Three months ago, if I had seen this article about the ctenophore genome, I would have moved right passed it without a second look.  What is a ctenophore and why would I care about the sequence of its DNA?  But then I taught Bio 2 this spring and learned about animal diversity and the evolutionary tree (a day before I taught it).  This is a great example that the more you learn, the more interested you become in the subject.  Today’s article by Moroz et al. was published recently online in Nature (this one is open access, so take a look).  The results totally change the roots of the animal tree and invalidate what we taught to our students this semester.  Before we get into the paper, let me answer my own questions:
What is a ctenophore?
Ctenophores are also known as comb jellies, because they look like jellyfish and have a comb-like structure that they wiggle around to move through the water.  They have sensory organs to sense light and gravity.  They have tentacles that they move with their nervous system in order to catch prey.
Comb jelly (from Wikimedia Commons)

Although they look like jellyfish, they are in a totally different phylum, or branch of the evolutionary tree (also known as a phylogenetic tree).  Jellyfish are in the phylum Cnidaria, along with sea anemones, coral and hydras.  Comb jellies are in their own phylum known as Ctenophora. 

Why should we care about ctenophores? 
Ctenophores, along with cnidarians and sponges, represent some of the most ancient lineages of animals.  Studying them can give us a clue about how animals evolved.  All the rest of the animals are in the large taxonomic group called Bilateria, because they have bilateral symmetry (which is symmetry across a single axis).  This includes humans, insects, crustaceans, worms, fish, molluscs, etc.  Think about a jellyfish or a sea anemone; they have radial symmetry, which means they can be bisected in lots of different axes and you would still have symmetrical halves.  The bilateral animals are more complicated in lots of other ways, such as having a greater variety of tissues and more complex physiology.
The phylogenetic tree according to the biology textbook
Sponges don’t have organized tissues and they don’t have a nervous system, so based on that, researchers have considered them to be the most ancient lineage (i.e. the “basal” animals).  So if we are building a phylogenetic tree based on morphological characteristics, we are going to put them as the first branch.
Cnidarians and ctenophores look very similar, so it would make sense to put them right next to each other, followed by the bilateral animals.  Thus, based on morphological observations, the tree should look something like this:
No one ever explained to me why cnidarians get to be closer to the bilaterals than ctenophores.  Perhaps this is because the cnidarians come in so many different body plans, so maybe they are considered to be more complex and thus, an evolutionarily “newer” animal.
We told our students over and over: “Sponges are the most basal animals”.  But like many phylogenetic theories that have come before, new DNA sequencing data is challenging this view.
What does the ctenophore genome tell us?
First off, for the non-biologists out there, you need to understand one fundamental thing about gene evolution.  Two species that are highly related will have very similar DNA sequences.  The further apart two species are in evolutionary time, the more time there is for mutations to change the DNA sequences and the gene functions.
Moroz et al. sequenced one of the ctenophore genomes and then compared it with the genomes of sponges and cnidarians.  One of the main findings was that there are many missing animal-specific genes that are involved in animal development (Hox genes), regulating gene expression (no miRNAs!) and innate immunity.  Although some animal-specific genes are absent, the ctenophores have many unique genes that are not found in other animals, indicating that these genes evolved independently in the ctenophore lineage. 
The researchers devoted a lot of the paper to looking at genes involved in nervous system function.  Ctenophores, like cnidarians, have neural nets, as opposed to organized bundles of nerves.  Bilateral animals have many different neurotransmitters, which are the signals that get sent between nerve cells.  The ctenophores only have genes for making the neurotransmitter glutamate (and GABA), but they have a ton of glutamate receptors, more than other animals.
All of these findings led the authors to conclude that ctenophores are the most basal animals, not sponges.  Alternatively, it is still possible to keep the same phylogenetic tree, but there would need to have been massive gene loss in the ctenophore lineage.  The most parsimonious explanation is shown here:
The main difference between these two trees is that the sponges and ctenophores have swapped positions.  Note that this would require a nervous system to have developed twice independently.  That’s totally insane.  The ctenophores and the cnidarians “needed” a method of controlling their body to capture prey and both lineages “came up” with the same solution (of course evolution is random and doesn’t have a particular goal in mind).  When similar structures evolve independently, this is known as convergent evolution.
Next year, instead of devoting half a lecture to sponges and tossing in a single slide on ctenophores, I think I’ll have to give ctenophores their due, as potentially the most ancient lineage of animals still in existence. 
Carl Zimmer always beats me to the punch, so here’s his take on the same article.  Better writing, but fewer trees!

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