A bunch of cool things

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

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

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

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

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

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

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

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2. Cambrian explosion: evolution on steroids.

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

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

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

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

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

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

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3. Chitons to sausages

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

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

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

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4. Does adaptation constrain mammalian spines?

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

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

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

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

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

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

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

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Thornbushes – it’s not just molecular data.

While I love phylogenetics, I rarely venture into the land of morphology-based phylogenetic trees.

Molecular sequences make sense to me as data. In a protein sequence, a proline is a proline, and if two proteins can acquire a proline in the same place by convergent evolution, well, you can look at large-scale patterns of amino acid substitution and estimate the chance of that. Genomes contain exactly 4 kinds of bases, they encode exactly 20 kinds of amino acids, and that’s that at least as far as conventional molecular phylogenies are concerned. Sequences are exactly the sort of neat, discrete data that you can describe and explore and simulate the heck out of to make sure that the assumptions you are making when you use them to infer relationships between genes or organisms are realistic.

Morphology, my brain says, is fuzzy and difficult and full of human subjectivity. In the anatomy of two animals, a limb and a limb can be totally different things with totally different evolutionary origins, and there’s no guarantee that you can tell them apart. Something can be “sort of” a limb, and there’s no well-defined number of ways of “limbness”.

Truth be told, morphology as a way of figuring out relationships kind of scares me.

However, I do love phylogenies. I’m also interested in the relationships of extinct creatures (where, unless they are very recently extinct, you simply don’t have molecular data to play with). Plus limitations intrigue me, not to mention that the limitations of the methods we use to arrive at conclusions have a huge practical importance. (As in: they can lead to bullshit conclusions.) Hence I thought a paper titled “When can clades be potentially resolved with morphology?” would be an interesting read.

And it absolutely was, only in a totally different way than I expected. I thought it would be all about the limitations I was thinking of – convergent evolution, defining and interpreting traits, the statistical biases of treebuilding methods, that sort of stuff. Instead, it ignored those issues completely in favour of a much more fundamental limitation. Bapst (2013) doesn’t talk about information that you or your fancy algorithms misinterpret. He talks about information that, due to the very nature of evolution, just isn’t there.

A modern classification of organisms is built out of clades: groups including all descendants of a single common ancestor. Phylogenetic trees are clades within clades within clades – or branches splitting into smaller branches splitting into twigs. A fully resolved tree consists only of two-pronged branching points. That is, if you pick any three creatures, you can tell which two of them are closer to each other than the third. (Resolution is determined by statistical support from methods such as bootstrapping. Bootstrapping basically asks whether all your data agree on the same tree.)

Clades are recognised by what their members share with one another but no one else: for example, a subgroup of dinosaurs that includes birds has feathers, which they inherited from their common ancestor. Each clade can have many such shared derived traits or synapomorphies. However, sometimes there are no synapomorphies. Take, for instance, the case of a single ancestral species “budding off” a series of descendants without changing much itself, like so:

unchangedAncestor

(You could say that three-spine sticklebacks are doing exactly this – the ancestral form that lives in the sea is largely similar all over the northern hemisphere, but it keeps getting stuck in rivers and lakes and sprouting a huge variety of descendants.)

In such a scenario, Descendant 1 is kind of closer to Ancestor than Descendant 2 is, since there’s been less time since they split. However, because Ancestor didn’t change in all that time, there are no synapomorphies that unite it with D1 to the exclusion of D2. A morphology-based phylogenetic tree of these three species would be intrinsically unresolvable – no matter how much data you collect and how well you analyse them, you’re not going to get the true tree, only a sad little bush. (A molecular phylogeny may be able to resolve a history like this, since genomes aren’t going to stop evolving just because the creatures that have them look the same.)

This is the sort of limitation Bapst explores through his simulations. The simulations don’t actually model the evolution of morphology itself. They compress all morphological change into “differentiation events”, i.e. the point at which two taxa become distinguishable. (He later makes the important point that “taxa” could be anything on the traditional Linnaean scale – species, families, classes, whatever -, and his conclusions would remain the same.)*

Differentiation events then might happen in a variety of ways, illustrated by Bapst’s Figure 2 below:

In other words, there can be branching without differentiation, differentiation without branching, and anywhere in between.

The simulations investigate how many intrinsically unresolvable clades we should expect under various mixtures of the four scenarios above, combined with more or less complete sampling of the fossil record. Some of the observations I found fascinating:

  • More complete sampling actually decreases resolvability, since your dataset is then more likely to include both ancestors and their descendants.**
  • Unresolvable clades are spread evenly throughout the whole model phylogeny – they aren’t disproportionately older or younger than their well-behaved counterparts. This is very important to me because it means that intrinsic unresolvability could also affect the levels I’m most interested in, i.e. the phylum-level relationships of animals.
  • No realistic simulationi.e. those whose parameters and results are compatible with the real fossil record – produces fully resolvable phylogenies!

It’s worth noting that it’s actually close to impossible to tell whether the lack of resolution in any given real dataset is due to this intrinsic effect or some other issue. However, the take home message of this study is that however well you’ve eliminated other sources of ambiguity, you should pretty much never expect a fully resolved phylogeny if you are working with the morphology of real creatures. If you got one, you probably did something wrong!

(Considering that molecular data can be just as incapable of correctly resolving relationships under certain circumstances, I dearly hope that the problem groups are at least going to be different for the two kinds of data… :D)

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*This is a distinctly punk eek-flavoured model, BTW; if morphological change is evenly spread out through time, the whole thing falls apart. But, then, if change is evenly spread through time, you wouldn’t have scenarios with unchanged ancestors like the one above, and I gather that the existence of those is an established palaeontological reality.

**However, this doesn’t mean that trees obtained from patchy fossil records will be more accurate – having a poorer sample also means potentially overlooking misleading changes like reversals to an ancestral state.

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Reference:

Bapst DW (2013) When can clades be potentially resolved with morphology? PLoS ONE 8:e62312

Score one for punk eek

Speaking of macroevolution…

I think it’s fair to say that the concept of punctuated equilibria is one of the most famous and most misunderstood ideas in 20th century evolutionary biology. PE, or “punk eek” was proposed by palaeontologists Niles Eldredge and Stephen Jay Gould  (Eldredge and Gould, 1972) as a reconciliation of the Modern Evolutionary Synthesis and the fossil record. Its core idea is that most (visible) evolutionary change happens during the formation of new species, and that this process is usually quick compared to the lifetime of a species. (An excellent layperson-friendly explanation of punk eek is available here.)

Of course, punk eek is not a law of nature – it’s only one way evolution might proceed, and it’s a decent explanation of the dearth of low-level (species to species) transitions in the fossil record. But there’s nothing to say that this is how evolution always proceeds, and consequently, exactly how often it does so is a valid (and still actively debated) question in evolutionary biology.

A related question is how often new species arise by the wholesale transformation of the ancestral species (anagenesis) or by the splitting of the ancestor into two or more descendants (cladogenesis). Since punk eek posits that most new species come from small isolated populations of the ancestor, under punk eek scenarios you’d expect most speciation to occur by cladogenesis.

However, assessing the exact contribution of each requires an exceptionally good fossil record where ancestor-descendant relationships and precise times of appearance and disappearance can be determined. This makes the investigation difficult to impossible in most groups. In the latest issue of PNAS, Strotz and Allen (2013) went to one of the few groups with a good enough record to answer such questions and analysed the living shit out of them.

Foraminiferans of forams for short are single-celled creatures that build hard shells to live in. They are very abundant, widely distributed in the world’s oceans, and because of their shells they make excellent (if tiny) fossils. Their relationships have also been studied with molecular methods, so we have a pretty good understanding of who’s related to whom and how well morphology meshes with genetics.

Therefore, as Strotz and Allen point out, we can say with a fair amount of confidence that what we’ve identified as species in the fossil record are likely to actually be species, not just varieties. (It doesn’t always work the opposite way – some “species” that look exactly the same on the outside are known hide several genetically distinct lineages.) The genetic data also help sort out who begat whom.

Armed with this knowledge of genetics and the detailed fossil record of planktonic forams in the last 65 million years, the pair formulated criteria for identifying cladogenetic events:

  • If morphologically distinct ancestor and descendant(s) overlap in time (factoring in dating and classification error), the descendant must have arisen by cladogenesis.
  • Likewise, cladogenesis must have occurred if the two species occur together in the same sample even if their morphologies overlap at that point.
  • Third, if an ancestor gave rise to a series of descendants, all but the last of those must have formed by cladogenesis – the ancestral form has to continue existing for it to sprout more descendants!

Thus, the possibility of anagenesis only remains for ancestor-descendant pairs that didn’t get caught on any of the above filters. And the number of those turns out to be very low.  Depending on how you estimate the errors associated with identifying fossils, only around 43-64 out of 337 speciation events (less than a fifth of the total) in the last 65 million years shows no evidence against anagenesis. The numbers are even lower, dipping below one-tenth of all events, if you only consider the last 23 million years, for which more precise dating information is available. In conclusion, for planktonic forams since the death of the dinosaurs, splitting an old species has been by far the more common way of forming new species.

It’s important to talk about the things this paper doesn’t say. It doesn’t, for example, say that its findings apply to all organisms. Speciation need not work the same way for all groups, and a subset of forams need not be representative of anything. It also doesn’t say – and the authors are quite explicit about this – that morphological evolution only occurs when species split. Instead, they argue, their findings support a modified view of punk eek in which species do change throughout their lifetimes – but the changes are fluctuations due to short-term influences, and they only persist if populations get isolated.

(Myself, I just think the simple fact that we have a fossil record where such ideas can be tested is pretty amazing. You can complain about the patchiness of the record all you like, but in the meantime it’s worth stopping and appreciating what we do have!)

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References:

Eldredge N & Gould SJ (1972) Punctuated equilibria: an alternative to phyletic gradualism. In Schopf TJM (ed) Models in Paleobiology. Freeman, Cooper & Co., pp. 82-115

Strotz LC & Allen AP (2013) Assessing the role of cladogenesis in macroevolution by integrating fossil and molecular evidence. PNAS 110:2904-2909