The outgroup for multicellular animals: ctenophores

Ctenophores, or comb jellies, are a phylum of animals whose relative position in the Great Tree of Life—along with the other metazoan (multicellular) animal phyla of Cnidaria (jellyfish, corals sea anemones), Porifera (sponges)  Placozoa (a single species resembling a multicellular amoeba, which forms its own bizarre phylum), and Bilateria (all the other animals we know, from worms to clams to squirrels)—has been a mystery.  It’s now being resolved, and a paper in the latest Science by Joseph Ryan et al. (see also the nice short summary by Antonis Rokis; references and links with free download at bottom) may have resolved at least these major groups.

But first, here’s a weird placozoan, the species Trichoplax adhaerens, which is the only monspecific phylum I know (there may be others). It’s a marine animal that eats algae:

Trichoplax_mic

This is a multicellular animal

There have been been lots of arguments over the years about how these phyla are related, and that’s important because some of them have common features (colenterates, ctenophores, and bilaterians, for example, have nervous systems; others don’t; while only bilaterians and ctenophores have “mesoderm”, a middle layer of tissue in the zygote that forms, among other things, bilaterian muscles), common features that imply common ancestry.  Just those similarities I described would imply that our closest relatives—and by “our” I mean Bilateria—may be ctenophores, but their mesoderms are different from ours.  And they strongly resemble jellyfish. When I was younger I learned that sponges, because of some peculiar cells with flagella they have, may be the outgroup for all animals (the sister group of all the other groups).

All in all, the grouping of metazoan phyla has been contentious and unresolved, but now the advent of whole genome-sequencing offers one way to sort it out.

The paper by Ryan et al is based on whole-genome sequencing of a single species of ctenophore, Mnemiopsis leidyi (one species from each group will do when you’re trying to resolve such anciently-diverged taxa, which diverged around the time of the Cambrian explosion, over 500 million years ago). Here’s M. leidyi:

7698693-md

Photo by: Krister Hall; portfolio here: http://photo.net/photodb/member-photos?user_id=880342

But let’s look at some ctenophores first, as they’re among the most beautiful of animals, iridescent marine species with shimmering waves of light:

I don’t want to dwell on the paper too long, but several of the main findings come from comparing the genome of this species (both DNA sequences and which genes are present or absent in the groups) with those of representatives of the other four phyla as well as a definite “outgroup” (single-celled animals; they used a “choanoflagellate“: a one-celled animal with a flagellum surrounded by a collar).  The phylogenies differed a bit depending on how they did the analysis, but the most definitive one, statistically more supportable than any other family tree, involved using the presence or absence of groups of genes as a way to judge relatedness. Here’s their phylogeny as redrawn in the summary of Rokas:

Picture 1Now this is weird in several respects:

  • It shows that ctenophores are the outgroup of all other metazoans. That is, their ancestors branched off before the ancestors of sponges, placozoans, cnidarians, and bilaterians. That’s a surprise because ctenophores look far more similar to jellyfish than to anything else. But that similarity is superficial, and belies the true genetic relationships. (Looks are deceiving; genomes less so.)  There’s no doubt that this is correct, and that the sister group to ourselves (Bilateria) is cnidarians. That’s a surprise. We are in fact more closely related to sponges and those weird placozoans than to ctenophores.
  • The only animals in this tree that have nervous systems are Bilateria, Cnidaria, and Ctenophores; placozoans and sponges don’t. And, as the new DNA sequencing study shows, those nervous systems rest on the expression of similar genes in the three groups, so they didn’t evolve independently.
  • The finding above implies either that 1.) the ancestor of all multicellular animals had a nervous system, which was later lost in sponges and placozoans, or that 2.) the ancestor had the requisite genes for building nervous systems, but they were originally used for something else and later co-opted in Bilateria, Cnidaria, and Ctenophora to build neurons and other components of that system. Although the latter may seem less likely, it’s not unknown for the same genes to be co-opted in different lineages to build similar structures. (The eyes of humans and fruit flies evolved independently, for instance, but both involve the important involvement of a gene called Pax6.) The representation in Rokas’s figure implies possibility 1)—a full nervous system in the common ancestor—but we don’t know that yet.
  • Finally, the genes that make the mesoderm of ctenophores—the middle layer of tissue—are different from those making the mesoderm of bilaterians, like the layer of tissue that builds our muscles and connective tissue. It’s thus pretty clear that the mesoderm evolved twice independently, and that depiction in Rokas’s diagram is accurate.  The mesoderms of Bilateria and Ctenophora are analogous but not “homologous”, i.e., they are similar in structure but not evolutionary origin.

There’s other stuff in the paper of Ryan et al. as well, but this is what most of us need to know. The paper is free if you want to read more.  What strikes me most strongly is that the similarity between comb jellies and jellyfish does not reflect close relationship, and probably evolved independently—unless the common ancestor of all metazoans was jellyfish-like (unlikely!). And the possibility that the common ancestor also had a nervous system is also intriguing. That won’t be resolved until we can figure out what those genes in sponges that make nervous systems in ctenophores and bilaterians (but not in sponges really do)—that is, we need a functional analysis of sponge “nervous-system-type” genes.

_________

Ryan, J. F., K. Pang, C. E. Schnitzler, A.-D. Nguyen, R. T. Moreland, D. K. Simmons, B. J. Koch, W. R. Francis, P. Havlak, S. A. Smith, N. H. Putnam, S. H. D. Haddock, C. W. Dunn, T. G. Wolfsberg, J. C. Mullikin, M. Q. Martindale, and A. D. Baxevanis. 2013. The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science 342:1336-1344.

Rokas, A.  2013. My oldest sister is a sea walnut? Science 342:1327-1329.

77 Comments

  1. marksolock
    Posted December 20, 2013 at 6:48 am | Permalink

    Reblogged this on Mark Solock Blog.

    • Jesper Both Pedersen
      Posted December 20, 2013 at 8:12 am | Permalink

      sub

  2. Charles Jones
    Posted December 20, 2013 at 7:01 am | Permalink

    I am shocked by these results: The common link between the choanoflagellates and the choanocyte cells (collar cells) in the sponges, plus the fact that sponges do not have true tissues, seems to make sponges the perfect intermediate step between choanoflagellates, which sometimes come in small colonies, and truly multicellular life, like the ctenophores or cnidarians.

    These results have ruined a nice narrative! Damn!

    • TJR
      Posted December 20, 2013 at 7:07 am | Permalink

      Ah well, Sophisticated Biologists have always known that that narrative was only metaphorical.

    • Posted December 20, 2013 at 10:22 am | Permalink

      I agree! The choanocytes of sponges seem so much like the choanoflagellates. And some of the choanoflagellates are colonial, with a gooey matrix and I think a crude division of labor among cells.
      Another nice narrative that was upended by genetic analysis was the finding that the platyhelminthes are really protostomes. They sure looked like nice, less derived bilatarians. Took me a while to get over that one.

  3. Kelton
    Posted December 20, 2013 at 7:32 am | Permalink

    I love reading about new discoveries in phylogeny like this – thank you Dr. Coyne!

  4. John Harshman
    Posted December 20, 2013 at 7:41 am | Permalink

    The phylogenies differed a bit depending on how they did the analysis, but the most definitive one, statistically more supportable than any other family tree, involved using the presence or absence of groups of genes as a way to judge relatedness.

    To each his own, but I would have said that the most definitive was the analysis of fourfold degenerate protein-coding sites in 50+ species and various outgroups. Different strokes, I suppose, and anyway they mostly say more or less the same thing.

    • Nmatzke
      Posted December 20, 2013 at 4:41 pm | Permalink

      Haven’t read the paper in depth, but I don’t see why fourfold degenerate sites are best here. They evolve hella fast so are subject to saturation, which is particularly bad for 500 my+ divergences and long branches. Or did I miss something about what you are saying?

      • John Harshman
        Posted December 20, 2013 at 7:16 pm | Permalink

        Whoops. I was thinking of a different paper. These folks used amino acid sequences; so substitute that for fourfold degenerate sites in my comment.

        Still: Transversions might not be saturated, and anyway sequences that are saturated over the whole tree can still provide information given dense enough taxon sampling. But I repeat that this isn’t relevant to the actual paper in question.

  5. anaxyrus
    Posted December 20, 2013 at 7:45 am | Permalink

    I think it is more likely that ctenophores have undergone loss of great numbers of genes. Not buying them as outgroup of other metazoans.

    • Posted December 20, 2013 at 2:29 pm | Permalink

      Agreed! Resolving (some of) these deep divergences is a very complex business, and gain/loss characters are some of the most problematic, every year there is some paper or other on some group that uses some presence/absence characters, announces revolutionary results, and then it doesn’t hold up.

      Also, ctenophores are on a loooong branch which makes everything hard and makes it very easy to get artifacts. It looks like the authors did a serious analysis but you’ve got to read a few back-and-forth analyses to get a sense of what will really hold up.

      My gut instinct goes with the hypothesis that ctenophores are basically a case where the larval form became the adult, so they could go almost anywhere, but probably above sponges!

      • John Harshman
        Posted December 20, 2013 at 7:19 pm | Permalink

        Note that the straight protein-sequence analysis gives the same result, and that they also tried an analysis without outgroups, whose topology is not compatible with the two most common prior hypotheses — ctenophores sister to cnidarians or sister to bilaterians.

        • Noma take
          Posted December 20, 2013 at 10:22 pm | Permalink

          I read the paper somewhat carefully on the plane. Actually the protein results were pretty mixed, the Bayesian runs didn’t give the same allegedly clear picture that the ML analyses did, and some of the Bayesian runs never converged. When looking at individual protein trees, it was apparently kind of a 60-40 thing whether or not the proteins backed their result. They did a heck of a lot of work of course, but the methods I felt were kind of standard when this sort of case in particular you really need to go the extra mile testing for saturation issues, comparing super-slow and fast sites/proteins, etc. The branches they are trying to resolve are short ones at the bottom of long ones-the worst case scenario! Any little non-phylogenetic signal could throw off the inference in that situation. So, don’t be surprised if you see this all disputed by other groups.

  6. Diana MacPherson
    Posted December 20, 2013 at 8:11 am | Permalink

    Hmmmm I guess humans owe a lot more to ctenophores than sponges after all.

    • gravelinspector-Aidan
      Posted December 20, 2013 at 9:41 am | Permalink

      Nope, other way around. If you accept this analysis (I’m off to RTFA shortly, so I’m fence-squatting), then humans are more closely related to sponges than ctenophores.
      It certainly is a peculiar and unexpected result.

  7. JBlilie
    Posted December 20, 2013 at 8:18 am | Permalink

    Cool. Thanks Dr. Ceiling Cat!

  8. Posted December 20, 2013 at 8:24 am | Permalink

    The diagram neglects to show that the common ancestor must have also had true tissues which were lost in sponges and tricoplax.
    The first ctenophores as outgroup paper came out a few years ago and I’ve been hoping since then that they put their tissues together differently. That would mean sponges are not degenerate ( the choanocyte observation is real) and development will be completely different in ctenophores….oh well.

    (JC – “which is the only monspecific phylum I know” )
    I think Ginkgo’s should count.

    I already know how the IDers will spin this.

    • gravelinspector-Aidan
      Posted December 20, 2013 at 9:45 am | Permalink

      Gingkos are not a phylum ; they’re somewhere around the family or order level, taxonomically. Whatever that means generally, and for plants in particular.
      The Gingkos have a long and well-established fossil record. Wikipedia lists ten fossil species. Or morpho-species, if you want to be picky.

      • aspidoscelis
        Posted December 20, 2013 at 10:37 am | Permalink

        Ginkgo has traditionally been treated as a phylum (or division, for those who prefer to call plant phyla “divisions”):

        http://botit.botany.wisc.edu/courses/systematics/Phyla/Ginkgophyta/Ginkgophyta.html

        However, since taxa within a given rank are not necessarily comparable units (and between widely divergent organisms -rarely- are comparable; e.g., families in mammals and birds are more or less equivalent to genera in plants, fungi, & insects), this isn’t terribly meaningful…

        • gravelinspector-Aidan
          Posted December 20, 2013 at 11:13 am | Permalink

          However, since taxa within a given rank are not necessarily comparable units [...] this isn’t terribly meaningful…

          Aye, ain’t that so. One of these days I’m going to have to get back into Margulis’ “Five Kingdoms” book (uhhhh … can’t seem to find an ISBN for the edition I’ve got ; about 1997), but they keep on changing the number and specifications of the phyla. I almost got as far as the animals proper before I ran out of energy.

        • chascpeterson
          Posted December 20, 2013 at 6:46 pm | Permalink

          “families in mammals and birds are more or less equivalent to genera in plants, fungi, & insects”
          I’d go with ‘less’. That’s an indefensible generalization.

          • aspidoscelis
            Posted December 21, 2013 at 1:41 am | Permalink

            Do you think I went too far or not far enough? :-)

          • aspidoscelis
            Posted December 21, 2013 at 1:55 am | Permalink

            Admittedly, it’s very hard to address the question meaningfully in a vacuum–there simply is no generally accepted criterion available to decide whether or not taxa are comparable. However, to me the tendency for taxonomic inflation among groups of organisms that are easier for us to observe, more similar to us in size and morphology, and more “charismatic” is such an obvious and striking aspect of taxonomy across major lineages that it seems undeniable. And given that the size of taxa at any particular rank is governed entirely by subjective assessments of how much variation is “too much” or “too little” for the rank, how could it be otherwise? The more appealling and relatable we find a group of organisms, the more we study their taxonomy and the more the variation among them is intuitively obvious to us, “needing” more genera, more families, etc.

        • Peter Nyikos
          Posted December 27, 2013 at 1:56 pm | Permalink

          Alfred P. Romer, in his classic _Vertebrate Paleontology_, said that most orders of birds are equivalent to most families of mammals, if that.

          For many years, a widespread practice was to include all spermatophytes (and IIRC all vascular plants) within a single phylum and to refer to monocots as forming an order, and dicots as forming the other order of angiosperms. That may have been too extreme in the direction of lumping.

          Anyway, if ginkgoes are sufficiently disparate from other known spermatophytes, it might be all right to call them a phylum, but the disparity that is evident between all ginkgoes, fossil and extant, may also call for them all forming one family within the phylum.

  9. Posted December 20, 2013 at 9:33 am | Permalink

    Two things.

    First, my mind is again blown at the concept of Deep Time.

    Second, the colors in the ctenophore are obviously the result of refraction or diffraction. The whole rainbow is there in proper order, and the colors themselves don’t move even when the patterns of intensity move. Wikipedia suggests it’s the comb rows responsible, which means diffraction. This, in turn, implies very regular spacing of very small structures, on the rough order of 500 lines per millimeter. I’d be interested to know if there’s a specific purpose to those structures, and if the diffracting properties are a curious byproduct or the primary purpose.

    Cheers,

    b&

    • gravelinspector-Aidan
      Posted December 20, 2013 at 9:59 am | Permalink

      They certainly are beautiful animals, and I heartily recommend snorkelling with some – not likely in Arizona, I suspect. But be careful – they are toxin-using predators, and even the common sea-goosberry can leave you (well, me) with numb lips around your snorkel. The possibility of allergic reactions is non-trivial.
      A number of species that eat ctenophores recycle intact stinging cells to their skin surface where they are co-opted into their new host’s defences. High praise indeed!
      The iridescent lines – eight normally – are lines of cilia that are part of the animals propulsion system. There are two tentacles coated with stinging cells which capture food items and bring them to the mouth.

      • Michael Hart
        Posted December 20, 2013 at 12:58 pm | Permalink

        Is it possible you’re thinking of the toxic cnidae (stinging organelles) of cnidarians? The analogous cells of ctenophores are called colloblasts and are not toxic. They produce a glue to attach the tentacles to prey, instead of a toxin to paralyze prey. Some animals (nudibranchs are famous for this) do steal cnidae from sea anemones, but I don’t think there are any examples of stolen colloblasts used by other animals.

        • gravelinspector-Aidan
          Posted December 20, 2013 at 1:37 pm | Permalink

          Sorry, you’re right. I was getting Cnidarian “jellyfish” and Ctenophoran “sea goosberries” confused. An object warning.

        • Diane G.
          Posted December 21, 2013 at 12:54 am | Permalink

          So we no longer use the term “nematocysts?”

      • Posted December 20, 2013 at 7:26 pm | Permalink

        Sadly, you’re right — the chances of finding a ctenophore in the middle of the Sonoran Desert…well, maybe there’s one in an aquarium….

        One of these days I’ll make my way to some tropical snorkeling paradise. (And one that has a cat-friendly hotel for Baihu to stay in — I’m guessing snorkeling would be just a wee bit too much for him.) No clue just how far in the future, or where, or any of the rest…but I’ll try to make sure that it’s somewhere I might have a chance of seeing one of these beasties.

        b&

        • gravelinspector-Aidan
          Posted December 21, 2013 at 2:02 pm | Permalink

          I’m guessing snorkeling would be just a wee bit too much for him.)

          I cannot avoid Googling for “snorkelling cat video”. I just can’t avoid it. One set from the “Happy Cat” vessel ; another set is about attaching a snorkel to an “Arctic cat” swamp-mobile. Someone has done it though : http://shows.howstuffworks.com/7605-howstuffworks-scuba-cat-commercial-video.htm with some sort of fish-bowl helmet arrangement with a continuous bleed of air into the cat suit and … well I can see how to build one. “Why?”
          is a different question.
          Does Baihu enjoy watching the fish tank? Could you build a surround-cat fish tank and see how he reacts in that. He’s already used to using a harness when he’s out for a walk, so getting him used to a body suit of some sort isn’t beyond the realm of the possible.
          This is one of the stupider ideas that I’ve heard. Which isn’t necessarily a criticism.

          • Posted December 21, 2013 at 4:16 pm | Permalink

            Holy shit, that’s fucking insane!

            No fishtank; I don’t think he’s ever seen a fish except for small cut-up portions thereof — and, of course, those were soon eaten. (Ignoring, for the moment, that you and I and he and the lizards and the dinosaurs are all fish.)

            After he, as Gary Larson put it, got “tutored,” he didn’t care much for the “cone of shame.” No clue how I could build a variation on that theme big enough to hold fish that didn’t weigh at least several times as much as he does

            I think any attempts at that would have to start with normal walks, with him on my shoulders, where I waded through some body of water. And it would take several days, weeks maybe, of me wading deeper and deeper until I was neck-deep and he was ankle-deep, at which point I could presumably start submerging briefly to get him to swim. Then when he’s okay with swimming, I could finally think about SCUBA for him…and even that might take as long to condition him to as swimming itself.

            Seeing how there’s no suitable body of water for hundreds of miles around, that’s not going to happen any time soon, if ever….

            b&

            • gravelinspector-Aidan
              Posted December 25, 2013 at 5:19 pm | Permalink

              How about working from the other end. Consider the diving suit as a (rigid- ish) helmet with a continuous air feed ; the body in a loose bag, with a vent valve located … appropriately. A collar-tightness constriction at the neck – or a shoulder harness outside the bag, if that’s what he’s used to – to keep the air flow direction as desired … and use waterproof material. There’s no real shortage of water-tight zips. That would serve as a basic model – indeed, it’s a conceptual cousin for the old “brass hat” type of diving suit.
              After that … strategically-placed elastic or draw-cords to fit the bag to the body well enough to let the limbs (front only? For starters?) function as fins (Neil Shubin’s “Your Inner fish” was indubitably correct.) and …
              Introducing Baihu – the incredible SCUBA-Cat.
              Sorry – SCUPA : Self-Contained Underwater Purring Apparatus.

              • Posted December 26, 2013 at 11:06 am | Permalink

                Upon further reflection of your proposal, I have expanded upon it a bit and decided that this is the optimal method for not only introducing Baihu to the depths of the ocean, but conquering any fears (or anything else) that might stand in his way.

                Now, if you’ll excuse me, I do believe I need to locate that missing monocle….

                b&

              • gravelinspector-Aidan
                Posted December 26, 2013 at 1:27 pm | Permalink

                Well, that’s a start. Didn’t Jacques Cousteau and NASA build underwater habitats which might be more cost effective?
                Baihu knows exactly where your monocle is. And you’re not allowed to play “World Domination, Fast” until after dinner time.

              • Posted December 26, 2013 at 2:18 pm | Permalink

                Cost-effective, perhaps…but you gotta admit that there’s a certain romanticism to the Carter that a mere stationary habitat can’t match.

                And mine or his? Never mind — he’s right now informing me that it’s his lunch time, so dinner will have to wait, I guess….

                b&

    • chascpeterson
      Posted December 20, 2013 at 10:36 am | Permalink

      Locomotion. They are tiny paddles made of fused cilia.

      • lkr
        Posted December 20, 2013 at 11:56 am | Permalink

        And diffraction because the unit repeating[cilium] is about the width of visible light waves.

    • chascpeterson
      Posted December 20, 2013 at 10:38 am | Permalink

      The combrows are for locomotion; they’re tiny paddles made of fused cilia.

      • Posted December 20, 2013 at 8:05 pm | Permalink

        Thanks!

        Must be very, very tiny….

        b&

    • Posted December 20, 2013 at 6:22 pm | Permalink

      Just a reminder that large numbers of very regularly spaces small objects can cause iridescence as well as diffraction. Ridges on Morpho wing scales are the classic example.

  10. Latverian Diplomat
    Posted December 20, 2013 at 9:35 am | Permalink

    I’m not verty knowledgable in this area, but is there a reason the common ancestor couldn’t be jellyfish-like?

    It’s a very successful body plan that works well at small scale and in a variety of environmental conditions.

    • gravelinspector-Aidan
      Posted December 20, 2013 at 10:11 am | Permalink

      That’s precisely what the journal article is saying isn’t the case – that the jellyfish are not particularly close to the root of the animal kingdom. In particular, the jellyfish use different genes to generate their mesodermal layer compared to the ctenophores.
      That ctenophores are anatomically different to jellyfish (cnidarians) has been known for a long time – I’m not sure how long, but I’ve got biology text books from the mid-1950s where that was taken as given. The gross anatomy is different – much higher degrees of radial symmetry in cnidarians for starters – and the microscopic anatomy is different, the two having different types of stinging cells. Jellyfish, bilaterians and placozoa are related to similar deggrees, i.e. not very closely.

      • Erik Verbruggen
        Posted December 20, 2013 at 11:27 am | Permalink

        Also, the closest ancestor can’t have been a carnivore, unless it was a cannibal :-)

        • Latverian Diplomat
          Posted December 20, 2013 at 11:43 am | Permalink

          Young jellyfish are some enough to be part of the zooplankton ecosystem. At that size, I’m not sure the carnivore/herbivore distinction exists (honestly, I’m ignorant as to whether it does).

          But again, the question is could a simple, “jellyfish-like” body plan at that small scale, feeding on single celled organisms of all types, have been the common ancestor.

      • Latverian Diplomat
        Posted December 20, 2013 at 11:38 am | Permalink

        You misunderstood me. I was specifically asking about this sentence in the writeup:

        “unless the common ancestor of all metazoans was jellyfish-like (unlikely!)”

        I tool jellyfish-like to not mean jellyfish, but a body plan resembling jelly-fish. Perhaps I’m reading more into this offhand remark than was intended.

        It’s reasonable but by no means necessary that the common ancestor would resemble one of the descendant phyla.

    • Posted December 20, 2013 at 10:18 am | Permalink

      I was wondering that as well. It seems reasonable to me that an early animal design could be based on a single body axis, as seen in jelly fish today, with radially symmetric structures built around it. I am not saying that the earliest animals would be specifically ‘like’ jellyfish with tentacles and stinging cells.
      Then addition of other body axes would add bilateral symmetry and a dorsal-ventral axis.

    • Torbjörn Larsson, OM
      Posted December 20, 2013 at 2:30 pm | Permalink

      is there a reason the common ancestor couldn’t be jellyfish-like?

      Generally no, but specifically here the body plan isn’t generic for all development stages.

      What I mean is that the young stage of cnidarians is larva resembling bilaterians (“A planula is the free-swimming, flattened, ciliated, bilaterally symmetric larval form of various cnidarian species.” ; http://en.wikipedia.org/wiki/Planula ), while the young stage of ctenophores is plankton resembling ctenophores (“The young are generally planktonic and in most species look like miniature cydippids,” ; likely because “all the other traditional ctenophore groups are descendants of various cydippids”; http://en.wikipedia.org/wiki/Ctenophora ). Maybe the new phylogeny is informative on the development stages, maybe not. But evidently the “jellyfish-like” body plan wasn’t used at all times.

      FWIW, the cut through of a cydippid (first figure) looks simple enough, like a veritable Pac-Man.

      [Disclaimer: I'm no biologist.]

      • lisa parker
        Posted December 20, 2013 at 5:08 pm | Permalink

        I have never seen nor heard the word “planktonic” before, but just sitting and reading it here, it suddenly and incredibly blossomed, whole and totally developed before me the wondrous glory of how many ways such a term could be used. I will remain humbly and eternally in your debt.

        • Torbjörn Larsson, OM
          Posted December 21, 2013 at 10:52 am | Permalink

          Wow. Thanks!

          But I too was immediately immersed into the context of that term. It is, as they used to say in the previous millennium, “nifty”.

  11. SteveCarb
    Posted December 20, 2013 at 10:03 am | Permalink

    M. leidyi is the jelly that decimated the Black Sea and has now made it’s way into the Mediterranean. Just finished Stung! by Gershwin – excellent but scary book on jellies and the current state of the oceans. She does not really go into the jelly phylogeny very much but does have a few relationships.

  12. gravelinspector-Aidan
    Posted December 20, 2013 at 10:14 am | Permalink

    It looks as if those links are only free if you’re on a subscribed (university and some other) network.

  13. aspidoscelis
    Posted December 20, 2013 at 10:17 am | Permalink

    “(one species from each group will do when you’re trying to resolve such anciently-diverged taxa, which diverged around the time of the Cambrian explosion, over 500 million years ago)”

    This is accurate only if the members of each group are invariant for all of the characters involved. Otherwise, including multiple members of each group will change the inferred character states for the common ancestor of each group which, of course, can change the inferred relationships among groups. If you use only a single representative of each group, you are implicitly assuming that the observed character states of that lone organism are identical to the character states of the ancestor of the group as a whole. This is independent of the age of the groups involved.

  14. Gregory Kusnick
    Posted December 20, 2013 at 10:51 am | Permalink

    As a non-specialist I’m having trouble swallowing the idea that the earliest metazoans already had functioning nervous systems.

    I suppose one alternative is that once it was invented, phyla with nervous systems outcompeted phyla without, and drove them to extinction. And yet the poriferans and placozoans seem to get by just fine without.

    • Latverian Diplomat
      Posted December 20, 2013 at 11:50 am | Permalink

      If I understand what the study can actually address, then the claim is just that the common ancestor of all known animal phyla had a nervous system, call this species N.

      That is not a claim that N did not have earlier ancestors or cousins without a nervous system, just that those cousin have no modern descendant phyla, and those ancestors to N left no descendants whose line of descent did not pass through N.

      • Latverian Diplomat
        Posted December 20, 2013 at 12:13 pm | Permalink

        Sorry, I guess your second paragraph encompasses that point. Didn’t mean to wax pedantic on you.

      • Gregory Kusnick
        Posted December 20, 2013 at 12:22 pm | Permalink

        Right, I get that; that’s what my second paragraph was about.

        Nevertheless this scenario posits two things that together seem implausible: first, that all the nerveless relatives of N became extinct, and second, that two descendent phyla of N independently lost their nervous systems without becoming extinct. So clearly there were niches available for nerveless metazoans.

        What I’m saying is that I find Jerry’s scenario #2 more plausible (“the ancestor had the requisite genes for building nervous systems, but they were originally used for something else and later co-opted in Bilateria, Cnidaria, and Ctenophora to build neurons and other components of that system”).

        • Latverian Diplomat
          Posted December 20, 2013 at 1:09 pm | Permalink

          Those are good points. One might argue that perhaps Species N were the first animals to be large enough that a sessile filter feeding strategy, as opposed to a floating strategy, worked.

          I say this because all the sessiles I’m aware of have a mobile larval stage. This may be because a certain minimum size is necessary for success, or just because mobility in larva is a desirable dispersal trait. Once sessile, discarding expensive organs is common. I think this might work for the

          This doesn’t work at all for the Placozoa, which remain small, floating, and would seem to occupy exactly the niche that Species N’s nerveless ancestors would have. Perhaps some other new trait of species N gave them competitive success, and the nervous system was discarded after (or as) the battle was won.

          • Latverian Diplomat
            Posted December 20, 2013 at 1:11 pm | Permalink

            Sigh. Not a good day for typing. The 2nd paragraph should end “I think this might work for the Porifera.”

  15. Posted December 20, 2013 at 11:41 am | Permalink

    One of the strange things about this illustration is that it has annotations that make it look rather non-parsimonious (that is, it points out several redundant events). The illustrator chose to show that nervous systems were lost twice, and a third mesoderm developing layer was gained twice. The tree would be easier to swallow if the annotations indicated why it is still the simplest tree.

    • Erik Verbruggen
      Posted December 20, 2013 at 11:53 am | Permalink

      I suppose this the simplest sequence of
      Trait gain or loss taking the tree as a given, which is based on dna sequences. With this tree there is no simpler configuration of trait evolution. Or am I misunderstanding your remark?

      • Posted December 20, 2013 at 3:42 pm | Permalink

        As was said in this posting, this was the simplest tree. I just would like to see the main traits that pull some groups together. What are the traits that bring the the sponges and placoz in toward the bilataria? The tree does not say.

        • Erik Verbruggen
          Posted December 20, 2013 at 4:57 pm | Permalink

          Now I see what you mean, sorry for that. From reading the papers it appears it is just sharing gene families (and EST’s), that are not found or more divergent in Ctenophora. So, what traits would be more similar among bilateria and sponges is not apparent at all…. they should have dug into that, interesting question for sure!

    • Diana MacPherson
      Posted December 20, 2013 at 12:59 pm | Permalink

      Swallow a tree!? How ghastly!

  16. Torbjörn Larsson, OM
    Posted December 20, 2013 at 2:42 pm | Permalink

    I read somewhere it isn’t a closed case (and even the paper seems to be cautious as I browse). But the gain-and-loss scenario seems analogous to many other trees that are derived from genomes (meaning trees this layman seen lately).

    It’s thus pretty clear that the mesoderm evolved twice independently, and that depiction in Rokas’s diagram is accurate. The mesoderms of Bilateria and Ctenophora are analogous but not “homologous”, i.e., they are similar in structure but not evolutionary origin.

    That reminds me of the claims to see an epidermis analogue in D. discoideum (“slime mold”) fruiting body growth tip, which is feasible on gene level (i.e. independent evolution from shared genes).

  17. Torbjörn Larsson, OM
    Posted December 20, 2013 at 3:08 pm | Permalink

    It’s thus pretty clear that the mesoderm evolved twice independently, and that depiction in Rokas’s diagram is accurate.

    Ha! I just realized the “first” (dunno about the timing) mesoderm muscle-giving layer evolved for eating, not locomotion. “The mouth and pharynx have both cilia and well-developed muscles” vs “comb rows … are used for swimming.” [ http://en.wikipedia.org/wiki/Ctenophora ]

    Seems my “Pac-Man” characterization was more apt than I realized. Animals, always looking for food first and everything else later.

  18. Joe
    Posted December 20, 2013 at 4:17 pm | Permalink

    IANAB, and was somewhat surprised to learn in this thread that “families in mammals and birds are more or less equivalent to genera in plants, fungi, & insects”. I am just back from four days treking through Haleakala “Crater” on Maui. On our way down Sliding Sands Trail, we always are on the lookout for the very striking Silversword-Dubautia hybrids, Argyroxiphium sandwicense X Dubautia menziesii. (Google silversword alliance to read about the 50 or so species evolved from a single introduction (a wayward North American tarweed?) about 5 million years ago). Note these are hybrids between different genera! Are there any known hybrids between mammal or bird families?

    • chascpeterson
      Posted December 20, 2013 at 6:49 pm | Permalink

      no.
      Nor are mammal & bird ‘families’ equivalent.
      You can’t believe everything you read.

    • aspidoscelis
      Posted December 21, 2013 at 11:42 pm | Permalink

      Regarding comparing families & genera – as should be obvious from chascpeterson’s response, there is disagreement on this point. :-) It is my opinion that taxonomists working on mammals and birds tend to proliferate genera, families, orders, etc., to such an extent that each rank in mammals & birds is more or less equivalent to the next lower rank in the less “charismatic” plants, insects, & fungi, but that opinion is probably not widely shared among biologists.

      Regarding hybrids – plants, for whatever reason, are much more prone to hybridization among species and, to a lesser extent, genera, than vertebrates. I’ve never heard of interfamilial hybrids, but in some plant families (orchids & bromeliads particularly) intergeneric hybrids are easily produced in artificial crosses (such hybrids are a large segment of the horticultural trade in these families) and hybrids between species are frequent in many plant families. Such hybrids may be sterile, reproduce sexually (and often conduits for gene flow where the parental species come into contact), or reproduce asexually (and often forming a new hybrid species reproductively isolated from its parents). In any case, taxonomic inflation aside, the rules for hybridization are dramatically different in plants compared to most vertebrates. Although there are a few vertebrate lineages that engage in hybrid speciation (e.g., the lizard genus Aspidoscelis!) or can produce fertile intergeneric hybrids in artificial crosses (e.g., between the snake genera Lampropeltis, Pantherophis, & Pituophis), these are rare and exceptional phenomena in vertebrates but frequent in plants.

  19. lisa parker
    Posted December 20, 2013 at 4:44 pm | Permalink

    1. The first picture you posted is very obviously the footprint of a Sasquatch. (So, does this mean that God is a Sasquatch and has been trying very hard to leave us messages? This will need to be investigated more thoroughly later.)
    2. This information will never ever make any difference in any way or any time to my health and well-being, nor likely to do so with the vast majority of humans scrambling around on this planet. Never the less, I am very pleased to know it. Thank you.

    • Gregory Kusnick
      Posted December 20, 2013 at 6:50 pm | Permalink

      If it pleases you to know it, then it’s already made a difference to your well-being (and possibly to your health as well, since happy people tend to be healthier).

      • lisa parker
        Posted December 27, 2013 at 12:31 am | Permalink

        You are right. I hadn’t thought of it that way. Now I’m even more pleased to know about it.

  20. chascpeterson
    Posted December 20, 2013 at 6:56 pm | Permalink

    I just can’t buy this narrative. To get from colonial-at-best choanoflagellates (the undisputed sister-group to Animals) to multicellularity at the level of cnidarians or ctenophores, an stage pretty much exactly like sponges is a logical necessity. Either
    a) the common ancestor of extant ctenophores and cnidarians (and probably, therefore, all extant animals) was already at the tissue level of organization and extant sponges are degenerate, including the re-evolution of choanocytes
    or
    b) ctenophores represent an entirely independent evolution of tissue-level multicellularity, neurons, mesoderm, etc. from cnidarians+all other non-sponge animals
    or
    c) these genetic analyses are confounded by long-branch attraction and/or other problems and the traditional narrative–with sponges as the sister-group to all other animals–is correct.

    My money’s on c.

    • dave-uh
      Posted December 23, 2013 at 4:35 pm | Permalink

      choanozoans and choanocytes are not the same thing, one is an adult cell type of some, not all sponges, the other is a single celled organism. there are a few published papers that discuss this. the larvae of some sponges have previously been proposed as their link to metazoa and quite a lot of research has gone into describing them, they can swim, crawl, sense light etc.

      if you based the metazoan tree upon the simplicity of traits the base would be trichoplax. as is, if the base is sponges trichoplax lost the morphological traits shared by sponges or sponges independantly evolved them, the former being the widely accepted hypothesis.

      longbranch attraction may be an issue but unless someone can show this to be the case in the analysis, at best it is a guess.

  21. Diane G.
    Posted December 21, 2013 at 1:05 am | Permalink

    Fascinating story, no matter if it prevails or is overturned by a later analysis. Guess “they” (another they) knew what they were doing back when they split up the Coelentera. :D

  22. Jim Thomerson
    Posted December 21, 2013 at 4:10 pm | Permalink

    I did fish taxonomy, mostly at the species and genus level. When I described a new species of fish, I was pretty sure I was describing an actual entity which existed in nature. When I moved a species from one genus to anorther, or even created a new genus, I though I was expressing my understanding of relationships among species as clearly as I could. I think taxonomists of other groups are doing something similar.

    As the saying goes, Ceiling Cat may make a species, but genra, families, and all higher categories are made by fools like me.

  23. Biff
    Posted March 3, 2014 at 2:46 pm | Permalink

    The article says:

    “The finding above implies either that 1.) the ancestor of all multicellular animals had a nervous system, which was later lost in sponges and placozoans, or that 2.) the ancestor had the requisite genes for building nervous systems, but they were originally used for something else and later co-opted in Bilateria, Cnidaria, and Ctenophora to build neurons and other components of that system.”

    There is a third option: The nervous system evolved twice; once in Ctenophora and once in the common ancestor of Bilateria and Cnidaria.

    If the nervous system evolved more than once, it’s important to understand how and why it evolved in the first place. I think this is an interesting theory:

    http://rspb.royalsocietypublishing.org/content/early/2010/11/26/rspb.2010.2027.full.pdf

    More about how different they really are from us:

    “Molecular components of signaling pathways involved in cell growth and metabolism are missing in comb jellies and sponges. The Hox genes, key to early development and responsible for signaling where the brain, limbs or other body parts should form, are also absent in comb jellies and sponges. And comb jellies may be the only animals that lack both gene-regulating molecules called microRNAs as well as the molecular machinery to create them.

    Some species chase down prey and others cast out their tentacles like fishing nets. Yet neither team located genes encoding serotonin, dopamine and most other classic neurotransmitters that send messages between neurons in other animals. Absent too are proteins that, in other animals, guide the growth of neurons.

    Also not present in the comb jellies’ genomes were the usual lineup of genes associated with muscles in other animals. And the muscle genes that were present in comb jellies appeared to function in unusual ways. For instance, genes that in other animals form the middle tissue layer (from which muscles arise) turned on in nerve cells in comb jellies.”

    Link:
    https://www.sciencenews.org/article/evolutionary-enigmas?mode=pick&context=118

    And:

    “We find that the sets of neural components present in the genomes of Mnemiopsis and the sponge Amphimedon queenslandica are quite similar, suggesting that sponges have the necessary genetic machinery for a functioning nervous system but may have lost these cell types.”

    Link: http://www.sciencemag.org/content/342/6164/1242592.abstract


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