| This article is within the scope of the following WikiProjects: | | | edit · history · watch · refresh  To-do list for Cladistics: | | | As it stands, this article confounds "cladistic" and Linnaean classification. What is being contrasted is not "cladistics versus Linnaean" but "Phylocode versus Linnaean." Fact is: any classification that contains monophyletic groups and is logically consistent with the underlying phylogeny is a "cladistic" classification. it may be Linnaean, an indented list, a classification that uses numerical prefixes, or a system that uses Phylocode. The article also confounds "Linnaean and evolutionary taxonomic classifications." A Linnaean classification that contains known paraphyletic groups is an evolutionary classification. A Linnaean classification that contains only monophyletic groups is a cladistic classification. In short, this article is in serious need of revision. Eowiley (talk) 19:57, 6 April 2009 (UTC). - 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) Eyu100(t|fr|Version 1.0 Editorial Team) 15:36, 22 August 2007 (UTC) | [edit] What about a warning? If I have made my point clear by now (i.e., that cladistics is inconsistent, self-contradictory and empirically erroneous), I would like to proceed to the next step requiring that this information is included in the beginning of the article about it. The reason for this choice of position is that it simplifies understanding of the apparent inconsistencies in the article, like, for example, the definitions of the terms: - A clade is an ancestor species and all of its descendents, - A monophyletic group is a clade, - A paraphyletic group is a monophyletic group that excludes some of the descendants where anyone with clear eyes can see that the definition of monophyletic group equalizes it with clade, and the definition of paraphyletic group equalizes it with monophyletic group, and thus also with clade, at the same claiming a difference between paraphyletic group and clade in "some" and "all". The definitions are simply not distinctions, but, on the contrary, a confusion of the concept clade with the concept monophyletic groups. The truth is that this mess arises because cladistics does not understand conceptualization of phylogenies (i.e., dichotomously propagating processes), and that it leaves out the concept holophyletic groups (see Envall in the Criticisms section). Inconsistencies like these are much easier to understand if one knows from the beginning that cladistics per definition is inconsistent, self-contradictory and empirically wrong. It is simply founded on an inconsistent definition that two things in a row equals a single thing, and thus that several equals single, and on the top of this that such several-single things can be defined by properties. It confuses one and many, and thing and kind, that is, everything that possibly can be confused, by definitions. In the light of this knowledge, inconsistencies like the confused definitions above is just what one can expect. (The cladistic battle is to "realize" lines of descent by defining the abstract as the concrete. It piles definitions on the top of each other trying to nail its abstractions in reality, at the same time trying to hinder the concrete from being nailed in the abstract, In practice, it means turning two into one by definitions, like turning me and C.Fred into one by definitions. It is, of course, just as impossible as eating a cake and keeping it). I thus suggest that a warning about cladistics' inherent inconsistency is included in the beginning of the article about it. Consist (presently at 83.254.20.53 (talk) 10:30, 23 September 2008 (UTC)) -
- Yes, clade and monophyletic group are equivalent. However, there is no rule in language or in science that terms cannot be synonymous. Clade is used in situations where the term monophyletic group would be unwieldy. All mammals are a monophyletic group. All birds are a monophyletic group. Both mammals and birds (along with other groups) belong to a larger monophyletic group. Each of these groups is a clade, the clade of mammals and the clade of birds are contained within the larger clade (vertebrates). The definition of paraphyletic group is imprecise and colloquial,but is not inherently false. Just imprecise. A paraphyletic group might include ancestral species A, descendant species B, and descendant species D while excluding species C which is also a descendant of species A. To put it in more day to day terms, a group that included you, your cousin and your grandfather but excluded your sister would be paraphyletic. The term monophyletic group can exist without cladistics, cladistics depends on the concept of monophyletic groups. In cladistics ONLY monophyletic groups are allowed, these groups are retermed clades to help emphasize this point.
-
- PS -- I know that the original post was made several months ago, but I felt that it was important that someone rebut it, especially as it was the first post visible on the talk page when I came here.Khajidha (talk) 04:29, 16 December 2008 (UTC)
-
-
- No, clade and monophyletic group are not equivalent. Clade is confused with monophyletic group and defined as holophyletic group. Monophyletic group is actually the generic concept for holo- and paraphyletic group. The definition in the article about clade confuses mono- and holophyletic group (i.e., the generic concept with one of its specifics by the expression "A clade is a monophyletic group - that is, a single common ancestor and all its descendants (my bold). It's analogous to stating that "A cladist is a biological systematist - that is, a person that accept the conceptual confusion of the concept clade" (thereby excluding non-cladists from both persons and biological systematists), or even worse, "A cladist is a human - that is, an organism that accept the conceptual confusion of the concept clade" (thereby excluding non-cladists from both humans and organisms). The correct definition of the concept clade (as it presently (19/1, 2009) is defined in the article): "A concept that inconsistently and empirically erroneusly confuses the generic with the specific, that is, reality with representation". It is just an inconsistent and empirically erroneous play with words. Mats, presently at 83.254.23.241 (talk) 07:07, 19 January 2009 (UTC)
-
-
-
- Monophyletic group (as defined by every professor in every biology class I took to obtain my degree) is "a single common ancestor and all its descendants". Holophyletic is a trivial synonym of monophyletic. Paraphyletic is "a single common ancestor and some of its descendants".Khajidha (talk) 23:24, 31 January 2009 (UTC)
-
-
-
-
- Mats is using a prescriptive definition of "monophyletic"; i.e., what he thinks it should mean, not how the term is actually used. Understandably, this generates some confusion.Paalexan (talk) 20:02, 15 November 2009 (UTC)
[edit] Proposed merge of Clade into Cladistics - oppose Right now the structure of WP's "cladistics package" is too up in the air, so a merge now would be premature. In fact there may be a case for splitting Cladistics into two artciles, one that describes the method clearly (posts at archives of this Talk page suggest there's major room for improvement) and another that summarises the scientific debate about the pros and cons of cladistics compared with other taxonomic methods. There already seems to be enough material for a "debate" article - see Talk:Clade#Sources_-_recognised_scientific_publications; I've hardly started tracking down sources and already see signs that botanists are less pro-cladistics than zoologists, which itself is a phenomenon that's worth investigating. --Philcha (talk) 23:24, 12 November 2008 (UTC)
- See also doi:10.1016/j.jas.2007.11.009.
- In any case, I have shuffled the sections around a bit, undo if you don't like it but I think it's an easier read now.
- However, as I have tagged it, the entire long-winded technobabble about how to do cladograms warrants to be split off and be replaced by an extended summary. Maybe 1/3rd the length in total. Some sections (avoid homoplasies, mol and morh and whatnot data, extinct spp etc) should be discussed in more detail perhaps, others (the entire tech stuff) can be cut away entirely perhaps.
- Also, I'd really recommend beefing up Phylogenetic nomenclature with the bit that is just about it and not really cladistics (it is "cladism" but that's a term of the Traditionalists.). The PN article is nice, but it's a bit orphaned, it lacks the information that is in overload here. The PhyloCode seems to be the way to go in PN, but altogether (see the paper above) the "advantages and disadvantages of 'cladism'" are irrelevant to the guys who found out the new stuff about the Clovis culture by using cladistics as well as to most entomologists as far as I can tell.
- The last ppl I have seen to roundly reject cladistics (as opposed to 'cladism') were perhaps Olson, Kurochkin et al.. And they have been pretty silent about the matter for the last years. So it is safe to say that while the "cladism" dispute has only startet, the dispute about cladistics is over. So instead of having 2 POVy articles let's just put it together in one; even the botanists who do use phenetics generally acknowledge the value of cladistic methods. It's just that they do not have enough data and rigs beefy enough to crunch the numbers ;-) Also, if you have much introgression, cladistics DOES suck. So botanists are generally "yeah right, pay us the phat computers and we'll do cladistic analyses... provided it is not about Hieracium or Rubus..."
- "Other disciplines" needs to be beefed up. See also stemmatics for more sources.
- Then I would support the proposed merge. Dysmorodrepanis (talk) 22:35, 13 November 2008 (UTC)
- oppose - to me, the merge would be analogous to merging "entomology" and "insect", i.e., the subject, and the field that studies the object. de Bivort 22:51, 13 November 2008 (UTC)
- oppose - Clade is such an important term (and has a few variant interpretations) so it certainly deserves its own article. On the other hand, the user of this encyclopedia needs a "one stop shopping" place to learn about Cladistics in general, and so the Cladistics article must contain a summary of Clade and Cladogram. Also, the Clade and Cladogram articles (the latter doesnt exist yet, true?) should cite Cladistics as the "main article". --Noleander (talk) 14:23, 16 November 2008 (UTC)
Oppose merger. absurd since both terms can evolve into huge articles. the relationship is obvious. Plumpurple (talk) 14:56, 18 November 2008 (UTC)
This is a huge mess. We have huge overlap between clade, cladistics, phylogenetic nomenclature, monophyly, Phylocode and possibly other articles. I think the best way to fix this is going to be to use a 'summary style' approach. A main article, probably cladistics, should give a brief section-length overview of all these topics. Each section should have a 'Main article' link to a more in-depth discussion. We might usefully separate historical background more clearly from the status quo, perhaps by creating articles such as 'history of phylogentic nomenclature' if they become necessary. Does this approach sound suitable? We have to do something to deconvolute our coverage of the topic. Martin (Smith609 – Talk) 06:21, 7 December 2008 (UTC)
- The term 'clade' could be defined without much trouble, but 'cladistics' is a school of thought. It's not a subject like Euclidean geometry whose conclusions have few doubters. (Felsenstein says that our Cladistics article gives the impression 'that we know ancestral states, and that there is no homoplasy in practice'). I agree that there is duplication within the set of articles you mention and there might be ways of addressing that. EdJohnston (talk) 07:31, 7 December 2008 (UTC)
-
- You're darn right I say that about this article. It is a mess, because it faithfully reflects the state of thinking in this area, and that is a mess. There are two ways in which the problem affects this article. One is the confusion between making groups using nested synapomorphies and using algorithmic approaches. The former needs ancestral states to be known and assumes no homoplasy. The latter can be done in cases where there is no outside information about what is an ancestral state and what is a derived state (though one then gets an unrooted tree). The article presents the one as deriving from the other. I don't think the connection is that simple. The second problem is the failure to distinguish clearly the task of constructing a classification system and the task of inferring the phylogeny. Even if you want the former to be rigidly constrained by the latter, these are distinguishable tasks. For example, an evolutionary systematist (who does not insist on a monophyletic classification) might use a parsimony algorithm to infer the phylogeny, prior to deciding on what groups to make in the classification. Is she doing cladistics? not? The article makes it sound as if, as soon as you infer a tree (even an unrooted tree?) you are doing cladistics.
-
- Having said all this, which is correct and relevant, I have to acknowledge that my opionions on matters like this are opposed by most systematists, who do not want to distinguish these two tasks. My views on this are usually regarded as marginally crackpot. As Wikipedia is a dominant-consensus view, they can perhaps thus be ignored. Felsenst (talk) 05:31, 25 December 2008 (UTC)
-
-
- On the evidence so far, you're no crackpot - and since it's Christmas Day I won't tell you where in WP to find a real one. I don't know enough clado-theology to have a strong opinion about your points, but they sound like items the article should make clear. --Philcha (talk) 09:36, 25 December 2008 (UTC)
-
-
-
- I would agree that classifications can be artificial and exist for human purposes. That is, they might simply have functionality, whilst biologists also uncover phylogeny. Would be nice if that could be done in practice. However, if groupings are not real, then they're of no use to biologists. As biologists, we employ groupings frequently, and there should be a clear and consistent meaning for what a grouping entails. The history of modern classification has followed a general course in which we've kept monophyletic groups and discarded non-monophyletic ones. Sort of. We've hung on to a lot o paraphyletic groups until cladistics came along, but they still hang around from time to time. The fact remains that a classification is a clustering of organisms. As such, it may compete with a phylogeny. That said, I agree that nomenclatural issues should be only briefly touched upon here (as in a statement that the cladistic nomenclatural practice is one in which taxa are exclusively monophyletic). Then leave all the phylocode particulars to another linked article. —Preceding unsigned comment added by 141.20.246.151 (talk) 09:43, 2 November 2009 (UTC)
[edit] resource doesn't support table I have the reference listed at the head of the table in .pdf. It is a published paper. It does not have the points listed in the table. There is no other reference by or near the table that tells where the info came from. Christian Skeptic (talk) 05:55, 12 April 2009 (UTC) [edit] Please use some care with edits Reminder: Please proof-read your edits before saving them. This is an old article on an important topic, so please take some time. Recently, an edit was made in the Intro paragraph (!) resulting in the sentence "It differs from heavy emphasis on objective, quantitative analysis". Huh? I fixed that, but please use more caution in the future.--Noleander (talk) 15:14, 10 July 2009 (UTC) [edit] Definition of Cladistics The current definition of classifying based on shared ancestry is both deeply wrong and uninformative. Ancestry cannot be known in advance of cladistic analysis, so it cannot be said to be a basis for it. Cladistics is distinguished from other fields by classifying according to monophyletic groups (hence cladistics), which are based on shared derived (or unique) features—synapomorphies. The concept of grouping by synapomorphy, and only by synapomorphy, is the novel and distinguishing contribution of cladistics. The notion of grouping by ancestry is not novel to cladistics, and is in fact a better characterization of evolutionary taxonomy. Secondly, cladistics does not attempt to "construct a tree representing the ancestry of organisms and species." In fact, cladograms are completely silent on the question of ancestors, as all taxa are grouped hierarchically as sister taxa. I think we should restore my edits to the first paragraph from several months ago. —Preceding unsigned comment added by The Braz (talk • contribs) 08:14, 2 November 2009 (UTC) - I don't understand some of your criticisms. For instance, you are correct that "ancestry cannot be known in advance of cladistic analysis", but incorrect in thinking that this means a cladistic classification is not based on shared ancestry; the classification comes after inference of phylogeny, and is based on the inferred phylogeny. Your comments on ancestry appear to be rather semantic. A cladogram is a representation of the inferred ancestry of a set of (usually) extant species. The goal is to infer how species within a certain slice of time (usually, but not necessarily, the present) are related to each other, i.e., in what order they are united by common ancestors. If we have fossils that may represent some of those ancestors, these can of course be mapped onto the tree; but while they will often be quite helpful (especially in attempts to determine the ages of lineages), including ancestral taxa is not necessary to infer relationships among the extant taxa. IOW, based on shared similarities at the present, we can infer that two species shared a recent common ancestor even if we don't happen to have a fossil specimen that we believe to represent that common ancestor.Paalexan (talk) 19:17, 15 November 2009 (UTC)
-
- A cladogram contains no ancestors, and thus is mostly silent on ancestry. A cladogram is only a summary of the most parsimonious distribution of character states. The problem of course, is that defining cladistics as a field of systematics that classifies according to ancestry is not a good start to the article. Evolutionary taxonomy also classifies according to ancestry (or some perception thereof). Cladistics groups things according to shared apomorphy (synapomorphy) which diagnoses monophyletic groups, and that is what distinguishes it from other methods that preceded it. Cladistic classifications are not based on shared ancestry, rather inferences of shared ancestry are based on cladistic classifications. I don't think this is semantic, I think it matters because one approach is purely circular and the other is not.
-
- Cladistics might be described as a method of trying to infer evolutionary relationships, but it consequently cannot be said to offer a classification based on evolutionary relationships. Otherwise, it is circular reasoning.The Braz (talk) 15:38, 23 November 2009 (UTC)
-
-
- Why must an assessment of ancestry directly include the ancestors? For instance, suppose we were grouping a set of children into families. The parents of the children are assigned no place in such a grouping; is the grouping therefore independent of ancestry? Of course not; the parents simply aren't members of the set of individuals being grouped based on ancestry. Your suggestion that cladistic classifications are based on "inferences" of shared ancestry rather than on shared ancestry itself is accurate, but does not seem relevant. All scientific knowledge that extends beyond direct observation (we could argue even on direct observation, but there would be no apparent purpose in doing so...) involves inference; should we then preface every scientific article on wikipedia with some sort of statement that the knowledge discussed in based on inferences? Pointing out that cladistics involves inference does not provide any noteworthy or unique information; the same will be true of any scientific alternative.
-
-
- I also do not understand your suggestion that there is circularity involved. A phylogeny is an inferred set of evolutionary relationships, which can then be used as the basis for nomenclature. First we try to understand relationships among terminals, then we apply names to groups of terminals based on the inferred relationships. Perhaps you could explain what is circular about this?
-
-
- Further, the issue is to some extent moot as far as the article itself goes; an encyclopedic article on an academic subdiscipline should reflect mainstream understanding of that subdiscipline, rather than being a venue to attack that subdiscipline. This page already suffers from that problem rather severely... hopefully I can get around to poking at it at some point.Paalexan (talk) 08:06, 29 November 2009 (UTC)
[edit] PhyloCode The article at present seems to suggest that cladistics and the PhyloCode are inseparably linked; that all cladists are inherently advocates of the PhyloCode. For instance, the link for "phylogenetic systematics" in the introductory sentence discussing Hennig leads one instead to phylogenetic nomenclature, i.e., the PhyloCode; Hennig never advocated such a system, but the naive reader would likely be led to think otherwise. Later, we encounter the sentence: "These traditional approaches, still in use by some researchers (especially in works intended for a more general audience[23]) use several fixed levels of a hierarchy, such as kingdom, phylum, class, order, and family. Cladistics does not use those terms, because one of the fundamental premises of cladistics is that the evolutionary tree is so deep and so complex that it is inadvisable to set a fixed number of levels." This is simply false. Advocates of abandoning ranks are "cladists" in only the broadest possible sense, and in that broad sense they are a small (but admittedly vocal) minority. Similarly, the figure demonstrating different PhyloCode approaches for delimiting taxa has no place here. Unfortunately, there are so many errors embedded throughout this article that I am not sure I can fix them without simply rewriting the whole thing! Paalexan (talk) 19:26, 15 November 2009 (UTC) [edit] Apomorph Apomorph redirects here, but is not even mentioned in the article! 24.14.159.149 (talk) 05:39, 22 November 2009 (UTC) - There is a discussion of apomorphy, synapomorphy, and symplesiomorphy, all terms that are defined within the field of cladistics. Unless there is another meaning of "apomorph" that I am not familiar with, this would seem to be the appropriate place for a redirect to point to.Paalexan (talk) 08:12, 29 November 2009 (UTC)
|
