A bunch of cool things

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

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

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

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

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

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

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

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2. Cambrian explosion: evolution on steroids.

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

Lee et al. (2013) used phylogenetic trees of living arthropods to estimate how fast they evolved at different points in their history. They looked at both morphology and genomes, because the two can behave very differently. It’s basically a molecular clock study, and I’m still not sure I trust molecular clocks, but let’s just see what it says and leave lengthy ruminations about its validity to my dark and lonely hours ๐Ÿ™‚

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

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

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

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

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3. Chitons to sausages

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

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

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

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4. Does adaptation constrain mammalian spines?

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

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

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

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

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

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

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And… I think that approximately covers today’s squee moments ๐Ÿ™‚

Of really old maybe-sponges, molecular clocks and common ancestors

If you’ve ever visited this blog before, you probably know that the early evolution of animals is one of my many random interests. You could say it’s my main interest, though that may be less obvious from my posting record so far. Well, knowing that, you could imagine my face when my labmate pointed me to this National Geographic news piece.

It doesn’t surprise me much that the earliest known animal would be like a sponge. Although for what they do, their construction is nothing short of ingenious, sponges are comparatively simple animals. While it’s possible that they weren’t always like that, it appears that their genomes are devoid of lots of the genes other animals have added to the “toolkit” that fashions their complex bodies (Larroux et al., 2008). They also retain morphological features that were probably present in the ancestors of animals and lost in pretty much every other animal lineage alive today. Notably, their food-capturing cells look an awful lot like the cells of choanoflagellates, which are thought to be the closest living relatives of animals and perhaps similar in appearance to our distant ancestors.

What looks positively amazing about the newly described sponge-like thingies, who go by the deceptively Italian-sounding name of Otavia (they’re actually named after the Otavi Group of rock formations in Namibia), is their age. The oldest ones, apparently, are close to 760 million years old, perhaps 180 million years older than the earliest occurrences of the famous and mysterious Ediacaran animals (Narbonne, 2005). (By the way, that difference is about the length of the “age of dinosaurs”!) The news, and Brain et al. (2012), point out that this date also precedes some events that were thought to set the stage for the rise of animals: the giant ice ages known as Snowball Earths, and the rise in atmospheric oxygen levels towards the end of Precambrian times.

We could talk about the significance of that, I suppose, but the issue the whole discovery brought to my mind is, strangely, molecular clocks.

Let’s face it, the Precambrian fossil record of animals is not brilliant. It’s getting better, as more Ediacaran fossils are dug up and analysed with more sophisticated methods, but it still raises as many questions as it answers, and the earliest history of animals is still shrouded in mystery. For one thing, when did animals even evolve? All we know from fossils is that it must have been “before”. If a particular fossil is not only an animal, but member of an identifiable subgroup of animals, it means that the branch separating that subgroup from all other animal lineages must have split by that time. A number of Precambrian animals may be members of groups that are many such splits into the animal family tree, and things that look like the predecessors of those splits are difficult to identify in the fossil record. So where did they come from? Where did it all begin? Kind of hard to say based on the bunch of hard to interpret blobs, fronds and strange fractal bodies that is the Ediacaran biota.

When the fossil record speaks gibberish, people sometimes query another keeper of deep evolutionary history: DNA. Molecular clock methods date splits between lineages by counting differences between their living members. The basic idea is this: if most mutations have no effect on fitness, then most mutations are created equal, with the same chance of fixing themselves in the gene pool. If that is true, then genomes change at roughly constant rates – dependent only on mutation rate – over time. Using that assumption and lineages whose divergence time is known (usually, from good fossil records), you can translate the genetic differences between two or more groups into evolutionary time.

The problem is that real life is not so simple as that. Evolution is not always neutral. The same gene may behave like a clock in one lineage or during one time period and not another. Part of a gene may be a good clock while another part isn’t. Even if all of a gene evolves in a clock-like manner in all lineages under study, there’s no guarantee that the clock will tick at the same rate in all of them. Different genes or parts of a gene can tick at different rates, and this can vary over time. If we’re trying to measure very long times, it can be hard to correctly estimate the amount of change in a gene. There can be error in the fossils used for calibration, or the calibrating lineages may evolve differently from the ones we’re interested in. And so on.

And thus, published estimates for early divergences among animals range from numbers that make reasonable sense with the fossil record (e.g. Peterson et al., 2004), to some that throw another billion years on top of those numbers (see Chapter 11 in Knoll [2003] for an accessible discussion).

The problem, as I see it, is this. With a billion-year margin of error, some of those estimates must be wrong. As Andrew Knoll noted, they all require that animals began much earlier than their fossil record (at least as it was known at the time). How can we trust any of them? Even for the ones that match what we think of the fossil record โ€“ well, stopped clocks are accurate twice a day. For a scientist, being accidentally right is no better than being wrong.

I suppose Otavia, if it’s really a sponge-ish creature, fits the Peterson & co. estimates quite neatly. Fairly certain bilaterians like Kimberella are known from the White Sea assemblage of the Ediacaran, somewhat under 560 million years ago (Narbonne, 2005). The origin of bilaterians is somewhere between two and four splits[1] after sponges diverged from other animals. Peterson and colleagues estimated it between 573 and 656 million years ago โ€“ so if sponges are indeed a conservative bunch, sponge-like animals must have been around quite a bit earlier, but perhaps >1 billion years ago is really stretching it. 760 million sounds kind of nice, farther back than the Kimberellas and Dickinsonias but not too far.

Kind of. But, seeing as we’ve had to wait this long for a maybe-sponge that old, who’s to say even older animals aren’t hiding in some unexplored fossil bed? Who’s to say that the next “oldest animal” find won’t validate some of the more outlandish estimates?

The other thing I’m wondering about re: Otavia is: is it a sponge (assuming it’s an animal at all), or could it belong to a lineage ancestral to both sponges and other animals? (Were early sponges ancestral to other animals? The idea has been played with in phylogenetic circles…) I guess we’ll never know for certain. I still think it’s worth raising the question. Creatures that might be ancestral to more than one phylum are extremely valuable to evolutionary biologists, but they might be very hard to recognise for what they are. Part of the problem with Ediacaran animals is that many if not most of them lack features associated with living phyla โ€“ but that’s exactly what we would expect from creatures that preceded the divergence of those phyla! Given how little, say, a jellyfish and a snail have in common, what on earth would their common ancestors look like? Would they have any fossilisable characteristics at all that could give us a hint as to their family ties?

And I guess I’ll close today’s musings with that question. If I spent more time reading Brain et al. (2012), there’d probably be a lot more to discuss, but after doing lab work all day and spending an extra couple of hours writing this, my brain doesn’t feel up to it ๐Ÿ™‚

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[1] You can refer to the rough animal phylogeny in the Nectocaris post for the moment. Being slightly out of the loop in this area, I wouldn’t hazard a guess as to the relationships of ctenophores, cnidarians and placozoans, hence my uncertainty. It’s possible that these three all form a single branch with bilaterians on the other side. Or they could represent three different branching events, or anything in between. I really should make an animal phylogeny page, I think, since I keep finding myself wanting to talk about bilaterians and lophotrochozoans and things that don’t make much sense unless you know at least the basics shown in tree I made for Nectocaris

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References:

Brain CK et al. (2012) The first animals: ca. 760-million-year-old sponge-like fossils from Namibia. South African Journal of Science 108:658; doi:10.4102/sajs.v108i1/2.658

Knoll AH (2003) Life on a Young Planet. Princeton University Press.

Larroux C et al. (2008) Genesis and expansion of metazoan transcription factor gene classes. Molecular Biology and Evolution 25:980-996

Narbonne GM (2005) The Ediacara biota: Neoproterozoic origin of animals and their ecosystems. Annual Review of Earth and Planetary Sciences 33:421-442

Peterson KJ et al. (2004) Estimating metazoan divergence times with a molecular clock. PNAS 101:6536-6541