Talk:Cladistics

What is the topic of this article?
I find this article confused/confusing because it seems to me that it's not clear what its topic should be: is it "phylogenetic systematics" as used by Hennig (and called "cladistics" by its opponents), or is it the whole field of modern methods grouped under this term?

"Phylogenetic systematics" as Hennig used the term is not identical to "cladistics" for two reasons: firstly, "cladistics" was the preferred term of those hostile to "phylogenetic systematics"; secondly, "cladistics" is now used to cover a much wider range of methods than those of "phylogenetic systematics", some of which are directly contradictory to Hennig's methods.

Hennig advocated two main ideas which are related but logically different:
 * 1) Systematics should be based purely on evolutionary relatedness and not on morphological similarity. The only groupings (taxa) of value are monophylies (clades). The key aim should be to construct a hierarchy which corresponds to the evolutionary history of the species concerned.
 * 2) The only morphological features (characters) that are of value in determining phylogenetic relationships are (syn)apomorphies. Overall morphological similarity is irrelevant, since this may be due to symplesiomorphies, which are valueless in determining relationships.

(1) is now accepted as the aim of phylogenetic studies, although some taxonomists are then prepared to name a few paraphyletic groups in special cases, but with full awareness of their nature.

(2) is simply not a feature of modern computer-based methods. Parsimony, which still seems to be the dominant method for analyses based on morphological characters, considers all characters used in the analysis equally, although the choice of characters may be influenced by whether they are considered derived or primitive. Statistical models (Bayesian, etc.) used with molecular data treat all sequences equally, although again the choice of sequences to be used may be based on the selection of homologs. But careful selection of synapomorphies which define clades simply doesn't feature. Although these methods aren't exactly the same as phenetics (numerical taxonomy), they are in many ways more similar than it to Hennig's manual methods.

However, I'm unsure how to fix the article. The Methodology section is particularly confused between the first part – an explanation of Hennig's terminology and methods, and the second part – an over-brief survey of the very different methods used now and their development. Peter coxhead (talk) 15:50, 19 October 2013 (UTC)

Proposal
Having thought about the article and the related ones in Wikipedia, I propose that: Peter coxhead (talk) 18:12, 19 October 2013 (UTC)
 * This article be restricted to "phylogenetic systematics", i.e. "cladistics" in sense of Hennig and his opponents.
 * Material which relates to the broader sense of "cladistics" be moved to "Phylogenetics".


 * I completely agree. I am not going to edit the Cladistics page, as I am a partisan in various disputes with people who think of themselves as practicing cladistics.  But I do want to express myself here.  There seem to be various positions:

  Cladistics is the position that all groups in the classification system be monophyletic.  Cladistics is that, plus reconstructing the tree by nested synapomorphies.  Cladistics is those, plus using parsimony methods when you have reversals or parallelisms in your data.  Cladistics is all those, but only if you're a paid-up member of the Willi Hennig Society.  Cladistics is numbers 1-3, plus using likelihood or Bayesian methods to infer trees.  Cladistics is numbers 1-3 and number 5, plus inferring trees by distance matrix methods. 


 * This page seems to take position number 6, or perhaps number 5. To me this seems deeply incoherent.  The straightforward and coherent definition seems, to me, to be #1.  It is a position on classification, not on how the phylogeny should be inferred.  As such it is a sensible position, and certainly the dominant one these days.   This page is basically talking about two things at once -- how we infer phylogenies and how we define groups in the classification system.  It is a mess.  But people should realize that my view on this is my own, and not shared by most systematists, who are wildly divided among the various posiitons listed above.  The confusion in the main article about what "cladistics" is simply reflects the state of the field and the wildly mixed messages that it gives to the outside world.  'Nuf said.  Felsenst (talk) 11:36, 31 October 2014 (UTC)


 * Our task is not to take any position, but to say what the positions are (in one article, or several). That allows us to say that the term is used in different ways, and indeed that there is confusion about it. What an article must not do is to get sucked into the confusion. The way to avoid this is to say clearly and verifiably who said what. Chiswick Chap (talk) 12:25, 31 October 2014 (UTC)


 * I don't think it's quite so simple. As Felsenst's analysis above demonstrates, I think, a large part of the problem is that the term "cladistics", when interpreted broadly, doesn't correspond to a, and a good Wikipedia article – indeed any encyclopedia article rather than a dictionary entry – needs to be about a topic. The term "cladistics" has been used in so many different senses that trying to cover them all in one article would still produce a confused and confusing article even if each sense could be clearly explained using reliable sources (which I doubt).
 * Going back to my suggestion, what exactly distinguishes this article from Phylogenetics? If there are two articles, there must be some demonstrable distinction between them. What exactly makes the Methodology section and the two Terminology sections part of "Cladistics" rather than "Phylogenetics"? Peter coxhead (talk) 14:49, 31 October 2014 (UTC)
 * So we just say clearly up front that this article covers Cladistics in some narrow sense (say, #1), and see Phylogenetics for the rest? That sounds sensible and defensible (and I'd be happy to !vote for that). It means removing all uses of 'cladistics' in the broad sense from the article. Chiswick Chap (talk) 16:07, 31 October 2014 (UTC)
 * The problem is that among systematists there is general confusion as to which of the above definitions of cladistics is correct. To me #1 is the only really defensible one, but my views on this are controversial, to say the least.  No matter what position the page takes a lot of people in the field are going to say it is wrong.  Enjoy, folks.  Felsenst (talk) 05:50, 2 November 2014 (UTC)
 * ... and I should add that while systematists have wildly different positions on what is "cladistics', the one thing that unites all of them is the belief that their position is the one everyone else also agrees with. Felsenst (talk) 14:40, 4 April 2019 (UTC)
 * - your excellent analysis, above, may help clear the confusion for laymen like me - especially if it were included in the article, as it would expose the confusion that (you believe) still exists in the minds of (professional) systematists. But of course, as user:Chiswick Chap rightly says — and it bears repeating, "What an article must not do is to get sucked into the confusion. The way to avoid this is to say clearly and verifiably who said what".  yoyo (talk) 00:46, 19 January 2020 (UTC)
 * Yes, thanks. I'm glad that I still think so all these years later. Our task is to report, accurately and reliably, no matter how many different positions the experts hold (whether we personally have a "side" or not). Chiswick Chap (talk) 10:12, 19 January 2020 (UTC)
 * Good luck. Over the years every one of those positions has been taken by one or multiple systematists.  If there is one thing I have no time for, it is to chase down all those positions, some of them quite vaguely stated, and carefully attribute them.  Perhaps some of the people who created this muddle could take it on, instead of leaving it as a massive burden to us poor drudges. Felsenst (talk) 11:59, 21 January 2020 (UTC)

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Too technical
The first sentence of : The cladistic method interprets each character state transformation implied by the distribution of shared character states among taxa (or other terminals) as a potential piece of evidence for grouping. contains or implies the following technical terms:
 * character
 * character states
 * character state transformation
 * grouping
 * taxa
 * terminals

— none of which have not been explained adequately — or at all! — to our intended audience: interested laymen. Also, a "method [that] interprets [x] as a potential piece of evidence for [y]" sounds awfully vague and … unsystematic. So I've marked it as needing clarification. It's beyond opaque; more akin, perhaps, to a black hole, that actively destroys any attempt at examination! ;-) Will somebody - perhaps a topic expert who is also an expert educator and explainer - please step up and make this sentence — and ideally, the whole article — more accessible to the likes of me?  That is, to somebody who is fascinated by the diversity of the natural world, yet sure that scientific methods can help them make sense of it all.  yoyo (talk) 01:06, 19 January 2020 (UTC)

Cladistic Revolution?
Being that there is no Wikipedia page for the Cladistic Revolution, I assume that this is the article that covers it. However, there is no reference within the article to the term and nor is there a redirection. This is a problem as several Wikipedia articles refer to such a thing as a "Cladistic Revolution". For example: https://en.wikipedia.org/wiki/Aysheaia

Not being at all familiar with how things are done on Wikipedia, it seems to me that the solution is to create a section within this article to define what the Cladistic Revolution is/was. 122.58.212.69 (talk) 05:36, 17 September 2021 (UTC)

paraphyletic: fruitless
Wrote precisely delineating paraphyletic groups (grades) are fruitless to precisely delineate, especially for extinct species. There are actually two meanings to this: It is virtually impossible to do, and the results are meaningless. Contenting that both hold. In principle one could define "all descendents of X, which are not the descendents of the last common ancestor of Y and Z", or "all descendents of X which are not descendents of Y", but as stated before, under the mantra of parsimoniousness, one should make a case about why that would be a particular interesting group. It necessarily is another layer of unnecessary complexity, at least while it is still being figured out what the basic relationships are. Lumping e.g. stem groupings together, which is what typically happens, is anti-helpfull, as it appears as a validation that it's ok that it is not further resolved. Further resolving stuff would often reveal that the stem grouping do not belong together, but that the one of them is most closely related to the resulting branch, and that the other stem branches are usually further apart from each other. Purposely ignoring here all kinds of arguments that continued evolution brought certain groups closer together or further apart in the way they live, which probably changed anyway from the moment these branches separated. Jmv2009 (talk) 16:17, 20 April 2022 (UTC)