Nomenclature is for naming
August 7, 2017
Matt just sent me an email entitled Are there “basal” sauropodomorphs?, in which he pointed me to Mario Bronzati’s (2017) opinion piece in Palaeontologia Electronica, “Should the terms ‘basal taxon’ and ‘transitional taxon’ be extinguished from cladistic studies with extinct organisms?”
Here’s the reply I sent Matt, which at his suggestion I am posting here essentially unedited. Note well that this is not a response to the Bronzati paper, but my own quite separate thoughts on the same issue.
I’ve not read the article, but here’s my position on This Kind Of Thing. I remember back when we used to talk about primitive and advanced taxa. Then someone managed to impose their liberal guilt on the world of vertebrate palaeontology and we all had to change to basal and derived instead. That change bought us nothing; and whatever new terminology this paper is proposing will buy us nothing, either.
The bottom line is, we all know what a basal sauropodomorph is, and when we want to talk about them we need a term for them. For myself, I reject the cladistic-police orthodoxy that says we should avoid “prosauropod” because of their irrational fear of paraphyletic taxa. “Prosauropoda” is a perfectly well-boundaried group, and can be defined (if we want a definition) as those sauropodomorphs that are not sauropods. (Note: this is a definition using phylogenetic principles.)
Ultimately terminology is there as an aid for us to talk about things, not as a political tool. “Prosauropod”, “primitive sauropodomorph” and “basal sauropodomorphs” were all perfectly good terms that named the same important group; and each them has been knocked out, one by one, by well-meaning nomenclatural puritans who could have been using their abundant energy and creativity on solving some actual problems instead.
So: how d’ya like them apples?
Sauropod Vertebra Picture of the Week 
August 7, 2017 at 9:32 pm
Surely the problem here is not that we keep shifting names for the same group; it’s that the group is an uninformative wastebasket in the first place.
We all have this familiar hierarchy of taxa in our heads (birds above other dinosaurs, sauropods above other sauropodomorphs, tetrapods above other vertebrates, etc.), and we shouldn’t. We keep trying to fix this problem by switching our nomenclature, but then we keep subverting the new nomenclature to fit our comfortable old hierarchy. And we end up with bizarre usages, like calling Carnotaurus a “basal theropod” (even though it postdates the ancestor of the avian crown).
There’s potential for “basal” to be a useful term, but I’m in agreement with Bronzati — it’s abused so much, we might as well drop it.
August 7, 2017 at 9:35 pm
I don’t at all agree that it’s an “uninformative wastebasket”. It’s the group whose evolution explains how we got sauropods from basal dinosaurs. You don’t need an arbitrary hierarchy to recognise the reality of paraphyletic groups.
August 7, 2017 at 9:45 pm
You reactionary, you – next you’ll be crying, “Grade as well as clade!” and burning PAUP* in the streets!
I see the point of the purists; it becomes easy to talk about a paraphyletic group as though it is a lineage unto itself, instead of a basket of lineages surrounding one we think is special enough to be its own thing. It has led to much taxonomic nonsense. Besides, there’s no objective set of criteria for where to place the breaks (part of the critique of Linnaean taxonomy in general, I suppose) – what makes one clade worthy of recognition on its own, and another clade relegated to a group of other sequentially branching clades? The division of “crown” and “stem” based on which members happen to be extant at this instant in time has always seemed arbitrary to me.
But I also see your more practical point of view; we shouldn’t have to stop talking about lizards just because snakes make them paraphyletic, or about wasps because bees and ants make them paraphyletic. They share enough commonalities in morphology and ecology to be a sensible unit. Besides, the branching order of “basal” taxa is so often difficult to pin down that it becomes a taxonomic mess if strict monophyly is insisted upon.
Perhaps what we need is parallel taxonomies – a rigorous, strictly monophyletic taxonomy for the clado-nerds, and a more rough-and-ready, old-fashioned taxonomy for everyone else, that would be more stable (because it doesn’t matter which prosauropod lineage branched from the “main” sauropodomorph line first, they’re still prosauropods) and acknowledge morphological grade as a legitimate criterion for taxonomic separation.
August 7, 2017 at 10:16 pm
I have no problem thinking of snakes as a type of lizard, or ants and bees as types of wasp. (Or termites as a type of cockroach, fleas as a type of scorpionfly, and butterflies as a type of moth, while we’re at it.)
August 7, 2017 at 10:21 pm
@Mike Taylor, see, you’re still thinking in terms of this hierarchy where sauropods are the interesting thing and other sauropodomorphs are only important for what they tell us about sauropod evolution.
August 7, 2017 at 10:36 pm
Sure I am — because I’m a sauropod worker, working on sauropods. If I was a titanosaur worker, no doubt I’d think titanosaurs are the interesting thing and other sauropods are important for what they tell us about titanosaur evolution.
And every one of us (except Darren) is an X worker for some X, and reads and writes papers about Xs that employ assumptions and nomenclature that relate to Xs. When I write “tibia”, a fellow sauropod worker knows I mean the lower hindlimb bone of a tetrapod, not the fourth section of an insect leg. All our terminology is relative to what we’re working on.
August 8, 2017 at 2:18 am
…Yeah, about taxonomy and nomenclature…
Home
(My article mainly deals with species-level taxonomy, but I do hint at frustration about using terms like “primitive” and “advanced” especially when they aren’t appropriate in a cladistic context.)
Personally, I think the term “prosauropod” is fine as long as you mention that it is an informal term for the paraphyly of basal sauropodomorphs leading up to Sauropoda, and that includes a number of diverse clades (Guaibasauridae, Thecodontosauridae, Plateosauridae, Massospondylidae, etc.), not all of them close relatives (let alone putative ancestors) of true sauropods.
August 8, 2017 at 2:56 am
Really, the phrase “non-sauropod sauropodomorph” is no more objective than the phrase “basal sauropodomorph”, because it implies that sauropod sauropodomorphs are more important than other sauropodomorphs just as much as the latter phrase. Indeed, it’s actually worse, because it specifically spells out Sauropoda is the “special” group in question rather than just saying the taxon is a basal member of the clade Sauropodomorpha.
The problem is that in evolution we do get these radical shifts in ecology and functional morphology that cause the members of one morphofunctional group to product offshoots that are ecologically and evolutionarily nonequivalent to other members of that clade. The classic case of this is birds and non-avian dinosaurs. The factors that affect bird evolution are going to be very different from those that affect the vast majority of non-avian dinosaurs, because of things like powered flight affecting dispersal, behavior, and extinction risk. Does this mean that birds are somehow separate from dinosaurs? No. Does this mean birds should not be classified as dinosaurs? No. What it does mean is we need a term for all of the taxa that are not part of the clade that has undergone this paradigm shift, and still conforms to the ancestral morphology (even though they may be just as successful in their own right). Basal works while not violating cladistic methodology (i.e., it recognizes that while the term is useful for communication or gross characterization of morphology/ecology, it non-monophyletic).
The other issue is that some nodes are more important from an evolutionary standpoint, simply because of their greater effect on the history of life. For sauropodomorphs, there was this one group that because of several adaptations ended up being wildly successful and flourished for more than a hundred million years, whereas others…didn’t, for various reasons.
That said, I agree that defining crown and stem group based solely on extant taxa is really arbitrary. It could be useful if simple used in terms of things like the extant phylogenetic bracket, but you get a lot of cases where extant taxa do not really form a distinct group relative to extinct ones and you have different terms for each one. And yes, this does cause confusion. I have seen people think that because clade X is part of the stem group, they are only “distantly related” to the crown taxa and hence are completely different in biology, even if they missed being part of the crown group by bad luck less than a million years ago.
August 8, 2017 at 3:34 am
See, Mike, you’re using “basal” to mean, “The ones I’m not as much interested in.” This is exactly the problem — using what’s supposed to be a scientific term in a subjective way.
August 8, 2017 at 3:35 am
“Really, the phrase “non-sauropod sauropodomorph” is no more objective than the phrase “basal sauropodomorph””
They’re not synonymous terms! One is precise, the other is vague.
August 8, 2017 at 3:37 am
“The classic case of this is birds and non-avian dinosaur…. Basal works while not violating cladistic methodology.”
“Basal dinosaur” and “non-avian dinosaur” are very, very much not synonymous!
August 8, 2017 at 3:40 am
“That said, I agree that defining crown and stem group based solely on extant taxa is really arbitrary.”
No, it’s not! Whether something is extant or not is an objective, testable assertion (relative to a chosen time, at least). And that is *always* what crown/stem/total group has referred to, since those terms were coined.
“It could be useful if simple used in terms of things like the extant phylogenetic bracket”
Precisely why the terms are useful.
August 8, 2017 at 4:59 am
“See, Mike, you’re using “basal” to mean, “The ones I’m not as much interested in.” This is exactly the problem — using what’s supposed to be a scientific term in a subjective way.”
I don’t see it that way. I just see it as, “members of a clade who do not possess the synapomorphies of the morphologically distinct subclade”. I don’t care whether a taxon is a basal member of a group or not. There is no aspect of hierarchy or “this taxon is more interesting” in it.
“They’re not synonymous terms! One is precise, the other is vague.”
Precise versus vague has nothing to do with synonomy. And my point wasn’t even about that. My point was they both fall into the issue of putting one clade on a pedestal that you were mentioning before. In terms of being objective in referring to something, there is no difference because they are both saying “this taxon is a member of group x but not a member of subgroup y” (and imply that subgroup y is somehow more important according to the argument above).
““Basal dinosaur” and “non-avian dinosaur” are very, very much not synonymous!”
I did not say they were synonymous. I was using it as an example of why using exclusionary terms (e.g., basal X, paraphyletic groups) are useful for communicating information, as long as we keep in mind they are informal terms and do not equate that with monophyly.
August 8, 2017 at 5:12 am
“I don’t see it that way. I just see it as, “members of a clade who do not possess the synapomorphies of the morphologically distinct subclade”.”
*The* morphologically distinct subclade? Is there only one? People sure act like there is.
“And my point wasn’t even about that. My point was they both fall into the issue of putting one clade on a pedestal that you were mentioning before.”
I can see that point in cases where a particular paraphyletic group is repeatedly mentioned even when a slightly different group would be more precise. E.g., a lot of times people say “non-avian dinosaur” when they really mean “Mesozoic dinosaur” or “non-avialan dinosaur” or “fossil dinosaur” or “stem-avian”, etc., just because they’re used to hearing “non-avian dinosaur” over and over. And the main reason we hear it over and over in the first place is because Aves has a history of being placed on a pedestal.
But in many cases, “non-X Y” does seem to me to be the best way to delimit a particular paraphyletic group.
August 8, 2017 at 5:13 am
“No, it’s not! Whether something is extant or not is an objective, testable assertion (relative to a chosen time, at least). And that is *always* what crown/stem/total group has referred to, since those terms were coined.”
Relative to a certain time. That’s the problem. If a meteor were to crash into Australia today and wipe out all the monotremes, are multituberculates no longer mammals because they have no living forms bracketing them? Is Smilodon outside Felidae because it had the bad luck to get wiped out before the invention of the scientific method? What about the thylacine? If it turns out to be basal to Myrmecobiidae + Dasyuridae does that put it outside Dasyuromorphia? If it doesn’t, then there has to be some defined cutoff in time where the last common ancestor of a crown group “counts” these extinct taxa. Which would have to be arbitrary.
It is useful to say “these taxa are bracketed by living relatives, and these are not”. It is not when the taxonomic classification of a group changes based on this (and is based entirely on the subjective criterion of when one primate species happened to exist in time). It violates rule one of nomenclature: maintain nomenclatural stability as best as possible for ease of communication.
August 8, 2017 at 5:21 am
“*The* morphologically distinct subclade? Is there only one? People sure act like there is.”
No, but in many cases there is. In other cases there is not. See below.
“But in many cases, “non-X Y” does seem to me to be the best way to delimit a particular paraphyletic group.”
I disagree. I work in a group where there is a big polytomy within one group in particular (hereafter termed group Z) where the relationships between subgroups A, B, and C have been unresolved despite years of work and several phylogenetic analyses. There are also several taxa that branch off before the polytomy between the three. So to refer to them I can either say “non-A, non-B, non-C Z” every time I refer to it, or just say “basal Z” and get on with my day, because everyone still knows what I am talking about.
August 8, 2017 at 5:42 am
“Relative to a certain time. That’s the problem. If a meteor were to crash into Australia today and wipe out all the monotremes, are multituberculates no longer mammals because they have no living forms bracketing them?”
I think we’d have bigger problems to worry about at that point! (Also, plenty of zoos outside of Australia have echidnas.)
“Is Smilodon outside Felidae because it had the bad luck to get wiped out before the invention of the scientific method?”
Yes. We can’t observe its behavior. We don’t have any preserved specimens. Inferences about its soft anatomy, behavior, etc. must be made from extant felids and their extant sister group (Prionodon). And it’s not an original member of Felidae. I can’t think of any good reason not to place it outside.
“What about the thylacine?”
Now this is a good edge case. We have film and preserved specimens. And there is even a remote chance it is still extant. (Very, very remote.)
The PhyloCode has some provisions around this. Basically, by default “extant” means “extant on publication date”. But if you want it to mean something else, you can specify that: https://www.ohio.edu/phylocode/art9.html#art9
“If it turns out to be basal to Myrmecobiidae + Dasyuridae does that put it outside Dasyuromorphia?”
How is Dasyuromorphia defined? If it’s a simple node-based definition, then it depends on whether Thylacinus cynocephalus was included as a specifier. If it’s a branch-modified node-based definition, then it depends on the definition’s provisions for being considered “extant”. (If none provided, then presumably it would be considered extinct.)
“It violates rule one of nomenclature: maintain nomenclatural stability as best as possible for ease of communication.”
Absent complete knowledge, nomenclature *shouldn’t* be entirely stable. The best we can do is to make the definitions relatively stable, so that we have some landmarks in our ever-shifting trees.
August 8, 2017 at 5:46 am
If they branch off before the A-B-C polytomy, why not just name the A + B + C clade?
August 8, 2017 at 12:09 pm
I dunno, shouldn’t you maybe read the paper before you attack it? Dismissing it as the work as that of a “well-meaning nomenclatural puritan” without actually reading the paper seems like pretty poor practice to me.
August 8, 2017 at 12:12 pm
Anonymous, it’s pretty clear that I am not attacking the paper. I am stating my own position on This Kind Of Thing, inspired by but not in response to the existence of the new PE paper.
August 8, 2017 at 12:31 pm
Seems pretty dismissive of a paper you haven’t read.
August 8, 2017 at 4:05 pm
It’s a short paper, Mike!
August 8, 2017 at 4:39 pm
I’m not going to read it as background for this post, which (I repeat myself) is “my position on This Kind Of Thing”. If only I’d thought to mention that right at the very start of the post.
August 8, 2017 at 4:48 pm
It’s clear that you are disparaging this paper, essentially saying that it is pointless, as shown by the sentence I quoted above which explicitly refers to this paper. Maybe Bronzati addresses all of the issues you raise – maybe he doesn’t. But to dismiss the paper without even reading it is disappointing. Especially as Bronzati is a student.
August 8, 2017 at 5:42 pm
Anonymous, you seem extremely certain that you know better than I do what the purpose of my post was. I tell you once more that this post is “my position on This Kind Of Thing”. If you want to continue this line of argument, please do it by email rather than further clogging up the comments.
August 8, 2017 at 6:05 pm
I apologise – I accept that it was not your intention to denigrate Bronzati’s paper in particular, rather to make a general point. But regardless of your intention, you should be aware that it appears to the reader that you are publicly dismissing a paper you couldn’t even be bothered to read.
That’s it, I won’t bother you any longer.
August 8, 2017 at 8:08 pm
Thanks, Anonymous. I happily accept your apology. I will tweak the wording of the post to make it even more explicit that I am laying out my own position rather than critiquing Bronzati’s.