One of the recurrent topics of this blog is the controversy around the acceptance of paraphyletic taxa. Although I have become a bit jaded over the years, my original stance was, and to a certain degree still is, that I am trying to understand the reasoning offered by colleagues who think that paraphyletic taxa are acceptable or even unavoidable. Because, who knows?, there may be a novel argument that shows cladism to be misguided after all, and I want to keep an open mind.
Sadly, however, it is mostly the same few talking points that lost the discussion in the 1970s and 1980s, resurfacing again and again. It is rare, although not unheard of, that a new and truly interesting argument is presented.
Today's candidate paper freshly online is
Baranow et al. 2017. Brasolia, a new genus highlighted from Sobralia (Orchidaceae). Plant Systematics and Evolution. DOI 10.1007/s00606-017-1413-zThe authors present phylogenetic analyses and change the classification of the titular orchid genus. The only point of interest for present purposes is that they argue for the recognition of Sobralia section Sobralia at the genus level despite that group being paraphyletic, and in what follows I do not want to imply any criticism of any other part of the publication or of the hard work the authors have put into their study. It is only the theory of classification that I like to hash out.
The argumentation in favour of paraphyletic taxa runs across three paragraphs in the discussion section. Let's see if I can learn something new!
In the light of phylogenetic outcomes, the proposed taxon is paraphyletic, which means that its species have a common ancestor, but the taxon does not include all its descendants (e.g., Elleanthus).Polyphyletic taxa also have a common ancestor, so by the reasoning implied here one could justify any classification whatsoever. I am consequently unsure what the point of this first sentence is.
Monophyly in its broader definition describes groups with a common ancestry, including both paraphyletic and monophyletic groups (sensu Hennig 1950); therefore, Hörandl and Stuessy (2010) advocate returning to this broader definition of monophyly and, adopting Ashlock's term, holophyly for monophyly s.str.Again I am afraid I must be missing the point. The controversy is really about whether we should consistently classify by relatedness or not. I don't mean to be uncharitable, but this could potentially be taken to mean the authors hope that recognising non-monophyletic taxa would become more palatable to mainstream systematists if one could hoodwink them into forgetting what monophyletic means. It would then be equivalent to hoping that your child will accept a mountain hike instead of the promised trip to the beach if you just said "mountains are also a kind of beach" with enough conviction. Nice try, but there will still be no swimming in the ocean, and little Tommy sees right through it.
Paraphyly is a natural transition stage in the evolution of taxa (Hörandl and Stuessy 2010). According to Brummitt (2002), paraphyletic taxa are ''products of the evolutionary process, which is left behind as evolution moves on to a new level of organization.''The logic of these quotations appears to be as follows: "We really, really want to recognise paraphyletic taxa. So we draw a paraphyletic taxon onto the phylogenetic tree. Look, cladist, there is a paraphyletic taxon in the evolutionary process! Why are you so unreasonable not to accept it?" Unfortunately, circular reasoning does not become more convincing just because it has been published somewhere and can now be cited.
To clarify, there are no paraphyletic taxa out there in nature; there is only a tree of life, and phylogenetic systematists consistently circumscribe taxa on that tree to be monophyletic, while 'evolutionary' taxonomists circumscribe some taxa on that tree to be paraphyletic.
We realize that this is in conflict with commonly accepted phylogenetic methods which declare that monophyly s.str. should be the only criterion for grouping organisms.A "phylogenetic method" is what produced the orchid phylogeny, so I assume what is meant here is "approach to classification". But whatever, that is not the point, so onwards.
However, a somewhat analogical situation has been recognized within Coelogyne (Gravendeel et al. 2001). In this case, the authors interpreted the morphology of the studied species as not corresponding to the cladograms, probably as a result of convergent evolution and they decided to maintain polyphyletic Coelogyne. Kolanowska and Szlachetko (2016) postulate to maintain paraphyletic Odontoglossum.This appears to be an instance of the argumentum ad populum, and not even very much populum at that. Consider: is it a good idea to shoot a stapler into your own foot? Okay, so there will have been at least two people in the history of humanity who have done that, so you could now cite them for support. But does that make shooting a stapler into your foot any more sensible? Exactly; a better argument is needed here.
Also, as I only realised some time after first drafting this, the senior author of the present paper is the same as in one of those two references. So this is apparently also an instance of the rarely seen ipse dixit. (It is, of course, valid to cite one's own prior research results, but in this case we are dealing not with an empirical question but simply with the argument that an action is acceptable because it is not unprecedented.)
Recognition of distinctive characters which have evolved in a group is essential for an understanding its evolution (Brummitt 2006).Quite the opposite, in my eyes: having an accurate classification is essential for understanding evolution, because paraphyletic taxa mislead us about relationships. In the present case, treating Elleanthus as a subgroup of Sobralia would (correctly) show that Elleanthus evolved out of Sobralia, whereas treating Sobralia and Elleanthus as separate genera implies (wrongly) that they are evolutionarily distinct units, side by side.
This point of view is shared by numerous other authors (Sosef 1997; Dias et al. 2005; Nordal and Stedje 2005) who state that traditional classification is the optimal tool for cataloging biodiversity and requires recognition of paraphyletic taxa.This reads like more argumentum ad populum, and sadly it is left unmentioned why paraphyletic taxa are supposedly required.
We decided to follow the Darwinian (evolutionary) classification, which requires consideration of two criteria: similarity and common descent.Leaving aside the obvious argument from name-checking here, which is exactly as relevant as using Newton to reject Einstein (and for the same reasons), the problem remains that trying to classify by two criteria at the same time will lead to a useless classification that is not reliably reflecting either.
Assume I have never heard of Sobralia before, and then it is mentioned to me for the first time. Given a phylogenetic classification, I know that it constitutes a natural group whose members are each other's closest relatives. Given a classification as argued for in the present paper, it could be a natural group... but it could also be a group defined by similarity that includes species more closely related to another genus than to any other species of Sobralia. I just won't know.
The approach will allow us to propose a classification based on the phylogenetic relationships, but at the same time it will be practical--with clearly defined and recognizable units.No, sorry to say so, but it quite simply will not. First, it will not be based on phylogenetic relationships, because in one crucial instance phylogenetic relationships will be ignored. Second, and again, it will not be practical, because if two criteria are mixed the end user cannot know without going back to the original publications whether a given group was circumscribed based on relatedness or based on 'similarity', see above.
Now obviously I understand that this is not a theory paper arguing for a wholesale shift in our practice of classification. What is more, I know we cannot expect all solutions to be easy or all groups immediately to be circumscribed as monophyletic the moment somebody looks at them. I can happily accept a paper concluding "we know this group is probably paraphyletic, but for the moment we don't have a better solution, let's wait until more data are in", or "the group is clearly polyphyletic, but at this moment we do not want to make hasty taxonomic changes", or something along those lines.
But the three paragraphs quoted above were specifically meant to justify the ultimate recognition of paraphyletic genera, so one would expect to find a convincing justification. Sadly I, personally, have to admit to being anti-convinced by this paper, which as previously mentioned I take to mean an argument had the effect of making me even more convinced of the idea it was meant to refute, in this case classification by relatedness.
"I am trying to understand the reasoning offered by colleagues who think that paraphyletic taxa are acceptable or even unavoidable" Seriously, you think you are trying? I see only confirmation biases, not open mind as you claim. See below.
ReplyDelete"I don't mean to be uncharitable, but this could potentially be taken to mean the authors hope that recognising non-monophyletic taxa would become more palatable to mainstream systematists if one could hoodwink them into forgetting what monophyletic means." Irony? Isn't it what has been historically done by cladists? Surprisingly, it worked!
"To clarify, there are no paraphyletic taxa out there in nature; there is only a tree of life"
"having an accurate classification is essential for understanding evolution, because paraphyletic taxa mislead us about relationships."
These two sentences are opposite. If there is only a tree of life and no taxa out there in nature, then any classification is artificial, so any classification is valid, and no classification is more "accurate" than any other. You, as a cladist, don't want a classification, you want the tree and only the tree. So why not allowing those who want a classification reflecting similarity to have one, besides the tree?
"treating Sobralia and Elleanthus as separate genera implies (wrongly) that they are evolutionarily distinct units, side by side." Yes, they are. Treating them separately means that Elleanthus has become radically different from its Sobralia ancestors. You want to read a classification as a tree, and then you complain it does not work. Yes, a classification is not a tree. It is just a misuse of a classification. Use a tree if you want to know about relatedness.
"the problem remains that trying to classify by two criteria at the same time will lead to a useless classification that is not reliably reflecting either."
This is obviously wrong, otherwise cluster analysis would not exist as a part of data science. Maybe you should seek a MOOC about data mining or something like that to learn a non-biological point of view about classifications and clustering.
"Given a classification as argued for in the present paper, it could be a natural group... but it could also be a group defined by similarity that includes species more closely related to another genus than to any other species of Sobralia. I just won't know." There is no dilemma as you argue: the group is ALWAYS defined by similarity in evolutionary taxonomy and ALWAYS constrained to include the most recent common ancestor of all its members, so both criteria are ALWAYS respected. You just cannot imagine that holophyly is not a criterion at all to establish our classification. Of course, taxa are randomly holophyletic or paraphyletic and we just don't care about it. You care? Right, use the tree, not the classification.
Hey, long time no see.
DeleteSeriously, you think you are trying?
I did not say "I am super-eager to be convinced", especially after having seen so many bad arguments over time. But yes, I try to understand the reasoning.
Isn't it what has been historically done by cladists?
As I have written before, I do not have the feeling that the term was considered all that important before Hennig published his definitions. I don't think I would care either if you could go back in time and convince Hennig to use holophyletic, but now the terms are well-established in Hennig's sense, and trying to change them again will only cause disruption.
"To clarify, there are no paraphyletic taxa out there in nature; there is only a tree of life"
"having an accurate classification is essential for understanding evolution, because paraphyletic taxa mislead us about relationships."
These two sentences are opposite.
Not at all. What I am saying in the first is that taxonomists define taxa, so one cannot simply assume one's preferred circumscription as natural and argue from there; whether it is natural is the question, and thus has to be demonstrated with more than mere assertion. The second is entirely compatible with that. As an aside, and as mentioned before, I believe that clades have an extremely strong argument for being natural units, because they are what a species turns into when it diversifies; the clade IS the ancestral species plus time. Consequently I hold that one cannot coherently accept species as natural units without accepting clades as the same, or be a cladist while rejecting the existence of species.
you want the tree and only the tree (etc.)
You could just as well say that a librarian wants the books and only the books, but no, it is useful to have a term like "novels" or "travel guides", and thus the librarian would not hand the classification over to those who want a category as useful as "books with blue covers".
So why not allowing those who want a classification reflecting similarity to have one, besides the tree?
I myself constantly use similarity based classifications, for example when I say "tree".
This is obviously wrong, otherwise cluster analysis would not exist as a part of data science.
You conflate analysis and classification.
the group is ALWAYS defined by similarity in evolutionary taxonomy and ALWAYS constrained to include the most recent common ancestor of all its members, so both criteria are ALWAYS respected.
I have explained in the original post what the issue is. The mixture of two criteria means the end user cannot know what a taxon name means, and the classification has no use case beyond satisfying 'evolutionary' taxonomists. The best argument that can be made is that of tradition or stability, and I see the point from an archivist's or data manager's perspective, but it has never convinced me from a scientific perspective because it is anathema to what science is about.
"Hey, long time no see." I have to say I regularly read your blog, it's interesting when it's not about cladist catechism.
Delete"whether it is natural is the question, and thus has to be demonstrated with more than mere assertion." I agree, but your definition of natural = holophyletic, so your reasoning is circular.
"the clade IS the ancestral species plus time" I strongly disagree with this equation for several reasons. Firstly, an ancestral species can give birth to a descendent species without changing at all, or so slightly that recognizing the result as a different species would be ridiculous. Secondly, your time dimension is the same in all branches, but evolution can have very very different speeds in the distinct branches.
"I believe that clades have an extremely strong argument for being natural units, because they are what a species turns into when it diversifies" I believe that grades have an extremely strong argument for being natural units, because they reflect the real tempo of evolution.
"You could just as well say that a librarian wants the books and only the books, but no, it is useful to have a term like "novels" or "travel guides" (etc.)" I agree, this why I think that clades should have names. The classification of "books with blue covers" is useless of course, this does not mean that ONLY ONE is useful.
"I myself constantly use similarity based classifications, for example when I say "tree"." Great. Now, what about having a systematized and latinized one? Why a similarity based classification would be OK if it is incomplete and the names are in English, and evil if it is complete and the names are in Latin.
"You conflate analysis and classification." Classification is a synthetic representation of the results of the analysis. Say the analysis of morphological similarity or the analysis of the different speeds of evolution. Why would be the analyses OK, and then a classification representing the results not OK?
"I have explained in the original post what the issue is. The mixture of two criteria means the end user cannot know what a taxon name means" I explained you were searching an information we don't care, so you don't find it. What is surprising? It is a misuse, not a good use of our classification. Read me again. All our taxa respect all our criteria, not randomly some.
"the classification has no use case beyond satisfying 'evolutionary' taxonomists." It is perfectly subjective to think that having boxes with only similar plants and animals is not useful, and I really cannot understand your opinion. Nearly all classifications in all sciences try to achieve such a goal. Besides, I am not a nominalist, so like you I am more interested in the scientific meaning: taxa are natural grades. Evolution slows down, then accelerates, then slows down again, etc. This dynamic is real.
No, I explain why I think that clades are natural groups, and there is simply no doubt on either side that common descent produces nested clades; I do not see how it produces objectively delimited paraphyla, given the graduality of evolution, but we had that discussion before.
Deletean ancestral species can give birth to a descendent species without changing at all, or so slightly that recognizing the result as a different species would be ridiculous.
The ancestral species has still turned into both descendant lineages. I know you try to treat everything like an individual animal birthing a baby or laying an egg, but that ignores the massive differences between those two scenarios.
this does not mean that ONLY ONE is useful, etc.
What is the problem? To repeat: I constantly use many similarity-based classifications. I don't want to do away with terms like herbivore, population, lichen, or rheophyte (note that all these are also based on single criteria, which is what makes them informative). You, on the other hand, want to destroy the only classification that is being optimised to be relatedness-based. There is an assymetry here.
they reflect the real tempo of evolution ... Evolution slows down, then accelerates, then slows down again, etc. This dynamic is real.
Certainly it is real, but it has never become clear to me why that, of all things in nature, should be the criterion for a border between two same-rank taxa. Again, what is the use case? If somebody says clade Hypotheticopsis, I know that this is a group for which it makes sense to compute a diversification rate; a group which I can compare against other such groups; a group that is complete, so that I can study its biogeography or character evolution or biochemistry without first having to search the literature for missing subgroups that also need to be in the analysis. I somebody says Hypotheticopsis ('evolutionary' classification) I don't even know if it is a grade or a clade! And if it is a grade, I don't know what that tells me about the group or what the heck it is good for.
You should also realise that your view re tempo is nearly completely unique to you (although it may be that Zander agrees - his views may be similar but if so they are expressed in very different language). Read again that special issue they produced in Ann MO Bot Gard; every contributor had completely different views on why cladism should be rejected and with what methodology a different classification should be produced. The only thing that they had in common was that taxa shouldn't have to be monophyletic.
"The ancestral species has still turned into both descendant lineages." Here is the point, you changed "species" into "lineages", so your nested clades actually represent population history, not species history, these are not the same entities. I disagree with Velasco's cladist philosophy, but you should read Velasco 2013 "Phylogeny as population history".
ReplyDelete"You, on the other hand, want to destroy the only classification that is being optimised to be relatedness-based." No, I don't want to destroy anything, I have always said that naming clades is useful (as well as Cavalier-Smith for example). You can keep your relatedness-based system, evolutionists generally just want that their system is formally allowed to exist. I have always advocated a bifid classification with clear rules to distinguish clades and grades.
"Certainly it is real, but it has never become clear to me why that, of all things in nature, should be the criterion for a border between two same-rank taxa." The basic (or cynical) answer would be "why not?", besides, why should relatedness be used as a criterion? It seems completely arbitrary. But a more complete answer would be simply because it reflects a natural property of the tree of life. Topology (relatedness) and speed of evolution are both natural properties of this tree, so both need to be represented by two classification.
"I somebody says Hypotheticopsis ('evolutionary' classification) I don't even know if it is a grade or a clade!" No, you are wrong, it is always a grade. It tells you they evolve at roughly the same speed, so they have roughly the same morphology, the same ecology, etc. So it is a basic biodiversity unit.
"You should also realise that your view re tempo is nearly completely unique to you" Well, no, the tempo and its relationship to paraphyly has been explored at least since the famous Simpson's book in 1944 (maybe it is more a zoological traditional point of view?). What I realize is that botanists often complain about cladism from an end-user point of view, which is a valid point of view, but not my preferred one.
I used the term lineage merely for clarity in this context; independently evolving lineages are the same as species under most species concepts, or one might say under all that were formulated by people who understand genetics, unless taking morphospecies as a pragmatic proxy.
DeleteGeographic ranges of the species-lineages are also a natural property of the tree of life, and there are many other processes that play out. That alone is no reason to use those particular processes to delimit supraspecific taxa. For why it should be relatedness see e.g. my previous response.
it is always a grade. It tells you they evolve at roughly the same speed, so they have roughly the same morphology, the same ecology, etc.
Nothing of this makes sense to me. It cannot always be a grade because even your system would have to recognise come left-over clades. That the species of one of your grade-taxa would evolve at roughly the same speed does not mean that they have roughly the same traits, especially if their shared speed is very high. What is more, "invertebrates" is such a paraphyletic taxon, an what is striking about it is its heterogeneity.
As mentioned above, there does not seem to be an "often" to any particular pro-paraphyly botanist's complaint. They are variously based on "information content", losing island genera for conservation lobbying, misunderstandings of phylogenetic systematics, "but they look so different, how can they be the same taxon" (a logic that is curiously never applied to taxa that the relevant person already learned about when they were young), nomenclatural stability, the claim that Linnean taxonomy and phylogenetic systematics are incompatible, the really weird claim that there is no evolutionary biology in the absence of paraphyletic genera, or simply one's favourite genus or family having been recircumscribed differently to how one was used to. And I am sure I have forgotten a bunch.
Going to bed now, so if you comment again it will not show for quite some time.
"independently evolving lineages are the same as species under most species concepts" Most paleontogical concepts disagree with this idea, and I disagree even for extant species. And I think I understand genetics, thanks.
Delete"Geographic ranges of the species-lineages are also a natural property of the tree of life" Yes, it may be considered a subset of characters, it can be useful to argue about clades as well as grades. So your example does not extent the properties of the tree of life.
"It cannot always be a grade because even your system would have to recognise come left-over clades." Grades can be clades (see Cavalier-Smith explanation in its 1998 classification), I just don't care about paraphyly vs holophyly. Grades and clades are not opposite at all.
"especially if their shared speed is very high" Then the rank is higher to reflect this. If the high speed only concerns a short amount of time then it is just a border between two grades.
"What is more, "invertebrates" is such a paraphyletic taxon, an what is striking about it is its heterogeneity." No it is not. I have never seen an evolutionary classification younger than 150 years including Invertebrata.
"but they look so different, how can they be the same taxon" Behind this caricature, there is just the common sense that the process of evolution is misrepresented. If random Brownian evolution were true, then you would be able to reconstruct the tree of life with a similarity-based index and a phenetic algorithm like UPGMA. This discrepancy shows that something (I think they sometimes don't know what or don't make it clear) is missing in the representation of the process as just nested clades. Clue: it's related to speed.
"the really weird claim that there is no evolutionary biology in the absence of paraphyletic genera" I agree with this for several reasons. You misrepresent the species concept and you misrepresent evolution by eliminating the varying speeds.
"(a logic that is curiously never applied to taxa that the relevant person already learned about when they were young)" A trial of intent. Evolutionary systematists often recircumscribe the taxa or the subtaxa they study, because of new information about grades.
Most paleontogical concepts disagree with this idea
DeleteIn practice. Well, no suprise, they don't have that kind of data, which is why I put that caveat at the end of my sentence.
So your example does not extent the properties of the tree of life.
I do not understand this sentence.
Grades can be clades (see Cavalier-Smith explanation in its 1998 classification), I just don't care about paraphyly vs holophyly. Grades and clades are not opposite at all.
Nor this one. Words have meanings, and a grade simply has a different shape than a clade.
Then the rank is higher to reflect this.
See, this is why it has never become clear to me how that would work in practice. Imagine a grade of shrubs that has a clade of 200 emphemerals nested within it, with the latter having massively higher rates and more morphological heterogeneity than the former. So the shrubs are a genus that has produced 200 monotypic classes? That is clearly ludicrous, so I assume you cannot mean that.
I have never seen an evolutionary classification younger than 150 years including Invertebrata.
Which brings us back to the point that pro-paraphyly people generally accept better classifications as long as they were improved before the relevant person went to uni. It boils down to an aversion to major change.
something is missing in the representation of the process as just nested clades
There is still no argument for why it needs to be considered in circumscription, and still no answer to the problem that the end user cannot extract any information from knowing the species belonging to a taxon under this approach, and still no use case.
I agree with this for several reasons. You misrepresent the species concept and you misrepresent evolution by eliminating the varying speeds.
The sentence "I misrepresent the species concept" does not make any sense in this context; I assume what you mean is that my species concept is a bad one? And no, evol biol is perfectly happy without paraphyletic genera. Show me an evolutionary biologist (not pro-paraphyly crusader taxonomists, but non-taxonomists studying evolutionary processes as their speciality) who thinks that genusification and familification events are meaningful concepts. I believe you will find, instead, cladogenesis and speciation, that's it.
A trial of intent.
I do not understand this fragment.
"Words have meanings, and a grade simply has a different shape than a clade." No. See reference, as well as my own paper you criticized on your blog some time ago.
ReplyDelete"So the shrubs are a genus that has produced 200 monotypic classes?" Yes, I cannot see any problem with this.
"Which brings us back to the point that pro-paraphyly people generally (etc.)" Pseudo-psychology, not an argument, historically wrong.
"the problem that the end user cannot extract any information from knowing the species belonging to a taxon" Then you consider similar morphology and similar ecology as "not an information". Weird point of view.
"Show me an evolutionary biologist (not pro-paraphyly crusader taxonomists" Ad populum not an argument. Besides, when I read "stem groups" everywhere I see people using the concept of paraphyletic grade without naming it.
"genusification and familification events are meaningful concepts" Yes, they are. Your circular reasoning doesn't work "paraphyletic genera don't exist, so generification don't exist, so paraphyletic genera don't exist"... Besides, evolution acceleration is the process you named generification. It's also the same process you named speciation and familification, it's all the same. If generification and familification don't exist, then speciation don't exist. Example of how it works: small and short acceleration = new species ; higher and longer acceleration = new family ; etc. It's really simple.
You could just as well refer me to a book that argues that blue is really yellow, that still won't make me forget what the words mean.
Delete200 monotypic classes? Yes, I cannot see any problem with this.
I don't think we can reach any sort of agreement here. I can kind of see the idea with trying to make each burst of speciation its own genus (although I'd disagree with that too), but raising something to a high rank just because its rate of evolution is high doesn't compute for me. It seems totally random.
Then you consider similar morphology and similar ecology as "not an information".
No. The point is, as I have written repeatedly, that telling me that taxon x in an 'evolutionary' system contains species a, b and c does not tell me anything about abc. They could be each other's closest relatives, or not; they could be similar in some way that I consider important, or not, because the taxonomist who circumscribed x did not consider that way to be more important than relatedness, in this particular case.
Hoerandl always writes that classification needs to reflect a lot of information, but the best you can hope for is that a lot of info went into the taxonomic decisions; the point is that the end user cannot get any information whatsoever out of the classification if it has more than one criterion.
Ad populum not an argument.
Sorry, but that is utter nonsense. The question is whether evol biol needs paraphyly, and it is answered precisely by looking at the actual work practice of evolutionary biologists. You could just as well claim that it was an ad populum fallacy to observe that painters generally don't use bulldozers in their art.
Besides, when I read "stem groups" everywhere I see people using the concept of paraphyletic grade without naming it.
Yes, and I read "species occurring in South America" all the time, and still those are not treated as a taxon.
it's all the same
I don't think that is how speciation works, or at least not how it always works. It can be really slow - which is what I would expect in vicariance, for example - or instantaneous, e.g. with polyploidisation or founder effects. And sister species can look virtually indistinguishable.
"You could just as well refer me to a book that argues that blue is really yellow, that still won't make me forget what the words mean." Yeah... Bad faith, are you going to argue that the Earth is flat because flat means round? And then if I show you a dictionary would you reply "this book won't make me forget what 'flat' means!". It's not surprising with this kind of attitude that you make no sense of what evolutionists are saying. I am jaded now.
ReplyDeleteYou say you are jaded? Clade and grade are simply defined in a mutually exclusive way, and you are the one who does the equivalent of claiming flat means round! This is disconcerting.
DeleteIt also has not escaped my attention that my repeated questions about the use case of 'evolutionary' classification were only ever answered with the observation that rate changes happen or something on the lines of "why not do it that way?", neither of which is comparable to the end user benefit of knowing that a group is complete, as required for downstream biogeographic, evolutionary, spatial, biosecurity or bioprospecting studies.
"You say you are jaded?" Yes. "Clade and grade are simply defined in a mutually exclusive way" They are not. Wikipedia is wrong. It should be corrected. See references, for example Huxley 1958 and Huxley 1959 which is cited in the Wikipedia article but misunderstood (note that Huxley uses "monophyletic" sensu Haeckel, not sensu Hennig, of course). Huxley uses Teleostei as an example of holophyletic grade. Vertebrata is also a grade because it has a unified organization plan, but it's also holophyletic, we just don't care about topology to decide what is a grade what it is not. If I was going on psychology like you, I would say cladists have a propensity to not understand things that are not topology-related and then distort terminology so that it becomes topology-related. Then they arrogantly claim that we changed the meaning!!!
ReplyDelete"It also has not escaped my attention that my repeated questions about the use case (etc.)" There are enough papers that complain about the uselessness of cladism in many situations and where similarity-based classification would do a better job, I won't repeat them here. I have already said that my own research do not involve end-user point of views but only a fundamental one, does something exist? If yes, how can we represent it in a synthetic way? Grades exist, they are hierarchized, so they can be made into a classification. I would let the end-users choose the classification (the cladist or the evolutionist one) that fit the best their needs, not impose it like cladists do.
This is just unbelievable. It is not some sinister cladist conspiracy, it is all of evolutionary biology that uses the term grade to describe a certain topology on the phylogeny. That is what the word means. I have seen dozens of talks and papers from biologists who couldn't care less about whether taxa are monophyletic but who use the term grade in this way.
DeleteAgain, I do not doubt the utility of similarity-based classifications. 'Evolutionary' classification is not a similarity-based classification, however; it is a bizarre hybrid of similarity-based and relatedness-based, putting both types of information in with the end result that the user cannot get either out.
"It is not some sinister cladist conspiracy" No it is not, it is called a paradigm, I understand the distortion may be widespread and unintentional. However, people using loosely a word should not bias a scientific rigourous terminology used by others.
Delete"'Evolutionary' classification is not a similarity-based classification" Yes it is.
"it is a bizarre hybrid of similarity-based and relatedness-based" No, it is not. Relatedness (holophyly) has nothing to do in evolutionary classification. It is not sometimes a criterion, it is NEVER a criterion, so there is no imaginary dilemma. Similarity-based taxa are just constrained to be monophyletic (contain their most recent ancestors). In other words, similarity includes symplesiomorphies and synapomorphies but excludes homoplasious relationships. There is nothing bizarre.
I just find it amazing how you can dismiss all the experts in the field as mistaken on a matter of, notabene, not even empirical truth but definition, which is generally decided by expert consensus. If tomorrow everybody except you starts calling rate of evolution "urts", then that is the word for rate of evolution, whether you like it or not.
DeleteIn your last paragraph, you used the words until "dilemma" to argue that relatedness is not a criterion, and then you used the remaining words to explain exactly how you would make relatedness a criterion. I am genuinely puzzled: How can you write such a paragraph without at least experiencing some cognitive dissonance? Is it not clear that if you used only similarity then you would not be an evolutionary systematist but a pheneticist?
Note also that the most prominent pro-paraphyly botanists are emphatic that their system is such a muddled hybrid of two criteria. Read any contribution by Elvira Hoerandl - she argues that that is its main advantage, its whole point, because it takes "more information" into account!
Certainly if we have such different perceptions of reality we will find it hard to achieve a meeting of the minds.
"If tomorrow everybody except you starts calling rate of evolution "urts", then that is the word for rate of evolution, whether you like it or not." If everybody except me starts using "flat" to mean "round", then yes I would dismiss the loose use of this word by these "experts", claiming that the "old" meaning was better. You seem to forget that evolutionary systematists are also experts. And above all, they are experts about grades.
Delete"how you would make relatedness a criterion" You are conflating relatedness and relationship. Moreover, you are also confusing optimization criterion and constraint criterion, so you should learn about constrained clustering to understand that both types of criteria are always recovered. Moreover, in this case, it is easy incorporate the monophyly constraint in the similarity evaluation by just dismissing homoplasies, so that it remains only one criterion.
"Is it not clear that if you used only similarity then you would not be an evolutionary systematist but a pheneticist?" As I said, similarity is not defined in the same way, homoplasies are dismissed, moreoever weighting is allowed, so this is a completely different philosophy.
"Note also that the most prominent pro-paraphyly botanists (etc.)" Yes they say things like that, but like you they are not rigorous at all with clustering terminology, but they are definitely right that their classification is more informative.
"Certainly if we have such different perceptions of reality we will find it hard to achieve a meeting of the minds." Yes, as I said, it is a question of paradigm, you have certainly note that "informative" does not even mean the same thing for you and me. But I am young I don't despair that when I am old a unified paradigm will rise from these conflicting philosophies, or at least a compatible way to make them coexist without fighting about every word. That's why I am still writing theoretical papers to make things clearer and clearer.
There is a limit to how often it is fun to go around in circles and express our mutual disagreement, so I think this may be my last response on this particular thread.
Delete1. You are the one here who is trying to muddle two mutually exclusive concepts like flat and round. Also, homeopaths are experts in homeopathy; that alone doesn't demonstrate anything.
2. I consider that sophistry. The classification uses both relatedness (your 'constraint') and similarity as criteria. You can argue, as Hoerandl does, that that is great, or, as I do, that that makes the classification useless, but you cannot simply deny that that is the case.
3. Yes, dismissing the homoplasies is how you make relatedness a criterion.
4. I have explained before that I think there is confusion here between "considering a lot of information when building the classification" and "the classification is informative for the user", and that while the former is certainly happening the latter fails, unavoidably, and precisely because of the former.
5. It seems rather we see an increasing focus on genomics and bioinformatics in evolutionary biology, with less and less people caring about the details of taxonomy and nomenclature. And that cohort seems to be a mixture of people who are for paraphyletic taxa because they don't understand phylogenetic systematics and the difference between gene trees and species trees, people who are for making everything monophyletic, including species, because they don't understand phylogenetic systematics and the difference between gene trees and species trees either, and people who just don't care about that issue at all as long as they get to give talks about this new sequencing method they tried out or their new Bayesian method for species delimitation under the multi-gene coalescent model.
"There is a limit to how often it is fun" It has never been to me, I don't try to make friends.
DeletePoint 1 is obvious provocation. Point 2 and 3, you simply don't understand that both criteria reduce to the same mathematical parameter, so they are really only one criterion. Point 4, there is no confusion, these statements are equivalent, not exclusive, contrary to your belief. It seems you conflate precision and accuracy, this is where there is a trade-off.
"people who are for paraphyletic taxa because they don't understand phylogenetic systematics"
"people who are for making everything monophyletic, including species, because they don't understand phylogenetic systematics"
Isn't it arrogant to think that people don't agree with you because they don't understand? This is like politicians saying "stop your strike and your demonstration, if you are against my reform that's because you didn't understand it is good for you!" No, we are against this reform, or against this philosophy of classification, because we understand it.
I did not say that this applied to everybody who disagreed with me. But if somebody points at a single gene tree showing a species as 'paraphyletic' and concludes from that that phylogenetic systematics can't work because all taxa are paraphyletic if a species is 'paraphyletic', then that merely demonstrates that they do not understand (a) incomplete lineage sorting, (b) the difference between gene trees and species trees, and (c) phylogenetic systematics.
DeleteThat is just a fact. If somebody argues that the earth is flat because if it were round the people on the other side would fall off, would you call it arrogant to conclude that they don't understand something?