Talk:Cladistics/Archive 1

This is an archive of past discussions about Cladistics. Do not edit the contents of this page. If you wish to start a new discussion or revive an old one, please do so on the current talk page.

Archive 1

Archive 2

Archive 3

Archive 4

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Cladistics is first and formost distinguished from other phylogenetic approaches by its consistent denial of paraphyletic groups, that is, its literary interpretation of the illustration of phylogenies. That's the original reason for its name. On the Swedish Wikipedia page a cladist called this a distinction of relative relationships as different from absolute relationships. However, Envall (2008. On the distinction of mono-, holo- and paraphyletic groups - a consistent distinction of process and pattern. Biol. J. Linn. Soc. 94:217-220) recently showed that this distinction rests on a confusion of pattern and process, which actually is falsified by a fact. The reason is that the confusion equalizes space and time, leaving no possibility for time to be relative to space, which it obviously is. It means that this fact falsifies the cladistic denial of paraphyletic groups, It is simply impossible to deny paraphyletic groups without contradicting facts.
This falsification appears far-fetched, but is none the less a fact, and it actually indicates much worse problems with the approach. It is just the small top of a huge ice-berg of paradoxes relating to its consistent inconsistency as being the orthogonality to science. It is simply totally wrong.
I have tried to include this information as a disclaimer at the top of the article about cladistics, but the editors have decreased it into a small note in the criticism section saying that "Envall claims to have falsified cladistics' denial of paraphyletic groups empirically" just as if falsifications are claims. It's unfortunate that Wikipedia's editors lack understanding of science. They probably think we should vote about whether it is a falsification or not, or wait to see if it is. The truth is that opinions are irrelevant; cladistics will, of course, continue denying the difference between space and time, and thus the fact that time is relative, whereas time will, just as of course, remain being relative to space despite cladistics' denial that it can be.(Read this comment fast. Cladists will delete or remove it as soon as they lay their eyes on it. It isn't easy to be falsified on a fundamental level. Many of these cladists are teachers on governmentally sponsored universities spreading their confusion to our kids using tax money). Consist (talk) 22:01, 1 July 2008 (UTC)

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. :)

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

-user:aezram

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 group, 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.

I must beg to differ with both Jaknouse and Josh. Both are partially correct and both are partially mistaken. It is true that _if_ birds are descended from dinosaurs, AND _if_ Aves are excluded from Dinosauria (AND hence excluded also from Reptillia), THEN both Reptillia and Dinosauria must (by definition) be paraphyletic. I happen to believe this to be the case, but I am no longer really in the dinosaur business. I believe that the cladistic purists now use the group "sauropsida" to indicate the clade that includes turtles, lizards, snakes, crocodillians, dinosaurs, birds and any other descendants of their common ancestor. HOWEVER, mammalia is definitely the living sister group to the sauropsida. The position of turtles is poorly understood, but it is generally believed to be either basal to the squamata (snakes and lizards) or somewhere around the archosauria (with a converent anapsid condition of the skull). In either case, they are probably not closer to the mammalia than to other sauropsids. The Mammalia and the Sauropsida seem to be the only living Amniotes if the latter are defined as a node-group. I agree whole-heartedly with Stephen about using the fish as an example of a paraphyletic group. Another choice to consider would be the invertebrata. --Cladist Jan 12 2005

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)

"Cladistics" in biology came about millenia after scholars began comparing features of manuscripts to develop a stemma; scholars in Alexandria had collected manuscripts of Homer and had published a critical text long before monks got around to doing the same thing in their spare time between prayers, in turn long before biologists began applying the same methods to taxonomic classification. Textual criticism has its own set of traditional tactics, such as "lectio difficilior," corresponding to the "cladistic" tactics such as "maximum likelihood." It seems to me that "cladistics" does not inform criticism so much as vice-versa -- to the point that this is another example of modern scholarship reinventing (and renaming) the wheel.

The idea of classification based on shared derived characteristics appears to have independently invented in systematics (as "synapomorphy"), stemmatics (as "common errors"), and historical linguistics (as "shared innovations"). In fact, one researcher has proposed that these three seemingling different fields could all be thought of as belonging to the field of palaetiology (see http://rjohara.net/cv/1997Scripta.html ). Unfortunately, there has not been a whole lot of cross-polination between the biological field and the other two philological fields until the 1970s. The "traditional tactics" or more commonly, the "canons of textual criticism," seem to be more more analogous to various ways of polarizing the characters (as the outgroup criterion is not so available in textual criticism.) Stephen C. Carlson 13:37, 2005 September 11 (UTC)

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

The classifications I'm referring to don't allow groups based on convergence, which would be polyphyletic, but do allow classifications based partly on plesiomorphies, which are paraphyletic. I don't think I have the terms confused, or if I do, so do enough biologists that I'd say their meanings aren't really set in stone. See the following note.

Part of Henig's genius was in recognizing the distinction between paraphyly and polyphyly (which had hitherto been treated as the same phenomenon), and showing that the exclusion of descendants from a group was as problematic as excluding the common ancestor.

I've removed this, because it seems wrong on several counts. First, it doesn't make any sense for him to have discovered that paraphyly is as bad as polyphyly if nobody noticed the difference before. Second, I'm pretty sure paraphyly was originally identified with monophyly, and a few biologists still use the term that way.

Third, and most importantly, not everyone agrees paraphyletic groups are bad. In fact, they're necessary to provide a comprehensive classification of ancestral organisms, as argued by people like Cavalier-Smith and more or less admitted in the PhyloCode guidelines. To put it simply, what family did the Hominidae evolve from? Either there is no answer, or the answer is a paraphyletic family. It's hard to say the former is a definite improvement, and Hennig certaintly didn't show it was. Josh

Josh: I have restored the quote that you excised, with the correction that it was monophyly, and not polyphly, that was confused with paraphyly. I think you will find that this makes more sense. As for your objection that some biologists accept paraphyletic groups, this is true; however, they are not cladists. Many biologists reject cladistics outright because it is inconvenient.

Also, I have a problem with your comment about Hominidae and subjective classifications. Your arguments do apply to species, but not to other ranks of taxonomy. In cladistics, all clades are expected to have descendants, and these are automatically included in the clade. Thus, the hominidae will always, automatically include all of the descendants of humans, of chimps and of gorrillas (etc), even if they should become something very different. Linnaean taxa do not have this property, and this lack makes them problematic. Thus Linnaean ranks are artificial (because human priority determines which species will be included or excluded), and I don't think anybody who undestands the issue would seriously dispute this notion. SPECIES on the other hand, are a different matter. Species are notoriously poorly defined. Check the literature for the phrase "species problem." There are as many definitions of the word species as there are hairs on your head, and not all of them assume that a species is a real, natural unit. One real problem with some species definitions is that species are paraphyletic: that is, the descendant of a species is automatically excluded from the species. There have been species definitions that seek to avoid this issue, however.

In any event, the Homo sapiens problem you point out is a problem of species definition, not of cladistics. The best that the authors you allude to can say is that we should not require all taxa to be monophyletic, because we cannot require species to be monophyletic. This is a straw-man argument because cladistics is about higher taxa, not species.

Personally, I see it this way: Higher taxa/clades are sets whereas the species are elements of the sets. We expect a set to include all subsets, but we need not expect an element to include anything. The set of all primes includes all the primes we can count, plus the ones we haven't counted yet, but each prime is only a number, and does not include anything. If you object that species include individual organisms, I can respond that a prime number is equal to the sum of some other set of numbers - but this is a different kind of set. If you object that a set of primes is not analagous to higher taxa in that it includes only elements, but no sets, I can respond that the argument works just as well (or better!) with the set of all pairs of prime numbers, or the set of all pairs-of-pairs of prime numbers, ad infinitum. ----Cladist 05:49, Feb 14, 2005 (UTC)

I'm sorry, Cladist. You missed my point regarding the article. Hennig did not prove paraphyly is as bad as polyphyly. Many biologists don't think it is. Some of them accept cladistic methodology in full for uncovering and describing evolutionary trees, but think clades and taxa should be kept as distinct notions. I don't know if you count them as true cladists, but their opinions means that the the evil of paraphyly can't be described as a fact.

Also, I'm not convinced nobody noticed the difference between monophyly and paraphyly. It's true the latter have been called monophyletic, but in that case there is still a separate word for the former, holophyletic. When were they introduced, and was it a new distinction, or did it reflect something people already discussed in other terms? There is so much material that assumes everything besides clades is garbage and bends the truth, I would like to see a reference.

I'm entirely aware how cladistics works, and this includes both its strengths and weaknesses. First, one should realize that neither monophyletic nor paraphyletic groups exist in nature, since the evolutionary tree is essentially continuous. They're labels you apply to sections of it. Every cut you make gives a monophyletic section above and a paraphyletic section below. It's not inherently more valid to name either one.

The argument I gave does apply to taxa at all levels. The common ancestor of the Hominidae and Cyprinidae can be placed in a phylum, but it is impossible to give it a monophyletic family. Some take one way out of this, abandoning ranks. Some take another, abandoning the requirement of monophyly, although they may still use clades to describe relationships. Neither option is inherent in nature, and I think we need to keep this in mind.

As such, I think we shouldn't have the passage, or anything else that asserts that clade-based classification is inherently better. It isn't, just appropriate for different things. Josh

Josh:

You make some good points and some bad ones. I can see you have put a lot of thought into this. You are correct that I mis-read your argument re: Hominidae and Cyprinidae. It had nothing to do with the species problem. I especially appreciate your desire to see references. I recommend (a) Phylogenetic Systematics, by Willi Henig and (b) Inferring Phylogenies ch. 10 ("A Digression on History and Philosophy"), by Joseph Felsenstein. Would you be so kind as to tell me which of Cavalier-Smith's articles provided you with so much information?

I am going to ask you to agree to restore my paragraph, but precede it with a clause such as, "Proponents of Cladistics believe that..." or "For cladists,..."

The essential reason is this: If we qualify the paragraph as I requested, it is certainly true, whereas if we remove the paragraph, we remove essential information about cladistics and the history of Systematics.

Now I have the following comments to make on your paragraph:

1. "Evolutionary taxonmist" is a phrase that is unfortunately similar to "Evolutionary Systematics." The latter was an early school of Taxonomy / Systematics proposed by Ernst Mayr and George Gaylord Simpson. You might in fact have been reading their works. In that case, you want to say "The School of Evolutionary Systematics, propounded by... etc." and state who said these things (Instead of "Other evolutionary...". Mayr and Simpson are not nobodies. Their work on Systematics and Population Ecology/Genetics are foundational to the rest of modern biology. However, their works on Evolutuionary Systematics are very much out of date. Active systematists mostly disregard the ideas you have cited, because it no longer matters what you call an organism, so long as you know its relationships to other organisms. Your sentence makes it sound as if there are many of these people, rather than a few hangers-on.

2. I looked up one of Cavalier-Smith's articles. He does use the term holophyeetic to mean monophyletic, and probably does this to distinguish monophyly from paraphyly. However, he also seems to be expressly concerned with whether or not a group is paraphyletic. Your paragraph would have it seem that modern writers do not care about this distinction. Cavalier-Smith may wish to keep the taxonomy as-is, but difference between paraphyly and monophyly is meaningful for him.

3. Your discussion of Hominidae is very unclear; at least it does not mean what you later described in this discussion page. I think this is where my confusion came from.

I suggest this alternative:

Other taxonomists argue that paraphyletic taxa provide information about significant changes in organisms' morphology, ecology, or life history; in short, that taxa and clades are both useful but separate notions. A few use the term monophyly in its older sense, where it includes paraphyly, and many use the alternate term holophyletic (which means monophyletic, sensu Henig) to emphasize the distinction between monophyly and paraphyly.

I have removed the Hominidae argument because it needs severe re-working, both in terms of content and clarity. But note that this is only a suggestion. For now I leave the decision to you.

--Cladist 12:44, Feb 20, 2005 (UTC)

Cavalier-Smith gives a quick defense of Mayr's system in A Revised Six-kingdom System of Life. He is not trying to keep the taxonomy as is, and in fact many of the paraphyletic taxa are ones he introduced. He doesn't distinguish them from monophyletic taxa because they are inferior, but because the distinction is still important to anyone studying evolutionary relationships.

For classifications of Protista, Cavalier-Smith is the only one who explicitly uses a system other than Hennig's, but I have seen a number of others that use paraphyletic groups without comment. I have seen various arguments against clades-only systems, and palaeontologists in particular seem to have issues with them, as one might expect since they deal largely with ancestral groups. Treatises on vertebrates that avoid paraphyletic groups seem not to exist. As such, while they appear to be in the minority, I am not convinced evolutionary systematists are only a few hangers-on.

I will try to find copies of the references. In the mean time, rather than restoring your quote, I've tried altering the entire section to make both positions less opaque. Please let me know if you have any complaints. Thanks, Josh

Josh:

Much better. I added a phrase that clarifies the reason why cladists regard non-synapomorphic characters as arbitrary. I still have problems with the next paragraph, but I can't think of a good replacement for now. Good work! -- --Cladist 18:10, Feb 21, 2005 (UTC)

Terms

Hey! Looks like we get a gold star -- nifty! Just a comment on semantics: I notced that someone used the term "developed" where "evolved" might have been more appropriate. The two are interchangeable in common parlance, but "develop" is unfortunately used in biological jargon to describe ontogeny (i.e. growth and differentiation of an organism), not evolution, and it is extremely important to distinguish the two. I corrected the example I found. Hope I don't sound like a word-nazi. --Cladist

Could someone please explain the term basal? The page was a redirect, but the term does not even occur in this article! Sebastian 07:04, 2005 Feb 7 (UTC)

References

Hi, I am working to encourage implementation of the goals of the Wikipedia:Verifiability policy. Part of that is to make sure articles cite their sources. This is particularly important for featured articles, since they are a prominent part of Wikipedia. The Fact and Reference Check Project has more information. Thank you, and please leave me a message when you have added a few references to the article. - Taxman 18:50, Apr 21, 2005 (UTC)

Teleology

I must take exception to one particular statement in this article, but before I do, I want to give kudos to the authors, and especially Josh and Cladist (who seem to have done a large share of the work, at least it appears so from the talk page). I am a common layman in terms of knowledge in cladistics and other specialized sciences. Before reading this article, I couldn't tell a clade from a synapomorphy. After reading the article (and the talk page, which was interesting in its own way), I can tell you that I have some idea of what all this is about, which is exactly what an encyclopedia article is supposed to do. Great job! On a sidenote, I think that in some cases I've learned as much about a subject by reading talk pages as I have from reading the actual articles. It is just a different side of the subject. Perhaps someone should create some sort of celebration of talk pages and their inherent value as sources of information, aside from their obvious and intended use as discussion forum. Perhaps someone has.

Back to my small criticism. Towards the end of the article, under "Cladistic classification," there is one sentence which I feel should be reworded to maintain NPOV. I am somewhat disappointed that, though earlier in the article a specific reference was made to avoiding value-judgments, in this particular line there is one. The line is: Many argue that they lead to "gradistic" thinking, where groups advance from "lowly" grades to "advanced" grades, which can in turn lead to the error of teleology.

I will admit that I did not know the exact meaning of teleology when I read that sentence, so I followed the link. Now that I know what it is, I take exception. Calling teleology an error is definitely a value-judgment, and therefore POV by definition. The problem with a cladist accepting teleology as a presupposition is not that it is erroneous, if it is. That is beside the point, and should not be addressed in this article. The problem with a cladist accepting teleology is that teleology is inherently non-scientific. It addresses questions outside the realm of science, which science cannot and will never be able to answer. Therefore it, along with philosophical naturalism (its opposing approximate equivalent), must be excluded from scientific discussion, as outside the realm of scientific inquiry. Therefore, the line should read something like: Many argue that they lead to "gradistic" thinking, where groups advance from "lowly" grades to "advanced" grades, which can in turn lead to teleology. Teleology should be avoided as outside the realm of science.

Since Wikipedians should be bold, I will be, and go ahead and change that line, but I wanted it here for the record.

I hope I myself have been NPOV and clear-speaking in this comment, and I welcome any comments pro or con. --Cromwellt | Talk 03:05, 30 September 2005 (UTC)

Cromwelt: Thank you for the many compliments paid to this page. I know I worked hard on it, and it was well developed before I found it, and it has changed substantially since I last had time to play with it. Good work Everyone! Regarding Teleology: Would it be fair to say that teleology is outside the bounds of a historical science? Teleology implies a plan that in this case cannot be detected by empirical means. In fact, I'll just add that bit and see what happens. --Cladist 5/15/2006

Featured article review of December 7, 2005

This review resulted in the passing of a new version of the article. Some minor extant issues remain unsolved, including remove "see also"s and "see below"s, add inline citations, generally copyedit (passive voice), make examples in text match the images.

This was the version promoted in february of 2004, and here's how it has changed. Looks like largely a rewrite, though at least a few bits are the same. All in all, apparently positive changes, certainly quite a bit clearer (at least to me). One new diagram, the last -- maybe it's just me, but I find that caption confusing: are these three ideas different formulations of the same idea, or are they competing schemes? The new version could probably use a little copyediting (I notice a good bit of passive voice, for example), and inline citations would be very nice. At the very least, I note at least one weasel-wordy "cladists argue" which should be attributed. The "see also" section looks like it isn't really necessary; if those links are not already in the article, they should be, and the section removed. Tuf-Kat 18:23, 17 November 2005 (UTC)

Points to improve on the current version:
- differentiate the two intro sections, with an unhelpful first sentence. (I actually prefer the original Feb 2004 opening)
- integrate the "see below"'s into useful prose.
- make examples in the text match the images.
- integrate "See also" list into article.

--maclean25 05:33, 21 November 2005 (UTC)

- - I have closed this review. Removed the introduction section header, which is redundant with the lead (which was short anyway), and partially reverted the first sentence to the original version because I agree with Maclean on that. Some of the see alsos I integrated and removed, some I didn't because I wasn't sure how. Tuf-Kat 09:23, 8 December 2005 (UTC)

Cladistics as method not compatible with Linnaean Taxonomy

Cladistics is a method that suggests hypotheses of phylogenetic relationship based on the statistical analysis of similar elements, detecting traits (characters) derived (apomorphics) or primitive (plesiomorphics) in a certain taxonomic group, generating cladograms, that are graphic representations of the several clades (hypotheses of relationships according to the homology criterion). The main function of Cladistics would be support to the classifications such as Linnaean Taxonomy (Darwinian); excluding the elements that represent evolutionary convergence which are not similars (not affined). Then Cladistics is only a method, but this by itself doesn't mean anything! The problem is in Cladism and Cladonomy!

As method of relationship analysis (actually hypothetical) among similar beings, it can be made a cladistic analysis of the elements (even objects) but not to establish your "relationship degree" or kinship; it is only applied by Systematics (that is, general science of classification, including among others: Taxonomy), as approach, when using of the phylogenetic criterion. To establish the relationship degree implicates in using a ordering system of hierarchical and formal type like taxonomic categories, which are mutually exclusive and that assign live beings (taxa) at the ranks (several classes) that form a taxonomic system.

To classify phylogeneticly, we should to apply the darwinian concepts of the descent (cladogenesis) with modification (anagenesis). Cladism only applies cladogenesis criterion, thus it makes a "cladification" (after Mayr & Bock, 2002). The basic error of Cladism is to ignore that to classify means to analyze similarities and differences, and not only similarities, like they do. And to classify doesn't mean merely to create genealogies of species. Its terminology is "funny" (sister groups, etc).

By the way phylogenetic criterion is not exclusive of Cladistics. It must not be called "Phylogenetic Systematics" because it is not the unique to use this criterion (that is arrogance!).

The Truthful Taxonomy is based (solidly) in rules established by Linnaeus, initially, and defined later by International Code of Botanical Nomenclature or ICBN and International Code of Zoological Nomenclature or ICZN. Thus Cladistics is not taxonomy!

Clades do not fit the taxonomic categories (taxa), like Genus, Family, Order, etc, they are just informal hierarchical levels (and therefore must not be named, it is preferable to use numbers to not to augment the confusion, that already is great). Another common error is the "taxonomization" of clades, that is, the creation of several useless "pseudotaxa" to fit to clades.

Clades do not exist in Nature! They do not have exact correspondence to natural beings. They are just hypotheses of relationships among taxa according to their homologous similarities. Taxonomic categories are abstractions (with the important exception of the category species, see below), but they correspond to natural and concrete elements (= taxa), specimens of plants or animals registered at the several herbaria and Natural History museums from world-wide as holotypes, isotypes, syntypes, neotypes, epitypes or lectotypes (nomenclatural types). The nomenclatural type is permanently associated with name of taxon. Clades are distinguished for its informality and instability (see Critic of Method), and therefore they represent a risk for Biology.

The Phylocode (system of rules for Cladonomy) will never substitute the Linnaean Taxonomy and ICBN.

Phylogenetic Concepts

Phylogeny's corollary: "The characters which naturalists consider as showing true affinity between any two or more species, are those which have been inherited from a common parent, all true classification being genealogical." Charles Darwin: On the Origin of Species.1859:391 [cited by Judd et al. 2002] This is the criterion that distinguishes a natural classification of an artificial one. August W. Eichler is the first person to recognize this criterion in Botany and therefore his system was also the first one to be considered phylogenetic (that is, natural).(after Aaron Goldberg (1986). Classification, Evolution and Phylogeny of the Families of Dicotyledons. Smithsonian Contributions to Botany 58:1–314.)

Note: To qualify a classification as artificial, not at all, reduces your practical importance, as in the identification of specimens.

"One of these original five theories of Darwin, and indeed the most important one to biologists in the latter part of the 19th century was that of common descent. In 1866, Haeckel introduced the term ‘phylogeny’, which corresponded quite strictly to this theory of common descent of Darwin’s bundle of five theories. That is, Haeckelian phylogeny is equivalent to Darwinian common descent (genealogy: theory 2 of Darwin, Mayr 1985. [Darwin's five theories of evolution. In D. Kohn, ed., The Darwinian Heritage, Princeton NJ: Princeton University Press], p. 758) and not to the entire bundle of Darwin’s five theories of evolution as often assumed by biologists and philosophers. Haeckelian phylogeny clearly does not include Darwin’s mechanism for evolutionary change (= Darwinian natural selection). But Haeckelian phylogeny clearly does include both the amount of evolutionary change (anagenesis [= modification sensu Darwin]) and branching (cladogenesis)." (from Mayr & Bock 2002)

Then it is deduced that in 1859 the term phylogeny was not applied and therefore Darwin used the ambiguous term genealogical.

Yet, phylogeny is totally different from genealogy.

Definitions of genealogy:

1. A record or table of the descent of a person, family, or group from an ancestor or ancestors; a family tree.
2. Direct descent from an ancestor; lineage or pedigree.
3. The study or investigation of ancestry and family histories.

[Middle English genealogie, from Old French, from Late Latin geneâlogia, from Greek : genea, family + -logia, -logy.] (from The American Heritage Dictionary of the English Language, Third Edition)

It is totally evident that this is a notion (only) applicable to humans.

This is the first (of many, see below) errors: the humanization of the phylogenetic criterion.

Definitions of phylogeny:

1. The evolutionary development and history of a species or higher taxonomic grouping of organisms. Also called phylogenesis.
2. The evolutionary development of an organ or other part of an organism: the phylogeny of the amphibian intestinal tract.
3. The historical development of a tribe or racial group.

[Greek phulon, race, class + -GENY.](from the same source cited above)

Then the first meaning is the one used in Systematics.

Evolution must not to be analysed genealogically, like a family tree, point-to-point, but collectively (at level of populations, populational criterion, with several elements = plural, "poly", not singular, mono = one).

Monophyly

Monophyly is a concept totally erroneous and obscure.

Distinction between Haeckelian and Hennigian concept of Monophyly, Hennig's concept is called Holophyly by other: There is a great confusion on this concept (monophyly):; "If all the species of a tentatively delimited taxon are the descendants of the nearest common ancestor, the taxon following Haeckel (1866) is called monophyletic (Mayr 1969, Mayr and Ashlock, 1991 pp. 253–255). Hennig (1950) introduced an entirely different concept. The study of phylogeny was for him a forward (to the future) looking process; its starting point was a stem (mother) species. The Hennigian distinguishes a phyletic branch containing the stem species and all its descendants as a taxonomic unit, as a clade, no matter how different the beginning and the ending of a clade may be. Hennig transferred the traditional term monophyly to his new concept of phylogeny, causing great confusion. To terminate it, Ashlock (1971) introduced the term holophyly for Hennig’s new concept. The traditional monophyly concept and the Hennigian holophyly concept have drastically different consequences in taxonomy. A holophyletic clade encompasses a stem species and all of its descendants. A monophyletic taxon consists only of the descendants of the nearest ancestral taxon." from Mayr & Bock 2002.

Takhtajan also draws the attention to the difference of the Hennig's concept of monophyly and the one of Haeckel. Takhtajan, A.:Diversity and classification of flowering plants, pp. 2-3, 1997: "The Hennigian concept of monophyly and paraphyly is misleading and, as Cronquist (1988:40) pointed out, 'is destructive to the taxonomic system'. The acceptance of this Hennigian concept would mean the destruction of many of the best-known taxa. It is quite clear that the traditional evolutionary concept of monophyly [in the Haeckelian sense] is entirely unambiguous and creates no difficulties in its application to taxa..."

From page Evolution: "In biology, evolution is the change in the heritable traits of a population over successive generations, as determined by shifts in the allele frequencies of genes. Over time, this process can result in speciation, the development of new species from existing ones."

It is important to point out that the subject of the speciation and consequently of the evolution is the population (populational criterion, collectively, that is, plural) and not a species or isolated individual (singular).

Then, which evolves are several (prefix poly) lineages (phyle) that are in this case, divergent and that eventually form new species, which is called speciation. Contrarily to the many people think it is not a species that originates (directly) the other ones, that is a vestige of the typologic concept of species.

Primary error of Monophyly: a species don't create directly the other, they have to surpass (to leap) the barrier of the reproductive isolation (pre-zygotic and post-zygotic mechanisms) and ecological (occupation of habitats - different and isolated niches) and only divergent lineages can make this, and it is therefore that there is an evolutionary leap. The reproductive isolation initially inhibits the formation of species and later it protects them of the mutual assimilation.

See: Judd et al. 2002. Plant Systematics, 2nd. Ed. p. 4: "An important exception to the rule of monophyly in the recognition of taxa occurs at level of species. The problem with monophyly at the species level has to do with nature of relationships above and below the level of species...This is so because blackberries and cherries, for example, do not cross or hybridize with one another. Within species, in contrast, branches join through mating between members of a species. Thus, during the separation of one species into two, matings may occur between members of the nascent lineages such that one cannot identify a common ancestor that is unique to either or both species.

Brummitt (2003) citing J. Cullen & S. M. Walters: "...the value of monophyly as a principle in classification has been shown to be zero."

Thus Monophyly does not exist, it is an erroneous phylogenetic concept.

Paraphyly

On the other hand "Paraphyly does not exist in a Darwinian classification" [= Linnaean Taxonomy]. (!) from E. Mayr & W. J. Bock 2002, J. Zool. Syst. Evol. Research 40:181. Berton 13:19, 5 October 2006 (UTC)

Polyphyly

Then only it remains the polyphyly of taxa. Berton 13:26, 5 October 2006 (UTC)

Evolution Concepts

Evolution is by leaps (that is, not continuous) (similar to the Thomas Henry Huxley's saltationism and punctuated equilibrium, but contrary to the phyletic gradualism).

This is an extremely easy concept: the divergent lineages have to give an evolutionary leap to surpass (to leap) the barrier of the reproductive isolation (pre-zygotic and post-zygotic mechanisms) and ecological (occupation of habitats - different and isolated niches) to form new species.

It is therefore that transitional fossils are not found.

Evidences in this sense: adaptive radiation, rapid changes caused by abrupt niche shifts (see Levin, D. A. 2005. Systematic Botany 30(1):9-15) lead to speciation. See also rapid modes of evolution.

The evolutionary lines are always discontinuous, suffering a true genic conflict, complex interaction of factors (mechanisms of speciation): genotypic (mutations, alleles, polyploidy, etc) and phenotypic (natural selection, allogenomic processes as endosymbiosis, plasmid transfer, infections for retrovirus: important mutation vectors, transposons and retrotransposons, etc) besides interferences of environment (hybridization, etc). See also Horizontal gene transfer#Evolutionary theory.

The hybridization (major mechanism of speciation, mainly in plants) is the principal evidence of polyphyly of taxa. Judd et al. 2002. Plant Systematics, 2nd. Ed. p.122: "Interspecific gene flow (hybridization, sometimes referred to as reticulation) plays a dual role in speciation. On the one hand it may reduce diversity by merging species. On the other hand, it can be a powerful force leading to speciation, especially when coupled with polyploidy, an important source of genetic variation within plant species". Berton 16:09, 5 October 2006 (UTC)

The changes are never gradual, but abrupt, because the "ancestries" either are adaptable or not, not existing middle term.It happens multiple structural divergences in the ancestries, and not isolated divergences.

Evolution is much more complex than the point of view of Cladistics!

Critic of the Method

Moreover, this method is highly distortional, the distortions can be:

resolution: as it has to be objective, it doesn't ponder the characters, it means that vegetative characters that have minor phylogenetic importance are equivalent (have same weight) to the sexual characters (actually, much more important phylogeneticly) and this is a great error; it needs of many characters and will look for them in genic polymorphisms, but from allogenome (that is, prokaryote DNA), and again a great error!
polarity: according to the choice of outgroup, cladograms will vary, becoming the system very contingent.
parsimony analysis made by beta softwares (that is, with bugs).
"configuration" (topologies): according to the elements (the "ingroup") that will be analyzed, the configuration of the cladogram could change completely. Now, do we know that the fossils have a primordial importance in the explanation of the phylogeny, and however I almost do not see analysis of fossils in the cladograms, how is that possible?
cladogram is not the same as phylogenetic tree. See Potter, Daniel & John V. Freudenstein. 2005. Taxon 54:1033–1035. "Since we never can know the true underlying phylogeny of a group of organisms, the only phylogenetic trees we can draw are hypothetical ones in which the ancestors depicted as giving rise to real (i.e., observable) taxa are based on speculation. Such phylogenetic trees are generally derived from cladograms, but there is a distinction between the two, and it is the latter that are derived directly from phylogenetic analysis of character state distributions, i.e., via the formulation and testing of hypotheses. Thus, cladograms fall strictly under the realm of science while hypothetical phylogenetic trees do not, and only the former should be used as the basis for constructing and revising classifications." But Hörandl, Elvira in Taxon 55:567 says: "So far the theory; now to the practice of classification. I do not agree with Potter & Freudenstein (2005) that 'we can never know the true underlying phylogeny of relationships' but I would rather say that usage of tree-building methods alone will fail to give insights in the underlying phylogenies. Admittedly, only at lower (species and generic) levels we may have a realistic chance to get insights into the kind of evolutionary processes..."
cladogram also is not the same as true tree, it is a inferred tree, likewise, true phylogeny is not the same as inferred phylogeny.
cladogram, its graphic representation, induces to evaluation error. When you look at a cladogram, you don't notice clearly that many branches are not simply supported (not even indicated the support percentage, a lot of times inferior to 50%).It should be represented in a clear way the ramification pattern that is supported by the robustness indexes (= support, in percentage) of the phylogenetic tree: Bootstrap or Jackknife or NNI (= Nearest-neighbour-interchange) swapping > 90%.
cladogram, its treelike model is a bad simplification of the evolutionary complexity, see Vriesendorp, Bastiaantje & Freek T. Bakker. 2005.Reconstructing patterns of reticulate evolution in angiosperms: what can we do? Taxon 54:593–604. "Hybridization is thought to be an important phenomenon in angiosperm evolution, and it has been suggested that a majority of all plant species may be derived from past hybridization events (e.g., Stebbins, 1959; Raven, 1976; Grant, 1981; Arnold, 1997).In addition to species-level hybridization, other (genome-level or molecular) evolutionary processes such as recombination, gene conversion or horizontal gene transfer can confound the phylogenetic signal in the data to such an extent that it may become non-treelike, and phylogenetic methods are not appropriate for analysis. It is best to check prior to phylogenetic analysis whether this applies, and if so, then use network methods to represent it (Bryant & Moulton, 2004)."
dichotomous branching patterns (= "each inner node is ideally binary"), see E. Hörandl (2006) for more details.
completely complex methodology ("esoteric").
counter-intuitive results: birds regarded as reptiles, cactus as portulacaceous, frankly!

Debate Cladism X Taxonomy (references)

Mayr, E. & Bock, W. J. 2002. Classifications and other ordering systems. J. Zool. Syst. Evol. Research 40: 169–194. for more details PDF file available here.
Brummitt, R. K. (1997). Taxonomy versus cladonomy, a fundamental controversy in biological systematics. Taxon 46(4):723-734: "Those who argue for eliminating paraphyletic taxa from classification, and recognizing only monophyletic (in the modern cladistic sense) taxa, are in fact arguing for a classification based on clades, not on taxa, which is quite different concept. Referring organisms to clades is perfectly possible, but it is not Linnaean classification. In an illumining recent paper Mayr (1995) has stressed the distinction between classifying organisms into a taxon and referring them to a clade, which he has designated a 'cladon'. "
Grant, Verne:INCONGRUENCE BETWEEN CLADISTIC AND TAXONOMIC SYSTEMS. American Journal of Botany 90(9):1263-1270. 2003.
Brummitt, R. K. (2002). How to chop up a tree. Taxon 51:31-41.
Brummitt, R. K. (2003).Further dogged defense of paraphyletic taxa. Taxon 52:803-804.
Brummitt, R. K. (2006), Am I a bony fish? Letter to the editor. Taxon 55(2)268-269): "The question of paraphyly is, I feel, the most important issue debate in Taxonomy today.

...The theory of cladistic classification is so wrong that distinctive groups which are sunk into another family or genus can usually no longer be recognized even at subfamily or subgeneric rank because they would just make another subfamily or subgenus paraphyletic.... The statement of Nordal & Stedje noted that cladistic classification is causing chaos in taxonomy, but this has been denied in the responses. It depends on how you perceive chaos. The recent disintegration of the Scrophulariaceae may seem like chaos to some. If we have to sink Hydrostachyaceae into Hydrangeaceae, Podostemaceae into Clusiaceae, Hippuridaceae (flowers consisting of an inferior ovary and a single stamen) into Scrophulariaceae, the whole of the Juncaceae into Juncus, many distinctive genera into Lobelia, and many other cases, we are moving towards a generally chaotic situation in my opinion.... But I feel very confident that future generations will thank Inger Nordal and Brita Stedje for raising the profile of the discussion and showing that many taxonomists have serious objections to the theory and practice of cladistic classification."

See also this very important initiative, like a manifest against PhyloCode and excesses of Cladistics: "Taxon 54(1)(2005): 5-8 LETTERS TO THE EDITOR (Coordinated by: Nordal, I. & Stedje, B.): Paraphyletic taxa should be accepted. available online here (pdf file; page 18), including proposal, but without the 150 signatories, several notable botanists from world-wide, among them: Brumitt, R. K. (from Kew) and Sosef, Mark.

For updated information on the controversy "Cladistics versus Taxonomy", see Hörandl, Elvira. 2006:Paraphyletic versus monophyletic taxa—evolutionary versus cladistic classifications. Taxon 55(3):564–570. Example: "Here I want to show that a strict application of monophyly for grouping of taxa is problematic, because the commonly used tree-building methods result in a too strong abstraction and a too simplified visualization of evolutionary processes." Berton 18:17, 4 October 2006 (UTC)

Conclusions

Hörandl, Elvira. 2006.Taxon 55(3):569."Considering these different aspects, I suggest that clades retrieved by phylogenetic analyses should be not used solely as a basis for classification, but should be regarded primarily just as information for a better understanding of relationships. If there is any indication that phylogenies are not dichotomous, researchers should refrain from quick taxonomic conclusions and try first to understand better evolutionary processes leading to such tree topologies, whereby a broad array of analytical methods and datasets, including external evidence,should be used."

As the monophyly (its basic premise) doesn't exist, then Cladistics should be reformulated ab initio. Cladograms are not valid to represent reality (they are false).

Synthesis: several (poly) elements (= divergent lineages) suffering the influence of several speciation mechanisms evolve for several new elements (= new species), not existing place for monophyly.

Concludingly, Cladistics as systematic approach is erroneous method leading to erroneous conclusions...

P.S.:Wow! I have just known that the turtles are our close relatives! see polyphyly

Berton 18:28, 4 January 2006 (UTC)

Comments by other editors

Berton, all theory is false. Some of it is useful. Cladistics has its uses. - Samsara 13:49, 10 January 2006 (UTC)

"Thus, falsifiability is an essential characteristic of any scientific theory." Karl Popper-- Berton 03:44, 23 March 2006 (UTC)

Yet oddly enough, most systematists are now using cladistic methodology (which itself only produces phylogenies, not classifications) and are managing to translate their results into Linnaean taxonomy. (This is a major reason why I don't think the Phylocode will ever catch on, at least not as an "official" system--the Linnaean system is simply too useful.) The results aren't always pretty, but then classification has never been pretty. I challenge anybody to go back to the classification schemes of the 19th and early 20th centuries and tell me that those were better, more accurate, or more useful than the ones being produced by systematists using cladistic methodology. MrDarwin 15:11, 12 January 2006 (UTC)

See comment in Talk:PhyloCode#PhyloCode and nomenclatural chaos. Berton 18:05, 12 January 2006 (UTC)

Berton, "Nomenclatural chaos"--or what I would call "controlled chaos"--has reigned since 1753. The Phylocode isn't going to change that (I don't expect the Phylocode ever to be adopted, at least not officially) but at the same time cladistic methodology isn't going to mess things up more than they already were. Systematists are struggling with the concepts of monophyly, holophyly, paraphyly, polyphyly and how to translate those into classifications that are both useful and make sense, but they always have and they always will. The history of the classification of virtually any group shows major changes over the last 200 years but in general I would say our current classifications are better than those of 100 years ago, precisely because they are reflecting evolutionary relationships. Classifications are dynamic, precisely because they are subjective and artificial, as you pointed out in your commentary on the Phylocode, and our understanding of relationships itself continues to evolve. And I would reiterate that cladistic methodology does indeed seem to be as compatible with "Linnaean" taxonomy as any previous methodologies have been. As a plant systematist myself, I have seen no need to throw away Linnaean classification based on my better understanding of relationships within my group as inferred from cladistic methodology, although the classifications themselves have needed some adjustment. MrDarwin 15:14, 14 January 2006 (UTC)

I somewhat feel that this whole discussion is about a mute point anyway, because they textual classification will no doubt be replaced by trees that can be downloaded onto mobile devices even in the field (there are several different ways in which this could be done, but let's not get into this: my point is clear). The species names will then simply be names that indicate that the two species do not interbreed (at least by conventional sex). (Again, let's avoid discussing hybrids and species concepts, as this affects textual and graphical representations in equal measure!) - Samsara 15:45, 14 January 2006 (UTC)

cladogram, its treelike model is a bad simplification of the evolutionary complexity (see Critic of the Method above).Berton 11:45, 11 October 2006 (UTC)

Berton, can you please clarify what you mean by "Clades do not exist in nature"? The way that I understand it, a clade is a concept, not a biological entity. If that is what you mean, okay, I think most cladists fully accept this. It is perhaps useful to remember that a cladogram is a hypothesis about how evolution has proceeded; this is a central tenet of the cladistic method. If instead you mean that evolution doesn't look like a bifurcating tree, well, yes, there are biological phenomena (HGT, genome fusions, and hybridization) that make a strictly bifurcating tree a somewhat incorrect representation of the evolution of life, but for most of the evolution of life, such a tree does quite well.

I think that most biologists agree that phylogenetic systematics is here to stay. What is the alternative criterion for forming coherent groups? Only a system that is 'more' subjective. The debate you engage in here should be more directed towards the question of ranked vs. rank-free taxonomy. Linnean ranks are much harder to get rid of, because as stated elsewhere on this talk page, they are useful. That many taxa are paraphyletic disturbs phylogenetic systematists does not neccessarily have anything to do with the creation of a rank-free taxonomic code (PhyloCode) but rather that they believe that taxa should be monophyletic. It is possible to adhere to a monophyletic criterion and retain a ranked taxonomy (as stated by MrDarwin); it's just that we will end up with new taxa arising from split up paraphyletic taxa.

Cladistics is extremely useful. Parsimony is still the only evolutionary criterion for evaluating morphology, which is the only data we have for more than 99% of life that has existed on earth, that from fossils. It is indeed still a useful criterion for evaluating small molecular data sets. In a world where people are still using distance (phenetic, i.e., NJ and UPGMA) criteria for generating phylogenetic trees, cladistics is a useful tool pedagogically to explain how to make truly evolutionary hypotheses.

Safay 01:50, 13 April 2006 (UTC)

Done with great lateness, excuse me. See above. Berton 15:51, 5 October 2006 (UTC)

Berton wrote:

Monophyly does not exist, it is an erroneous phylogenetic concept.

Evolution is by leaps (that is, not continuous) (similar to the Thomas Henry Huxley's saltationism and punctuated equilibrium, but contrary to the phyletic gradualism), it must not to be analysed genealogically, like a family tree, point by point, but collectively (at level of populations, with several elements = plural, "poly", not singular, mono = one).

But that´s totally incorrect, as far as I know. The literal interpretation of "onophyly does not exist" would imply that every single organism is spontaneusly generated... I know that was not the claim, but shows the nonsense of the affirmation. Other things: punctuated equilibrium is not saltationist, it is yet gradual; it is just not phyletic gradualism, which means, that species are most of the time in evolutionary stasis rather than changing more or less homogeneoulsy during all its phyetic existence prior to cladogenesis. But the punctuated "leaps", are gradual in short term, i.e., there is no need for invoking sudden differences from one generation to another (saltationism), it all can occur with the usual continuum of variation. And, most importantly, does not matter if a clade arises gradually phyletically, or in a evolutionary spurt between periods of stasis, or out of a few "hopeful monsters". It would be monophyletic as long as they´re all coming from a common ancestor, without the inclusion of some other population that does not descend from the common ancestor of them all within it.

The only justification for all the fuss against monophyletic groups as a criteria for taxa, is that would be unnecessarily "atomizer" sometimes, for example, if not only the biological concept is taken as criteria, but also the eco-species concept. As there are many possible convergent eco-species sometimes, each one of these would have to be considered as a single, distinct, species, when in fact they´re still potentially capable of crossbreeding. But I think that it only causes problems as monophily as a criteria for certain species, not for higher taxa.

The hybridization (major mechanism of speciation) is the principal evidence of polyphyly of taxa.

I don´t know whether hybridization is the major mechanism of speciation or not, but however, I think that if a species that results from these hybrids is yet formed by all the descendants of these hybrids, without the inclusion of other groups, it would still be monophyletic... would not? Unless it´s referring on multiple instances of hybridization among two species (the same two all the times, probably). More or less like "ligers" being considered as a species. But even in these cases, I think that they could be considered "theoretically", or genetically monophyletic, even if they´re not actually monophyletic. I think that this whole "there´s no monophily" thing is more or less like saying that there are no rivers because there is rain (as an analogy of HGT), and rivers sometimes merge into one and etc. HGT and hybridisation need not be denied in asseting monophily, I think, what matters is that in a certain aspect, that group is like single "genetic river".

However, how much of this talk actually has something to do with the article? Should not it all be in a discussion forum? --Extremophile 14:10, 24 April 2006 (UTC)

Extremophile,

didn't you understand anything of what I said, do I think would be better than I expressed in Portuguese (are you Brazilian, right?).

Saying Monophyly does not exist, doesn't mean to say ancestors don't exist.

I didn't also say that saltationism was the same as punctuated equilibrium, but similar to this.

Population has not the common ancestor, that is ridiculous.

Besides, what is genetic river?

This is not discussion forum, this is talk page, and it is this that I am doing, talking...--Berton 17:22, 12 October 2006 (UTC)

"Cladistic classification"

Claims from famous people to the contrary, there is no such thing. Period. Cladistics is phylogenetics, not taxonomy (and not nomenclature).

What you are trying to talk about is phylogenetic nomenclature, which has nothing to do with cladistics except that historically it is an outgrowth of it. I think I'll get myself a username just to start the article "phylogenetic nomenclature" (which doesn't exist yet).

David Marjanović | david.marjanovic_at_gmx.at | 1:53 CET | 2006/2/17

Important note

Please note that Berton has been editing his comments in this discussion after others have already replied to them, sometimes weeks or months after posting his initial comments. MrDarwin 22:34, 19 March 2006 (UTC)

MrDarwin, I recently have noticed the same thing.

Berton, perhaps you should look at this from the perspective of other editors. Your contributions are valuable, but so is the discourse that flows among us here on the talk page. Going back and editing your talk page comments after others have replied disrupts this flow. Own what you have said in the past, and add new comments clarifying your views, if you feel they need clarification.

Respectfully,

Safay 18:18, 11 October 2006 (UTC)

MrDarwin, Safay

I promise to both of you that when I finish my argumentation I will stop editing in this talk page. Berton 14:21, 12 October 2006 (UTC)

I'm afraid I don't see the point of the "argumentation" in the first place. Article discussion pages are supposed to be for discussions about how the article is written, not for diatribes or critiques of the subject matter of the article. However strongly Berton feels about cladistics or how cladistic methodology has been used in formulating new classifications, it has no bearing on the subject of cladistics, and more importantly, on the article itself. MrDarwin 15:16, 12 October 2006 (UTC)

MrDarwin, if you gives yourself to the work of reading this talk page entirely, you will see that nor everything that was said is about how to write the article, that is important, clear, however, the fact is, that there are much more important things besides writing an article (obviously!), actually, I am writing an alternative article with my points of view (and of important researchers, see the references) on this subject because I don't want to influence this article that I consider very well written. Berton 20:26, 12 October 2006 (UTC)

Paraphyletic clades acceptable??

I thought only monophyletic was acceptable? And that's why the "Protist" kingdom has been split up??

"Paraphyletic clade" is an oxymoron. There are numerous paraphyletic taxa and it remains to be seen how those will be treated. MrDarwin 13:42, 5 April 2006 (UTC)

Yes, it's an oxymoron, but there is a word for paraphyletic and polyphyletic groups, "grade." The word for monophyletic groups is "clade." MOBOT's APG pages have a good cladistics glossary. KP Botany 18:49, 4 October 2006 (UTC)

What is "acceptable" depends on your perspective. Some systematists accept paraphyletic groupings. There are formalized codes out there which make "official" systematic declarations, such as the ICZN or ICBN. These two currently employ known paraphyletic groups (and probably a share of polyphyletic ones too). Some systematists accept only monophyletic taxa. These people would be called cladists. PhyloCode, whose mission is to expound phylogenetic systematics, is an emerging rank-free taxonomy of strictly monophyletic groups, and is thus an application of cladistics.

Whether Kingdom Protista is broken up depends on what textbook you read. - Safay 05:48, 11 October 2006 (UTC)

Typo in diagram

In the second illustration, the word "quillworts" is misspelled as "quillworths".

Kay Dekker 20:09, 12 April 2006 (UTC)

Molecular clock

Molecular clocks are calibrated with fossils, so how can it be true that a molecular clock is more precise than fossil dating? -Safay 23:44, 10 October 2006 (UTC)

Time?

The 1st diagram caption says: "In some cladograms, the length of the horizontal lines indicates time elapsed since the last common ancestor." I could buy "relative" time, but I'm pretty sure a main goal of cladistic analysis is to eliminate time from consideration and look solely at morphological characteristics.

Well, I'll try adding the word and see if I get flamed.

Aldenrw 17:05, 15 October 2006 (UTC)

It's not even true for that particular tree anyway. I say it should just be deleted. Your edit was an improvement, though. --Aranae 04:52, 16 October 2006 (UTC)

A cladogram specifically does not have a time component - its topology only shows a hypothetical branching pattern. Thanks for catching that. A tree that does propose to represent time is a phylogram. See [2]. So I'm going to get rid of the time reference altogether. Another minor point, Aldenrw: I think that cladistic methods can use molecular characters too. It's not so important what kind of characters you use as it that one uses the criterion of parsimony and chooses an outgroup to polarize characters. This stands stands in contrast to phenetic methods. -Safay 08:20, 16 October 2006 (UTC)

Actually in a phylogram branch length is representative of the number of characters. A chronogram is a type of tree where branch length represents relative time. --Aranae 14:35, 16 October 2006 (UTC)

Thanks for clarifying! -Safay 16:35, 16 October 2006 (UTC)

Featured Article Review

Cladistics has been nominated for a featured article review. Articles are typically reviewed for two weeks. Please leave your comments and help us to return the article to featured quality. If concerns are not addressed during the review period, articles are moved onto the Featured Article Removal Candidates list for a further period, where editors may declare "Keep" or "Remove" the article from featured status. The instructions for the review process are here. Reviewers' concerns are here. Gzkn 07:21, 14 December 2006 (UTC)

FAR suggestions (copied from FAR page)

Here are some suggestions to improve the article:

I think the distinction between cladistics and phenetics should be addressed a second time once plesiomorphic and apomorphic terms are introduced. Cladistics is interested in synapomorphies. Phenetics does not distinguish between the two. An example of how the two could come up with a different tree would also help.
I'm a bit unhappy with the discussion of what it means to be basal. I completely agree that usage of the term primarily refers to a taxon-poor clade that branches off early. I also think that the term gets used in reference to the ingroup, the taxon sampling, and the question being asked. For example, gibbons will commonly be said to be basal among the hominoids, yet there are 13 species of gibbons in four genera and only 7 species of great apes (also 4 genera). In this case, the research question usually being posed is really about a focus organism (us) and relationships among the gibbons is less important in that particular discussion. Bats and insectivorans are basal to the rest of the Laurasiatheria in spite of the fact that over 50% of described laurasiatherian species are bats and 20% are insectivorans. The research question is how are bats, insectivorans, carnivorans, pangolins, perissodactyls, and cetartiodactyls. From that perspective, bats and insectivorans to qualify as basal to the cetferungulates. Being "primitive" shouldn't qualify a group as basal (although it probably is used that way in some instances). Bats fly, echolocate, and look nothing like the ancestor of the Laurasiatheria.
The distinction between synapomorphy and autapomorphy should be clarified.
The second paragraph of the section titled "Cladistic methods" is confusing. Plesiomorphies were present in the last common ancestor of group discussed. Apomorphies arose subsequent to the last common ancestor of the group discussed. To say that an apomorphy was present in the last common ancestor of the ingroup is false. A synapomorphy was present in the last common ancestor of the clade it characterizes (and may have arisen anywhere along the branch leading to that clade). Autapomorphies are also a type of apomorphy and they weren't present in the last common ancestor of any two taxa in the analysis.
Eliminate the use of "we" in the 4th paragraph of the same section.
I think at least 50% of the field would consider maximum likelihood and Bayesian methods to be both Hennigian and cladistic. They are still constructed on the basis of synapomorphies, they just incorporate information about how characters evolve and attempt to incorporate the potential for additional evolution hidden in a final parsimony analysis. They are definitely not phenetic methods. I'm also amazed that there still isn't an article on maximum likelihood in phylogenetics.
The total evidence approach advocated in the 6th paragraph isn't universally accepted. I think it's safe to say that >50% of the field would agree, but there are those who argue that a little bit of quality data is better than a lot of noisy data or even a little bit of quality data + some noisy data. Most (but not all) do agree that data where homology is questionable should be excluded. That should be addressed in the paragraph as well and I'm not all that comfortable with the behavior example (without expansion and clarification) for that reason. That statement that molecular, morphological, etc. not are all equal is definitely an opinion and is definitely disputed. Homoplasy is more common in morphological data? Are we sure about that?
Paragraph 7. A small point, but cladistics does assume that evolution is bifurcating as opposed to hybridizing, reticulate, or having lateral transfer.
In my opinion, the "Cladistic classification" section can reasonably stay, but seesm to ramble on as if it was written by several editors who had differing opinions and tried to jump back and forth in such a way as to make it sum up to NPOV. I'm not happy with the notion that about half of the text of a featured article on cladistics is spent discussing the PhyloCode and Linnean hierarchy.
There is a subtle, but important philosophical difference between cladistics and parsimony. This article should address that clearly.
The "see also" is an odd list. It should have links to phenetics, parsimony, maximum likelihood (phylogenetics), maybe Bayesian (phylogenetics), as well as some of what's already there.

--Aranae 02:27, 15 December 2006 (UTC)