While working for a 2-piece post on the Genealogical World of Networks (A bit of heresy: networks for matrices used in Cladistics studies), I stepped over a threat on ResearchGate, where someone asked this. I browsed through the answers, and felt obliged to answer as well.
[The following is a fairly literal copy of my answer on RG, graphics are added]
Cladistics is about clades, defined as subtrees in rooted trees. There's a nice chapter in Joe Felsenstein's 2004 book, Inferring Phylogenies, on this; also pointing out why we actually should clearly distinguish between clades, a subtree in a rooted graph, and monophyla, an interpretative concept. It goes back to Farris (1983) and not Hennig (1950).
Hennig "just" provided a new (indeed better, because it can be tested) concept for monophyly in the framework of his "Kladistik" (which differs in quite some bits from what later became "Cladistics")
|The problem Hennig tried (half succeeded, half failed) to solve: evolution of two reciprocally ("mutually") monophyletic lineages, Roundish (all descendants of Rounded) and Pointish (all descendants of Pointed), in time and morphospace. Note each cladogenesis, i.e. dichotomous split, is accompanied by a unique change in form or colour. But whereas forms only evolved once, i.e. are or were(!) synapomorphies, colours were also evolved in parallel (lush blue octagon) or independently in the Roundish and Pointish lineages (olives).|
|Realising that form is more important than colour, we can put up an intuitive phylogenetic classification: all groups go back to a defined common ancestor, i.e. are monophyletic (in a pre-Hennigian sense). Hennig noted the difference between groups of inclusive common origin, his monophyla (green; Ashlock, 1971, proposed the term 'holophyla' to avoid confusion), and those of exclusive common origin, which he termed paraphyla (red). Since paraphyla are impossible to define without recognising monophyla, he suggested to avoid them at all cost. For example, Roundish is a monophyletic group defined by a smooth, rounded outline. They include one sub-monophylum: Donutia, which members are defined by a uniquely derived donut-shape, a synapormophy (found in all descendants of the first donut). But the other two shapes collect only part of the descendants of the first oval (Ovalia), also the ancestor of all Roundish, and first turned-over oval (Obovalia).|
|A proper Hennigian phylogenetic classification, recognising three monophyla instead of the paraphyla. It also illustrates what Hennig had to ignore and many cladists still do: change over time (also called evolution). The Pinkoids are all descendants of the first pink oval. Prior to the evolution of the monophyletic Donutia, pink was the synapomorphy of the Pinkoids. Today, due the evolution of darker shades, it is a symplesiomorphy — an ancestral, primitive, shared trait of some Pinkoids except for the Donutia. For their sister lineage, the Orangeoids, we have no synapomorphy at all — a dead end for Hennig. Nevertheless, we can characterise the monophyla viz clades (this is still a rooted tree) by their unique combination of traits: the Orangeoids are rounded, but not pinkish; the Turqoids greenish stars. This is where cladistics sets in: the tree topology is inferred from all traits, no matter whether they represent modern or ancient synapomorphies.|
We had last year two posts on this (on the Genealogical World of Phylogenetic Networks)
- Let's distinguish between Hennig and Cladistics
- Clades, cladograms, cladistics, and why networks are inevitable
PS Statements [see Victor Orrico's answer on RG] that NJ trees are "phenetic" are wrong (a common error): the NJ algorithm produces phylogenetic trees fulfilling either the minimum evolution (ME) or least-squares (LS) optimality criteria (depending how set up). The algorithms for UPGMA and NJ are both cluster-algorithms (so "phenetic", if you want), but for the NJ it has been shown that it succeeds in finding a good estimate for the ME or LS tree (which UPGMA does only by accident). NJ is just a shortcut to find a ME or LS-optimised phylogenetic tree from a distance matrix (again e.g. Felstenstein, 2004, Înferring Phylogenies). A perfect matrix, where each cladogenesis is represented by at least two subsequent synapomorphies will result in a perfect distance matrix, and the ME or LS tree inferred from this matrix, will be the true tree, and identical to the single MPT inferred from the character matrix. If convergences outcompete synapomorphies, the MPT will have clades that are not monophyletic, as will (to a lesser degree it seems) the ME or LS tree, whereas compatibility and probabilistic methods can handle this to some degree.
Phylogenetics is about phylogeny, evolutionary pathways, and goes back to Darwin and Wallace's age. The first phylogenetic trees were published in the 19th century, one of the earliest at my Alma mater, the University of Tübingen, by Franz-Martin Hilgendorf (who also published possibly the first phylogenetic network). Haeckel did a lot to advocate phylogenetic trees, and also coined monophyly, if I remember correctly). Regarding first phylogenetic trees including a definition of what a phylogenetic tree is, see this post by David Morrison
[Side-remark: A phylogenetic tree is a tree depicting ancestor-descendant relationships, which, ironically, no cladogram, the still commonly seen rooted trees without branch lengths, can; and phylograms, rooted trees with branch lengths, only indirectly by zero-length terminal branches.]
|Left, Hilgendorf's 1866 phylogenetic tree depicting ancestor-descendant relationships (monophyletic groups coloured); right, a cladogram depicting most of the monophyla, but no ancestor-descendant relationships.|
I gave it a quick search, and found this nice set of lecture slides giving a quite comprehensive introduction into "evolutionary (phylogenetic) trees" and three of the methods to infer them: "Parsimony; Distance matrix based; Maximum likelihood" [link to PDF].
Cladistics is hence a (quite restricted) subset of phylogenetics (not synonymous with Hennig's "Kladistik").
So, to be on the safe side, always go for phylogenetics.
And largely irrelevant these days. Not a few are aware (openly or shyly) that clades in rooted trees often correspond to monophyla, i.e. groups of inclusive common origin, but not necessarily do so. Incomplete lineage sorting is cladistics' greatest foe. Just take the many cases where different genomes tell different stories: the nuclear, mitochondrial and/or plastid trees may have different highly supported clades, but there can only be one monophylum (or two overlapping ones, in case of hybridisation). Which we try to infer based e.g. on the coalescent tree (which is a special form of coalescent network).
Or, think of a misplaced root or ingroup-outgroup long-branch attraction that easily turn a grade into a clade an vice versa. Especially parsimony trees can be severely misleading (see eg. this recent paper by Scotland RW, Steel M. 2015. Circumstances in which parsimony but not compatibility will be provably misleading. Systematic Biology 64:492–504).
|Ingroup-outgroup long-branch attraction. The outgroup flips around the ingroup tree, the splits remain the same, but all monophyla (green boxes) become grades (more in Clades, cladograms, ... on GWoN)|
Plus, there are many evolutionary/biological processes that inflict reticulation, i.e. ancestor-descendant relationships that cannot be modelled by a tree at all. A phylogenetic tree is just a special phylogenetic network, i.e. a phylogenetic network without reticulation.
A notable exception is classification. Cladistic classification, putting names to clades in inferred trees (under the implicit assumption that all clades represent monophyla fide Hennig), is still the holy goal.
Although, we often bend the rules and use (more general) phylogenetic classification concepts. Oaks being an example: the first multigene trees placed them in two separated, well-supported clades, but no-one was bold enough to divide this (most likely monophyletic) genus into two genera fitting the two clades in the trees or include the chestnuts etc. in the oaks. We formalised the two oak clades last year as subgenera (paywalled final version; free Pre-Print with one major change: Ponticae and Virentes accepted as additional sections in final version), the new infrageneric classification of oaks is hence a cladistic one based on nuclear oligo-gene and phylogenomic trees. But we are confident that it is also a phylogenetic one: our subgenera and sections are not only clades, but also monophyla (today and back into the past).
Cladistic or Hennig-phylogenetic classification (e.g. PhyloCode, using 'clade' as synonym for 'monophylum') is, however, impractical (to impossible, see e.g. Brummit 2002, How to chop up a tree) when being extended to fossils, we summarised the different concepts (those used in reality) in Fig. 8 of our 2017 Osmundales paper (open access). Naming (likely) paraphyla, or groups that may be para- or monophyletic, is inevitable. Ancestral forms and groups need names, too (no mention of fossil/ancestral taxa in the PhyloCode).
Why is there so much confusion?
Apparently many still hang on to parts of the 80s intellectual cladist package as summarised by Joe Felsenstein this list can be found in his 2001 piece for Systematic Biology, open access). So you not rarely get odd (and wrong) comments from (anonymous) reviewers (I got them quite often, since I usually used networks for phylogenetics and frequently had to deal with fundamentally "a-cladistic" data)
Quoted from Felsenstein (Syst. Biol., 2001, p. 466):
"The cladists of that era had accepted a number of points as an intellectual package. At one point in the mid-1980s I tried to summarize the package and came up with these points, in order of importance
- Use Hennig’s terminology—autapomorphy, symplesiomorphy, and so forth—rather than terms like ancestral or derived. [still very common]
- Classify cladistically; use only monophyletic groups. [still the official standard, see eg. dinosaur part of the Tree of Life/ Wikipedia (e.g. Coelurosauria and subclades); with funny consequences: the full hierachy for modern-day birds is (Wikipedia, 17/2/2020): Kingdom Animalia, Phylum Chordata, Clade Dinosauria, Clade Saurichia, Clade Theropoda, Clade Avetheropoda, Calde Coelurosauria, Clade Tyrannoraptora, Clade Maniraptoromorpha, Clade Maniraptoriformis, Clade Maniraptora, Clade Aveairfolia, Clade Pennaraptora, Clade Paraves, Clade Eumaniraptora, Clade Averaptora, Clade Avialae (= "flying dinosaurs"), Clade Euavialae, Clade Avebrevicaudata, Clade Pygostylia, Clade Ornithothoraces, Clade Euornithes, Clade Ornithuromorpha, Clade Ornithurae, Class Aves)]
- Do biogeography by vicariance (pace Hennig). [not exclusive anymore but still common, an (bad) example: How not to make a biogeographic study]
- Use only computer programs written by leaders in the Hennig Society, all others are fundamentally flawed. [both rarely openly stated, but I experienced this during review still in the zeroes]
- Use only parsimony methods. Compatibility methods are evil. [recent example: Ockham's Razor applied but not used...]
- Do not weight characters. [has become rarer, but often still frown about, even by those who then use TNT's post-inference character weighting option to increase branch-support]
- Be hostile to molecular data [see Ockham's Razor..., and follow-up post: Why we want to map trait evolution along networks].
- Consider your methods to be hypothetico-deductive. [see e.g. Wilf et al.'s response to Denk et al.'s comment on their 2019 paper]
- Fossils are to be treated the same as living species. [this is still standard, and beyond cladistics]
- Parasites always have exactly the same phylogenies as their hosts.
- It is important to go around saying that one cannot infer ancestor–descendant relationships. [this is a wide-spread belief, partly out of necessity: tree-inference programmes do not allow placing ancestors on the nodes or internal branches, all OTUs have to be tip taxa]
- It is important to go around saying that species are individuals, not classes. [many still think species are the only "natural" biological unit, fundamentally different from e.g. genera; which everyone knows to be nonsense, who worked with data from more than one individual per species]
- Be sceptical of the reality of the species as nonoperational. [see above]
- History: William of Ockham told Popper to tell Hennig to use parsimony." [still a belief, especially in palaeontology]
Das Grimm, thanks for reprinting my list of points that constituted the Hennig Society official thought package of the early 1980s. Could I ask for a little reformatting to make this an accurate quote from my 2001 account? There need to be separate list items for "Use only computer programs ...", for "Do not weight characters ...", for "Consider your methods ...", for "Fossils are to be treated ...", and for "It is important to go around saying that one ...". Otherwise people will be confused about whether the "computer programs" entry is somehow part of the point about biogeography. And so on. And thanks for your thoughts on the extent to which these points are still adhered to. I am somewhat horrified to see how valid these generalizations still are!ReplyDelete
Admittedly, I fused some of the points on purpose following my personal experiences with the cladistic ghost.
But you're right, since it's a quote, also the line breaks should be as in the original.
Regarding how valid they still are in certain subfields of biological sciences (study of extinct organisms, systematic botany), three recent examples:
A chair for botany told a colleague quite recently that all my research does not qualify for phylogenetics but is complete nonsense. Because it lacks parsimony trees, and, even worse, includes networks exploring the typcial non-trivial signal in our data.
And when you check out the dinosaur part of the Tree of Life, you find a huge wealth of superclass "Clades" := monophyla (see D. Marjanovic's comment), some based on (strict consensus) cladograms that don't even show Bremer support. The logic is: since the branch support is inevitably low (when using parsimony), we don't establish any branch support at all but assume that the collection of most-parsimony trees (estimated with TNT, which has replaced NONA as the 'Holy Tool') succeeds in finding the true tree. What we know from modern-day organisms – a) morphological evolution doesn't reflect 1:1 molecular evolution, b) there may be more than one possible tree that can be inferred from the data even when we have no evidence for evolutionary reticulation (lineage crossing) – simply doesn't apply to the extinct "sister" lineages of modern-day organisms.
Science (comment pointing out the paper's many weaknesses; the authors' "response") just published a "DNA-scaffold phylogenetic analysis", which, according to the authors, conclusively demonstrates that a modern-day East Asian genus originated in the Eocene of Patagonia. Using seven morphological traits, no molecular data partition and TNT to optimise the fossil's position (scorded as identical to the modern target taxon) in an taxon-wise incomprehensive preferred tree under parsimony (Ockham's Razor applied, but not used).
The "cladists of that era" are not only still alive but found new followers and make sure no-one straddles from the Holy Truth in the darker fringes of biological sciences such as palaeontology and systematic botany.
Hi Joe, Das Grimm,Delete
Would it be too much to suggest that all cladists are not the same. Our book, just published, should help, I hope, answer some of these questions, you may find what you are looking for within these pages: https://www.cambridge.org/core/books/cladistics/D3C3FC2E69F52FB3BDBDBA219157E625#
of course they are not the same, because many people that call themselves "cladists" are actually phylogeneticists, who know or subconciously realised that a clade in an inferred, rooted tree is neither a necessary nor sufficient criterion for monophyly.
But then you shouldn't call yourself a cladist at all. Or a book about phylogenetic methods and classification "Cladistics". A (post-Farrisian) cladist is a person who believes the inferred (or preferred) tree represents the true tree. If you cannot make that jump in faith (because your data tells your otherwise, as mine did, repeatedly and fervently), you are neither a cladist nor doing cladistics.
I stopped calling myself a cladist (as German, I'm a great fan of Hennig and the simplicity of his logic) after my Diploma thesis and went for "phylogeneticist", an evolutionary biologist doing phylogenetics. I realised very early in my career, how easy it is to get a tree with non-monophyletic* clades, i.e. subtrees in a rooted tree with tips probably not sharing an inclusive common origin at all (especially when using suboptimal data such as limited morphological data).
From a classification perspective, when you work with plant fossils of extant lineages (e.g our 2017 Osmundaceae classification paper), you simply cannot adhere to cladistic classification, i.e. only name holophyla (fide Ashlock = Hennig's monophyla). It will be instable and pointless (if I anyway need to infer a tree to classify, why bother giving names to the internodes?). You need to go for a general phylogenetic one, preferring (a) holophyla, (b) make use of easy-to-diagnose paraphyla (ancestral taxa, least-modified left-overs from fast ancient radiations), and (c)monophyla (s.l., pre-Hennig), where we have no way to conclude whether they are holophyletic or paraphyletic.
If the 2nd part of my post is what your books provides answers to, choose a more fitting title next time. But if its about the superiority of cladistics, equals clades with monophyla (Farris' school; and that of many of my anonymous expert peers), it's not worth a peak.
A tip for those who want to learn about how to infer trees, do phylogenetics, here's an open access, free-to-read textbook for the era of Big Data with all up-to-date methods.
Phylogenetics in the Genomic Era
"A book completely handled by researchers.No publisher has been paid."
PS Personally, I rarely found an answer in a textbook because all my research questions were data-based and very peculiar, dealing with the dark spots of evolution. And all textbooks and far the most papers I crossed having "cladistic" in the title were posing (and answering) just the wrong questions. Some papers tackled the right ones, but then not using a cladistic framework at all. Most younger ones don't get the difference between phylogenetics, identifying common origins using collections of trees and exploratory data analysis, and cladistics, clade = monophylum, no question asked. And real bioinformaticians simply don't care, knowing that any tree we infer is, at best, only an approximation towards the true tree.
* Not to be confused with "non-monophyletic" taxa commonly seen in molecular-phylogenetic studies, i.e. accepted taxa assumed to have a common origin but not being collected in a high-supported clade.
There's a lot in here that suggests, rather, you have been indoctrinated in a series of viewpoints and assumptions not held by myself nor my co-author. But that is not surprising given the way science unfolds -- or doesn't.Delete
"But then you shouldn't call yourself a cladist at all."
Well, now I can adopt whatever name I wish, that it doesn't conform to your notions is neither here not there. But names to one side...
"Or a book about phylogenetic methods and classification "Cladistics"."
Why do you think this is a book about phylogenetic methods? That's why I'm asking you to consider its contents.
"A (post-Farrisian) cladist is a person who believes the inferred (or preferred) tree represents the true tree. If you cannot make that jump in faith (because your data tells your otherwise, as mine did, repeatedly and fervently), you are neither a cladist nor doing cladistics."
If you read the book you will see we are not, nor have we ever been, followers of, supporters of, whatever of, Farris. Or any of his ideas.
We are interested in classification, if that helps at all.
You are entitled to take whatever view of me you want. But, as we state in this book over and over again, we do not want to be misunderstood. Which is what you are doing, without, seemingly, ever having read a word of what we write.
A classic: Of course, I must have been indoctrinated by viewpoints and (unbased, I suppose) assumptions (you may want to point them out in the post you comment to) because my "opinion" doesn't agree with your "knowledge".
So, if you are not a disciple of Farris' school, why did you choose the title Cladistics for an open-minded book about, phylogenetic(!) classification? And not, e.g. "Phylogenetic classification in the Genomic Era"?
PS Before you claim indoctrination by some (by the way, non-existing) philosophy, you may want to actually read any of the open access systematic papers I co-authored (all providing anonymous access to the used data) and posts (you are probably the first person noticing my indoctrination, many of my peers were appauled by my lack thereof)
And stop commenting on your pay-to-view book with its, as you clarified, misleading title, and point out the flaws in this very post. I hope, my post is not exactly doing what you wanted to do in your but simply couldn't get rid of the branding? After all, putting forward phylogenetic but not cladistic classifications is still a dead-end in systematic biology. But that has nothing to do with the peers being indoctrinated, of course.
Since when has cladistics = Farris school? That is your assumption not mine. it is incorrect. I am a disciple of no one.ReplyDelete
Yes, it is a pity that CUP charge -- I wish it were otherwise. But the answers to your question are within.
I have read some of your papers.
Re your first question: see the interlinked GWoN post by David MorrisonReplyDelete
Let's distinguish between Hennig and Cladistics
The reason he wrote it, is because (in our fields) many still equal Farris' cladistics with Hennig's Kladistik, and make no difference between a "kladistische" classification fide Hennig, naming monophyla (holophyla sensu Ashlock) and a cladistic classification fide Farris, i.e. naming clades in an outgroup-rooted, inferred tree (most-striking and funny example: dinosaur classification, based on nodes and branches seen in instable, parsimony consensus cladograms).
If you haven't experience this indifference, consider yourself lucky. We had to force papers through single-blind review because our peers simply didn't understood why we only take clades as indication for inclusive common origin but not as sole criterion. And didn't want to understand why we name groups that are not corresponding to a clade with a BS ≥ 70. To my experience the indifference is much more predominant in vertrebrate palaeozoology and botany (neo- and palaeo-) than in any other organismal group. Vertebrate palaeozoologists are sure there are no ancestors in the fossil record, and systematic botany was the last retreat of the Farrisian faction when they lost the so-called Phylogenetic Wars (I escaped the usual indoctrination because my background in genetics and geology, not systematic biology).
Re "...pity that CUP charge...answers to your question are within.", so, why not repeat it here for those who cannot (or are not willing) to pay the CUP?
My answer to the question, how to classify in the presence of ancestral taxa and topological uncertainty, not too mention reticulation and budding speciation, is very simple. Love to repeat it:
Don't classify cladistically but phylogenetically!
Make use of holophyla, paraphyla, and monophyla in a pre-Hennigian sense, and take into account lineage coherence and diagnosability (what Mayr called "overall similarity"), and the time-frame as evidenced in the fossil record (if there is any). See e.g. the Osmundaceae example and my posts on What is an angiosperm [pt 1] [pt 2] [casus belli].
As far as I can tell we (still, cf. Felsenstein, 2004, chapter 10) only have cladistic doctrine (!)-induced naming problems because neither Hennig's "Kladistik" nor Farris' "cladistics" considered the existence of actual ancestors in the fossil record, not to mention evolutionary stasis and positive selection. If A and B are well-established extant monophyla and I go deep enough into time to stumble across their ancestor(s) (ancestral forms), I just call them C, even though any ancestor with its own name is per se paraphyletic. Hennig's or Farris' only option is to fuse all into A (something neontologists generally don't except, getting their good taxa destroyed because of a too primitive fossil)
Once you stop trying to classify cladistically, there are no questions anymore, only quick-and-easy answers. Pinpointing common ancestry (monophyla sensu Haeckel) is quite straightforward (especially when you have molecular data), discerning Hennig's monophyla (= holophyla) and eliminating paraphyla is not (why both Farrisians and the PhyloCode failed in producing handy and stable classifications).
If you check with the original post of Morrison's you'll notice I offered a correction to one of his statements:ReplyDelete
"Second, parsimony analysis was developed independently of Hennig, by people such as Farris, Nelson and Platnick." Farris, maybe -- but cladistics sensu Nelson has no connection to Wagner Parsimony (Nelson, Gareth G. 1979. Cladistic analysis and synthesis: principles and definitions, with a historical note on Adanson’s Familles des Plantes (1763–1764). Systematic Zoology, 28: 1–21.). This paper may tell you a great about cladistics and how it should have been understood.
The key point: cladistics sensu Nelson has no connection to Wagner Parsimony. Morrison never replied.
I am not responsible for your experiences with reviewers or persons you seemingly feel belong to a faction. Maybe I agree with your last comment. Maybe I have suffered too. But it doesn't matter much. I am not interested in factions, schools, disciples etc. or feeling sorry for myself.
I don't want to simply argue with you, it serves no purpose. Let me just comment on one or two things:
"Vertebrate palaeozoologists are sure there are no ancestors in the fossil record". That is a very odd statement and suggests to me, although I could be wrong, you don't understand anything about recognising ancestors.
So, you want to resurrect 'overall similarity'. Good luck, you are not alone.
Actually, you seem to want to resurrect all sorts of things.
Again, with respect, one needs evidence for monophyly, paraphyly is a consequence of discovering monophyly. It is lack of evidence.
Right now I don't care if you don't read my book. You seem to know all sorts of things.
There's no reply by David because none is needed. It's a valid point to make. If it wouldn't have been, David would have replied.Delete
But, it's not something widely known and taught in systematics courses (I first heard about Nelson because of Felsenstein's book). I actually cited Hennige (1950, never read really the English translation, because the Kladist who introduced me to Hennig and phylogenetics told me, it much looses in translation) more than once to rebut the opinion of a "cladistic" (Farrisian) peer. No self-declared cladist I met and discussed with in the last 20 years has ever mentioned Nelson, you are the first. So, apologise me putting you in the wrong drawer.
Regarding no ancestors in the fossil record: Since I worked at evolution's coalface (mostly plants but including foraminifers), I know, it's nonsense. I actually posted on it, too, in response to an according comment.Delete
Where have all the ancestors gone
Re: Overall similarityReplyDelete
I don't want to "resurrect" overall similarity (Mayr's 2002 paper was convolute and a bit pointless); but one should not ignoring lineage coherence when doing classification. Especially not in an era, where species are erected based on 3% rules and environmental bulk DNA samples in order to replace good alpha-taxonomy.
Just to give a concrete example: To classify the angiosperms cladistically sensu Hennig (Nelson?), I don't need to infer any tree at all. It's obvious from a heat-map of genetic distances: members of likely monophyla (holophyla) are much more similar to each other than to any other taxon in the data set. That's why they give us highly-supported (and model-independent) clades. Morphologically, we have such trivial situations, too (an example from the dinosaurs), but often we face much more complex data situations, e.g. when putting up a matrix for extant and extinct angiosperms.
Re: Paraphyly; not "just lack of signal"ReplyDelete
Paraphyly is the lack of lineage-conserved, uniquely derived character suites—homoiologies and Hennig's rare synapomorphies. What makes paraphyletic groups useful in classification is exactly what you point out: we can define them via (nested) monophyla.
Paraphyly is furthermore also a common consequence of population dynamics (interesting case: individual-based fossil phylogenies), and, subsequently, genetic drift, active population sizes, and effect and frequence of bottleneck situations, in short: asymmetric speciation processes. If I remove one population (or species) from a master population (source species), it may become quickly different but the master population doesn't change. As soon as I give the isolate a name (being beyond doubt monophyletic and visiblydifferent), the still-unchanged remainder becomes a paraphylum and becomes invalid. Fast ancient radiations popping up easy-to-diagnose, highly-supported clades with prominent roots, i.e. easy-to-argue monophyla, quite often keep leftovers that are genetically ambiguous and morphologically poorly differentiated. Which we, using cladistic classifications, solve by erecting monotypic genera of little diagnostic value, or simply not recognising the easy-to-diagnose monophyla within the larger group (see e.g. certain much-inflated angiosperm families).
I guess, in most aspects, we are not that far apart. It's only (pretty dogmatic, sorry) statements like "paraphyly is lack of evidence" that distinguish your (in principle, good-)cladistic (in contrast to Farrisian naive-cladistic) doctrine ("Only monophyla must be named!") from my real-world inspired (as in this post), utterly doctrine-free solutions to complex (non-trivial) cases, hence, different solutions for different sets of data and data situations.
If you have time to waste: Just try one of the many freely accessible datasets I covered in my papers and posts, following the suggestions in your own book to demonstrate that (the original, pre-Farris) cladistics are still the only possible classification system and are applicable also to non-trivial situations (rather to those where Mayr's overall similarity would suffice, see example in the response above). Proof me wrong, there are many examples to choose from.
Postscriptum and epilogueReplyDelete
Absolutely not sorry for myself; I'm very happy in my early retirement because I don't have to fight anymore utterly useless fights with anonymous shadows shooting from the dark, who occassionaly demonstrated to even know less about their own data/papers (one example) than they had about ours. But, and apparently in contrast to you, I met many people who suffered during peer-review without really knowing why having been indoctrinated by cladists. That's why I have such an illustrious collection of co-authors ranging from micropalaeontologists to bioinformaticians: people came to me with data that was not trivial to analyse, and required some open-minded creativity. In my early retirement, I can afford to give all those victims of doctrines a voice, and a helping hand, pointing them to solutions that worked for us. And call-out challenging hindering doctrines, such as cladistic classification (be it Hennig, Nelson or Farris-style).
I've been trying to find out about the "cladist wars," which produced a revolution in biology, whose fallout you, Das Grimm, are ably dealing with. The essays I've read so far are (1) long on generalities and short on details and (2) have little to do with the issue of which I am most concerned: the demise of the Linnean system of classification, including the banishment of paraphyletic taxa and the resulting forcing of all organisms to the branch tips of phylogenetic trees.ReplyDelete
The only specific event of those wars that I have ever read about (from two different sources, one of which I own: Kenneth S. Thompson's LIVING FOSSIL: The Story of the Coelacanth) is the 1978 event "the lungfish, the salmon, and the cow". It had to do with a corollary of item (2) above, the radical redefinement by cladists of the word "related". The anti-cladist side claimed that it was absurd to regard a lungfish to be more closely related to a cow than to a salmon, but that was a naive choice of taxa, and the outcome was an undeserved victory for the cladist side.
Had a competent vertebrate paleontologist been involved, the choice of taxa could have been very different. One choice readily available at that time was "Bos, Ichthyostega, Elpistostege." [Nowadays, the third is better replaced by the more familiar Tiktaalik.]
It does violence to our ordinary idea of human relationships to claim that Ichthyostega is more closely related to us human beings than it is to Elpistostege. It's almost as bad as saying that Mitochondrial Eve is more closely related to everyone alive today than she was to anyone in her family at the time she was born.
Had the victory gone the other way, we might be far advanced in a definition of "more related" that combines phylogeny with measures of disparity. As it is, the theory of macroevolution, to which disparity is an indispensable tool, has made comparatively little progress to date.
I wouldn't say it made little progress because there are whole groups of organisms (such as bacteria, single-cell metazoans like foraminifera, invertebrates at various levels, fungi, primitive plants, any research close to the speciation horizont, any research involving fossils, ancestors, and their modern counterparts, descendants, like everything I was involved in) still or just now classified dominately using combination of tree inferences and absolute disparity.Delete
It's just not so visible, not promoted so fiercely that it sipped into the mainstream of the great classifications: vertebrates and angiosperms.
But it may be just a matter of time: the more dense our phylogenomic datasets become, the more difficult it will be to infer that single-best tree cladistics needs to classify. The only reason, cladistics have become mainstream for classification is its simplicity: one doesn't need any prior knowledge to define groups based on a tree.
I guess, in the long run, defining "valid" taxa solely based on high-supported clades in inferred trees (inferred clade = holophyly, an equation that too often just doesn't hold) will only survive at mid-/high-hierachical levels in (i) angiosperms because the big lineages are data-wise trivial to discern having high coherence: their members are much more similiar within than with anyone outside the tribe, family, order) and (ii) extinct groups of vertebrates, where one has a huge amount of morphological-anatomical characters to code but runs no risk that molecular data reveals the character suites behind clades or detected synapomorphies are at worst composed entirely of convergences, at best homoiologies and/or (ironically enough) Hennig's symplesiomorphies.
Thank you for letting me know of an ongoing effort to combine tree inferences and disparity; I didn't know such an effort existed on such a scale.Delete
I've been reviewing discussions in sci.bio.paleontology back in 2016, and it impressed on me the way doctrinaire cladists are still stuck in the false dichotomy between cladistics and phenetics. This also seems to have been the blind spot of both sides in the "cladist wars". In both cases, the paleontological point of view of Romer was missing, because the majority of systematists deal in extant taxa.
In our 2016 discussion/debate, the cladist side could see no use for tools from graph theory such as finding the length of the path from one species to another, given that the graph was a tree. That is, of course, because they were thinking purely in terms of the number of nodes separating the two species in the tree.
But here is exactly where disparity between two successive nodes comes in. The line segment joining them is given a number estimating degree of disparity, and the numbers are added together to compute the length of the path.
The concept of "more closely related" then could be given a whole new meaning -- or, rather an old meaning but now quantified. We would be able to say that vertebrate A is more closely related to B than it is to C even when the LCA of A and B is strictly ancestral to the LCA of B and C.
Example: A = Panderichthys, B = Tiktaalik, C = Homo. A cladist would say B and C are equally distant from A because they are in a clade that excludes A.
A pheneticist would agree with the disparity measurer in this example, but I think it is not hard to cook up an example where evolutionary convergence could make the pheneticist disagree with the disparity measurer, because the latter takes a plunge down the tree and back up to do the measuring, but the pheneticist hops across the tree in a beeline from one species to another.
For extinct-extant groups it's very straightforward to assess the phylogenetic distance, i.e. the distance between two tips over the tree (or all possible trees, i.e. the species network) or all members of a subtree/ putative taxonomic group to each other, in relation to their absolute distance. And use this as guideline for erecting taxa (holophyletic and paraphyletic ones) because we can use the molecular data (supposedly neutrally evolved) to correct inherent bias in the morphological data (e.g. due to positively selected traits, homoiologies, symplesiomorphies misinferred as synapomorphies (and v.v.; clades easily become grades and v.v. in phylogenetic trees in any part comprising short internodes). And the morphological (dis-)similarity to decide which of the 2n+2 clades in the rooted tree should be named. This is now pretty much the standard when neosystematicists talk about “monophyletic” groups (genera, tribes, families, orders), you may read “cladistic classification” but in strictly speaking it's a clado-phenetic or pheno-cladistic classification.Delete
For extinct groups, it's much more difficult, since we lack the much needed comparative data. It's obvious morphological evolution was not parsimonious and that similarity can be severely misleading, too. So, one really needs to assess the stability of the background tree and explore the signal in the matrix. And keep an critical eye on one's “synapomorphies” or unique character suites characterising a holophylum.
As exemplarily seen in king fern rhizomes, for (palaeo-)systematics fusing “cladistics” (in the traditional sense, i.e. pre-Farris) with phylo-phenetics (viewing distance distributions in an explicit phylogenetic context) is a viable way to do it (open access paper):
Bomfleur et al. (2017), The fossil Osmundales (Royal Ferns)—a phylogenetic network analysis, revised taxonomy, and evolutionary classification of anatomically preserved trunks and rhizomes
The same procedure and logic could be applied to all purely or mostly extinct
groups, and I've no doubt it would lead to much more stable phylogenetic classifications: having names and explicit thresholds for when we should give a clade a name, and where we have to do with (potential) paraphyla to keep things simple and applicable (the number of unranked "Clades" between the MRCA of today's Aves and the MRCA of all related dinosaurs is simply ridiculous and pointless).
Just a quick question for now: what do you know about PeerJ.com? I only came across it last month, through an article in one of its many journals, PALEONTOLOGY AND EVOLUTIONARY SCIENCE (yup, it's in all caps). The 2019 article I skimmed included the cladism zealot Mickey Mortimer as one of its co-authors, and so far I am unimpressed by it. Do you happen to know anything about its reputation among evolutionary biologists, and of PeerJ.com among scientists in general?Delete
Paleontology and Evolutionary Science is the topic section within the journal PeerJ. PeerJ is, to my opinion, currently one of the best journals (if not the best) and honest publisher on the market (reasonably low APC, highly professional paper handling and proofing) because they have a very strict open data policy, and actively promote peer review transparence. If the authors opt for it. So, it's very easy to see how good a paper is. If an established veteran author doesn't opt to publish the peers' reports on the articles page, it's a sign it was pal-reviewed or included some unpleasant (to the veteran author) reviewer comments. Note that pal-review is pretty common, and including flagship journals such as Science or Nature (a recent example). Review transparency (see my second Res.I.P post) is the only counter-measure against (inevitably) compromised peer review.Delete
Furthermore it promotes post-publication discussion by its (starting to be used) Q&A option. Which is a good thing to do. We cannot expect anymore that a single reviewer knows all there is to know about a study, and being an handling editor, having to find people willing to do proper reviews, is the worst possible job in all of science.
We hence explicitly chose PeerJ as venue for all our research including the Osmundaceae systematics, where we could expect hostile fire from the Mighty (incl. cladistic) Beasts of the Forest of Reviews. Because they don't like to see their profoundly destructive otherwise "anonymous" and "confidential" reviews out in the open.
For more on the topic, see my #FightTheFog posts.
With PeerJ we still got critical but profoundly constructive reviews, much in contrast to most reviews for studies we published with Holtzbrinck's (SpringerNature) or RELX's (Elsevier) cashcows. Because, cladism is the Holy Truth in palaeo- and neobotany, too, and, very obviously, most fields of palaeozoology. I have not yet crossed any palaeoverterbrate study that would fulfil my minimum standards for phylogenetic analyses. Those dealing with groups that still live today (bears, wolves, hominids) are much better in all methodological aspects (probably because any gene sequence kills the finely tuned morpho-cladogram, so you have to be a bit more open-minded rather than keep spinning the rat-wheel).
Really can recommend publishing there.