Cavlier - Smith

[Placozoa]

Catalogue of life 2021 edition just started working for me today, and I couldnt help noticing that many of the new and strange taxonomic changes Cavalier-Smith has been proposing seem to have been accepted. I find this mind boggling, an advance in science that we havent seen since Newton. It was obvious that the classical system was complete garbage, and the newer version with ciliates, flaggelates, algae, fungi, sporozoa, and amoeba was hardly any better, but wow! I am just stunned by the advances in microbiology lately. How does everyone else feel about this? Has anyone noticed?

[Bruce Taylor]

I always read Cavalier-Smith with interest, and admire the huge contributions he has made. However, I have a lot of misgivings about his high-level classification scheme. I strongly prefer the unranked system proposed by the International Society of Protistologists (current version: https://onlinelibrary.wiley.com/doi/ful ... /jeu.12691). Here's an article about the current states of the eukaryote tree, by some of the signatories to the ISOP consensus: https://www.cell.com/trends/ecology-evo ... 19)30257-5

And a current tree, from that article:

Eukaryote Tree.JPG (89.8 KiB) Viewed 4813 times

Cavalier-Smith's scheme is an attempt to reconcile traditional ranked taxonomy with current phylogenetics...but the result, to my mind, is a mishmash of the old and the new, unsatisfactory on both counts.

Take his Kingdom Protozoa. It is a paraphyletic group, deliberately excluding animals and fungi, both of which, in terms of ancestry and evolution, should branch within it. His reasons for carving out Animalia and Fungi as separate "kingdoms" are pragmatic, not phylogenetic. It preserves continuity with old and familiar models used in schools and textbooks...and I can certainly see advantages to that. For one thing, it makes his system an attractive framework for general-purpose databases like CoL and WoRMS. However, it means that our little one-celled sisters, the choanoflagellates, are in an entirely separate kingdom, far from their nearest relatives, the animals. And the fungus-cousins Fonticulida and Nucleariida are waaaay over in Protozoa, instead of snuggling up to the mushrooms and yeast, where they belong. This way of organizing the taxa obscures real evolutionary relationships.

But at least his Kingdom Protozoa preserves the colloquial sense of "protozoa" as single-celled heterotrophs, right? Well, no. While Cavalier-Smith can accept paraphyletic groups, he draws the line at polyphyletic ones. So, the ciliates, dinoflagellates, rhizarian amoeboids and heterokonts are (justifiably) put aside in a group of their own, to which C-S gives his own idiosyncratic name: Kingdom Chromista. The word "Chromista" (derived from the Greek "chroma," or colour) reflects his own hypothesis that all members of the group share an ancestor that possessed a plastid containing photosynthetic pigments. Recent evidence does not seem to support this, but unfortunately it is baked into his name for the group. And to add another twist, his Kingdom Chromista...is likely polyphyletic! The Cryptista (Cryptomonas, etc., which Cavalier-Smith puts in Chromista, under Hacrobia) appear to be more closely related to the plants, and green and red algae.

But to return to your real point...yes, great strides are being made in figuring out the eukaryotic tree! Cavalier-Smith has been a major player in this revolution, but there are many others, notably Alastair Simpson, Patrick Keeling, Fabien Burki, Matt Brown...and, among the younger ones, Yana Eglit, Gordon Lax, etc. The restructuring of the tree hasn't attracted a lot of attention from the popular science press (except when something sensational happens, like the recent discovery that Hemimastigophora form a whole new superkingdom!), but it is a huge story.

[Challenger007]

Catalogue of life 2021 edition just started working for me today, and I couldnt help noticing that many of the new and strange taxonomic changes Cavalier-Smith has been proposing seem to have been accepted. I find this mind boggling, an advance in science that we havent seen since Newton. It was obvious that the classical system was complete garbage, and the newer version with ciliates, flaggelates, algae, fungi, sporozoa, and amoeba was hardly any better, but wow! I am just stunned by the advances in microbiology lately. How does everyone else feel about this? Has anyone noticed?

Well, you have to be completely blind in order not to notice the huge progress in science. And in microbiology, and in the field of space exploration, and in the development of technology. After all, this is all a scientific base, a huge amount of studied theory and out-of-the-box thinking in order to discover something new.

[charlie g]

Thanks 'placozoa' for this posting...I enjoy the arguments Dr. Cavalier-Smith makes for our tree of life. Current ultra-structure studies, current (gasp!) ribosomal DNA sequence studies contribute now to how we go about naturally relating our worlds organisms. It is a robust and vastly detailed , and quite evolving area of life studies, this good doctor contributes to.

Just google: Cavalier-Smith 2015 taxonomy, you get a sense of how dominant microscopic life forms are on our planet.

BTW, 'placozoa'..when ever I have a chance to view a large saltwater aquarium...I always look on the glass walls for a placozoan. charlie guevara

[Placozoa]

I just recently got back to this. I have been very busy dialling in on current research in taxonomy and phylogenetic studies. Just finished today.

I am new to microbiology, but I certainly will pay more attention at the aquarium from now on. We have a nice one here, its not big but it is interactive. I have not been to it since CoVID and I have to admit, I miss it.

I just finished going over Adl, et. al. (2018). This was a large group of microbiologists, 50 or so, that went over the Cavalier-Smith stuff (and everything else) with a fine tooth comb. Some stuff did not hold up (Chromista was messy like Bruce said, and viridiplantae was no good cause they arent all green, etc.) but a lot of it is highly successful (and being integrated into "mainstream"). I am interested in ecological microbiology (local especially), and since the vast majority of microbiology focuses on medical, it requires a lot of sifting to avoid information overload. I drew up a phylogenetic tree with all the plants from my area a year ago, and over the last month I added the microbiology that supports them to it. I am starting to get a handle on it, but greatly appreciate any good leads.

It has really sunk in how easy it is to identify things under the microscope incorrectly at genus/species level, but I think sorting critters at a higher level (colpodea for example) should not be impossible without DIC on my scope.

Edit: That was funny, bruce. One of your two links was the exact paper I just described, the one I just finished. I checked your links after posting this.

[Bruce Taylor]

Edit: That was funny, bruce. One of your two links was the exact paper I just described, the one I just finished. I checked your links after posting this.

The list of authors in Adl et al. (in its 3 incarnations, since 2005) is basically a list of the major players in eukaryotic deep phylogeny...with one notable absence: Cavalier-Smith! He has been harshly critical of the ISOP scheme, which he dismisses as a "cladification". In the latest version of Adl et al. they take a swipe at his classification, as it appeared in Ruggiero et al., 2015: "This effort may be reasonable in their classification of the prokaryotes, but the eukaryote section does not pass standards of modern biology. Specifically, it is their refusal to use monophyly as a guiding principle, but to argue to retain 'ancestral (paraphyletic) taxa when it seemed beneficial to do so' instead, even where monophyletic clades are already established. Their insistence on using a hodge-podge of names that do not have nomenclatural priority and poorly describe the taxa included, further reduces its usefulness."

My sympathies lie with ISOP, mainly, though I do see why the big databases opted to follow Ruggiero et al., which keeps the good old "plants n' animals" at a status equal to that of the protistan groups. One of the odder consequences of this choice is that the important and robustly supported supergroup Opisthokonta--which Cavalier-Smith himself proposed in its current form--is entirely eclipsed, depriving young biologists of a clear view of the way animals nest within the eukaryote tree.

[actinophrys]

His reasons for carving out Animalia and Fungi as separate "kingdoms" are pragmatic, not phylogenetic. It preserves continuity with old and familiar models used in schools and textbooks...and I can certainly see advantages to that. For one thing, it makes his system an attractive framework for general-purpose databases like CoL and WoRMS. However, it means that our little one-celled sisters, the choanoflagellates, are in an entirely separate kingdom, far from their nearest relatives, the animals. And the fungus-cousins Fonticulida and Nucleariida are waaaay over in Protozoa, instead of snuggling up to the mushrooms and yeast, where they belong. This way of organizing the taxa obscures real evolutionary relationships.

I mean, this is a very cladistics way of looking at it. To traditional evolutionary taxonomists like Cavalier-Smith, the point of these divisions is not just pragmatism at the expense of illustrating the evolution, but a part of illustrating it. Because evolution is not just a question of what diverged off what, but how they changed and what the significance of it is.

Very often it becomes difficult to discuss groups without resorting to paraphyletic groups at least informally...you need only look at the continued use of terms like fish, non-avian dinosaur, or green algae. And sometimes that problem applies even in a formal taxonomic context. For instance in some of the discussions of the Colpodea, a class of ciliates, I have seen the use of paraphyletic Colpoda argued for as a way to better represent the reality. Because sure, this one species might be closer to Maryna or Tillina in terms of evolutionary divergence, but those have changed in morphological and ecologically significant ways, and they haven't. Or at the very least we should wait to figure out how they have...and I think you will agree some of the genera that result seem to differ in ways that are very hard to understand any significance of, save the desire for genera to be clades.

Cavalier-Smith's kingdoms are meant to be the same idea writ large. The choanoflagellates are our sister group, but they remain little single-celled or colonial flagellates that feed by phagocytosis, much like many others...while the sponges are something functionally very different, with many cells, differentiated tissues, and an internal chamber for food collection you won't see in other groups. The argument goes it is easier to understand the evolution of the groups if you acknowledge that sort of major change.

Needless to say there are arguments against that too. The one that speaks loudest to me is that this is a subjective call where to draw these lines, so that biologists can argue endlessly over where to put them, without any real way to decide and with no real meaning in terms of underlying ideas. It is not hard to see why so many have gotten sick of them. In my opinion, though, which taxa you actually use is always a subjective call anyway...by not deciding, you only end up with a multitude of names someone needs to be ready to know. Where are we on the tree you just showed? I recognize Opisthokonta, but now some other papers will only say Obazoa, so I need to know two because you never know who cares about apusomonads and who doesn't.

Whereas everyone knows not to skip groups like Animalia for weirder ones like Bilateria or Deuterostomia, as something we have generally agreed is a taxon that tells you a lot about the organisms in question, encoded in its rank of kingdom. In other words, I don't think it is a coincidence that Cavalier-Smith's system works better for things like CoL and WoRMS...and for the record, what I have chosen to use on my webpage too. It is because it is based on a different philosophy, that sacrifices strict objectivity and dedication to representing absolute positions on the evolutionary tree for general utility and describing more about the organisms in question. I know it's not in vogue, but don't agree that it results in an unsatisfactory mismash at all. I think it's reasonably good as a traditional scheme, better than anyone else has tried for certain.

Notable exception: the name Protozoa does seem to me a really unfortunate choice for a group that does not contain the ciliates (which were the most obvious under the microscope), foraminiferans (which were the most important as fossils), or apicomplexans (which were the most important as pathogens). Especially since he had another name kicking around, Archezoa, that better matches the idea of "eukaryotes not diversified into other groups yet". Chromista...well, it's a name he introduced a long time ago, and I can hardly fault him for others not picking it up, especially when the alternatives have been things like SAR or now TSAR. That he includes Cryptista and Haptista is of course his own guess, not well-supported (although placing Cryptista next to plants honestly seems very questionable too). But see, that's a nice thing about traditional systematics. If he's wrong, the core of the group still gets to be called Chromista, instead of everyone now learning a whole new kindgom for all the others.

My thoughts anyway. Again, I know a lot of real biologists would scowl at me for them, and I do understand...our priorities simply aren't quite the same.

[Bruce Taylor]

Thanks for some great comments, Josh! I don't think we're that far apart. I do recognize that taxonomy and phylogeny serve different ends, and can see that Adl et al. might make a poor framework for CoL, or a site like yours.

In fact, I don't object to paraphyletic grades...though I do have a philosophical objection to justifying them as "evolutionary taxonomy". When the taxonomist draws a circle around the "fish" and excludes anything downstream from Devonian amphibians (conventionally, the Icthyostegalia) it highlights an evolutionary innovation that sets our group apart: colonization of land. However, "evolution" also gives us grounds for drawing the circles differently, should we choose to do that. The ancestor we share with a mackerel had lungs. Our branch of the tree, the lobe-finned fishes and tetrapods, conserved these as air-breathing structures, while the ray-finned fishes went on to evolve their fabulous swim bladders (which enabled their remarkable diversification). If it served our purposes, we could erect an evolutionary grade consisting of "fish that did not evolve bladders", which would include all fish and tetrapods, but exclude the Actinopterygii. We don't do it, because evolution of bladders seems less momentous and consequential than adapation to life on land, but of course, that is a human judgement that has less to do with the evolutionary process than with "things people consider significant."

That brings me to the thing that makes me most uncomfortable, which is that evolutionary gradism subtly implies that those fish which "kept on being fish" somehow stopped evolving, or evolved "less"...when, of course, they radiated and diversified, just as members of our branch did, and are every bit as highly derived from our common ancestor as we are. It misrepresents evolution itself. To my mind, this encourages the kind of thinking that leads questioners on Quora to ask (over and over again!) why humans "evolved" and chimpanzees did not. So, when the traditional taxonomist asks, as R.K. Brummit famously did in the pages of Taxon, "Am I a Bony Fish?", I enthusiastically say, "Yes! Yes, you are a bony fish!" and have always encouraged my kids to do the same.

With microbial eukaryotes--which is to say, most eukaryote diversity--we are particularly likely to overlook important adaptations (biochemical innovations, for instance), and to overvalue trivial ones (differences in lorica shapes in tintinnids). Crucial secretory innovations won't necessarily leave changes in body plan, yet may arise to meet "significant" adaptive challenges that happen to be invisible to us, simply because we still know so little about microbial ecology. Rooting classification strictly in phylogenetics has the proven advantage of not locking organisms into categories based on biological processes we don't fully understand (yet).

When we segregate metazoans from choanoflagellates on the grounds of multicellularity we are imposing an arbitrary criterion on the group (however useful that may be for pedagogy, etc.). The closer we look, the blurrier the line becomes. Choanoflagellates do form colonies, and their cell signaling is of considerable interest for those studying the origins of animal multicellularity. The feeding behaviour of sponge choanocytes is actually not very different from the feeding behaviour of free-living choanoflagellates. Of course, sponges have specialized tissues, such as the amoebocytes that lurk behind the collared cells. That draws a hard line between the groups...or so we thought, until recently! New work shows that free-living choanos can enter an amoeboid phase (switched on by entrapment or compression), so that particular difference between the groups no longer exists. This reinforces the notion that the embryological differentiation of tissues in metazoans actually recapitulates serial life phases in a unicellular ancestor. That's pretty interesting, and if it turns out to be true I wouldn't want those important evolutionary relationships to be pushed into the background, in the name of "evolutionary" taxonomy.

[actinophrys]

So, when the traditional taxonomist asks, as R.K. Brummit famously did in the pages of Taxon, "Am I a Bony Fish?", I enthusiastically say, "Yes! Yes, you are a bony fish!" and have always encouraged my kids to do the same.

Well, see, I would differ on that. In this case I am glad to see classes like Actinopterygii used in formal classification...and generally would avoid paraphyletic groups whenever it doesn't ruin everything to do. But we already have a word for fish and all their descendants, namely vertebrates...or, you know, craniates if the hagfish turn out to be basal, as per what I just said about multiplying terms. Meanwhile, although we could divide the same evolutionary tree differently, it turns out the concept of vertebrates that still have gills and fins is obviously one people have found tremendously useful. Not just in casual speech but in scientific contexts like ecology, where the functional similarities are important. It's good to have a word for them. Thinking of humans as specialized land fish comes with insights, but calling whales "marine fish" obscures their nature instead.

And of course when it comes down to it, any line is going to be separating very similar things. Taxonomists are sort of lucky the common ancestors are all dead, because if we could only see what was happening at the time, we would always be separating parents from children or siblings from siblings. That's just the nature of classifying what is really a much more continuous reality. There is no real line between the desert and savanna, but we pick something arbitrary because the endpoints are so different from one another. And when you hit something in the middle, like biologists do with members of ring species, you just have to shrug and say that our models only go so far.

Personally I haven't much felt the ill consequence you bring up, that this hides groups' real diversity. The incredible success and diverse adaptations of the teleost fish especially has always stood out to me, and that lungs predated swim bladders seems to me surprising either way, simply because of the story it implies. I grew up with books that called the choanoflagellates the closest protozoan relatives of animals, and never felt their relationship and significance any more hidden by that than listing them both in clades like Opisthokonta. Of course the changes that made multicellular animals possible had to be based on things there, new genetic innovations and proteins and cellular changes that made the subsequent structural changes possible.

I mean, that could just me. I'm not the sort to wonder why chimpanzees stopped evolving. I am one to wonder why some groups have changed so much more than others...because I think the answers are significant for understanding their place in ecology and the evolutionary history of the world. That does involve making judgments, calling some evolutionary changes more important than others. But the truth is some mutations are neutral or relatively so, and some open up whole new possibilities for a group to diversify into, and trying to judge which is which is I think at the heart of understanding the living world in as more than just a catalogue of names, no matter what standards you pick for those.

[Bruce Taylor]

Well, there's a lot of good sense in what you're saying, Josh. We seem to be on different sides of the "bony fish" question, but that's OK. The consequences of choosing one classification scheme over another are not particularly dire.

One of the specialized land fish I raised is currently finishing his Ph.D. in marine biology, and, like most working biologists, doesn't have a lot of interest in taxonomy. He feeds Rhodomonas to his sea urchin larvae, and keeps referring to them as "brown algae". I ask him why he calls them that, and he shrugs. "The water in our cultures is kind of brown."

[Placozoa]

I have just learned microbiology so these issues you guys mention hit me particularly hard. I did not bother learning Linnaeus (what for? Its wrong, and learning microbiology is a massive undertaking already without adding more to it). For this reason I actually started with Cavalier-Smith. It was insanely confusing, I cant lie. I drew up several phylogenic trees, finally got it nailed down, and once I started using it found it to be not particularly useful. I drew up some zoomed in additions for alveolata and stramenopiles, and I could get by with it then.

After going through Adl, et. al (2005) and Adl, et al (2018) I redid my phylogenic tree, focusing on soil organisms, and its crystal clear now and everything makes sense. To be fair, really nothing much has changed, there is still a divergent line through SAR leading to the chromista, and it was Cavalier-Smith that made me me aware such a thing even existed. Ultimately a taxonomic tree is far simpler than a phylogenic tree but only provides limited insight in how it all fits together. I have seen recent papers that still treat flaggelates as if they were as real as ciliophores and not a colossal failure like algae, and it severely weakened the paper, leading to mistakes all over the place. Thats what a sloppy taxonomy can do.

That said, Paddy was right when he said that each species carries its data with it, and the taxonomy is an evolving thing and having multiple active taxonomic systems is not a problem. Calling one species two things (testate amoeba, Im looking at you), having two names for the same species, having names for species that dont exist, these are the real problems.

I think that microbiology is a bit like quantum mechanics. There are multi-unicelled creatures (films and slimes), there are symbionts all over the place, there are numerous creatures whose lifecycle takes them through forms where they seem to be something completely different. The world of the small is not just a scaled down version of the macroworld, and classical ideas will not always work there.