:

The precise position of the mouth is unknown but was presumably located around the area between the base of the comb-like segments and the stomach. (p16 in the PDF)

 

and this:

Food particles would have circulated down towards the gut, through a central mouth which has not been identified, but is suggested by the concentration of organic matter in this area. (p18)

Someone please explain why that implies a separate mouth? I mean, they found well over a thousand specimens of not too bad quality. These people have a few thousand times more expertise than me in interpreting weird Cambrian fossils. I would assume they didn’t pull the idea out of thin air, but they don’t exactly make it convincing for non-specialists there 😦 (Not that a single-opening digestive tract makes the animal any easier to interpret…)

TwoSiphusauctum apparently has sixfold symmetry. I don’t know if that’s significant, it just struck me as something that isn’t terribly common in living bilaterians. Hard corals and sea anemones work in multiples of six, but they aren’t bilaterians. But maybe I should go check a zoology textbook…

Three – I found it funny that in true Cambrian style, the creature most similar to Siphusauctum is… Dinomischus? Which is another weird Burgess Shale fossil no one can really place. Well, at least now they have company in being complete riddles. 😀