Animals, amoebae and plant scientists’ concerns

I recently wondered, in response to an “ideas” paper in BioEssays, whether animals, fungi, slime moulds etc. actually had a multicellular common ancestor. Dickinson and colleagues’ argument (partly) hinged on the shared presence of epithelia, “barrier” cell layers with distinct insides and outsides, in animals and the social amoeba Dictyostelium discoideum. The most recent crop from BioEssays includes a short letter by František Baluška of the botany department at the University of Bonn that challenges this argument.

Plants, Baluška reminds us, also have epithelia. These epithelia are functionally more similar to animals’ than the one Dickinson’s team found in the amoebae. While there may be doubts about amoebae, plants almost certainly became multicellular independently of animals. Ergo, convergent evolution can clearly produce similar tissues in two distant lineages. So why would we take the possession of an epithelium as evidence for a multicellular common ancestor?

Which is a perfectly valid argument, but it misses the point in my opinion.

The botanist writes,

[Plants] evolved their own plant-specific epithelia 3–5, obviously via convergent evolution. This fact alone not only continues to make plausible the traditional independent origin of multicellularity in the metazoa and social amoebae, but it also indicates that the power of convergent evolution should not be underestimated.

Of course it shouldn’t, but Dickinson’s team wasn’t arguing that “the traditional independent origin of multicelluarity” in animals and amoebae was not plausible any more. They find it unlikely that the functional and molecular similarity (does the latter exist between plants and animals?) between animal and amoeba epithelia is convergent, but they are suggesting that we investigate their new hypothesis, not that we summarily throw out the old one. Baluška is attacking a straw man.

Furthermore, he only addresses this one argument, but the thing in the Dickinson article that made me think the most was phylogeny. According to the traditional scenario, it seemed more likely that all those different unikont groups evolved multicellularity independently. But multicellularity is very widespread among unikonts, so precisely what makes the traditional scenario more likely? (Incidentally, has anyone done any actual statistics on this?)

As far as I’m concerned, the letter said nothing to change my mind. Dickinson et al. presented an interesting idea that’s definitely worth a closer look. I don’t think the evidence is currently strong enough to upset the consensus, but the proposal is not at all daft. I have to say I agree that plants should not be ignored, though. Because we can assume that any similarity between them and animals when it comes to being multicellular is the result of convergence, they’d be a wonderful “control group” when people start testing Dickinson et al.‘s hypothesis.

I think that’s something students of evolution should always keep in mind. Plants and animals have little reason to do things in the same way – they diverged very long ago, adapted to completely different lifestyles, etc. If they do so anyway, that might tell us something deeper about the way living things work. A limitation imposed by physics, a very ancient genetic predisposition, or simply the best way to do something – either way, finding the reason will enrich our knowledge of life and evolution. Animal scientists would be well advised to remember that.

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Reference:

Baluška F (2012) Rethinking origins of multicellularity: Convergent evolution of epithelia in plants. BioEssays, available online 26/10/2012, doi: 10.1002/bies.201200134

A small planet hidden in plain sight, and a must-read book

Random squeey post!

Squee number one: Dumusque et al. (2012) found a probably earth-sized planet literally next door to the solar system. The newly announced rockball orbits α Centauri B, one of the three(?)* stars making up the star system closest to the sun. Alas, it’s unlikely to harbour life of any kind given its very close orbit – it goes around a star not much cooler than our sun in slightly over 3 days. However, the authors point out that small planets are most likely to be found in multiplanet systems, and given the difficulty of finding this one, the star may well have even harder to detect, more distant companions. I think this is a nice reminder of how much more we need to learn about other solar systems – this little guy has been circling there, a mere four point something light years from us, and we only found it now. Keep it up, planet hunters, you’re doing amazing stuff!

Reference: Dumusque X et al. (2012) An Earth-mass planet orbiting α Centauri B. Nature advance online publication available online 17/10/2012, doi: 10.1038/nature11572

*I’ll let the real astronomers argue whether Proxima Centauri is part of the α Centauri system…

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Squee number two: I totally must read this book. It’s the ultimate evo-devo book: it’s about fossilised development, basically. It seems overwhelmingly vertebrate-centred based on the review in Developmental Dynamics, but hey, there is an invertebrate chapter and I take what I can get 😀

And wow, it’s not even that expensive as far as university-published hardcover sciencey books go! Hmm. Shall we give in to temptation right now or save it for a Christmas present?

 

Interpreting ‘omics: a good example this time

Remember how I complained that people often seem to forget the scientific method when it comes to transcriptomics? Well, I’m glad to say some scientists still remember those all-important steps between data and conclusion. When looking at the predicted functions of the genes active in these cute little baby worms* during the first three days of their lives, Kenny and Shimeld (2012) not only compared their data to a “background” dataset from a well-studied animal, but also

• did statistical tests to confirm that the differences they saw were real,
• discussed several possible causes for them.

… including those that weren’t biologically interesting at all, like limitations of their methods. In the end, they couldn’t really draw strong conclusions from this particular part of their analysis, but the best thing is they sound perfectly aware of the difficulty and careful not to go too far in interpretation.

Folks, this is how you should write a transcriptomics paper. Not look at a few out-of-context numbers and concoct a story around them.
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*Okay, am I the only one who finds trochophores adorable? :$

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Reference:

Kenny NJ & Shimeld SM (2012) Additive multiple k-mer transcriptome of the keelworm Pomatoceros lamarckii (Annelida: Serpulidae) reveals annelid trochophore transcription factor cassette. Development Genes & Evolution Online First™ article available online 8/10/2012, doi: 10.1007/s00427-012-0416-6

So… much… STUFF!

Gods, this is what I’m faced with all the time. Someone needs to tell me how proper science bloggers pick articles to discuss, because I just get my RSS alerts, start squeeing, and end up not writing about anything because damn, I WANT TO WRITE ABOUT EVERYTHING!

I give up. I’ll just dump all the cool stuff that’s accumulated on my desktop and bookmark bar here and return to lengthy meandering whenever I don’t feel like I’ve been caught in a bloody tornado 😉

So, here is some Cool Stuff…

(1) A group measured the rate of DNA decay in 158 moa bones of known age from three sites. Really cool stuff, to go out and directly measure how ancient DNA disappears from dead things under more or less identical conditions. The unsurprising result is that DNA decays exponentially, a bit like radioactive material. This suggests that the main cause of the decay is random breaking of the strands. The surprising bit is that this happens much more slowly than previously estimated, suggesting that in ideal (read: frozen) conditions, it might be worth looking for preserved DNA in samples as old as a million years.

(On a side note, if you ever get a chance to see a talk by Eske Willerslev, one of the authors and a leading expert on ancient DNA, don’t miss it. The man is absolutely hilarious.)

– Allentoft ME et al. (2012) The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils. Proceedings of the Royal Society B FirstCite article, available online 10/10/2012, doi: 10.1098/rspb.2012.1745

(2) The beaks of the finches, or mixing and matching developmental recipes. This study examines the genetic basis of beak shape in three little birds closely related to Darwin’s famous finches. The three finches, just like Darwin’s, share the same basic beak shape, only bigger or smaller. However, there seem to be two distinct developmental programs at work, using different genes and parts of the skeleton to orchestrate beak development. One of the three newly investigated species (the one most closely related to Darwin’s finches) apparently uses the same developmental program as its more famous relatives, even though its beak is shaped more like the other two birds studied here. I told you – genetics, development and homology are complicated 😉

– Mallarino R et al. (2012) Closely related bird species demonstrate flexibility between beak morphology and underlying developmental programs. PNAS 109:16222–16227

(3) Armoured fossil links worm-like molluscs to chitons. There’s a little-known group (or groups) of molluscs called aplacophorans that have only a coat of tiny spicules instead of shells and look more like worms than “proper” molluscs. Exactly where they fit into our picture of mollusc evolution has been controversial to say the least – they could represent an old lineage separate from other molluscs, they could be related to cephalopods, they could be related to chitons, they could be one group or they could be two lineages in completely different places on the tree… Well, a new fossil named Kulindroplax seems to argue for the chiton connection: the animal has the characteristic armour plates of a chiton on an aplacophoran-like body. Similar creatures have been discovered before, but this guy with its detailed 3D preservation provides the clearest evidence of the link so far.

– Sutton MD et al. (2012) A Silurian armoured aplacophoran and implications for molluscan phylogeny. Nature 490:94-97

(4) More cool fossils – this time straight from my beloved Cambrian. Nereocaris, a newly described Burgess Shale arthropod, suggests to its discoverers that the earliest arthropods weren’t predators prowling the seafloor, but swimmers who might have been filter feeders and certainly weren’t predators. The animal has a bivalved shell around its front end, similar to many other Cambrian swimming arthropods, and a long abdomen with paddles at the end. It bears the arthropod hallmark of a hardened and jointed exoskeleton, but it lacks specialised limbs such as antennae or mouthparts. In a cladistic analysis of arthropods and their nearest relatives, the new species comes out on the first branch within true arthropods, and the next few branches as we move towards living arthropods all contain similar shelled, swimming creatures. Since the non-arthropods closest to the real thing (i.e. anomalocaridids) were also fin-tailed swimmers, this arrangement makes the transition between them and true arthropods smoother than previously thought. It also suggests that the hard exoskeleton so characteristic of arthropods originally functioned in swimming – perhaps as an anchor for swimming muscles.

– Legg DA et al. (2012) Cambrian bivalved arthropod reveals origin of arthrodization. Proceedings of the Royal Society B FirstCite article, available online 10/10/2012, doi: 10.1098/rspb.2012.1958

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And … there was also

• a well-preserved Cambrian arthropod brain with an unexpected structure,
• a bunch of algae that evolved an ability to subsist on organic food (and some even lost photosynthesis) when left in the dark long enough,
• a simulation examining the properties of “evolvable” genetic networks,
• a review of the complexity of the genetic switches belonging to developmental control genes,
• some really cool stuff about making mouse fingers regenerate,
• another Kepler binary star with planets,
• a cyanobacterium fixing nitrogen for an alga that photosynthesises for it,
• fruit flies evolving the same reproductive traits through different genetic and developmental mechanisms (it’s not just finches, you see!),
• the genetic basis for a famous evolutionary novelty in the Lenski long-term evolution experiment,
• and the freakish and wholly un-mammal-like skin regeneration abilities of African spiny mice…

… but it’s almost bedtime, and if I wanted to summarise every one of those, I’d be here all weekend 😦

See, this is why being a science nerd today is both amazing and frustrating. There’s just so. Much. Stuff.

Virtual squirtlet

Sea squirts are not the most endearing creatures, but they are pretty interesting in their own way. Although their adults are basically cellulose-covered bags of jelly, their larvae and their genomes reveal their dirty secret: they are actually close (probably the closest) relatives of vertebrates. Squirts and their kin – collectively known as tunicates – also have some of the fastest-evolving, most crazily scrambled genomes among animals (e.g. Denoeud et al. 2010).

(Say hi to your long-lost cousins! A whole crowd of grown-up Ciona from Wikipedia)

To be fair, not all of them are as bland and ugly as Ciona species. Some of them are actually quite gorgeous with all the colourful extravagance you’d expect from a tropical marine invertebrate (below is one example from Wikipedia’s squirt entry).

But, anyway, I got a bit carried away there. In truth, I just wanted to squee about a new virtual squirt embryo (Nakamura et al., 2012). Because 3D reconstructions of animals down to single-cell resolution are pretty damn cool.

Unlike the adults, baby squirts actually look a proper chordate, with a plump little body and a long tail supported by a good old notochord. They float in their little eggs for a while, developing their tails and simple sensory systems, and then they swim around for a few days before settling and transforming into those unappealing jellybags for a life of filter-feeding and spawning. (Below: the tadpole larva of the colonial squirt Botryllus schlosseri by Richard Grosberg via this site)

Because squirts are so close to vertebrates, and some of them (like Ciona) are relatively easy to breed and grow up in the lab, they’re among the favourite model organisms of evo-devo researchers. That means some people are bound to put serious effort into community resources about them. The good folks at Keio University in Japan have been building this amazing resource for years, where they painstakingly document the development of Ciona intestinalis from fertilised egg all the way to jellybaghood using photographs, microscopic images and 3D reconstructions from optical sections made with a confocal microscope. The virtual embryo is the latest addition to this project. It represents a stage where the embryo is growing its tail, and it is packaged into an interactive PDF with all sorts of annotations on cell types and stuff (that my PDF viewer can’t handle :(). I’m not much into sea squirts, but an interactive embryo you can manipulate and examine cell by cell and use as a free reference to interpret your own experimental results? That’s seriously awesome.

(Almost as cool as the digital zebrafish embryo movies)

(Above: A, an example of the confocal images used to build the virtual squirt, with a few views inside the 3D model: B, rear view of the “skinned” virtual embryo, C, side view of same, and D, virtual cross-section of the tail. Tissues like muscle, notochord and nerve tube are colour-coded and labelled. From Nakamura et al. [2012])

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References:

Denoeud F et al. (2010) Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate. Science 330:1381-1385

Nakamura MJ et al. (2012) Three-dimensional anatomy of the Ciona intestinalis tailbud embryo at single-cell resolution. Developmental Biology in press, available online 27/09/2012, doi: 10.1016/j.ydbio.2012.09.007