Comb Jellies for the Win

Sponges May Not Be the Oldest Anymore. What Does This Mean for the “Tree of Life”?

I first witnessed the ethereal beauty of comb jellies when I was about eight years old. I was peering down into the dark waters of the Puget Sound from the edge of a pier when suddenly, they were right there. Comb jellies come in many kinds, and I recognized these from one of my field guides: they were sea gooseberries, swept in from the open water by the current. They passed by in a group, drifting along like ghosts, and were soon gone.

If you’ve never seen a comb jelly before, they’re a little hard to picture. Translucent to the point of invisibility, the various species look a bit like alien spacecrafts and a bit like glass figurines of their namesakes (“sea gooseberries,” “sea walnuts,” “Venus’ girdle,” etc.). But mostly, they just look like themselves. They glide through the water slowly, propelled by comb-like ridges of tiny, beating cilia, with two long tentacles trailing behind. To see them drift, it’s not immediately obvious that you are looking at something even capable of independent movement, but in fact, they are predators. Beautiful predators. They are both bioluminescent and iridescent —the bioluminescence is visible in the dark, and their iridescent rainbows when the sun reflects off their rowing combs.

On the day I saw them, comb jellies captured my heart. They became my favorite animal and remain so to this day, though in those (sadly rare) social situations when someone asks me, “What is your favorite animal?” I sometimes say “owl” because explaining what a comb jelly is gets old and makes me seem like a weirdo. Besides, comb jellies comprise a whole phylum —Ctenophora —so it is a little odd to give them as my favorite animal. It would be like saying my favorite animal is “chordates.”

Comb jellies truly are a whole category unto themselves. At first glance, one might say they resemble jellyfish, because both comb jellies and jellyfish are transparent and gelatinous. But one would be wrong. They are completely different.

For one thing, their shapes and structures are nothing alike. Neither is their means of locomotion. Unlike jellyfish, comb jellies swim using cilia, which is very unusual, because cilia swimming is typically found in single-celled protozoans, not animals. Comb jellies also lack stingers; instead, their tentacles are equipped with unique sticky structures called colloblasts that spring like a trap when touched. Also, comb jellies have a complete gut, while jellyfish have an incomplete gut. The list goes on, and even at the tissue level, comb jellies are unique.

Because comb jellies are delicate and difficult to raise in captivity, they remained understudied for a long time. They were initially placed in the same phylum as jellyfish, based on superficial similarities. But as biologists studied comb jellies further, they gradually discovered that they are stranger than anyone at first realized, and they were given their own phylum.

Then in 2008, a new genetic study seemed to show that, beyond deserving their own phylum, they might even comprise themostdistinct of all animal phyla. This has surprising implications for evolutionary theory.

An Intruder in the Evolutionary Tree

One of the original arguments for Darwin’s theory of evolution was the fact that we seem to see in the fossil record a progression from simpler to more complex lifeforms. The Cambrian explosion —the sudden appearance of diverse phyla of complex animal life —was always a bit of a problem, but it was assumed that as more fossils were discovered, we would see a transition from some simple ancestor to the various phyla of the Cambrian period.

For a long time, the best candidate for this common ancestor was sponges. Not that modern sponges are the ancestors of anything (important to note, so as to head off the pedantic protester), but that an organism similar to modern sponges was the common ancestor. Phylum Porifera, the modern sponges, would then be considered the “sister of all other animals,” the first branch of the tree to split off.

The main reason for this assumption is that sponges are relatively simple. They don’t have all the complex organs and tissue types that other kinds of animals have. They have no brain or nervous system. Instead, they almost seem to be collections of single-celled organisms gathered together into vase-like shapes. The similarity between sponges and single-celled organisms that live in colonies has led evolutionary biologists to use sponges as the basis for the model of how animal life might have evolved multicellularity.¹ Specifically, it has been speculated that multicellularity arose from free-swimming, single-celled eukaryotes² that somehow gathered together and ended up as something rather like a larval sponge.

The sponge-first theory seemed to be supported in the fossil record, because sponges appear in the record going back even to the Precambrian era. Ancient sponges were therefore seen to be the link between the simpler single-celled lifeforms of the Precambrian and the wide, wild diverse lifeforms of the Cambrian. In this way, the whole animal evolutionary tree rests on sponges as the ancestor of all. Take away sponges as the trunk of that tree, and you have no real tree at all, but rather something more like a field.

That’s why quite a hullabaloo arose when a 2008 genetic study placed comb jellies as the earliest diverging branch of the tree of life. The significance of this is hard to overstate. Comb jellies have nervous systems, muscles, and a complete gut —all of which were supposed to have evolved after the sponge lineage diverged from the rest of the animal kingdom. From an evolutionary perspective, the comb-jellies-first theory would have to mean either that (1) sponges devolved from a more complex ancestor possessing neurons, muscles, and a complete gut, or else that (2) these complex tissues and structures arose independently twice in evolutionary history, by chance —once for comb jellies and once for all other life forms.

The first option makes hash of the tree of life as it has been envisioned up to now. If ancient sponges aren’t allowed to be the first step on the evolutionary ladder, the animal tree of life is cut down at the trunk. A question mark covers everything between single-celled eukaryotes and complex animals like comb jellies.

The second option gives the distinct impression of foresight: what are the odds of something as complex and specified as neurons evolving twice? Even if one fully believed that Darwin’s mechanism successfully explains how complex structures could arise by chance, it doesn’t explain why the process would turn out the same way twice. This sort of “convergent evolution” has no good explanation. It has been speculated that maybe there are only so many viable biological options to choose from, so that life would naturally evolve the same way multiple times.

But . . . really? An evolutionary pathway producing something as complex as neurons reoccurring . . . by chance? Any elementary school teacher, looking at the tree of life, would say that we higher life forms had plagiarized our neurons from Ctenophora.

For the Darwin faithful, you have to pick your poison: lose evidence for common descent or admit evidence for foresight in the evolutionary process.

The Ctenophore War

Naturally, the 2008 study could not be left unchallenged. After almost a decade of debate, a 2017 paper, “Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals,” declared that new genetic analysis had shown sponges were, in fact, the earliest-diverging animal. The early placement of Ctenophora had been a mere modeling artifact, it said.

One imagines the biologists of the world collectively letting out their breath, some in disappointment, others in relief. The Economic Times suggested that the study could finally mark “an end to a long-standing row over animal evolution.” The report allowed scientists to fall back to the comfortable old position of a Precambrian sponge-like organism as the common ancestor of all multicellular animal life, the trunk of the evolutionary tree, with modern sponges as the sister phylum to everything else.³

When I read the 2017 study, I was frustrated, because I suspected it was ultimately driven by sheer opposition to the idea that anything other than Porifera (sponges) could be the earliest branch of the tree. Not that I thought the authors were being willfully deceptive. But somebody simply had to come up with a model that would result in sponges splitting off at the base of the tree. One way or another, a model needed to turn up, so it did.

Of course, I had no way to prove this. So I waited. I figured time would tell if the comb jellies would be finally vindicated. (Yes, I’m rooting for the comb jellies as if they cared about all this. I’m not sorry.)

Comb Jelly Coup

Last year, it finally happened. The tide has shifted in favor of the comb jellies, probably for good. In May 2023, a new study presented unambiguous evidence for ctenophoric primacy in the hypothetical tree.⁴ It seems unlikely that this evidence will be overturned. Even staunch ID critic Jerry Coyne called it “pretty unequivocal” on his Why Evolution Is True blog.⁵

That’s not surprising, really. To reject the argument of this paper, Coyne would have to reject one of the main lines of genetic evidence for common descent. The argument is based on syntenic groups —areas on the chromosomes of two different organisms that have gene blocks arranged in the same order. This shared order is considered evidence of common ancestry. The evidence is considered especially strong for syntenic regions that seem to be the result of a fusion and mixing event —an area of one chromosome breaking off and fusing to another chromosome, then mixing with it. When two organisms have the same order of genes in a given chromosomal region, and the order seems to be the result of this sort of fusion/mixing process, then this is taken as evidence of common ancestry on the theory that the fusion/mixing event happened at some point in the two organisms’ common past.

The absence of such regions can likewise be treated as evidence against common ancestry at a certain level of the tree, because the mixing is thought to be irreversible; once a chromosomal section has been fused and mixed in with another chromosome, the odds of it unmixing and returning to the original chromosome would be vanishingly small.

In the 2023 study, the researchers found seven syntenic areas that were shared between specimens from Porifera (sponges), Bilateria (chordates and other groups), and Cnidaria (jellyfish) but that were not shared with Ctenophora (comb jellies). Four of these syntenic areas showed evidence of gene mixing. That is important, because it means that for the sponge-sister theory to be true, those chromosomal regions would have had to unmix and return to their original chromosomes at some point in the comb jellies’ evolutionary past, which is probabilistically unviable.

By contrast, they found no syntenic areas shared between all the groups to the exclusion of Porifera, which you would expect to find if Porifera was the earliest divergence of the evolutionary tree.

Weirder than Thought?

The New York Times report on the new paper stated that the biology community had been reluctant to accept the ctenophores-first conclusion “because it meant animal evolution was weirder than they had realized.”⁶

I don’t believe that assessment is quite right. Biologists have no problem with things being weird. In fact, biologists are famous for loving weird things. Biologists are comfortable with weirdness. What biologists —and scientists of any discipline —don’t tend to be comfortable with are findings that threaten to disrupt the whole framework everyone is working with.

The great physicist Max Planck said, “A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it.” We seem to be witnessing that phenomenon now.

Back in 2019 the Times interviewed biologist Claus Nielsen on the state of the sponge/comb jelly controversy. “I’m 81 years old, and I’ve been a zoologist since my 20s,” Dr. Nielsen said. “My whole concept of the animal kingdom would crash with this ctenophores-first idea.”⁷ Nielsen had published an article that year arguing that sponges have to be first in the evolutionary tree, because it simply wouldn’t have been adaptive for the ancestors of sponges to have lost all the complex features found in ctenophores. “To lose the ability to digest larger organisms —to me, that is nonsense,” he told the Times.⁸

This is true —within the framework of the neo-Darwinian evolutionary model. The question is, what if the whole model needs to be torn down and rebuilt from the foundation?

The old guard in the scientific community may be reluctant to question the received model. But people become scientists because they like exploration and discovery, and new generations of scientists are not always going to be satisfied staying in a model that doesn’t work. Sponges may be forced to sit in place, but comb jellies are free. I am hopeful that biologists of the future will be free as well.

Notes
1. “Sponges as the Rosetta Stone of Colonial-to-Multicellular Transition,” Australian National University
2. A eukaryote is a single-celled organism whose cells have a clearly defined nucleus bound by a nuclear membrane.
3. “Sea sponges are common ancestors of all animals: Study,” The Economic Times (December 3, 2017).
4. Darrin T. Schultz, et al, “Ancient gene linkages support ctenophores as sister to other animals,” Nature (May 17, 2023).
5. “A major problem in animal phylogeny seems to have been solved,” Why Evolution is True (May 21, 2023).
6. Carl Zimmer, “Bizarre Sea Creatures Illuminate the Dawn of the Animal Kingdom,” New York Times (May 17, 2023).
7. Cara Giaimo, “A Battle Is Raging in the Tree of Life,” New York Times (August 2, 2019).
 8. “Early animal evolution: a morphologist’s view,” Royal Society Open Science (July 31, 2019).