Talk: Cladistics

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I am amazed at the rate of progress of this article. The Wikipedia model is truly the most exciting, interesting and fulfilling model for an encyclopedia that I have ever come across! Congratulations! user:exigentsky

I don't think polyphyly, monophyly, and the like are really cladistics terms, are they? After all they refer first and foremost to the evolution of the group in question; for instance the claim that the arthropods are polyphyletic is a hypothesis about their origins, which certainly cladistics have been used to help evaluate, but also more traditional lines of reasoning. From what I have seen, to, the trees constructed usually come out reasonably close to one another.

Go ahead and fix it to your taste. I don't have anything against the concept of cladistics, but the current practice violates a principle that it took a lot of painful experience to absorb. Namely, if the practitioners of an art can't/won't speak in clear, simple language, that's usually a symptom of massive confusion on their part. I do think the subject deserves an entry. DJK

I've seen some cladistics and as far as I can tell it uses no more jargon then any other field. A lot of the terms, as stated, are used by other methodologists as well. But more to the point, except for perhaps clade each of the words expresses a concept which doesn't really have a compact synonym in normal English. So they're somewhat unavoidable, just like jargon like endoplasmic reticulum is unavoidable in protistology.

Ah, one more thing I noticed. Cladistics is not a classification system, as stated on talk:Linnaean Taxonomy. It's a methodology for elucidating evolutionary relationships. Taxonomy ties in because cladists intend it to reflect the phylogeny of organisms. However this intention is shared by pretty much the majority of biologists. If you look at some of the more recent Linnaean schemes for, say, protists and flowers, you'd find everything up in the air for precisely these reasons. So objections to the practice on these grounds have kind of been superceded.

On these grounds I think I'm going to take a stab at rewriting the article. Please don't be insulted by this! I'll try and leave all your points except the above, but move them to a criticisms paragraph down at the bottom, since that seems to be the standard way of presenting a neutral point of view. Personally I think cladistics is neat, at least when it works, but takes forever to get used to. :)

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Hmmm. I think we can all agree that the ASCII tree is rather attractive.

-user:aezram

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I strongly beg to differ with Josh Grosse. Turtles are no more closely related to snakes than are mammals. And if it's given that birds are dinosaurs but removed from them in taxonomy, then that's paraphyletic. jaknouse 02:26 1 Jun 2003 (UTC)

The reptiles are very definitely paraphyletic, for exactly the same reason as the dinosaurs: they include an ancestral form, together with some but not all of its descendants. Remember that the ancestral amniotes are traditionally considered reptiles, so it doesn't matter what the relative positions of mammals, turtles, and snakes are (just for the record, though, turtles are now considered somewhat closer to snakes and birds than to mammals). The problem with giving dinosaurs as an example of a paraphyletic group is that they aren't always taken to exclude the birds. Josh

Yeah, that's right. Amniota comprises Synapsida, which gave rise to mammals, and Sauropsida, which includes anapsids (turtles) and diapsids (snakes and birds). The controversy over birds being dinosaurs has died down in recent years, but I think it is still too controversial to be a good example of a paraphyletic group. A better example would be class Osteichthyes (bony fishes) being paraphyletic, since one group of fish gave rise to Tetrapods. SCCarlson

The fishes are a good example of a paraphyletic gropup, but the Osteichthyes are sometimes taken to include the tetrapods. The same sorts of extensions are done with the Sacropterygii, Reptilia, and Dinosauria, while the Amphibia may be restricted to a holophyletic group. Among the major vertebrate groups, the only formal taxon I can think of which is unambiguously paraphyletic is the Agnatha, which relatively few systems still use.

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I'm planning to add a brief section in the textual criticism article about the use of cladistic analysis techniques borrowed from biology. I just thought I'd run it past people here first for coherence:

"Cladistics is a technique borrowed from biology, where it used to determine the evolutionary relationships between different species. The text of a number of different manuscripts is entered into a computer, which records all the differences between them. The manuscripts are then grouped according to their shared characteristics. The difference between cladistics and more traditional forms of statistical analysis is that, rather than simply arranging the manuscripts into rough groupings according to their overall similarity, cladistics assumes that they are part of a branching family tree and uses that assumption to derive relationships between them. This makes it more like an automated approach to stemmatics.

The major theoretical problem with applying cladistics to textual criticism is that cladistics assumes that, once a branching has occured in the family tree, the two branches cannot rejoin; so all similarities can be taken as evidence of common ancestry. While this assumption is applicable to the evolution of living creatures, it is not always true of manuscript traditions, since a scribe can work from two different manuscripts at once, producing a new copy with characteristics of both.

Nonetheless, software developed for use in biology has been applied with some success to textual criticism; for example it is being used by the Canterbury Tales Project to determine the relationship between the 84 surviving manuscripts and four early printed editions of the Canterbury Tales."

Obviously it needs some wikifying, but I wanted to check I hadn't horribly misrepresented what cladistics is before posting it to the textual criticism article. Any thoughts? Harry R 12:20, 6 Jul 2004 (UTC)

OK, I've taken your silence as approval (or indifference?) and posted it to textual criticism. If anyone sees a problem, could you take it up there please? thanks. Harry R 09:35, 8 Jul 2004 (UTC)

Harry: Interesting idea. Only criticism: "stemmatics" is spelled "systematics." --Cladist

Hi Cladist. Thanks for looking at this. "stemmatics" is a technical term in textual criticism, "stemma" being the technical term for a family tree of manuscripts. [1] is an example of the kind of thing. Harry R 10:08, 20 Jul 2004 (UTC)

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All: I'm amazed at the depth of this article on a relatively obscure field. The authors are to be commended. However, there is some confusion in the Cladistic Methods section. It is certainly true that it has "taken some time for cladistics to settle in." There is much debate about the use of Cladistitcs. However, the sentence continues, "...and there is some questioning over in just what sort of circumstances cladistics is applicable." While there is debate about the use of numerical methoids like Parsimony and Maximum Likeelihood, I don't think there is much formal debate about the use of phylogenetic systematics (that is, the adherence to phylogenetically relevant, clade-based taxonomies). Phenetics does not have many supporters in the systematics world. In my experience, even those systematists who do not care for numerical methods would never purposefully erect a new paraphyletic taxon. Thus, it is not _cladistics_ that may be regarded as inappropriate under certain circumstances, but the methods of _numerical_taxonomy_, including parsimony. In fact, Henig never mentioned parsimony. This is a fine distinction that is often glossed over in the literature, but I would love to see it clarified in this article. Perhaps we could change the above-quoted sentence to read: "Cladistics has taken some time to settle in, and there is still wide debate over how to apply Henig's ideas in the real world." --Cladist July 20 2004 (incidentally, I chose my handle before I saw this article. I didn't intend to sound so arrogant)

Hi, thanks for the comments. Feel free to Be bold and improve the article in ways that you see fit. For large textual/structural changes (particularly for deletions), it's always good to discuss them here in Talk, but go for your life! We really need somebody to help work on the various articles on phylogenetics, systematics and the like. My knowledge is more in the population genetics area and my grasp of systematics is much less firm. There is much duplication and some of the various articles could be merged, or at least structured and interlinked in better ways. --Lexor|Talk 07:58, 20 Jul 2004 (UTC)

Thank you. I have begun working on it (check out the first section). Next I want to talk a bit more about synapomorphies in the Intro section. Eventually, I'd like to start tying all the systemtics articles together, but I don't think my advisor would count that toward my dissertation requirements... --Cladist July 21 2004

Cladistics can refer to numerical taxonomy or to clades-only approaches to classification. Note the latter is not the same thing as phylogenetic classification, which may allow paraphyletic groups, and is rejected by at least some notable biologists. In particular I think it is unpopular among those specializing in basal groups, like protists or extinct vertebrates, where it has led to numerous difficulties. I've notably changed the article to reflect this. Josh 10:03, 10 Oct 2004 (UTC)

Josh: I beg to differ. In common parlance (as if common people speak of cladistics vary often) you are correct, however, I believe you are missing the history of the terms. Numerical Taxonomy was a rising field before Cladistics became popular. Numerical Taxonomy referred to a suite of techniques in which mathematical "rigour" was applied to the science of taxonomy. Cladistics was a separate development in which the use of synapomorphies was held to be philosophically superior to the use of symplesiomorphies (not to be confused with symplesiosaurs, which were the first aquatic organisms believed to perform musical concerts). However, Henig did not recommend any particular numerical approach, and did not foresee the mathematical problems that are caused by excess homoplasy in the dataset. Parsimony Analysis, the first blend of numerical Taxonomy with Cladistics, was the solution proposed. Thus, we can use Cladistics in the original sense of "clades-only approaches to classification," or in the modern sense of parsimony-based cladistic numerical taxonomy, but we would be wrong to use 'Cladistics' as synonymous with 'Numerical Taxonomy'. Parsimony-based Cladistic methods are at best a sub-set of Numerical Taxonomy. Again, in common parlance students of "phylogenetic classification" might decide to use paraphyletic groups, but strictly speaking the two are mutually contradictory. "Phylogenetic Classification" is the use of phylogenies to produce classifications, and hence does not brook paraphyly. If it did allow paraphyly, there would be no limit to the arbitrary taxa that taxonomists could erect. Do you perhaps have "Phylogenetic Cassification" confused with "Evolutionary Classification?" In the latter, many evolutionary attributes (including similarity of adaptations) were collected to construct groups, and hence paraphyly was occasionally allowed. However, these are contentious issues. I would like feedback before changing anything in the article. --Cladist November 9, 2004