Talk:Cladistics/Archive 4

Opening definitions
The opening definitions are very confusing and appear to be confusing/confounding cladistics with phylogenetics, among other things.

Definition #1- Cladistics is not "the science of phylogenetics." This sentence has two problems. First, cladistics is a starting point method for figuring out a phylogeny. It is not the actual making a phylogeny, several of which could come from one cladistic analysis (see Cladograms and Phylogenetic Trees, Wiley EO, Systematic Zoology, 1979). Second, and in a similar vein, it is not "the" method as in the only one for figuring out a phylogeny (again, it doesn't even figure them out in the first place it is only a starting point). Third, and MOST importantly, this definition really doesn't tell the reader anything about cladistics. It just tells the reader that it is "a method", but never actually describes the method (in fact no where in the article is this so called "method of cladistics" ever defined or described, not even telling the reading what a shared derived characteristic is). Therefore I wanted to replace the opening definition with: "A method for establishing the relationships of various individuals, items, concepts, etc through the use of shared characteristics." This definition is backed up with the following citations:

"Cladistics: Theory and Practice of Parsimony Analysis" page 1: "Cladistics is a method of classification that groups taxa hierarchically into sets and subsets." page 2: "The aim of cladistics is to establish sister-group relationships, and the concept of two taxa being more closely related than either is to a third." "Sister groups are hypothesized through the analysis of characters"

"Transformed Cladistics, Taxonomy and Evolution" page 68: "On the basis of a comparison of organisms, perceived similarities are utilized to choose those characters that will be used for more detailed comparisons leading to the construction of a cladogram. Central to this endeavor is the recognition of shared derived characters."

UCMP University Of California Museum of Paleontology Website on cladistics: "Cladistics is a particular method of hypothesizing relationships among organisms." "The basic idea behind cladistics is that members of a group share a common evolutionary history, and are "closely related," more so to members of the same group than to other organisms. These groups are recognized by sharing unique features which were not present in distant ancestors."

Definition #2- This is confusing due to its wording. Its original form leaves it unclear if the words "phylogenetic systematics" are included because they are somehow a synonym for cladistics (if so why is that down here in definitions) or whether it is a whole different field and hence no longer a definition of the main heading word of the page. I tried to emphasize that the second definition is a narrower form of the first definition and that it goes by a specific name (phylogenetic systematics). Hence my definition: "phylogenetic systematics, is a narrower and more formal version of the above which uses the principle of only naming clades as its source of information for taxonomy. This is sometimes pejoratively called "cladism."" — Preceding unsigned comment added by Nathank2 (talk • contribs) 21:21, 29 October 2012 (UTC)


 * Certainly, your critiques are well founded. Your quotations, however, don't actually provide a definition and cannot be used in support of one. None of the three actually defines cladistics; the first and the third say that it is a method with certain characteristics but don't say just which such method should be called "cladistics" while the second doesn't use the term.


 * I see no support for the statement that the term "cladism" is perjorative. Donoghue and Cantino have no problem with it, as they have produced an article entitled "Paraphyly, ancestors, and the goals of taxonomy: A botanical defense of cladism".


 * You say that cladistics does not establish a phylogeny but does establish relationships between individuals. What is there to phylogeny besides relationships? Again, you object to the characterization of cladistics as a method and your cure is seemingly to characterize it as a method. . . .what am I missing?


 * There are indeed two senses of "cladistics". The first is a widely accepted research technique. The second is cladism, an approach to nomenclature. Neither is a "version" of the other.


 * Revision is definitely needed. It is well that you have started this discussion.


 * Peter Brown (talk) 22:52, 29 October 2012 (UTC)


 * I didn't add in the cladism part. It was originally introduced by Mayr and Darlington in the 1960's and 70's due to their perception of unfounded philosophical belief and borderline zealotry by followers of Hennig's newly created field of cladistics. But it's likely a long since forgotten concern.


 * Phylogeny is not just relationships between individuals (aka who is the most similar). Phylogenies shows the ancestor-descendant relationships that result from the various events of evolution.  Phylogenies take into consideration hypotheses of evolutionary events like budding and anagenesis which a cladogram (the result of cladistics) cannot account for or show.  Cladograms also don't show who actually evolved from who on a species/population level.  For example the famous horse evolution phylogeny  [picture] is not a cladogram, but it is a phylogeny.  Cladograms don't have real entities in the internal nodes only at the leaves, but phylogenies can have real entities at the internal nodes.  Hence different evolutionary theories about ancestor-descendent relationships will result in different phylogenetic trees from a single cladogram. (Again, see "Cladograms and Phylogenetic Trees, Wiley EO, Systematic Zoology, 1979" page 1, 1st paragraph.)


 * I see your point about simply restating that it is a method. It is a method, but the original definition is incomplete.  The new definition explains that the method is to compare shared characteristics for the purpose of figuring out relationships.  I wanted to put shared derived characteristics and then add a page link, but haven't gotten around to writing up a whole thing on shared-derived characteristics yet :)


 * Why does definition #1 not work? "The aim of cladistics is to establish sister-group relationships, and the concept of two taxa being more closely related than either is to a third." "Sister groups are hypothesized through the analysis of characters" I haven't been here long so I don't know but does wikipedia require only direct quotes as definitions? Can't we reword that mess into something a layman could understand?  That's basically what I tried to do.


 * How about a direct quote from the OED? Cladistics (OED 2nd Edition)- "Systematic classification of groups of organisms on the basis of shared characteristics thought to derive from a common ancestor."  It's just too narrow because it only includes organisms.


 * "Phylogenetic systematics" was Hennig's original term for his methodology which is now referred to as cladistics. His system emphasized "clades" to the exclusion of other grouping. "Phylogenetic nomenclature" is the new nomenclature based on cladistics, it has it's own page already."

Nathank2 (talk) 00:06, 30 October 2012 (UTC)

Looking back over the old revisions of this article, things seem to have been clearer before. The very old version from [09:22, 6 June 2003] is almost exactly what I am suggesting. It's clear and understandable for a lay person. Version [20:23, 19 January 2007] is a little more convoluted and difficult to understand at the beginning, but the entirety of the opening section is very good and does a good job of giving a basic explanation of the whole concept. Nathank2 (talk) 16:14, 30 October 2012 (UTC)


 * The 2003 version uses the phrase "derived similarity", which I don't think the lay person will find at all clear and understandable. The 2007 version, however, is admirably clear. It does use the term "organisms", which you object to; perhaps you would not mind "items (usually organisms)"?


 * What it doesn't do is distinguish the two senses of "cladistics". I would urge that the article be limited to cladistics1. As I understand cladistics2, it is simply cladistics1 as practiced by those favoring phylogenetic nomenclature. Rather than give cladistics2 any significant attention, let's just refer the reader to the Phylogenetic nomenclature article.


 * By the way, you misunderstood my use of the term "relationships". I didn't mean just "who is most similar" but included ancestral relationships. I suggest that the use of "relationships" in your proposed Definition #1 would be misunderstood in exactly the same way.


 * Peter Brown (talk) 19:22, 30 October 2012 (UTC)


 * Yeah, the "items" idea sounds good. I'm still not fond of the 2007 definition.  It just seems jargony ("morphological similarity", "branching", "evolutionary tree")?  However, if you like that definition, could we perhaps add something at the end which mentions that the process is carried out through the construction of a cladogram? The definition never mentions characteristics or that they are shared and derived or that they are even used in cladistics, but a link to cladograms could (if also cleaned-up) or a further explanation below as in the 2007 version.


 * "Cladistics is a philosophy of classification that arranges items only by their order of branching in an evolutionary tree and not by their morphological similarity. This is carried out through the construction of a Cladogram."


 * I totally agree that we can just dump def 2. It has really been replaced by the term cladistics in the general vernacular (It was just the original/official word for what we now call cladistics). A redirect from "Phylogenetic systematics" to here would be appropriate.  Phylogenetic nomenclature is not however Phylogenetic systematics.  Phylogenetic nomenclature came out in the mid 80's, Phylogenetic systematics was the title of Hennig's book on cladistics in 1966 (it was his official name for what is now called cladistics).


 * Not sure what you meant by the "relationships" comment, but it looks like that will be resolved with the current definition.

Nathank2 (talk) 21:11, 30 October 2012 (UTC)


 * You're right, characteristics are essential to the concept and must be mentioned in the lead. I reiterate that talk of derived traits can be most confusing. A trait can only be derived with reference to a clade (feathers are a derived trait within Archosauria but not within Aves) but the term is often used in a way that fails to make clear the relativity of the attribute. Peter Brown (talk) 21:47, 30 October 2012 (UTC)


 * completely agree. the "derived" concept can be really confusing and probably too much for an opening definition. Nathank2 (talk) 22:02, 30 October 2012 (UTC)


 * After reviewing still more versions of this article it kinda feels like we are just recreating the wheel and rehashing out the same stuff from the last 10 years :( The massive edit on "18:19, 23 September 2012" with no sources and no community discussion made many changes that were very good, but also introduced a lot of changes that make the article very confusing and inaccurate (as we have discussed here the last few days).  Our current discussion seems to be leading us back to the exact same article opening paragraphs that were already there prior to that massive edit. Nathank2 (talk) 15:37, 31 October 2012 (UTC)

Template
Hello, I need a help from people with knowledge in systematics and taxonomy to discuss the Template:SysTax. This template was removed from the pages where it appears for discussion and improvment. Thanks Zorahia (talk) 15:22, 22 March 2013 (UTC)

Reference Errors
RE: Maas, Philipp (2010), "Text Genealogy, Textual Criticism and Editorial Technique", in Jürgen, Hanneder; Maas, Philipp, Wiener Zeitschrift für die Kunde Südasiens (Vienna: Austrian Academy of Sciences), 52-53: 63–120, doi:10.1553/wzks2009-2010s63

The article title is wrong. At pages 63-120 of this volume, Maas's article title is "Computer Aided Stemmatics — The Case of Fifty-Two Text Versions of Carakasaṃhitā Vimānasthāna 8.67-157."

The title given to this issue of the journal, which Maas CO-edited, is indeed Text Genealogy, Textual Criticism and Editorial Technique. But in the references, that title for the journal is given as the title for the article. It is unclear what is being cited. — Preceding unsigned comment added by 50.133.222.248 (talk) 05:15, 19 May 2013 (UTC)
 * I have access to the article by Maas, and that seems to be what is being cited. It develops "A hypothetical stemma codicum, i.e. a branching diagram that reflects the transmission history of a given text" using "two complementary approaches: the computer-based cladistic analysis of variant readings (i.e. a quantitative approach) and the philological discussion of selected variants (i.e. a qualitative approach)." MacClade software turned out to be useful. That fits with reference 6 (I wish people wouldn't split bibliographies into two parts like this, as seems to be becoming more common in wikipedia). Sminthopsis84 (talk) 15:41, 19 May 2013 (UTC)

Neutrality issue
Peter Brown deleted my edits to the cladistic pages here, suggesting that they gave too much credit to Steve Farris. I see that he is not a systematist, and I wonder just how he justifies his editorial choices, given that the section called for greater detail, which I provided. Is he suggesting that the historical information I provided is not true? - Andy Brower — Preceding unsigned comment added by Abrower (talk • contribs) 13:00, 20 May 2013 (UTC)
 * Yes, I think that's the general idea. Not that Steve Farris didn't write what you said he did, but that his personal approach was somewhat divisive, and the legacy that you claimed for him is largely due to other people. Sminthopsis84 (talk) 17:11, 20 May 2013 (UTC)
 * I support the deletion, too. The issue is maintaining WP:NPOV and WP:UNDUE. You can say a bit about what Farris wrote, but his importance must be based on what reliable third party sources say. Peter coxhead (talk) 19:12, 20 May 2013 (UTC)

Etymology: minor edit-war
See here. A similar example, which thankfully hasn't escalated to an edit-war due to the timely intervention-edit of another user, can be found here. From my point of view, this is something trivial... Thanatos|talk 19:59, 24 May 2013 (UTC)

Stray citation and WP:3RR
The first sentence of the page currently has two citations for the parenthetical statement that the word "cladistics" derives from Greek κλάδος, klados, i.e. "branch". I see the first one as spurious because it says nothing about this, but the editor who inserted it has repeatedly reverted me. Could someone else please look at this matter? Thanks. Sminthopsis84 (talk) 20:01, 24 May 2013 (UTC)
 * A. See section above.
 * B. WP:3RR reads "more than 3 reverts" (emphasis mine); so please count before invoking it; I haven't in fact even reached 3 reverts yet; I'm presently at 2...
 * C. If you object so much (can't understand why) to this reference-entry-link, why haven't you instead e.g. proposed citing, linking instead to the hyperlinked one therein, i.e. cladism, or even linked it yourself without first proposing anything?? ;-)
 * Thanx. Thanatos|talk 20:08, 24 May 2013 (UTC)


 * Maybe we were seeing different things but when I followed the original first reference (to "cladistics" in the Online Etymological Dictionary) I got nothing (I think because there is only an entry for "cladistic"). The link I've used now shows – for me anyway! – both "clade" and the derived terms "cladistic" and "cladism". In my opinion we don't need a reference to a dictionary of classical Greek to permit the transcription between κλάδος and klados; transcriptions between writing systems are regularly given in Wikipedia without sources. So I think this is the only reference needed. Peter coxhead (talk) 19:21, 25 May 2013 (UTC)
 * Thank you Peter, that also looks good when I access the link. Sminthopsis84 (talk) 13:29, 28 May 2013 (UTC)

Taxonomy
What is the difference (if any) between cladistics and classic biological taxonomy? How do they relate to one another? What was there before cladistics was invented? Or is cladistics just a new name for an old discipline? The article on "Taxonomy (biology)" mentions "cladistic" only in passing, without any explanation of its role. — Preceding unsigned comment added by 213.207.170.238 (talk) 07:49, 29 July 2013 (UTC)


 * I would say that cladistics is just one method which can be used as part of taxonomy to derive hypotheses about the evolutionary relationships of taxa and hence provide evidence on which classifications are based. However, the word "cladistics" seems to be used very loosely in modern biology (e.g. cladograms produced by computer programs employing parsimony or maximum likelihood criteria are sometimes considered part of "cladistics" whereas their methodology is very different). What was there immediately before (but after Darwin) were judgements made by specialists in that group, based on characters and attempting to reconstruct evolutionary relationships, but in a less "algorithmic" and hence arguably more "subjective" fashion. Now, at least for living organisms, there is a related but different method based largely on patterns in their genes. Peter coxhead (talk) 09:26, 2 August 2013 (UTC)

Character-based clade definition
In Cladistics is the statement:


 * A clade is characterized by one or more apomorphies: derived character states inferred to have been present in the first member of the taxon, inherited by its descendants (unless secondarily lost), and not inherited by any other taxa.

Is saying that the character states were "inherited by its descendants (unless secondarily lost)" just a fancy way of saying that the states were inherited by its descendants unless they weren't? If so, the phrase is vacuous and could be omitted. Peter Brown (talk) 02:12, 2 August 2013 (UTC)


 * I think your interpretation of the phrase is correct, but I don't think it's vacuous. Firstly, if you omit the entire phrase, you get A clade is characterized by one or more apomorphies: derived character states inferred to have been present in the first member of the taxon and not inherited by any other taxa. This isn't right, because it doesn't say that the apomorphies were inherited by that taxon, only that they weren't inherited by any other. If you omit the parenthesised part, you get A clade is characterized by one or more apomorphies: derived character states inferred to have been present in the first member of the taxon, inherited by its descendants, and not inherited by any other taxa. Since bare plurals in English often logically mean "all", this can be misread as ... inherited by all its descendants ..., so the qualification is needed to avoid this interpretation. A fuller statement might be something like A clade is characterized by one or more apomorphies: derived character states inferred to have been present in the first member of the taxon, present through inheritance in most of its descendants (but not necessarily all since they may have lost it), and not inherited by any other taxa. Peter coxhead (talk) 09:14, 2 August 2013 (UTC)


 * A clade is characterized by one or more apomorphies: derived character states inferred to have been present in the first member of the taxon, present through inheritance in most of its descendants (but not necessarily all since they may have lost it), and not inherited by any other taxa.


 * This "fuller statement" of yours introduces most as a brand new element. ". . .most of its descendants"&mdash; are we counting individuals, species, families or something else? Of course, imprecision in a definition is acceptable so long as we are willing for it to be inherited by the defined term, "clade" in this case. Is imprecision in the concept of a clade tolerable? Notice that whether a character state satisfies the condition will vary through time; ovipary was relevant as an apomorphy (sensu Coxhead) for Synapsida as of the end of the middle Jurassic, but not today.


 * "Vacuous" was admittedly the wrong word. To say that a character state is either inherited or not inherited is, rather, a tautology, a proposition that cannot consistently be denied. When a tautology appears as part of a conjunction, it can simply be dropped. "I am American and all Kurds are Kurds and you are English" is equivalent to "I am American and you are English". If the result of dropping a tautology in a conjunctive context is unacceptable, then so is the original proposition. We agree that the result of dropping "inherited by its descendants (unless secondarily lost)" from the definition in the article is inadequate; it follows, I submit, that the definition is unsatisfactory as it stands. Peter Brown (talk) 18:16, 2 August 2013 (UTC)
 * Ah, right, I see you were making a slightly different point than I thought. First, a character state might not be (simply) inheritable; e.g. as I know from experience, many alpines have consistent growth habits in the wild which don't persist in lowland gardens. The genetic propensity to grow in a certain way when exposed to high levels of UV, snow cover, etc. may be inherited, but not the observed characters. Second, there is the word "secondarily" in the original. To say that a character is either inherited or secondarily lost isn't a tautology: "secondarily lost" doesn't just mean "not inherited".
 * However, I do agree that the definition you quote is unsatisfactory, because it appears to be circular. I think that what "secondarily lost" really means is "this is a clade, so the fact that some members don't have the character means that they lost it secondarily". Thus apomorphies of a clade not present in a member of the clade must be "secondarily" lost as opposed to the "primarily" acquired apomorphies. Can "primary" and "secondary" in this context be defined independent of "clade"?
 * Also, are the character-based 'definitions' really definitions in the context of this article? The 'real' definitions of a clade are the "all descendants" ones. In Hennig's method, characters are a way of coming up with hypotheses as to what are clades. Character-based seem to be a feature of the PhyloCode, not cladistics more generally. Peter coxhead (talk) 08:05, 3 August 2013 (UTC)


 * The propensity to grow in a certain way when exposed to high levels of UV, snow cover, etc. is not an observed character but it is one that you have observed???


 * Yes, bad example on my part. Although it does make the point that "character" requires very careful definition: a "propensity" is a character, but might not obviously be thought of as one. Peter coxhead (talk) 17:07, 3 August 2013 (UTC)


 * The only definition I quote is the one you offered; I would say that both it and the one in the article are circular for the same reason. However, suppose we adopt the the "all descendants" definition of "clade" so that it doesn't depend on "secondarily lost". Circularity disappears, but does this permit a principled way of saying whether oviparity was secondarily lost in the mammaliaform lineage leading to Theria or whether it simply disappeared? I doubt it.


 * The article's character-based definition of paraphyly does not use the term "secondarily" but, perhaps for that reason, it's in even worse shape.


 * A paraphyletic assemblage is characterized by one or more plesiomorphies: character states inferred to have been inherited from ancestors but not present in all of their descendants.


 * I take Monotremata to be monophyletic, though there are few careful studies of the matter. The combination of hair and oviparity is a good candidate for a characterizing feature. It was inherited from the last common ancestor of the crown mammals. But some descendants of that ancestor lack oviparity; is the characteristic then a plesiomorphy, so that the monotremes are paraphyletic as well as being monophyletic? No, the definition of plesiomorphy is unsatisfactory.


 * I do not conclude that character-based definitions are all unsatisfactory, for I think that the character-based definition of polyphyly, as I have now updated it, works. It is essentially the definition given in the articles Monophyly and Polyphyly.


 * Monophyly and paraphyly, in my view, are tree-based concepts and should have tree-based definitions. Polyphyly is a character-based concept and should have a character-based definition. The attempt to approach all three in a uniform manner is a mistake. Further, "was secondarily lost" is just a misleading way of saying "was not inherited".


 * Peter Brown (talk) 16:28, 3 August 2013 (UTC)


 * Two different issues here:
 * was secondarily lost" is just a misleading way of saying "was not inherited – well, this is at the heart of our disagreement. Clearly "was lost" is just a way of saying "was not inherited". However, the addition of "secondarily" here is an attempt to say more, although I suspect it fails through circularity. (But this is precisely one of the accusations that critics made against cladistics: the decision that a character is an apomorphy is informed by a prior view that the group it defines is a clade.) You and I may agree that adding "secondarily" fails to say anything extra, but I think that reliable sources do not, so we should be cautious about removing it.
 * I profoundly disagree that monophyly and paraphyly are tree-based concepts and polyphyly is character-based. First, the literature doesn't support this view. Hennig's definitions were all essentially character-based. (As elegantly summarized by Oosterbroek, monophyly = synapomorphous similarity; paraphyly = symplesiomorphous similarity; polyphyly = convergent similarity.) Later, others produced tree-based ones. I can source both kinds of definition for all three concepts, if you want. Second, it's very easy to give a tree-based definition of polyphyly: any group of taxa that is not either a monophyly (tree defined) or a paraphyly (tree defined) is a polyphyly (tree defined). Only Oosterbroek (1987) has managed to give a positive rather than a negative tree definition of paraphyly which can be shown to precisely match the negative one ("[a] group of taxa is polyphyletic if their most recent common ancestor has given rise to excluded taxa of which at least one of the sister groups is only partly included in the group").
 * Peter coxhead (talk) 17:43, 3 August 2013 (UTC)

Subjectivity and polyphyly
An earlier version of the article said:


 * "A polyphyletic assemblage is characterized by one or more homoplasies: character states which are inferred to have converged or reverted so as to appear to be the same but which the cladogram implies have not been inherited from a common ancestor."

Peter Brown changed this to remove the 'subjective' wording "inferred", "appear to be" and "implies", with the edit summary "Deleted phrases implying that polyphyly is subjective. Polyphyly does not depend on human inference."

Now I agree that polyphyly is objective: a set of taxa either is or is not polyphyletic (based on a given definition). However, my worry is that stated baldly this doesn't convey the science involved. We don't know for sure whether a character is a homoplasy; it's a scientific hypothesis that it is and hence it's a scientific hypothesis that a set of taxa is a polyphyly. Polyphyly does not depend on human inference, but whether or not we believe that a set of taxa constitutes a polyphyly does depend on human inference. I'm not quite sure how this is best conveyed, though. Peter coxhead (talk) 15:17, 3 August 2013 (UTC)


 * It's common on Wikipedia to hide the effort involved in establishing properties and relations. The Author article, for instance, ignores the immense effort involved in establishing the authorship of medieval works. On the other hand, the Atomic number article does discuss the means by which an atomic number is established. If someone wants to augment Author or Cladistics or Polyphyly with discussions of history or methodology, fine, but I don't see the absence of such augmentation as a shortcoming. The prior wording in Cladistics did imply that polyphyly was subjective, and it was therefore appropriate to remove that implication. Peter Brown (talk) 16:22, 3 August 2013 (UTC)


 * I don't think that the prior wording did necessarily imply that polyphyly was subjective, although it could be read that way. Another way of reading it is that the first part ("[a] polyphyletic assemblage is characterized by one or more homoplasies") is an objective statement, but that the second part says that the concept of a homoplasy is a subjective one. This does seem to me to be a view taken in some of the literature.
 * The problem for me is that what we should be doing in Wikipedia, namely paraphrasing reliable sources and not making up our own definitions, is difficult in relation to cladistic concepts, because reliable sources are regularly confused and contradictory. Peter coxhead (talk) 18:41, 3 August 2013 (UTC)


 * If homoplasy is subjective and polyphyly is defined in terms of homoplasy, then I think it follows that homoplasy is subjective too. And to define homoplasy in terms of what people have inferred makes homoplasy, and therefore polyphyly, relative to human endeavor.


 * I think you mean "... I think it follows that polyphyly is subjective too." if so, this is a nice semantic point. Is it subjective that there are eight planets? The definition of 'planet' seems to be subjective, but once the definition is accepted then I'm reluctant to say that the number (now eight, once nine) is subjective. Peter coxhead (talk) 21:37, 3 August 2013 (UTC)


 * I do have to acknowledge that some homoplasies are based on terms like "yellow" or "gracile" that are vague enough that whether two specimens both possess it is a subjective matter. The polyphyly of Diandria though, seems devoid of subjectivity; either a plant has two stamens or it doesn't.


 * As far as what we should be doing, the policy is that, if reliable sources conflict, we should be presenting both sides. It is surely OK, though to ignore sources that are self-contradictory or totally confused. The trick to to decide what sources can be used. Despite Hennig's historical importance, I'm doubtful as to whether he should be cited except in a strictly historical context; after all, he did die in 1976 before molecular sequencing became practical, and such sequencing dominates current literature (along with parsimony, maximum likelihood, and Bayesian techniques). You have not mentioned Oosterbroek except on talk pages, which I think wise; not only are his formulations too complex for the average reader, Google Scholar lists only 12 citations for his 1987 paper, less than one every two years. Even though he published in a major journal, I think his work must be considered fringe for that reason. He certainly does not represent a consensus.


 * Yes, some sources describe what's now done using genes and computer programs as what Mayr called cladistics. But its logic is entirely different. It doesn't begin by looking for apomorphies; it doesn't use the character concepts of Hennig at all. All it has in common are some prior assumptions (binary branching, all actual taxa terminal, etc.) Only tree based definitions make sense in the molecular phylogenetic context. Peter coxhead (talk) 21:37, 3 August 2013 (UTC)


 * You say in the previous section, " I can source both kinds of definition for all three concepts, if you want." Well, I do want sources, but Cladistics does provide sources, which may be adequate. I'll get back to you on that.


 * By the way, thanks for setting extended quotations off in separate paragraphs instead of using . Personally, I don't find the serif/sans-serif distinction easily to spot and green doesn't show up well on my screen.


 * Peter Brown (talk) 20:27, 3 August 2013 (UTC)

Definition of symplesiomorphy
Ignoring parentheses, the first two sentences of the definition at Cladistics read:


 * A plesiomorphy or ancestral state is a character state that a taxon has retained from its ancestors. When two or more taxa that are not nested within each other share a plesiomorphy, it is a symplesiomorphy.

Both crocodilians and insects have certainly inherited jointed legs from their ancestors so, from the first sentence, it seems that jointed legs are a plesiomorphy of the crocodilians as well as of the insects. Neither Crocodilia nor Insecta is nested within the other. Does that mean, from the second sentence, that the possession of jointed legs is a symplesiomorphy of these two clades? If so, this would be a good example to use. Peter Brown (talk) 23:01, 12 October 2013 (UTC)
 * As far as I understand it, it has to be the plesiomorphy. Crocodiles and insects didn't inherit jointed legs from their LCA. Peter coxhead (talk) 00:34, 13 October 2013 (UTC)
 * Tricky! The most obvious Wiktionary definition of "share" is "have in common", but jointed legs are certainly common to insects and crocodiles. These sentences need to be reworded if homology is relevant.


 * No, I think you are mis-reading the paragraph. It says that they "share a plesiomorphy" not that they "share a character", and a plesiomorphy is necessarily homologous. (However, "retained" has to be read as "retained by inheritance"; to be really precise perhaps this should be said.) Peter coxhead (talk) 01:07, 14 October 2013 (UTC)


 * There are further problems with this paragraph. The last sentence reads:


 * Since cold-bloodedness is a plesiomorphy, inherited from the common ancestor of traditional reptiles and birds, and thus a symplesiomorphy of turtles, snakes and crocodiles (among others), it does not mean that turtles, snakes and crocodiles form a clade that excludes the birds.


 * After a long subordinate clause, one finally reaches the subject of the sentence, which turns out to be "it". To me and perhaps other readers, the reference of "it" is quite unclear. Why should anyone think that it (whatever it is) means that turtles, snakes and crocodiles form a clade anyhow, never mind one that excludes the birds? Further, pelycosaurs are cold-blooded "traditional reptiles"; are they included in the group of which cold-bloodedness is a symplesiomorphy?


 * Why are birds mentioned at all?


 * Someone might say, "Hey, Peter Brown, you're a competent writer and the #2 editor of this article; if you don't like the paragraph, why not fix it up?" The answer is that I am not clear on what a symplesiomorphy is and therefore cannot provide a definition with any confidence. Peter Brown (talk) 18:05, 13 October 2013 (UTC)


 * I don't think that symplesiomorphy explains it very well either. Here's my take. Suppose we have three groups of organisms, A, B and C, and it seems that all members of A and B have a particular character and all members of C don't have the character. We are trying to decide whether A and B fall into a clade which excludes C. Evidence that they do would be that the character was an innovation (apomorphy) in an ancestor of A and B that was not an ancestor of C and that the character has been inherited from this ancestor by A and B (i.e. it is a shared apomorphy = synapomorphy of A and B). What would not be evidence that A and B fall into a clade which excludes C would be that A and B retain some character from an ancestor of A, B and C, but that C or C's ancestors lost it. Such a character is a plesiomorphy – a character inherited by many groups from an ancestor sufficiently distant that it has been lost in many of that ancestor's decendants. The character would then be a shared plesiomorphy = symplesiomorphy of A and B, and it would offer no evidence that A and B fall into a clade which excludes C.


 * Let A = cartilaginous fish (Chondrichthyes), B = ray-finned fish (Actinopterygii) and C = tetrapods (Tetrapoda). The character "possesses internal gills" was not an innovation (apomorphy) in an ancestor of cartilaginous fish and ray-finned fish that was not an ancestor of tetrapods. It was an innovation in an ancestor of all three, and has been lost along the line leading to tetrapods. Hence it is a plesiomorphy (a "basal" or "primitive" character) and a shared plesiomorphy = symplesiomorphy of cartilaginous fish and ray-finned fish. It offers no evidence that cartilaginous fish and ray-finned fish form a clade which excludes tetrapods.


 * To me an under-emphasized issue in many explanations of symplesiomorphy is that groups need to be considered, since to call a character a symplesiomorphy of two groups we have to rule out its being a synapomorphy, and two groups alone won't do this. "Possesses internal gills" is a symplesiomorphy of cartilaginous fish and ray-finned fish relative to tetrapods, but is a synapomorphy of cartilaginous fish and ray-finned fish relative to exchinoderms.


 * This need for a third group is why birds have to be mentioned in saying that "cold-bloodedness" is a symplesiomorphy of traditional reptiles. (Actually I think this is a poor example, since non-homeothermy isn't really a character, but rather the absence of one. You can see that if you ask "of what groups is 'cold-bloodedness' a synapomorphy?" No ancestor of clade-defined reptiles evolved the non-ability to control its body temperature.) Consider "possesses epidermal scales on the head and body" (not a terribly good character either). It's a symplesiomorphy of traditional reptiles relative to birds, but a synapomorphy of the clade Reptilia (=Sauropsida) relative to synapsids (or at least I think so). Peter coxhead (talk) 01:07, 14 October 2013 (UTC)


 * I'm not finding your four paragraphs easy to understand.




 * -valign = top
 * style=white-space:nowrap|Paragraph 1:
 * What would not be evidence that A and B fall into a clade which excludes C would be that A and B retain some character from an ancestor of A, B and C, but that C or C's ancestors lost it.

The fact that Gila monsters and monitor lizards have legs retained from an ancestor of Gila monsters, monitor lizards, and snakes but snakes' ancestors lost them is evidence that Gila monsters and monitor lizards fall into a clade (specifically Anguimorpha) that excludes snakes, isn't it?
 * No, it's not (in the strict Hennig approach). Replace "Gila monsters" by "crocodiles". Crocodiles and monitor lizards have legs retained from an ancestor of crocodiles, monitor lizards and snakes. Having legs is a plesiomorphy of quadrupeds; it's a symplesiomorphy for crocodiles and monitor lizards exactly as it is for Gila monsters and monitor lizards. Therefore it offers no evidence either that crocodiles and monitor lizards form a clade excluding snakes or that Gila monsters and monitor lizards form a clade excluding snakes. Peter coxhead (talk) 12:46, 16 October 2013 (UTC)


 * -valign = top
 * Paragraph 2:
 * The character "possesses internal gills". . .offers no evidence that cartilaginous fish and ray-finned fish form a clade which excludes tetrapods.

As with the Anguimorpha, I'd say that it does offer strong evidence. As it happens, there is even stronger evidence that there is no such clade. I suggest that consideration of evidence be excluded from these formulations; what matters are the traits and the phylogeny.
 * Again, it does not, because an ancestor of cartilaginous fish, ray-finned fish and tetrapods had internal gills. Sharing the of an ancestral feature which is also retained by other groups or has been lost in other groups is a symplesiomorphy by definition. In the Hennig approach symplesiomorphies never offer evidence for a clade (rather for a para- or polyphyletic group). Peter coxhead (talk) 12:46, 16 October 2013 (UTC)


 * -valign=top
 * Paragraph 3:
 * "Possesses internal gills". . .is a synapomorphy of cartilaginous fish and ray-finned fish relative to exchinoderms.

For symplesiomorphies, your preferred schema is "&sigma; is a symplesiomorphy of A and B relative to C". For synapomorphies, though, do we want the "relative to" part? Can't we just say that "Possesses internal gills" is a synapomorphy of cartilaginous fish and ray-finned fish?
 * No, not if we know that lobe-finned fish (for example) inherited the feature from the  ancestor. That by definition makes it a symplesiomorphy. There is (by assumption) a common ancestor for all deuterostomes and hence for cartilaginous fish, ray-finned fish and echinoderms. That ancestor did not have internal gills (so far as I know). So internal gills were an apomorphy of some ancestor of cartilaginous fish, ray-finned fish (and other groups, but not echinoderms). All the descendants of the first ancestor with internal gills form a clade; the evidence is that they all either have internal gills or have clearly lost them. If you want not to specify a "relative to" part for a synapomorphy then you have to include the total clade which is descended from the ancestor for which the feature was an apomorphy. Peter coxhead (talk) 12:46, 16 October 2013 (UTC)


 * -valign=top
 * Paragraph 4:
 * Same problem as in Paragraph 3. Also, are you saying that synapsids don't have epidermal scales on the head and body? What about armadillos?


 * I'm far from an expert on vertebrates! My understanding was that synapsids and mammals, including armadillos, have a different kind of scale, but this may be wrong. Ignore the example if my facts are wrong. Peter coxhead (talk) 12:46, 16 October 2013 (UTC)


 * }


 * Peter Brown (talk) 18:29, 15 October 2013 (UTC)

Another attempt
I think I need a diagram to help me explain what I mean (which is hopefully what Hennig meant, but I find this stuff confused in the literature).

Consider three features distributed among four groups like the following. "Yes" means "has or has lost".

The universe of discourse consists only of A, B, C and D and Features 1, 2 and 3.

Then in the Hennigian approach, we look for apomorphies.
 * Feature 1 is a synapomorphy of A, C, D, i.e. A+C+D are a clade
 * Feature 2 is a synapomorphy of C, D, i.e. C+D are a clade
 * Feature 3 is an autapomorphy of C

Then the only possible cladogram (bar rotations) is:

So far, so good. What about (sym)plesiomorphies? Since Feature 1 is a synapomorphy of A+C+D, it's a symplesiomorphy of any subset, i.e. A+C, A+D, C+D. C+D do form a clade but their shared possession of Feature 1 offers no evidence for this in the Hennigian approach because it's a symplesiomorphy with respect to A (in my terminology). [In other phylogenetic methods, e.g. parsimony, it would add support for this cladogram.] If Feature 3 is a radical innovation, and Feature 2 only a minor change, in traditional Linnean classification we could argue for putting A and D in one (paraphyletic) group and C in another. But there's no Hennigian evidence for this: all that A and D share is Feature 1, which is a symplesiomorphy (with respect to C). What about the of Feature 3? That's a (kind of) symplesiomorphy, in this case inherited by A, B and D from their common ancestor, but C has "lost" the absence. The absence of Feature 3 can define a paraphyletic group, but not a Hennigian clade, which must have a synapomorphy.

In the strict Hennigian approach, the only groups of real interest are monophylies; paraphylies and polyphylies are just different kinds of non-monophylies. In the same way, the only features of real interest are synapomorphies – those features which define a clade because they are shared by all members of the clade and are derived from the ancestor of the clade (although they may have been lost later). Symplesiomorphies are just features which aren't synapomorphies and hence characterize non-monophylies.

A synapomorphy necessarily involves at least one group the clade – an outgroup in modern phylogenetic studies – from which the "morphy" is "apo". That's what I mean by "with respect to". (For example, in my cladogram above, A is outside the clade C+D because it doesn't have the synapomorphy Feature 2. Feature 2 is a synapomorphy of C+D with respect to A – or indeed with respect to any other group.)

Can we describe Feature 1 as a synapomorphy of C+D? The simplest answer is "no". An "apo-morphy" must be "apo" something. In this case it's "apo" the absence of Feature 1. So the only group of which Feature 1 is a synapomorphy is A+C+D. Another answer, and here I think I may be departing from the Hennigian approach (although I find explanations of it unclear on this point) is that Feature 1 is a synapomorphy of C+D with respect to B. Feature 1 is a shared (i.e. syn) difference (i.e. apomorphy) of C and D from B. But it's not a shared difference of C and D from A, so it's not an "absolute" synapomorphy.

A symplesiomorphy necessarily involves at least one group a clade whose sharing of the clade-defining feature (or possibly having lost it) is being ignored – that's what I mean by "with respect to". (For example, in my cladogram above, if we group A and D on the basis of sharing Feature 1, we're ignoring C which also has Feature 1. Feature 1 is symplesiomorphy of A and D with respect to C.) Peter coxhead (talk) 14:22, 16 October 2013 (UTC)

Once you have defined a clade on the basis of a shared inherited feature which differentiates it from all non-members of the clade (i.e. a synapomorphy), that feature is of no value whatsoever in determining whether groups within the clade form subclades. From that point on it's a symplesiomorphy. Peter coxhead (talk) 14:31, 16 October 2013 (UTC)
 * Key summary


 * Thank you for all your work on the above. I'm certainly clearer on some points. I'm baffled, though, by the concept of "Hennigian evidence". Hennig was a recognized expert on the Diptera; surely, he had to adopt his colleagues' sense of evidence to be taken seriously. X is evidence for Y just in case Y is more probable given X than otherwise. The fact that cartilaginous and ray-finned fish both possess internal gills and tetrapods don't is evidence in this sense that the two fish groups are members of a clade that excludes tetrapods. The latter proposition is false, to be sure, but the former is still evidence for it. Facts, like the fact that an ancestor of cartilaginous fish, ray-finned fish, and tetrapods had internal gills, can be introduced as additional evidence for or against a proposition, so that the evidence relations get more complicated, but prior to their introduction, we have only:


 * X: cartilaginous and ray-finned fish both possess internal gills while tetrapods don't, and
 * Y: cartilaginous and ray-finned fish belong to a clade excluding tetrapods.


 * Here, X is evidence for Y. Hennig could not have been a respected scientist if he insisted on a nonstandard sense of evidence. Nor do I remember encountering this sense in my scattershot reading of Hennig. Peter Brown (talk) 00:01, 17 October 2013 (UTC)
 * Frustrating to try to communicate in this way! (In case it's not clear, by "Hennigian" I mean only "following the method espoused by Hennig" not that Hennig himself said this.)
 * cartilaginous and ray-finned fish both possess internal gills while tetrapods don't It's not so simple because features can be transformed and so apparently lost. There don't have to be fully functioning internal gills; the question is whether there are any features of tetrapods which are homologous to internal gills and which can't be explained other than by having ancestors which did have internal gills. Similar features may not be homologous and homologous features may not be similar.
 * The fact that cartilaginous and ray-finned fish both possess internal gills and tetrapods don't is evidence in this sense that the two fish groups are members of a clade that excludes tetrapods. If tetrapods really did have no trace whatsoever of internal gills, then sure. However, embryological development as well as adult morphology shows that actually tetrapods do have features which are homologous to the internal gills of the two fish groups. (Gill slits appear in mammalian embryological development, for example.) There's no doubt that tetrapods are descended from ancestors with internal gills.
 * However, you are, I think, right to raise these questions. There have always been those who worried that there is a circularity in the Hennigian method. Synapomorphies determine clades, but are we really sure that we can decide what is a synapomorphy independent of what is a clade? Given that we know that cartilaginous fish, ray-finned fish and tetrapods are part of the same clade we're likely to look for evidence that tetrapods' ancestors had internal gills and that tetrapods retain vestiges of internal gills, because that's what should be the case. Similarly we discount symplesiomorphies as evidence for a set of groups forming a clade, but is it only because we know that the total clade includes other groups that we are able to decide that a feature is a symplesiomorphy?
 * All this is of doubtful modern relevance, since the computer-based methods now used, whether based on molecular data or on character data, don't use strict synapomorphies to determine clades. Peter coxhead (talk) 01:28, 17 October 2013 (UTC)

Stem-based taxon
The term Stem-based taxon redirects to this article, which however does not even mention it! Could the term please be placed in boldface in the lead, with a brief explanation, and then discussed somewhere in the article? Chiswick Chap (talk) 15:51, 23 October 2013 (UTC)


 * It shouldn't redirect here. This concept is covered at Phylogenetic nomenclature. I'll alter the redirect. Peter coxhead (talk) 22:27, 23 October 2013 (UTC)

Parallel evolution: divergence versus convergence?
It gets even worse than the article and talk page seem to have suggested. You could in theory have 2 different (yet maybe closely-related) species/varieties experience a common environmental factor and thus have a preference for the same mutation/s. Eyes for example seem to have evolved several times since animal life evolved. Granted, they aren't physically identical forms of vision. ''Actually, I was wrong. It's more like dozens. '' O_o

How do you contend with timelines of family/group/genus/species/subspecies trees that seem paradoxical because of this issue? The article implies that only one of the cladistic trees is accurate, but it seems that simplistic trees might ALL be wrong for a given group of species. 2601:1:9280:155:6155:1881:4B26:F3D4 (talk) 12:25, 6 March 2014 (UTC)
 * This is dealt with by the parallel optimization of many characters on the same tree. The thought is that convergence is unlikely to happen in enough characters to dominate the tree topology, provided enough are included in the analysis. For the purposes of examples in the article however, it makes most sense to talk about one character at a time. de Bivort 14:26, 6 March 2014 (UTC)


 * It's also important to select and define "characters" carefully. There are many different kinds of eye, as noted above, so "possesses eyes" is not a useful character in a cladistic analysis. "Simplistic" trees (i.e. trees constructed using simplistic characters) are highly likely to be wrong. This is one of the serious objections to the original Hennigian method which relied on individual characters to identify branches in the cladogram, rather than statistical aggregation over many characters as in modern computer-based methods. Peter coxhead (talk) 21:02, 12 March 2014 (UTC)

For those interested in phylogenetics, and clade presentations
Could you have a look at this effort, here, to use clade diagrams to summarize pharma business mergers and acquisitions (M&A). My take at present is that the images created are devoid of standard quantitative meaning—nothing is captured by vertical and horizontal line lengths, as far as I can tell—and so they are a misapplication of this maths/graphic presentation method. Moreover, I argue that they are misleading (presenting a time axis, but not making spacing of events proportionate to the historical time differences), much harder to maintain (consider adding entries to a std Table versus this graphic), more likely to diminish article quality (in their ambiguity of content, again, over a std Table with clear headings), and therefore practically amenable to decay as a result. I would add to this, in this esteemed cladistics context, that they would make those who trained us, and other purists in methodology and meaning… turn in their graves/beds. After having a look at the User page and at a couple of pages linked on that sandbox page, leave your opinion [at the link give below], regarding the overall effort? Thanks for your opinion. Cheers. Le Prof Leprof 7272 (talk) 01:37, 23 March 2016 (UTC)
 * Jytdog deleted the above posting (edited slightly here for clarity), and moved the question to a new forum, the Business area, now here.
 * I reply in greater detail with my views there.
 * I stand by the fact that this Cladistics article is a gathering place for experts in cladistics, and so an appropriate venue to call out for experts, regarding how a tool of cladistics is being cross-applied (I argue misapplied) to an area of business graphics.
 * I ask your input, and apologize for your being left out of the conversation, by the overstepping deletion. (I acknowledge Jytdog's right to have an opposing opinion on the matter, but not to limit discussion, by deleting my Talk page entry. Enter a post saying inappropriate, but do not delete. That oversteps.)
 * All coming from the Cladistics area, to address the cross-application at the link above: I would appreciate if you state for the record there, the real practical knowledge you have on on this matter (e.g., if you have ever actually worked on a project involving cladogram computations/presentations), for sake of transparency, please. Le Prof Leprof 7272 (talk) 15:45, 23 April 2016 (UTC)

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