Sponges have 70% homologous genes with humans?

I liked Julia Galef’s article in Slate about keeping a “surprise journal” – and this seems as good a place as any.  Maybe I’ll call it “Surprise, Me” or something cute.  Also, the word “surprise” has a very low semantic satiation threshold.

Spongia_officinalisAnyways.  At PG’s suggestion, I went digging into the genomics of sponges:

  • Srivastava, M., Simakov, O., Chapman, J., Fahey, B., Gauthier, M. E. A., Mitros, T., … Rokhsar, D. S. (2010). The Amphimedon queenslandica genome and the evolution of animal complexity. Nature, 466(7307), 720–6. doi:10.1038/nature09201

  • Mann, A. (2010). Sponge genome goes deep. Nature, 466(7307), 673. doi:10.1038/466673a

  • Riesgo, A., Farrar, N., Windsor, P. J., Giribet, G., & Leys, S. P. (2014). The analysis of eight transcriptomes from all poriferan classes reveals surprising genetic complexity in sponges. Molecular Biology and Evolution, 31(5), 1102–20. doi:10.1093/molbev/msu057

Sponges are cool because they’re commonly accepted to be simplest animal.  (Remember, animals are multicellular (metazoan) eukaryotes.)  Actually, sponges are cool for lots of reasons – they live in incredibly diverse environments, have lots of different shapes (and ways of forming those shapes), and some are carnivorous.  (I’m imagining a fantastic sequel to Little Shop of Horrors here.)

But I’ve been reading alot about morphogenesis recently (how animals form tissues and structures and organs and appendages from a single cell), and it makes you wonder: what does a “minimal” animal look like?  We can take bacteria and remove genes, and remove some more, and remove some more and eventually you find the minimal set that lets the bacterium still eat and live and reproduce.  (Fred Blattner, who first sequenced the E. coli genome, made a business out of it.)  It’s hard to do that with an animal, of course: there’s so much complexity (in the technical sense) to animal development that perturb it a little bit and you don’t get an animal any more.

Genomics to the rescue!  You might think to ask “what genes are in the sponge?  It’s the simplest animal, right?”  And that would be a start — but sponges have genes that other animals don’t.  They live in places that other animals don’t (the sea floor) and have evolved genes particular to that environment.  Better to ask “what genes do sponges and other animals share?”  Lots of other animals have had their genomes sequenced, so if we sequence the sponge genome there’s a lot to compare it to.  In fact, with so much data available the best question to ask is “what genes did the last common ancestor of sponges and more complex animals have?”  Right before the split into the animals that became sponges and the animals that became, well, not sponges – that’s the genome we’re interested in, because comparing it to unicellular eukaryotes (protists and fungi and Dictyostelium and such) will tell us “what genes are required for multicellularity?”

You know the awful misquoted factoid about how humans and monkeys are 99% the same?  (It’s actually 96%, but who’s counting?)  It makes sense, though – chimps have the same body plan as us, the same organs, they’re intelligent.  How much of the genome do we share with the lowly sea-sponge?


Think about that for a moment.

All the wondrous complexity of human morphology, all the muscles and sensory organs and nerves and, you know, a two-ended digestive tract (little things), all are a relatively minor portion compared to what we do share.

The genes that we share, what are their functions?  Well, you find the things you’d expect: genes that relate to multicellularity, like genes responsible for cellular adhesion, programmed cell death, cell-cell communication and the like.  There are things that you might not immediately expect, but upon reflection make sense – much of the cellular differentiation machinery is shared, because sponges have different cell types like we do (just fewer, ~20 instead of ~200.)  Sponges share with us a relatively robust innate immune system (they have an associated microbiome, and they get sick too.)  And they share much of the machinery responsible for detecting and shutting down uncontrolled proliferation (ie cancer.)  Because apparently sponges get cancer too?

And then there are the real head-scratchers.  Sponges have genes that, in humans, code for neurons and muscles.  Neither of which sponges have.  Wut?  What do sponges do with them?  More interestingly, if the common ancestor had genes that, in humans, make nerves and muscles — what did the common answer use them for?

Why is this cool?  What it points to is not only how fascinating and complex sponges are (i wanna do synbio in sponges now), but how fascinating and complex our ancient common ancestor was.  Multicellular organisms have an evolutionary advantage over unicellular organisms because they can more efficiently utilize environmental resources (because of active transport between cells, your size isn’t constrained by the diffusion limit.)  What the lowly sponge teaches us is about the tradeoff: that a ridiculous amount of our genetic machinery goes into supporting our multicellularity.  And to keep all those pieces in working order, we need to copy our genes more faithfully, which means a lower mutation rate, which means slower evolution.  Or it would have, if transposable elements (Richard Dawkin’s “selfish genes”) hadn’t shown up.  But that’s another post.