Talk:Cladistics/Archive 3

Archive 1

Archive 2

Archive 3

Archive 4

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)

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)

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)

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)

To do list 2007

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:

1. 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.
2. 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.
3. The distinction between synapomorphy and autapomorphy should be clarified.
4. 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.
5. Eliminate the use of "we" in the 4th paragraph of the same section.
6. 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.
7. 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?
8. Paragraph 7. A small point, but cladistics does assume that evolution is bifurcating as opposed to hybridizing, reticulate, or having lateral transfer.
9. 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.
10. There is a subtle, but important philosophical difference between cladistics and parsimony. This article should address that clearly.
11. 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)

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)

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)

Popularity of phenetics?

The article says of phenetic classification that

For some decades in the mid to late twentieth century, a commonly used methodology was phenetics ("numerical taxonomy"). This can be seen as a predecessor to some methods of today's cladistics (namely distance matrix methods like neighbor-joining), but made no attempt to resolve phylogeny, only similarities.

I think this exaggerates the importance of phenetic classification as a method in wide use (it certainly had an important intellectual influence). I do not recall a single year from about 1963 (when Sokal and Sneath's Principles of Numerical Taxonomy was published) to 1980 (when phylogenetic systematics was becoming dominant) that phenetic classifications were more common than other approaches such as Mayr and Simpson's "evolutionary systematics". I am also intrigued by the idea that distance matrix methods are part of "cladistics" as they are also frequently denounced as "phenetic". Which goes to show how muddled much thinking is on this topic. Felsenst (talk) 21:44, 19 December 2009 (UTC)

Long article; split into sections as per summary style

As evidenced by the size of the article and the number of related articles and references, this is a big subject, hence the main article should be a summary with links to detailed sections. I suggest that the article be broken up into sections, with summary on the main page, as per:

• Wikipedia:Summary style
• Wikipedia:Article series

Nbarth (email) (talk) 01:18, 8 March 2008 (UTC)

See above, the entire "Cladistic vs Linnean" stuff really does not belong here. Dysmorodrepanis (talk) 12:50, 11 May 2008 (UTC)

This is a long-standing {{Split}} request. I will look into implementing the splits as they appear to make sense, and to have some support. I am not, however, familiar with this topic, so my efforts will need review and possibly reverting. SilkTork *^YES! 12:32, 31 December 2009 (UTC)

Tallapellet's Tree of LIfe

I cut this out. I know, Tallapellet, this is not going to endear me to you. Nevertheless this is my perception in good conscience.

• Tree of Life illustration - A high-level cladogram showing the complete tree of life.

Tallapellet is a programmer and a WP editor; in fact, he worked on this article. He has his own web site, in which he does not identify himself, unless Tallapellet is his real name. Unfortunately the poster is part of the personal web site. With a click you can get photos of him (my what a handsome man), house plans, blogs, and his personal views of religion. The deciding factor in my mind, however, was the fact that he invites us to buy it online. We can download it for free, he says, if we take it to the copy center and pay for them to print it, or we can purchase it from the web site he specifies. Well, Tallapellet. Wonderful poster, great work of art. If this were not WP I would urge anyone interested to buy it forthwith. My walls don't have room for it. However, this is WP. In my judgement this is a personal and commercial site and is really part of his blogs and other stuff. Tallapellet, you well know this type of material is not allowed on WP. What do do you say, hey, how abut playing by the rules! I don't know what your rank is on WP but if you use it to override me I will object on grounds of abuse of power. By the way I do think it is a worthy and saleable poster and I am glad you contribute to WP.Dave (talk) 15:36, 15 January 2010 (UTC)

The first vertebrate

"the first vertebrate is the common ancestor of all vertebrates" There seems to be a confusion here between taxa and individuals. There was no first vertebrate. And, there was no first human, no first chordate, etc. This is beginning to sound like Adam and Eve. As dearly as I love the myth, it is only a figure of speech. In considering fossils, no one ever has to deal with the problem of placing the dividing line in the middle of a continuous sequence of fossils, each very slightly different, so as to say, on this side of the line is one species, and on that, another. Fossils are always plucked out of their sequences by chance so as to appear totally discontinuous; in fact exactly what the sequence was can almost never be reconstructed. Have you not been listening to the critics of evolution? Suppose in a population of individuals gradually acquiring more and more distinctive individual variations a certain number cross some defined threshold for meeting the criteria of a new species. Statistically speaking it is most unlikely that the threshold would be crossed by one individual first. But supposing it was. He would not be related to any of the other individuals crossing it subsequently, unless you hypothesize that he and he alone produced this variation that exceeded the threshold. Well, suppose a single mutation occurred instead of the thousands and hundreds of thousands that regularly occur and that one was so advantageous the individual was able to multiply and transmit that mutation. There still wouldn't be any supposed clade of individuals as they would have other ancestors, unless you suppose asexual reproduction. All clades of individuals would have to be polyphyletic.

Cladistics cannot possibly refer to individuals. "Monophyletic" etc refer to phyletic, which are groups of a kind, not to single organisms. Suppose it did. How could you ever find any clades? Human descent is not actually a tree, it is a matrix. There is no such thing as a single ancestor to a group of individuals. Our family trees are cuturally defined, not biologically defined. There may have been a single person of my name, but at that time I must have been equally related to everyone in the population in which he lived. You know, the animals went two by two into the ark, two elephants, two giraffes. Even Adam and Eve were two people. How does that fit statements such as "the first vertebrate?" You mean, the first two vertebrates?

This language is really quite confusing to the public. They are very likely to conceive of the first vertebrate slithering around, perhaps named Charlie. Exactly how the second vertebrate got here would be a bit of a puzzle, or if one did get here at the other end of the world, how did the first and second find each other? So, I am going to alter the language to such an extent it is clear to the public "the first vertebrate" is really "the first taxon of vertebrates". While we are on the subject, let's consider the manuscripts. The method is analogous, not the same. Manuscripts are individual, not classes. Now, if I err, someone be sure and correct me.Dave (talk) 03:33, 16 January 2010 (UTC)

PS. As I edit through this thing I discover chunks that are actually well-written, well-referenced and well-formatted. You will find that I did not or hardly touched those.Dave (talk) 17:32, 17 January 2010 (UTC)

PPS. As I was perusing Albert, I noticed that he defines a semaphoront as a genetic slice of an individual organism. However, he doesn't mean individual qua individual, he means species represented by this instance of it. Of course you can only work on individual animals; the species only lives in them (in Aristotle anyway). If you had a pet named Fido you wouldn't be concerned at all with the species of dog, only with your pet - how tractable, whether healthy or not, and so on. If you analyzed a sample of Fido's genes, you wouldn't care in the slightest about Fido, you would be interested in the sample as an instance of dog. Albert's choice of words is in that sense unfortunate. Organism primarily refers to the individual but he is in no way interested in individuals. As a scientist he can make his meaning clear and use the term in such as way as to avoid confusion but as Wikipedia parrots we cannot. Everything I said about the use of organism here is true. As I clarify this thing I will be making sure there is no confusion. The readers report these articles are very confusing and one of the reasons is the failure to distinguish between multiple meanings or senses of a word. Seeing that the editors think the analysis of MSS is the same thing as the analysis of species it often appears they do not understand the distinction either. The species appears in the individual but it is NOT the individuals together or collectively, it is the universal.Dave (talk) 14:42, 18 January 2010 (UTC)

Complexity of the tree of life

This purports to present an advantage and disadvantage of the Cladistic method vis a vis the tree of life. But, the reference on the advantage does not mention the advantage and the disadvantage has been cited for a reference. Nor can I find it explicitly on the Internet. However, if we read a little further, we find that the whole topic is not only covered but referenced under the table of advantages and disadvantages! Presumably support of the reference there is implicit. Is there any point in repeating the material? I think not. But, we definitely want to mention the complexity of the tree of life under that title and as far as I can see at that location. That complexity is mainly fractal evolution and Gould's punctuated idea. The reference given is not as good as Albert on fractals so I want to switch to Albert and leave the assessment to later.Dave (talk) 08:09, 19 January 2010 (UTC)

Phony cladogram

• the lineage of Linux distros, a class of computer operating system.

This is not a cladogram. No lineages of distribution are being reconstructed here. The Linux article says nothing at all about it. The source is a programmer's personal site. He has lost his job, he says, and he would like some help with a donation (so would I for that matter). All he does is list releases of Linux software. That's a list not a cladogram. Whether innovated by him on the spot or in use as a vogue word among software people, this is not a true use of pairwise comparison and no graphic cladogram is the outcome. Whew. Sorry, buddy, I sympathize with your economic situation, and with everyone's economic situation, and if I can't sympathize with that than I sympathize with us all for one problem or another, but you still can't use WP to raise money for yourself. Best wishes and best of luck.Dave (talk) 10:21, 21 January 2010 (UTC)

Willi Hennig Society link

• Willi Hennig Society

This is a tough call. It does contain some biographical info on Hennig and a blurb for their magazine, but no information useful in figuring out cladistics. It does plug the magazine and it gives meeting and event information with various chatty blog site material. Now, the magazine has its own article accessed through a link at the top of the page and Hennig has his own article also, so we don;t need it for that. I judge this not to be an encyclopedic source for cladistics.Dave (talk) 13:34, 21 January 2010 (UTC)

I agree. I'd drop it the link. Btw... are you planning to submit this article for FAC? –Visionholder (talk) 16:01, 21 January 2010 (UTC)

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)

Sorry for the long delay in my response. However, I think you've almost entirely misunderstood what I said. Let's start from the beginning: You write: "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." You haven't specified here what the grouping was based on. So your example has no relevance to the question. What justifies the grouping? If you knew that the children were descended from certain parents, then you could indeed base the clasification on common ancestry, because that is knowledge you have in advance of the grouping. In cladistics, groupings are always justified by synapomorphy. They are never justified by hypotheses of common ancestry, because the degree or level of common ancestry (what cladistics can actually discover) is not known in advance of the analysis. Common ancestry is inferred by means of synapomorphy. Thus, synapomorphies are discovered and justify the hypothesis of common ancestry. This is what sets cladistics apart from evolutionary taxonomy. The search for synapomorphy is also what sets it apart from phenetics. Therefore, cladistics is best described by what it actually does.

You write: "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'm not sure what this means, or where you get this from. I said nothing at all like this. There is, however, a logical direction in which inference proceeds from evidence. Cladistics, by contrast with evolutionary taxonomy, is a great advance in formalizing this relationship between evidence and inference.

You write: "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?" This is nomenclature, not classification. I never said anything about names. What I said was: "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". If you use cladistics to infer evolutionary relationships, and then say that cladistics is based on evolutionary relationships, you're saying something that is effectively circular (we're then back in evolutionary taxonomy land). Cladistic results are based on synapomorphy.

I think I see the problem, though, and it's made clear by your earlier statement: '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'. You have your epistemology backwards because you see the classification as something distinct from the construction of a cladogram. At this point, we run the risk of descending into a debate about classification, etc. The point is that if you want to understand my arguments, then at least understand that I don't see classification as a distinct process from cladogram construction. I don't see why anyone should. Phylogeny, on the other hand, is a hypothetical abstraction we make beyond the inference of a cladogram/classification.

I'm not sure what sort of "attack" you're talking about. I'm in fact trying to keep this pared down to the basics, and refer to those aspects which would be least likely to cause controversy if a person were asked to describe what cladistics is. I think that by saying cladistics is based on common ancestry is vague, misleading, and not very informative. From a methodological point of view, it is wrong. The Internet, however, appears to have developed its own version of what cladistics is about. This is due, in part, to the wide spread notion that cladistics classifications are based on common ancestry. No they are based on synapomorphy. Cladistics is only a means of finding relative degrees of common ancestry. Thus, it may be described as a system of classification that makes statements of relative degrees of common ancestry, but it is meaningless to say that the classifications are 'based on common ancestry', since inferences of common ancestry are actually based on cladistic knowledge.The Braz (talk) 16:42, 25 January 2010 (UTC)

Unused bibliography

An article such as this could have a bibliography hundreds of items long. In general the topic of interest is the article not the complete bibiography (unless the article topic begins "Bibliography of ...."). So, whatever supports that belongs, whatever does not, does not. I'm removing the unused biblio items to here. Naturally there might be disagreements, in which case put the item you feel should be in there back.Dave (talk) 11:15, 21 January 2010 (UTC)

• CurrBiol16:R245. MolPhylEvol45:81,45:748,46:375;48:23,48:176,48:313. OrgDiversEvol5:89. SystBiodivers4:137. SystBiol49:202,51:369,55:46,55:245,55:740,56:252,56:389,56:400,56:543,56:887,56:896,56:956,57:131. ZoolScripta33:293,36:395,36:409,36:607,37:337,37:561,38:101.
• Cavalli-Sforza, L.L. and A.W.F. Edwards (1967). "Phylogenetic analysis: Models and estimation procedures". Evol. 21 (3): 550–570. doi:10.2307/2406616. {{cite journal}}: Unknown parameter |month= ignored (help)
• de Queiroz, Kevin; Jacques A. Gauthier (1992). "Phylogenetic taxonomy". Annual Review of Ecology and Systematics. 23: 449–480. doi:10.1111/j.1096-3642.2006.00293.x. ISSN 0066-4162.

• Felsenstein, Joseph (2004). Inferring phylogenies. Sunderland, MA: Sinauer Associates. ISBN 0-87893-177-5.
• Hamdi, Hamdi; Nishio, H; Zielinski, R; Dugaiczyk, A (1999). "Origin and phylogenetic distribution of Alu DNA repeats: irreversible events in the evolution of primates". Journal of Molecular Biology. 289 (4): 861–871. doi:10.1006/jmbi.1999.2797. PMID 10369767.
• Hennig, Willi (1950). Grundzüge einer Theorie der Phylogenetischen Systematik. Berlin: Deutscher Zentralverlag..
• Hennig, Willi (1982). Phylogenetische Systematik (ed. Wolfgang Hennig). Berlin: Blackwell Wissenschaft. ISBN 3-8263-2841-8.
• Kitching, Ian J. (1998). Cladistics: Theory and practice of parsimony analysis (2nd ed.). Oxford University Press. ISBN 0-19-850138-2. {{cite book}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
• Luria, Salvador (1981). A view of life. Menlo Park, CA: Benjamin/Cummings. ISBN 0-8053-6648-2. {{cite book}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
• Rosen, Donn; Gareth Nelson and Colin Patterson (1979), Foreword provided for Hennig (1979)
• Shedlock, Andrew M; Okada, N (2000). "SINE insertions: Powerful tools for molecular systematics". Bioessays. 22 (2): 148–160. doi:10.1002/(SICI)1521-1878(200002)22:2. ISSN 0039-7989. PMID 10655034. {{cite journal}}: Unknown parameter |doi_brokendate= ignored (|doi-broken-date= suggested) (help)
• Sokal, Robert R. (1975). "Mayr on cladism -- and his critics". Systematic Zoology. 24 (2): 257–262. doi:10.2307/2412766.
• Swofford, David L. (1996). "Phylogenetic inference". In Hillis, David M; C. Moritz and B. K. Mable (editors) (ed.). Molecular Systematics (2. ed.). Sunderland, MA: Sinauer Associates. ISBN 0-87893-282-8. {{cite book}}: |editor= has generic name (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)CS1 maint: multiple names: editors list (link)
• Wiley, Edward O. (1981). Phylogenetics: The Theory and Practice of Phylogenetic Systematics. New York: Wiley Interscience. ISBN 0-471-05975-7.
• Zwickl DJ, Hillis DM (2002). "Increased taxon sampling greatly reduces phylogenetic error". Systematic Biology. 51 (4): 588–598. doi:10.1080/10635150290102339. PMID 12228001.

I fully support dropping reference to my book. It was not about classification at all (as I was at pains to say in Chapter 10, in a passage that outraged many systematists). Most of it was (as the title implies) about methods for inferring phylogenies. Using nested synapomorphies, in cases where the apomorphic state is known, is Hennig's method -- all of the other numerical methods have only indirect connection to it, and they reconstruct phylogenies, and do not force one to classify monophyletically. So my book is mostly on the more interesting issues that are not what the term "cladistics" covers. Felsenst (talk) 17:50, 25 January 2010 (UTC)

False cladogram

The cladogram illustrating polyphyly, monophyly etc is nice looking, but it's inaccurate. Pisces is not a clade. I don't want to remove the picture until there's another one to take it's place, but I don't know how to edit images. --Danger (talk) 16:09, 22 July 2010 (UTC)

I agree. Pisces is not monophyletic, it's not a good inclusion in an article talking about cladistics. Moreover, this picture is maybe difficult to understand. Using a separate picture to illustrate monophyly, paraphyly and polyphyly could make the article clearer. Naldo 911 (talk) 13:45, 22 November 2010 (UTC)

Just incert "lobe-finned fishes" or "lungishes" instead of "pisces" would solve the problem. Alternatively one could use a more hypothetical tree, like the one in the clade article.--Petter Bøckman (talk) 18:22, 22 November 2010 (UTC)

Definitions of types of group

In the version of 12:47, 4 December 2010, if the text relating to the terms Monophyletic, Paraphyletic and Polyphyletic in the Terminology section is meant to offer definitions, then they are either unclear or incorrect.

• "Monophyletic groups are groups containing only taxa descended from a given ancestor taxon and all those descendants." This is just poor English, I think. A re-write would be something like "Monophyletic groups are groups containing all the taxa descended from a given ancestor taxon and no other taxa." However, this does not allow a group of extant taxa to be called a monophyletic group: the definition requires the group to contain all the ancestors. This is not how the term is used by many workers.
• "Paraphyletic groups are groups excluding one or more descendant taxa of the common ancestor, and thus contain some but not all of its descendants." This is only valid if you state that the "descendant taxa" being excluded are monophyletic groups; e.g. excluding a paraphyletic taxon from a monophyletic taxon doesn't leave a paraphyletic taxon.
• "Polyphyletic groups are groups containing taxa from two or more different monophyletic groups." A monophyletic Linnean Family which contains two or more monophyletic Linnean Genera is, by this definition, polyphyletic.

To be fair, I think it's very difficult to define in words what these terms mean in their current consensus usage (partly because authors aren't, in my view, consistent, and partly because they often don't give their definitions). However, what is written here is very problematic. I'm a bit reluctant to make editing changes without some input from others. There's also the difficulty of finding source references with clear and consistent definitions. Peter coxhead (talk) 22:34, 6 December 2010 (UTC)

Personnaly, I'll definite :

• monophyletic --> based on a synapomorphy
• paraphyletic --> based on a plesiomorphy
• polyphyletic --> based on a homoplasy

N@ldo (talk) 11:28, 7 December 2010 (UTC)

I agree with Peter coxhead. The descriptions are vague and badly worded. This is an important article, and these descriptions should be worded carefully. Petter Bøckman (talk) 18:39, 7 December 2010 (UTC)

I agree too. The definitions based on the notion of common ancestor are rather confusing.

• Monophyletic : Peter coxhead got the point. We can replace this with :

"All members of a monophyletic group are more closely related between them than they are with any other taxon situated outside the group. A monophyletic group is defined by at least a synapomorphy (= a character at a derived state)." Maybe we can also add that some will call them holophyletic groups.

• Paraphyletic : "The members of a paraphyletic group are defined by a plesiomorphy (= a character at an ancestral state). As a consequence, they form a truncated group, that excludes some monophyletic taxa from a monophyletic group."

• Polyphyletic : "The members of a polyphyletic group are defined by a homoplasy (a convergence or a reversion). In consequence, polyphyletic groups are totally artificial"

I took these definitions from diverse lectures and sources, including Darlu & Tassy 1983 (rather old, but still valid for such definitions). N@ldo (talk) 22:45, 7 December 2010 (UTC)

That looks better. I do however think that the concept of an ancestor and all the descendant need to be mentioned, as it is 1) a very common understanding of it, and 2) the definition used by Hennig. My suggestions:

• A monophyletic group consist of all members that are more closely related to each other than to any taxon outside the group. When extinct ancestors are regarded, a monophyletic group consists of an ancestor an all of it's descendants. Such a group is defined by at least a synapomorphy (= a character at a derived state)." The terms clade and holophyletic bout refer to this understanding of the term monophyletic.

• A paraphyletic group is defined by plesiomorphies (= characters at an ancestral state). As a consequence, they form a truncated group, that excludes one or more monophyletic taxa from a monophyletic group. An alternative name is evolutionary grade, refering to the ancestral character state within the group.

• A polyphyletic group is defined by a homoplasy (a convergence or a reversion of characters). In consequence, polyphyletic groups are totally artificial. Petter Bøckman (talk) 08:23, 8 December 2010 (UTC)

Sounds good to me. But I think it's better to not talking about "ancestors" as this notion creates confusion. We need to talk about ancestors but in an other section, where we explain that an ancestor biologically exists, but cannot be reconstructed into a cladistic framework.

It's better to use the term "hypothetical ancestor". And personnaly, I'll define the node as a synapomorphy more than as an ancestor : the tree does NOT show speciations !

Then, let's talk about the examples and the figure, which is awful ("Pisces" is monophyletic, as "Amphibia" !). I propose to draw an other figure, with examples of species as terminal taxa (for example, "salmon" instead of "Pisces" or "Teleostei", which is more understandable for a layman). And let's stop using "Reptilia" as an example of a paraphyletic group, because in some definitions, they are a clade which is more or less synonym with "Sauropsida". We shouldn't add to the confusion !

N@ldo (talk) 10:07, 8 December 2010 (UTC)

The figure absolutely needs changing (I've already removed "Pisces" from diagrams elsewhere -- see Monophyly, but the changes need to go further). Peter coxhead (talk) 12:32, 8 December 2010 (UTC)

Petter Bøckman and N@ldo: I have a problem with your suggestions. For me, they mix what should be two quite different issues. (1) What shape are the three kinds of group, in terms of tree diagrams? This is quite independent of any of the properties of the entities being classified and so you don't need to mention any kind of character issues, plesiomorphy, homoplasy, or whatever. (2) Why would a biologist want to use a group of this shape in a classification? Here characters are crucial.

Sometimes phylogenetic analyses produce trees on which monophyletic classifications are built without it being clear that there are any synapomorphies (other than in the gene sequences). For example, the plant family Plantaginaceae has recently been expanded based on gene-based studies. Botanists have then struggled to find any morphological synapomorphies ([1]). So I don't think that it's right to define monophyletic as requiring any kind of character properties in modern (post-Hennig) use.

The problem with producing definitions which mix (1) and (2) is that it makes it harder to clearly discuss the uses, advantages and disadvantages of particular classifications because these have been embedded in the definitions. Personally, I am in favour of definitions which depend only on shape, followed by an explanation of when and why groups defined in this way are used, and what their advantages and disadvantages are. However, it's clear to me that the literature does mix shape and property in definitions. As an example, consider Budd & Jensen (2000)([2] – not public access, sorry), who, following Jeffries (1979), define a phylum as a crown group with the extant restriction. This leads them to the conclusion that there cannot be an extinct phylum, which is, to say the least, an odd use of the term 'phylum'. The oddness is produced by mixing shape with the extant property. This is only one example among many. The difficulty within Wikipedia is how far to go in trying to produce clear explanations without at least violating WP:Synth, when many (if not most) sources use different/incompatible/confused definitions. I don't know the answer! Peter coxhead (talk) 12:32, 8 December 2010 (UTC)

Hm, seems there's no simple way through this. I do see the point of "mixed" approaches. However, as bout are used, bout should be covered. Would a table be better, where on column may show "tree topography" type of definitions and another one referring to traits? I really think we ought to put "ancestor" in there as well, in that it is central to the Hennig/PhyloCode type definitions. Perhaps a third column?

From a historical point of view, is what we are seeing here the slow splitting up of the terms "monophyletic", "clade" and "crown group" into several closely related meanings? Petter Bøckman (talk) 13:54, 8 December 2010 (UTC)

A table is a clever idea, and may well be the best solution. I think that you are right that there are actually several closely related meanings of these terms. We have to try to sort this out clearly for the 'typical reader' (whoever that is!) of Wikipedia. As always it's much easier to see what's wrong than to put it right. Certainly it's worth trying a two-column table first, to see how it works – I guess in user space rather than publicly at this stage. Peter coxhead (talk) 14:08, 8 December 2010 (UTC)

The table is a good idea : as we already said, it will make it easier to discuss the "ancestor" concept.N@ldo (talk) 15:10, 8 December 2010 (UTC)

Ok, I've attempted a table-based set of definitions at User:Peter_coxhead/Sandbox. Please edit/comment -- I suggest at that page not here. If you think the table works and we can agree on its contents, it can be copied to the article. Peter coxhead (talk) 09:28, 9 December 2010 (UTC)

I'm for replacing the current text! I think you have done a good job! Petter Bøckman (talk) 08:14, 10 December 2010 (UTC)

The revision is good ! However, I believe that our definition of paraphyly and the example both need to be revised. The plesiomorphy quoted here is the backbone which is a synapomorphy of the Vertebrates, but a plesiomorphy when you are inside the Vertebrates. I think it's important to emphasize that apomorphy and plesiomorphy are relative notions, that appear to us when we polarize a tree, using an extra-group (or, more rarely, ontogeny). So, the status of plesiomorphy depends on the ingroup considered.

The example, I think, is confusing. True, the backbone is a plesiomorphy if you are inside the Vertebrates. But no matrix can group birds and mammals as a paraphyletic group if you use backbone as a character at a plesiomorphic state, because there is no apomorphic state for the same character in the group considered. As an example of symplesiomorphy which leads to paraphyletic groups, we can use for example the pluribasal member. Inside the Vertebrates (or at least, the Craniata), it is a plesiomorphic character. The apomorphic state for Sarcopterygii will be "absence of pluribasal member", or "monobasal member". As a consequence, a group defined by the character state "pluribasal member" (Chondrichtyes + Actinopterygii if you don't include fossils) will be paraphyletic, as it excludes Sarcopterygii. Glad that this discussion had made the article better ! N@ldo (talk) 21:58, 11 December 2010 (UTC)

Note that there is a paragraph stressing the relativity of synapomorphy/plesiomorphy. One problem which comes up over and over again in writing this material is its circularity: it's very hard to write a linear explanation, because so many terms depend on the others for a full understanding. So the reader really must work through the whole section. However, I agree that the example isn't the best. However, it must relate to the diagram (which Chondrichthyses + Actinopterygii wouldn't, given the present diagram). As was commented earlier in the discussion, we really need a slightly better example diagram, but hopefully one which doesn't require the whole of the section to be re-written. Is there an example based on the present diagram which is better? Peter coxhead (talk) 23:50, 11 December 2010 (UTC)

Ok, I've tried again, removing the "backbone" example altogether. I think 'cold-bloodedness' works better. Note that we can't say, at this point, that "symplesiomorphy leads to paraphyletic groups" (which I nearly did) because the '-phyletic' terms haven't yet been introduced. Comments on this change, please. Peter coxhead (talk) 00:14, 12 December 2010 (UTC)

~Yeah, "Cold-bloodedness" is better, at least as a provisory example.N@ldo (talk) 10:28, 12 December 2010 (UTC)

James & Pourtless citation

In a discussion with user Peter coxhead we came to the conclusion that the bird-dinosaur example is not entirely appropriate. If no one objects, I'll remove it. Does anyone know of another case, easily understandable to the general public, in which homology might have been assumed because of a presupposed phylogeny?--MWAK (talk) 14:00, 26 May 2011 (UTC)

The bird-bats link may do? It was Linnaeus who solved that pickle. In Erasmus Darwin's time, the hot blooded creatures (birds-mammals) were generally thought to be related. Another possible candidate may be the "panda thumb" in pandas and red pandas, which both have despite not being very closely related. Another possibility may be falcons and eagles. Petter Bøckman (talk) 14:10, 26 May 2011 (UTC)

Just to make the point that the example needs to serve a very specific purpose, namely to point out that sometimes cladistic analysis can involve a circular argument (but of course doesn't always). A character is excluded because it is thought to be a plesiomorphy or included because it is thought to be an apomorphy. The resulting analysis (manual or computerized) then confirms the assumption. The best example I know (as a "plants person") is the early evolution of land plants. At one time it was thought that the algal ancestors of land plants had more-or-less isomorphic alternation of generations. On this basis, the gametophyte-dominant lifestyle of the bryophytes was an apomorphy, leading to the use of this character in deciding that bryophytes were monophyletic. However, molecular evidence later showed that that this was wrong, so now the plesiomorphic state is considered to be gametophyte dominance, leading to this character playing no part in deciding whether bryophytes are monophyletic. I don't know enough about the examples Petter suggests to know whether they fit this scenario or not. Peter coxhead (talk) 15:38, 26 May 2011 (UTC)

All my suggestions are off then, as they are all more or less pre cladistics. What about the debate over Ida the fossil, where the two sides really debate the character state for the early primates? Petter Bøckman (talk) 16:34, 26 May 2011 (UTC)

Merged Clade

I have determined that the Clade article and the Clades section of this article contain basically the same information, therefore making it pointless for Clade to have its own article. There is really no way to expand information on the term so as to necessitate a separate main article, since any discussions on clades refers directly to cladistics. This is just a heads up to anyone wondering where the Clade article went. Cadiomals (talk) 03:34, 2 March 2012 (UTC)

The new section on clade in the cladistics aricle lacks a lot of the information found in the old clade article. Though they necessarily will contain much of the same information, the two are not the same. I will revert if no-one comes up with a better reason for a merge. Petter Bøckman (talk) 07:40, 2 March 2012 (UTC)

I support a revert. The concept of a clade is derived from cladistics but logically independent from it. Information on what a clade is belongs at Clade. Information on how clades are used in the field/activity of Cladistics belongs here. If there's unnecessary overlap, the move of content should be the other way. Peter coxhead (talk) 14:50, 2 March 2012 (UTC)

Agreed. Is anyone up for moving the content the other way? Cladistics is a method and a controversial point of view while the concept of a clade is generally acknowledged to be useful, or at least well-defined, by all concerned. A reader who runs into the term in other reading and goes to Wikipedia for enlightenment is not looking either for a method or for a POV. Peter M. Brown (talk) 15:10, 2 March 2012 (UTC)

I've reverted the removal of the content of Clade. I do agree with User:Cadiomals that there is an issue with the overlap of the two articles, but as per User:Petter Bøckman and User:Peter M. Brown, removing Clade was not the solution. I hope that one or other of us will have time to look at these articles soon. Peter coxhead (talk) 15:17, 2 March 2012 (UTC)

My view: The content of the clade article is relevant to several parts of the cladistics article. Eventually, the content will defuse a bit, and anyone looking for a concise text on clade will have to trawl through the (necessarily) quite long article on cladistics. In my view we need both, even though there will be a bit of doubling of information. Petter Bøckman (talk) 19:56, 2 March 2012 (UTC)

Whatever; I don't ultimately care. Cadiomals (talk) 21:30, 2 March 2012 (UTC)

Turtles are too controversial

In view of mounting evidence to the contrary (such as this source), to imply that there is a clade containing birds and lizards but not turtles violates WP:NPOV. The diagram in the Clades section therefore needs revision. I suggest eliminating the Testudines side branch, eliminating the Reptilia and Diapsida legends, and specifying Sauropsida as the node for the Lepidosauria branch. If five side branches is not considered enough, one for the Hyperoartia (lampreys) could be added. Peter M. Brown (talk) 21:04, 24 September 2011 (UTC)

One possibility is to substitute the image shown here, which avoids naming the "traditional reptile groups". The text may needs some changing. Peter coxhead (talk) 09:31, 25 September 2011 (UTC)

Actually, the second paragraph of the section is devoted to emphasizing the tentative nature of cladograms, with an example of a possible result that would force a revision. We could leave the image alone and modify the paragraph so as to present a genuine possibility rather than a speculative one.

In the Monophyly, Paraphyly, and Polyphyly articles, where the image is also used, the caption could be modified to make the point.

My suggestion and Peter coxhead's evade the issue; why not confront it? Peter M. Brown (talk) 17:20, 25 September 2011 (UTC)

Cladogram (family tree)

The root of the reptilian (Amniote) tree is kind of fussy. Presenting the tentativeness of cladograms with the reptiles/turles/sauropsids as an example is a good idea. Peter Coxhead's suggestion to find another "standard" figure for the three -phyly articles would on the other hand also make the articles better in my view. The terminology in the present figure is vague ("reptiles" have multiple meanings, so has "Sauropdids" btw), we really should find another section of the tree where the mapping is a bit less back and forth. Perhaps we should go for a purely hypothetical figure in stead? The figure to the right might serve as an example of the latter. Petter Bøckman (talk) 06:37, 27 September 2011 (UTC)

Hm. Well, apes—on one common use of the term, excluding humans—are paraphyletic. Simians are monophyletic. Monkeys are polyphyletic. Will that do? Is there a better example? Peter M. Brown (talk) 19:25, 27 September 2011 (UTC)

Are monkeys as such polyphyletic? By what definition of monkey? Petter Bøckman (talk) 14:02, 28 September 2011 (UTC)

Old World monkeys and New World monkeys are each clades respectively, but the clade including both (Simiiformes) must also include great apes, which are generally not considered monkeys. So, yes, monkeys in the colloquial sense are polyphyletic. --Danger (talk) 14:20, 28 September 2011 (UTC)

That would be paraphyletic rather than polyphyletic. The monkeys have a single point of origin, so that make them monophyletic in the evolutionary taxonomic sense. A unit made up of night active primates (tarsiers and lorises) wpould be biphyletic. Petter Bøckman (talk) 17:15, 28 September 2011 (UTC)

Ugh, you're right. I don't know why I talk before tea. Danger (talk) 17:19, 28 September 2011 (UTC)

The monkeys are the Platyrrhini together with the Cercopithecidae. The last common ancestor, among the basal Simiiformes, was neither. The monkeys are therefore polyphyletic.

The fact that Petter Bøckman has to ask, though, means that this is not a good example. We're trying to explain what a clade is, and we can't clutter up the explanation with a definition of "monkey."

How about: Boreoeutheria monophyletic, Insectivora polyphyletic, Soricomorpha paraphyletic? Peter M. Brown (talk) 01:15, 29 September 2011 (UTC)

Are you really sure, Peter? This depends on how you define Platyrrhini and Cercopithecidae. If you use a crown group definition for the two you are right, but crown groups are not universally accepted. Using a trait or stem based definition will give you other results. I'd say the mundane understanding of monkey is a monophyletic grade, including their common ancestor and excluding their ape descendants. I would be careful imposing subtle scientific definitions on it, given that "monkey" is very much a vernacular term. The primate tree is useful for our purpose though, as it is well understood and branches fairly straight forward. Insectovores are a bit more fickle, not to mention there are alternative definitions about. Petter Bøckman (talk) 07:06, 29 September 2011 (UTC)

Prowling on Google (in English), I find some bloggers who say that humans are descended from monkeys and, not counting creationists, quite a few who say that they are not. Only the former (who generally seem less well-informed) conform to your assessment of "the mundane understanding." All the same, it would be best if we were neutral on the point.

If we do use the primate tree, though, what group—other than the monkeys—do we use to illustrate polyphyly? Do we just pick a homoplasy within the primates and point out that those with the character constitute a polypheletic group? We could use the absence of a tail, for example.

Alternatively: porcupines are a polyphyletic group, and rodents are monophyletic; is there a paraphyletic group closely associated? Peter M. Brown (talk) 22:03, 29 September 2011 (UTC)

Well, humans are descended from monkeys, if you go back far enough (just like we are ultimately descended from reptiles, amphibians, fish etc). We'll need to be careful when wording things. Prosimians are definitely paraphyletic any way we twist it, perhaps they'll do? For a polyphyletic unit is was thinking about a hypothetical unit for nocturnal primates. Then it dawned on me that primates may be primitively nocturnal, rendering "Nocturnalia" a grade. If so, a unit comprised of the diurnal primates would be nicely polyphyletic. I'll take it up with a primatologist friend up and the university and see what he can tell me. I'm making a primate version of the "standard cladogram" for such use. Petter Bøckman (talk) 19:53, 2 October 2011 (UTC)

Primate cladogram

Edit, here's the raw tree. Petter Bøckman (talk) 09:47, 3 October 2011 (UTC)

Part of the problem is that terms like "paraphyly" and "polyphyly" aren't used consistently in the literature; they may include or exclude hypothetical ancestors. The commonest uses of these terms in papers that I read are to classify groups of terminal nodes in cladograms produced by either morphological or molecular cladistic analyses. In such cases there is no question of ancestors being included. (This is well-discussed by Podani (2010) – reference here.) So if you use the term "paraphyly" solely in terms of the terminal nodes of this cladogram then traditional monkeys are a paraphyletic group. Whether or not they are paraphyletic if ancestors are included isn't clear to me; you would have to define "monkeys" as all the whole simian clade (i.e. down to its earliest ancestor) minus the whole hominoid clade. I don't think that the traditional term "monkey" would be used in the kind of source which discussed the fossil ancestors. Peter coxhead (talk) 17:06, 4 October 2011 (UTC)

I see your point. Again, there's subtle language phenomena at work here (words have ever so slightly different meanings in various languages). However, Prosimian should be a clearcut grade, no matter how you twist it, and Simian an equally clarecut clade. Petter Bøckman (talk) 18:01, 4 October 2011 (UTC)

Yes, I think it's better to use scientific names, not common ones like "monkey" which don't have clear meanings. Prosimii and Hominoidea are perhaps the best examples in the primates. The definition of the Suborder Prosimii, e.g. here, is a good example of a grade/paraphyly, so isn't accepted in current systems. Whereas everyone agrees that Hominoidea form a clade. Peter coxhead (talk) 18:28, 4 October 2011 (UTC)

They even have straight up vernacular names (lower and higher primates). I'll see what I can do with the cladogram tomorrow. Petter Bøckman (talk) 19:13, 4 October 2011 (UTC)

Yes, good point. I guess my point should be that "secondary names", i.e. ones that scientists and popularizers of science make up for scientifically defined taxa, generally have clear meanings. Whereas "real" vernacular words like "monkey" or "ape" don't have tight biological definitions (although people try to give them ones). So it may be better to avoid the latter. Peter coxhead (talk) 20:09, 4 October 2011 (UTC)

Monophyly, paraphyly and polyphyly

Sorry for being late, Gents! I have now made a primate version of the mono-, para- and polyphyly figure. Petter Bøckman (talk) 11:22, 9 March 2012 (UTC)

With Petter's OK, I have implemented his diagram with minor modifications. (Simia was abandoned by the ICZN in 1929). This is my first venture at uploading, so I welcome improvements. Peter M. Brown (talk) 19:06, 5 July 2012 (UTC)

Now someone needs to modify the section next to this diagram since it refers heavily to the previous diagram. (I know way too little about the topic to try myself ...) Ardik (talk) 12:16, 15 July 2012 (UTC)

I've made some changes to the text next to the diagram. The section Cladistics#Terminology for characters, however, is seriously in need of attention.Peter M. Brown (talk) 17:19, 15 July 2012 (UTC)

Real life events have unfortunately kept me from contributing much lately, but I just want to say you guys have done a very good job of clearing up this article! Petter Bøckman (talk) 06:51, 2 August 2012 (UTC)

ostriches and rheas

Hi Peter Brown - you asked if you were missing something in removing the sentence "The fact that ostriches and rheas both have four limbs does not provide any support for putting them into a separate group of 'flightless birds'." Perhaps. Isn't it an important concept that while ostriches and rheas share this character, it provides no evidence of their being closely related, because the trait is plesiomorphic for the larger clade containing those species - tetrapoda?

Reflecting on your response, I now think that the problem with the sentence is not so much that it is irrelevant as that it is false. Restricting the animals of interest to those with four limbs excludes most flying animals (insects), thereby providing some evidence that they are flightless; it also eliminates the most common animals of all, the nematodes, so every non-nematode taxon—including birds—becomes more likely in light of this evidence. Your formulation also seems incorrect: the fact that ostriches and rheas all possess four limbs places both groups among a tiny percentage of eukaryote genera, thus providing excellent evidence that they are closely related. Peter M. Brown (talk) 16:28, 10 August 2012 (UTC)

The context is within the tetrapoda. Yes, four limbs in rheas and ostriches is evidence that they are related, but only at the level of tetrapoda, and at no finer of a level. Having four limb is synapomorphic for the tetrapods, but plesiomorphic if you consider just rheas and ostriches. Four limbs provides no evidence for a closer relationship, even though there are tetrapods with other than four limbs (snakes, skinks, caelicians etc). de Bivort 17:18, 10 August 2012 (UTC)

Does this observation point the way to reformulating the deleted sentence in a way that is true, relevant, and not redundant? The text already says that "for a group within the tetrapods, such as birds, having four limbs is a plesiomorphy." I do not see a point in replacing the deleted sentence with one noting that this trait is a plesiomorphy for the ratites. Peter M. Brown (talk) 17:42, 10 August 2012 (UTC)

Well, clearly the point of the deleted sentence was to provide an example, to make the concept easier to understand for readers. And also clearly it didn't succeed, since it generated confusion. I think an example, either the original one re-worked, or a new one, is a good idea. Hopefully others will weigh in. de Bivort 18:11, 10 August 2012 (UTC)

Excessive commas

I am removing some commas recently added to the article. All are permitted by the rules, but many are optional and interfere with the flow of the text. For example, the edit added a comma after each occurrence of "e.g."; while this is always permitted, it is generally optional. The Blue Book of Grammar and Punctuation, for example, uses

You may be required to bring many items, e.g. sleeping bags, pans, and warm clothing.

as an example of acceptable usage; a comma is admissible after "e.g.", but it is not necessary. Peter M. Brown (talk) 12:37, 25 August 2012 (UTC)

Edit 23 September 2012

Argh. This whole series of articles was, and largely still is, a mess. So many articles on so narrow topics, all of them repeating large chunks of the same stuff (independently written, not copied & pasted!) that only fits one of them... Cladogram explains phylogenetic analysis at considerable length, the very topic of the Phylogenetics article, when a cladogram is simply the result of a phylogenetic analysis...

I have tried to begin unraveling this mess. Yesterday, I extricated Phylogenetic nomenclature from it; that was fairly easy, because I had created that article independently of the mess. I also restricted Clade to what it says on the tin; that article was relatively short.

Today, I:

• Wrote a new introduction, trying to distinguish phylogenetics from the principle of only naming clades.
• Reorganized the article according to that distinction. This distinction allows me to keep the Cladistics and Phylogenetics articles separate (I have elsewhere threatened to merge them).
• Made the paragraph about the problem of homology a "controversy" subsection within the "phylogenetics" section. The rest of that paragraph is now in the "controversy" subsection of the "taxonomy" section, see below.
• Moved the history section up, because it concerns both phylogenetics and taxonomy, and rewrote the part on phenetics.
• Exported the explanations of "nested", "sister group" and "basal" to Clade, because they belong neither quite to phylogenetics nor to taxonomy.
• Changed "Terminology for characters" to "Terminology for character states".
• Changed "Terminology for groups" to "Terminology for taxa". Apparently, it was meant to compare pattern cladistics to (process) cladistics, but it never once mentioned those terms, and pattern cladistics is dead, dead, dead. (It doesn't even have a WP article, unlike, say, the quinarian system!) I've still kept the subsection, because it is a nice conclusion to the rest of the taxonomy section, but I've removed the pattern-cladistic language with its "groups of nodes". If you want to bring it back, write an article on pattern cladistics. – Also, the stipulation that an apomorphy must be inherited by all members of a clade was flat-out wrong.
• Moved "Phylogenetic definitions of a clade" to Phylogenetic nomenclature, where it belongs. Once more, in chorus: Clades are not defined, they exist outside our skulls and are discovered by science; names are defined, they are conventions. Science and nomenclature aren't the same!
• Integrated part of the "Cladograms" section, which was in part a repetition of stuff higher up on the page, in the new "Phylogenetics" section. – "In cladograms, all species lie at the leaves" is flat-out false; datasets for cladistic analysis can have larger taxa than species as their OTUs, as well as smaller ones down to individuals (or genes) within one or a few species.
• Deleted the other part of "Cladograms", because it was just repetition of what it says in Phylogenetics and Phylogenetic tree.
• Removed the stuff about phylogenetic nomenclature. PN is not synonymous with the principle of only naming clades – it's not even a subset of it. The rest of the "cladistics in taxonomy" section is fine; I've made it a "controversy" subsection within the "taxonomy" section. This subsection also includes text from higher up; I've removed the reference to Mayr (1974) writing of "the essential unity of the reptiles", though, because almost 40 years later that's just silly – the fossil record has improved to such a point that the long, long transition from "reptiles" to birds is now known in itty-gritty detail, never mind the one from "reptiles" to mammals which was already pretty well understood in 1974. If you want to have a gradist statement, find a much more recent reference (Mayr himself only died in 2010, right?).
• Edited that subsection. As somebody said higher up on this page, Hennig's work didn't trigger any discussion about phylogenetic nomenclature; the first paper that used PN came out in 1986!
• Removed the "complexity of the tree of life" section because it's off topic. Calling the tree "the cladistic tree of life" doesn't make it cladistic.
• Changed "Application to other disciplines" to "Application to disciplines other than biology". Removed the simply wrong statements about pairwise comparison; phylogenetic analysis compares the entire dataset at once.
• Clarified the small distinction between cladistics and the comparative method of historical linguistics.
• Moved the ethology example high up, because ethology is part of biology – ethological data can be, and have been, used in the reconstruction of the relationships of animals.
• Removed "Bauplan", "Evolution of Mollusca" and "PhyloCode" from the "See also" section.
• Cut down the enormous bibliography to the references and a few other important works... which should probably be cited somewhere in the article or moved to other articles.

The article as it now is does not have enough references. I'll try to add more, but I won't have much time in the coming weeks. Feel free to scoop me!

Now on to Phylogenetics... but I won't do much there, it's late.

David Marjanović (talk) 18:19, 23 September 2012 (UTC)

Hi. I rewrote the subsection "Some criticisms of phylogenetic nomenclature" last week, spending some time researching criticisms. No question, it didn't belong in the Cladistics article. I don't see it in the new Phylogenetic nomenclature article either, though. Where are you planning to put it? Or will you be rerewriting it? Peter M. Brown (talk) 19:43, 23 September 2012 (UTC)

Linnaean definition of tetrapod

According to Cladistics#Example, Linnaean taxonomy defines the Tetrapoda "morphologically as vertebrates with four limbs (as well as animals with four-limbed ancestors, such as snakes)." The definition is not morphological if it includes the part in parentheses, which brings in the matter of ancestry. Without the parentheses, however, it is inadequate because it excludes snakes, moas, etc. Peter M. Brown (talk) 17:00, 6 August 2012 (UTC)

Well, it's how the term is used in Linnaean taxonomy. We just need a suitable way to express it. Petter Bøckman (talk) 20:23, 10 August 2012 (UTC)

I would like to replace the first paragraph of Cladistics#Example with something like the following.

The difference between approaches can be illustrated by the varying treatments of Tetrapoda.

Linnaean taxonomists do not have a firm definition of Tetrapoda or, indeed, of any higher-level taxon. Systematists like Benton see, as an important strength of the approach, the ability of the taxonomy to change based on the progress of science.​ The ICZN takes this flexibility as an underlying principle: "Nomenclature does not determine the inclusiveness or exclusiveness of any taxon".​

Historically, the classes Mammalia, Aves, Reptilia, and Amphibia were united in the superclass Tetrapoda based the evident fact that most animals in these classes have four limbs. All animals in these classes were therefore included despite the fact that some, including whales, moas, snakes, and caecilians, have lacked this feature. In addition, four-limbed animals like the Diadectidae known only from fossils were included even when they do not fall into the four extant classes. Going forward, the discovery of a new animal may require the scientific community to decide whether to call it a tetrapod or not; when the transitional fossil Tiktaalik was first described in 2006, for example, the discoverers called it a fish, not a tetrapod, but no firm rules required this designation.

Is my history accurate? Can it be sourced? If not, can something along the same line be used? Peter M. Brown (talk) 00:44, 11 August 2012 (UTC)

No, it seems that all early sarcopterygians were classified as fish, amphibians, or reptiles; no tetrapod was considered neither amniote nor amphibian. I'm working on it. Help would be appreciated. Peter M. Brown (talk) 14:16, 11 August 2012 (UTC)

OK, done. Please review and correct, or at least comment on the shortcomings. Peter M. Brown (talk) 23:01, 11 August 2012 (UTC)

Looks good, only there is actually a "firm definition" of Tetrapoda, i.e. having feet rather than fins. One might say that the back and forth over internal gills and fin rays (both found in Ichthyostega) would make the definition "unfirm", but the fins/feet definition has there all along. The same with mammals, where the definition eventually settled on the jaw joint/ear osicles.Petter Bøckman (talk) 20:19, 12 August 2012 (UTC)

Really? On the matter of defining Tetrapoda, Clack & Coates (1995) wrote, "Possession of digits remains the most compelling character in practice at the present, but we point out its potential inadequacies for the future." I might add that as a reference supporting my contention that delimiting Tetrapoda in a Linnaean framework is an ongoing process; that there is not a firm definition. Notice that they do not mention feet. Clack adds elsewhere that "limbs with digits" is unsatisfactory since it can be broken down into many separate characters. Peter M. Brown (talk) 21:12, 12 August 2012 (UTC)

I suppose it depends on the abruptness of the change. If the single-mutation scenario is right, then all, or most of, Clacks characters are linked. If it was a more gradual process, then more fossils will lead to new definitions. In that regard I believe the term "unfirm" is apt. Petter Bøckman (talk) 12:19, 13 August 2012 (UTC)

Do not confuse definition and diagnosis. Diagnoses – lists of characters that allow systematists to tell whether a specimen belongs to the taxon in question or not – belong to taxonomy, not to nomenclature; the ICZN (like its sister codes) stipulates that, when a taxon name is erected, a diagnosis must be provided, but this diagnosis can be changed at any time; the diagnosis need not ever be correct, and a change of the diagnosis is not a nomenclatural act.

Taxon names in the species, genus and family groups of ranks do have definitions under the ICZN; but those consist of a type and a rank. Homo sapiens is defined as the name of the taxon of species rank that Linnaeus belongs to, Homo is defined as the name of the taxon at genus rank that H. sapiens belongs to, and so on, till Hominoidea is defined as the name of the taxon at superfamily rank that Hominidae belongs to. And then it ends. Tetrapoda is high above the family group of ranks; on the rare occasions that it's given a rank at all, that is usually superclass or an unconventional rank.

The fun thing is that most rules of the ICZN only hold for the species, genus and family groups of ranks. Even the Principle of Priority does not hold for names of higher rank. They don't have types either. Therefore, Tetrapoda does not have a definition at all under "Linnaean" nomenclature.

There is a discussion about how best to define the name Tetrapoda = which clade to attach it to; but this discussion is entirely within phylogenetic nomenclature. As you say, some favor applying the name to a crown-group, which means they want a node-based definition, while others favor an apomorphy-based definition that lets Ichthyostega stay a tetrapod.

David Marjanović (talk) 13:27, 23 September 2012 (UTC)

A diagnosis is nomenclatural, not just taxonomic, as it is required as part of naming at the species level. If taxa were defined by necessary and sufficient conditions, it would indeed be an objection that the diagnosis may change and may not actually be applicable to the type. A diagnosis does not supply necessary conditions for membership, however; rather, it is a statement intended to provide characters that differentiate the taxon from others with which it is likely to be confused.​ It provides guidance to subsequent researchers and may be replaced by another formulation that gives better guidance. Peter M. Brown (talk) 16:57, 6 October 2012 (UTC)