Talk:Monophyly

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Untitled[edit]

In fact, biologists are discussing this issue with regards to the genus Homo at this very moment, though for different reasons. For example, H. heidelbergensis and H. neanderthalensis are thought to be subspecies of H. sapiens. Therefore, Homo is not strictly monophyletic!

That's wrong. If H. heidelbergensis and H. neanderthalensis were subspecies of H.sapiens, then they would by definition HAVE common ancestral form, and that wouldn't interfere with monophylecity of Homo in any way. --Taw

One way or the other, folks, Homo is not a good example. More enlightening quibbles are found in the Dinosauria/Aves cladistics, no?

This entry must mention cladistics/clades to be intelligible. User:Wetman

NPOV? Accuracy?[edit]

Portions of this are unintelligible or simply wrong. I'm not sure I'm up to completely rewriting it at the moment, but I will mention the basic problems here in case there is a strong defense of the status quo:

1) Holophyly vs. monophyly. Discussion of holophyly in this article is probable best limited to the current statement "The term is synonymous with the uncommon term holophyly." Yes, there was a brief interest in using the word "holophyly" for what we presently call "monophyly", but this is a minor side issue, while this article seems to suggest that it is the main event. If discussion of this rather defunct debate is necessary, it would best be placed in the article for the term "holophyly", since that term is wholly a creature of that debate, while "monophyly" is not.

2) There are a number of sentences in the article at present, such as "However, when considering taxonomic groups such as genera and species, the most appropriate nature of this common ancestor is unclear. Assuming that this is one individual or mating pair is unrealistic for species, which are by definition interbreeding populations.[1]" and "Naming is also a problem for monophyletic groups: because the number of ancestors from which to root monophyletic groups is almost infinite, giving each clade a unique name is impossible[4] - as illustrated by the failed attempts to instigate a system called the Phylocode. Names obfuscate the really interesting part, which is the branching order, and are therefore of little utility to the cladist [...]" that highlight eccentric objections to cladism. Through their inclusion, they give the impression that the concept of monophyly is shrouded in obscurity and controversy, and are obfuscatory rather than explanatory. An NPOV article should, presumably, attempt to highlight and clarify the mainstream usage and definition of the term. Discussions of disagreement with this mainstream view should not necessarily be removed entirely, but they should not dominate it.

3) Whether a taxon *includes* the common ancestor of the extant members is a somewhat thorny issue that should at least be mentioned in a coherent fashion. At present, the article advocates the inclusion of extinct species within a cladistic classification of extant species without discussion, but also disagrees with itself occasionally; this is not helpful.

4) There seems to be confusion between typological and phylogenetic classifications, e.g.: "For instance, Archaeopteryx appears more reptilian than bird - it has teeth and a number of other reptilian characteristics. But it also has feathers, which have traditionally been considered as an avian trait. It lacks a number of other traits shared by all birds, so can't fall within the bird clade." If Aves is defined phylogenetically, its membership is determined based on the common ancestry of its members and nothing more. Only if Aves is defined typologically are specific traits considered to be necessary and/or sufficient conditions for membership. But in this example, Archaeopteryx is claimed to be excluded from a *clade* (a phylogenetic unit) on the basis of absence of certain characters that are supposedly requisite for membership; i.e., a typological interpretation of taxon membership is applied to a clade. This example is further confused by the problems encountered by attempting to include extinct taxa consistently in a classification of extant taxa, as mentioned above.

5) And a very minor point; calling a clade "a monophyly" is a very unusual construction. I do not think I have ever seen it used in the phylogenetic literature; likely it is out there somewhere, but it is at least anomalous. Paalexan (talk) 00:19, 15 November 2009 (UTC)

definition of polyphyletic as distinct from paraphyletic[edit]

The definition of polypheltic, as distinct from paraphyletic, doesn't make sense to me. Could someone help clear up the following points and/or update the article.

In phylogenetics, a group is monophyletic (grek: of one stem) if all organisms in that group are known to have developed from a common ancestral form, and all descendants of that form are included in the group.

How is possible for the organisms in the group to not have a common ancestral form? If the evolutionary tree really is a tree then this will always be the case, and removing this condition would make no difference to the definition.

Taxonomic groups that contain organisms but not their common ancestor are called polyphyletic, and groups that contain some but not all descendants of a given form are called paraphyletic.

Every subset of the set of extant species will always have a latest common ancestor, so what does it mean for a taxonomic group to contain organisms but not their common ancestor?

The difference is whether the last common ancestor is in the group. For instance warm-blooded vertebrates all evolved from the ancestral reptile, but it wasn't itself warm-blooded, so they form a polyphyletic group.

I'm no expert in phylogeny/cladistics, but from what I remember, it might be possible for a clade to be polyphyletic if two species were grouped together based on say, physical & behavioural characteristics, but actually had different ancestors due to convergent evolution. I don't have a real-world example for you (nor even a good hypothetical one), but hypothetically, let's say that birds evolved from some dinosaurian ancestor, with the exception of ostriches, which first went partway down the mammalian/marsipupal path, then branched from there to their current form. The ostriches would then make the whole avian clade polyphyletic, but phylogenists might not want to revise the tree for historical reasons. Hope that helps (and that it's even partly correct: like I said, I'm not an expert).
Also, I made a minor edit so that paraphyly linked to that article. Potatophysics 04:13, 6 October 2005 (UTC)
There is no nonarbitrary distinction between paraphyly and polyphyly when classifying extant taxa alone. If the two terms are distinguished at all, a taxon is called "paraphyletic" if its members are relatively closely related, and "polyphyletic" if its members are relatively distantly related. It is only possible to make a distinction if extinct species are explicitly included in the classification of extant taxa; then one can make a distinction between taxa that do or do not include the common ancestor of the extant species included within them. However, including extinct species in a cladistic classification of extant species requires a very large can of worms to be opened. In practice, this can of worms is generally left closed; the result is that extinct taxa do not have any clear placement in a cladistic classification (i.e., classifications of extant and extinct species are generally incompatible unless both are typological rather than phylogenetic) and a distinction between paraphyly and polyphyly is generally not applicable except in the arbitrary sense mentioned above. Paalexan (talk) 23:37, 14 November 2009 (UTC)

Holophyly[edit]

Can anyone translate this into English that a lay person can understand?

  • Evolutionary taxonomists use the term holophyletic for the sort of groups discussed here, whereby monophyly includes both holophyly and paraphyly. (Unsigned, by user:66.44.102.50 on April 1, 2006)
I'd like to second this request. Does the statement mean that holophyletic a synonym of monophyletic? (And why is holophyletic a wikilink if it just redirects back to this article)? --SB_Johnny | talk 10:13, 28 July 2006 (UTC)

I've change the sentence; hopefully the new version makes more sense. Josh

Much better, thanks! SB_Johnny | talk 10:29, 29 July 2006 (UTC)

Still incomprehensible. The whole idea of an introduction is so that any reader can understand what the subject is all about. This has not been done. Way too much geekese and insider terminology. - 22:02, 22 February 2010 (UTC) —Preceding unsigned comment added by KitchM (talkcontribs)

Iragopogen miscellus[edit]

What is it and what is the source of the claim about multiple arisal? This article is the only one in the entire Wikipedia, as well as the internet (according to google), to ever mention such species. mathrick 00:14, 26 November 2006 (UTC)

Since Google corrects the spelling to "Tragopogon miscellus" and gives results about polyploidy and plants in Washington, I posit that "Iragopogen" is a typo. Rehevkor5 23:11, 5 December 2006 (UTC)

The claim that it has arisen independently over 20 times seems extraordinary. Can someone with more knowledge about this make a bigger deal of it, and explain it better? It sounds almost impossible to believe.23:59, 21 December 2006 (UTC)
It is cause by a confusing type of evolution variously referred to as reductive speciation, reticulate evolution or hybrid speciation. This is well known in some groups (e.g. plants) and represents a major problem for "typical" applied species concepts. Basically, it is caused by two species hybridizing. Their offspring eventually become reproductively isolated from the two "original" species, i.e. a new species. As the basis for this new species was formed by two other species, it can potentially "re-evolve" whenever the two original species come into contact. See hybrid speciation and polyploidy for more. Rabo3 02:13, 1 September 2007 (UTC)

Clades[edit]

Is a monophyletic group basically the same as a clade?23:59, 21 December 2006 (UTC)

Identical.Dave (talk) 03:54, 23 January 2010 (UTC)

Edit planned[edit]

I'm interested in getting some comprehensible cladistics articles so I'm going to do an edit. I'm also working on a few others. it's the fine points I'm worried about, the things that make good articles good, etc. What do they got that we ain't got? Fine points. I'll be interested in clarity first. It starts well I do believe. After that the style gets less encyclopedic; maybe it tries to be Stephen Jay Gould - but - out of context. The references - well, I'm pleased to see some. That first reference, can't we have a page number?

So, don't get upset, get helpful. I work very slowly, plenty of time.Dave (talk) 03:54, 23 January 2010 (UTC)

Translational English[edit]

The early work in cladistics was done in German, and it was translated into English. Sometimes, though, the word that seems the best translation is not used or is not used that way in English, especially if the translator has opted more for transliteration. The words look the same but they aren't the same. For example, we don't speak of the characters of a bird or a reptile - a character is a symbol on a page or a condition of ethical or moral rightness. We call a feature a characteristic. But, in translational contexts, once you understand the author's use of it, character is acceptable. For the clearest English, I want to avoid translational terms and use the regular equivalent.Dave (talk) 09:08, 24 January 2010 (UTC)

Gobbledeygook[edit]

  • "However, when considering taxonomic groups such as genera and species, the most appropriate nature of their common ancestor is unclear. Assuming that it would be one individual or mating pair is unrealistic for species, which are by definition interbreeding populations.[5]
  • However, using a broader definition, such as a species and all its descendants, doesn't really work to define a genus.[5] A satisfactory and comprehensive cladistic definition of a species or genus is in fact impossible, and reflects the impossibility of seamlessly impressing a gradualistic model of continual change over the 'quantum' Linnean model, where species have defined boundaries, and intermediaries between species cannot be accommodated.[6]"

There are such problems with the English of these passages as to render them incomprehensible. First we talk about "appropriate nature." Then we refer to it with an "it" calling it also an individual or a mating pair. I'm sorry, but individuals are not a nature do not have a nature (what is the nature of Tom, Dick or Harry, and are they a nature?) and neither do mating pairs. Only universals have natures: man, bird, mammal, and so on. There is the question of the nature and the question of the common ancestor. They are not identical; you can't mix the two. I presume by nature you mean a synapomorphy. Since when is a synapomorphy? You mean, we can ignore the synapomorphies that are NOT the most appropriate nature? And what happened to the plesiomorphy, or is that what you mean by nature?

In the next paragraph, what do you mean, "doesn't really work?" First the style level is inappropriate. Second, if you mean there is a logical inconsistency, you in no way have stated what that is or even hinted what that may be. I see you are telling us that a "cladistic definition" of a species or genus is "in fact impossible." I seems as though you are trying to say that species and genera cannot be in the stem of a clade. Well, if they can't be, I'd like to know just what can be, as there can't be any more general taxa without the subordinate taxa. But, you might not mean that. Just what you do mean is completely impenetrable.

A third problem is your references. You keep citing Simpson without any page numbers. In other words, we have to search the whole book to try to find out what you mean. This superficial non-reference may satisfy the cursory inspection of a sysadmin in a hurry but it is in no way a reference. In another reference you give us a link to the abstract of an article but that abstract has not a thing to do with the above passages. Maybe the article does, but we can't get that without paying for it. You may not link to pay sites, did you not know that? Whether the article is appropriate I do not know, as I cannot understand what is being referenced. First give us an idea, then give us the reference. No idea, useless reference.

For the moment I'm leaving this passage in to give you a chance to totally rewrite it. This approach has worked well on another article. Then I will look at the rewrite. If you don't respond I will do some additional Internet work to try to find out what problems you are referencing and rewrite it myself. In my experience, I think you would be happiest doing your own work on it, so go right ahead. For the moment I will tackle the next incomprehensible cladistics article. There is no hard and fast rule, cladistics must be incomprehensible to the genral public. Good luck.Dave (talk) 12:47, 24 January 2010 (UTC)

I agree with Dave that the article isn't as clear as it needs to be for such an important topic. The problem is however twofold:
  • There are problems with language, which can be sorted by a competent native speaker of English.
  • There are problems with the underlying concepts, in that they are used inconsistently and in a confused way by much of the literature.
The second problem is difficult to fix. I can, I believe, explain what monophyly, paraphyly and polyphyly ought to mean, based on the geometry of trees. But this isn't the usage the literature actually contains. This is a classic example of the conflict which arises between being neutral and explaining clearly. To bring in a professional bias, a good teacher of advanced topics cannot avoid being a scholar, if not an original researcher, since material often needs to be synthesised to be made clear. I am going to try to edit the article to make it clearer, but I may well end up being accused of synthesis/POV. Peter coxhead (talk) 09:51, 5 December 2010 (UTC)

Rewritten lead paragraphs[edit]

I have re-written the lead paragraphs to make them both clearer and more accurate. Comments welcome! Peter coxhead (talk) 10:34, 5 December 2010 (UTC)

Why have three articles?[edit]

There are currently separate articles on monophyly, paraphyly and polyphyly. Inevitably they repeat much of the same material. Worse, they are not wholly consistent with one another (I have been trying to correct this). If there are to be three separate articles, then there is material which is missing from some of them, e.g. each should have a discussion of its advantages or disadvantages in classification. The reality is that you can only understand at least two of these terms (paraphyly and polyphyly) by contrasting them with the others. I am strongly in favour of creating one main article under one of the headings and then having short definitional articles under the other two, which use "see" to point to the main information. I would be willing to try to do this, but not if there is significant opposition. Comments please. Peter coxhead (talk) 15:54, 6 December 2010 (UTC)

how about an example?[edit]

This is one of many WP articles which apparently thinks it is wrong to give a simple example of what is meant. Why not simply put in an example of some animal considered to be monophylatic (and say why) and one which is polyphylatic (and say why)? If a picture is worth a thousand words, then so is an example. To write an article on this subject without ONCE mentioning real instances of what they refer to is silly and pretentious. Myles325a (talk) 05:48, 23 August 2011 (UTC)

Actually there are examples in the article, but I would agree that they are not obvious. The problem is that the style of the article reflects the fact that these ideas (monophyly, paraphyly and polyphyly) are somewhat disputed among experts. So the writing is rather technical and defensive.
The examples are:
  1. Living birds are a monophyletic group. That is, biologists believe that all the species of birds which are alive today are descended from one ancestral species and that no other kind of animal is descended from this same ancestor.
  2. The group of animals commonly called "reptiles" – turtles, lizards, snakes, crocodiles, etc. – are not monophyletic. That is, biologists believe that although all of them can be traced back to one ancestral species, birds descend from this same ancestor, so "reptiles" do not include all the descendants of their common ancestor. The group "reptiles + birds" is monophyletic.
Not sure if this helps! Peter coxhead (talk) 10:40, 23 August 2011 (UTC)
Sure thing, sounds good (only you forgot mammals in the last example). Petter Bøckman (talk) 15:12, 23 August 2011 (UTC)

Definition of monophyly[edit]

For some time the definition in the lead has been "a monophyletic group is a taxon (group of organisms) which forms a clade, meaning that it contains all the descendants of the possibly hypothetical closest common ancestor of the members of the group." This has recently been altered to "... meaning that it consists of a species and all its descendants."

The minor problem with the new version is the word "species"; this is generally not insisted on by those who use this form of definition. The ancestor could just be a population.

The major problem is explained by Mishler (2009): "There have been two basically different ways of defining monophyly within the Hennigian tradition of phylogenetic systematics: one is synchronic (i.e., “all and only descendants of a common ancestor”); another is diachronic (i.e., “an ancestor and all of its descendants”)." Mishler goes on to prefer the synchronic definition. [See Mishler, B.D. (2009), "Species are not Uniquely Real Biological Entities", in Ayala, F.J. & Arp, R., Contemporary Debates in Philosophy of Biology, Oxford, UK: Wiley-Blackwell, doi:10.1002/9781444314922.ch6 . There's a more detailed explanation and a suggestion – not taken up alas – for the use of different terminology for the two definitions in Podani, J. (2010), "Taxonomy in Evolutionary Perspective : An essay on the relationships between taxonomy and evolutionary theory", Synbiologia Hungarica 6: 1–42 .]

So I'm not going to revert the change, but actually the original is just as correct as the new version. Sorting this out has been on my to-do list for some time. Peter coxhead (talk) 11:01, 17 April 2012 (UTC)

Two points:
  • I don't know that there's anything particularly "Hennigian" about our current concepts of monophyly. When Haeckel claimed that "the whole class of Mammalia is monophyletic," did he mean anything different? (Haeckel, Ernst (1899), The Last Link: Our Present Knowledge of the Descent of Man (2nd ed.), London: A. and C. Black, p. 36. )
  • "Population" seems a hopelessly vague term. In studies of energy flow at a locale, the primary consumers—insects, mammals, whatever—are sometimes treated as a population, but surely no one would regard their descendants as constituting a monophyletic group.
Peter M. Brown (talk) 14:47, 17 April 2012 (UTC)
In response to your two points:
  1. I haven't read Haeckel, but I have read most of what Mayr has written about the history of the subject. He is very clear that Hennig changed the meaning of the term (a change which Mayr always objected to): monophyly used to mean what is now called monophyly+paraphyly, i.e. descent from a common ancestor without any "all descendants" requirement. So I would be pretty sure that Haeckel did not use the term as we do now, post-Hennig.
  2. "Population" is a term used in some definitions, and it has a meaning in context, i.e. as an intra-species group. It's easy to give examples when "species" can't be correct. E.g. the current view is that the polar bear evolved from one population of brown bears (the brown bear is paraphyletic w.r.t. polar bears). Polar bears are monophyletic, but the ancestral species can't be included in the clade, only (possibly) that population which gave rise to the polar bear.
The key point that needs to be made in the article is that many definitions are in use. Sometimes it's clear which one is being used; often it's only implicit. In practice the synchronic definition is used much more often. All cladograms which result from molecular phylogenetics, for example, don't have actual species at the internal nodes; all the algorithms used place the units being classified exclusively at the leaves; there are no "ancestors" to be included in the clade. There isn't just one diachronic definition either. See the PhyloCode article: stem-based and node-based clades (=monophyletic groups) are subtly different. Peter coxhead (talk) 18:33, 17 April 2012 (UTC)
Quite. The small, but distinct differences in meaning is rather important here. Petter Bøckman (talk) 19:16, 17 April 2012 (UTC)
You guys are ganging up on me.
The Phylocode article does not distinguish stem-based and node-based clades, only stem-based and node-based clade definitions. Because of the limitations of our knowledge, we can never be certain that a stem-based definition is equivalent to a node-based definition, but surely it sometimes is. What is picked out by both definitions in such a case is not a stem-based clade or a node-based clade but simply a clade.
The polar bear, Ursus maritimus, is a species. I suppose that you can call a species—any species—monophyletic. The "ancestral" polar bear is simply the polar bear, however, and it is certainly included in the polar bears.
I have always thought that cladograms resulting from molecular genetics, the one in Euarchontoglires for example, had a lot to say about ancestry. That one says that there were species that were ancestors of primates and colugos but not of treeshrews. What makes you think that there are no species at the internal nodes?
Peter M. Brown (talk) —Preceding undated comment added 19:50, 17 April 2012 (UTC).
Lots of points here!
There are two kinds of diagrams which are called "cladograms". One simply shows the branching order between the leaf nodes; the internal nodes serve only to show branching points. In the other kind not only the internal nodes but also the lines represent actual organisms/populations. It's the first kind which is produced by all the algorithms used in cladistics, whether the old parsimony ones or the newer ones based on statistical models (Bayesian, maximum likelihood). Suppose you actually had data on the population at the time it was just about to split into two species, plus data on the two species some time later; it could be molecular data or morphological data. You put this data on the three entities into a program which produces a tree. All three entities will show up as leaves, because that's how the programs work: the trees just show the branching. Look at any of the papers which produce cladograms in this way: none of the species used as data points ever end up in the internal nodes. See, e.g., the cladogram at Polysporangiophyte#Phylogeny (taken from Kenrick & Crane's book). None of the extinct groups is ever shown as an internal node. Of course the first kind of tree is simply an abstraction/representation of the true historical events, which are more accurately represented by the second kind of tree.
The second kind of tree, in which all the internal lines and nodes correspond to evolving populations (not species, because these are arbitrarily imposed limits on the continuously evolving populations), is "what really happened". The fact that the lines as well as nodes correspond to organisms is important. The different definitions in the PhyloCode lead to different inclusion rules. Look at the diagrams at Cladistics#Phylogenetic definitions of a clade. When you start to be precise about the notion of "ancestor" in the 'short' definition of a diachronic clade, you can define "ancestor" differently. Is it just the population at the branching point (internal node) or does it include all the populations represented by the stem down to the previous branching point or does it include only some of the populations represented by the stem (those possessing some apomorphy)? These definitions lead to different clades. If we had, say, five fossils corresponding to four points along the stem plus the branching point, the three different definitions would place the fossils differently into the clade: the node-based one would exclude all four fossils below the branching point fossil from the clade; the stem-based one would include all five fossils in the clade; the apomorphy-based one would include some of the four stem fossils but not others.
Note that if all five fossils were put into the first kind of tree, they would all be leaf nodes, and the node/stem/apomorphy difference wouldn't arise: clades in this kind of tree are always and only all the descendants of a common ancestor, shown by the branching pattern.
All of this is discussed in the literature, but, like a lot of theoretical biology, is almost entirely ignored by most biologists, who don't worry too much about precision in definitions. This makes it very difficult to get right in Wikipedia; on the one hand there are theoretical articles in journals, etc. which explain all the fine distinctions carefully, but on the other hand there is what biologists actually do, which is much messier. Peter coxhead (talk) 22:24, 17 April 2012 (UTC)
You are arguing for two types of cladograms: those generated by cladistic algorithms, which I shall call Type I, and those representing historical events, Type II. Your thesis, as I understand it, is that Type I cladograms do not provide historical information. In support, you ask me to imagine a scenario in which we have data on a species as well as data on two descendant species, pointing out that a Type I cladogram would not represent the ancestral relations correctly. Though true, the fact provides negligible reason to distrust Type I cladograms as sources of historical information. Given the huge number of extinct species and the tiny sample of fossils we have to provide information about them, the probability that any fossil we find will be conspecific with an ancestor of another in a descendant species is so small that the hypothesis may be disregarded. A plausible Type II cladogram, one that is intended to represent historical developments, will never place an actual fossil at an internal node. The bare possibility that fossils may be related in the way you describe provides no reason against relying on Type I cladograms to provide information about historical events.
A Type I cladogram, you say, "simply shows the branching order between the leaf nodes." What is a "branching order" if it does not reflect historical branching events? Alphabetical order using ICZN/ICN nomenclature would be much easier to determine, without sophisticated software; what is the advantage to branching order?
No, I'm not at all arguing that Type I doesn't provide historical information; of course it does. All I'm saying is that the lines and nodes in Type I don't represent organisms, merely the branching order. So in a Type I cladogram, the question of which part of a line is in a clade is not relevant. Peter coxhead (talk) 21:43, 18 April 2012 (UTC)
I repeat, what is a branching order? It is not the same thing as a node, since a node represents it. What sort of thing is it? Peter M. Brown (talk) 23:26, 18 April 2012 (UTC)
See below. Peter coxhead (talk) 10:56, 19 April 2012 (UTC)
In your view, the internal lines of a Type II cladogram cannot refer to species "because these are arbitrarily imposed limits on the continuously evolving populations." The problem, as I understand you, is that of anagenesis: how dissimilar must an individual and its ancestor be for the two to count as different species? And that question is itself ambiguous, since there are a variety of measures of difference. Arbitrariness enters at two points, therefore: once in the choice of a measure and once in the choice of a limit to the extent to which individuals in a species may vary. To say that cladogram lines represent species, then, is vague to the extent that no similarity measure or cutoff is specified. But what of that? Outside of pure mathematics, all statements have some degree of vagueness. The vagueness associated with saying that the lines refer to species does not seem inordinate.
In ordinary and cladistic usage, there are three meanings to "ancestor," but they are not the three you list. According to the Ancestor article, an ancestor is "a parent or (recursively) the parent of an ancestor." Another sense applies to species: species A is an ancestor of species B if every individual in B has an ancestor (in the first sense) in A. Finally, in more ordinary usage, the ancestor of a human is limited to humans; this third sense is never used in a paleontological context, while the first two impose no limit on the time gap between an individual or species and its ancestor. It would be quite compatible with phylogenetic nomenclature to define Theria as the clade originating with the last common ancestor of humans (Homo sapiens) and eastern grey kangaroos (Macropus giganteus), although that ancestor is separated from humans by over 150 myr, the lineage passes through many branch points, and the definition does not involve apomorphies. None of your three definitions allows this quite standard usage.
There may well be other issues/definitions of ancestor; that wasn't my point. My point was that merely that stem-based, node-based and apomorphy-based definitions correspond to different sets of organisms/fossils/species/whatever being included in the clade, and in that sense, to different clades. Peter coxhead (talk) 21:43, 18 April 2012 (UTC)
No current example comes to mind but, for long time, the animals included in Crurotarsi, with a node-based definition, were exactly those included in Pseudosuchia, with a stem-based definition. The matter is discussed in Christopher A. Brochu (1997), "Synonymy, redundancy, and the name of the crocodile stem-group", Journal of Vertebrate Paleontology 17: 448–449.  Though Brochu does consider them different clades, there were not, to his knowledge, any sauropsids contained in either that were not contained in the other. He could not have said a priori that they were not coextensive nor, I suggest, can you confidently predict "that stem-based, node-based and apomorphy-based definitions [will always] correspond to different sets of organisms/fossils/species/whatever." Peter M. Brown (talk) 23:26, 18 April 2012 (UTC)
Finally, you correctly note that no extinct group is an internal node in the Polysporangiophyte cladogram. As this is not generally true of cladograms based on parsimony algorithms, I fail to see the importance. Cladogram B on page 21 of Rougier et al. (1996), with the taxa corresponding to numbered nodes identified on pages 36–38, is generated by PAUP but does have the extinct Triconodonta (node 6) as an internal node.
Peter M. Brown (talk) 18:15, 18 April 2012 (UTC)
Sorry, but you've misinterpreted this cladogram. The taxa put into the analysis all turn up at the leaves; these are the taxa in the table in Appendix II (p. 36). Then, after PAUP has generated the branching sequence, the authors discuss the clades which result. The numbers identify the stems of subtrees, i.e. clades. Clade 6 consists of Priacodon, Trioracodon, Triconodon and Cloverly triconodonts. This clade is given a name – they call it "node 6 triconodonts" but it's really "the subtree rooted at node 6" – and they look for common features of all the taxa in the triconodonts clade, which are then diagnostic of the clade. The fact that these internal nodes are not actual ancestors but names of the clades above them is clear from the fact that e.g. Node 10 is called "Mammalia". Of course if the branching shown in the cladogram is correct, then there must have been an ancestral organism or population from which all Mammalia evolved. However, as I noted above, if we had a fossil of this organism, and knew its features and added it to the Taxon-Character Matrix on p. 36, and then ran PAUP again, it would turn up as a leaf node: that's just how PAUP works. Precisely the same thing is being done in the Polysporangiophyte cladogram with the labels "tracheophytes", "euphyllophytes", etc.
The only example of a Type II tree I could find in Wikipedia, looking quickly, is at Hominid_evolution#Multiregional_model. Whoever drew it carefully put "thin necks" between the "blobs" for the species, but even so, it's clear that you can't precisely decide on clade boundaries without choosing some cut-offs – consider trying to colour in the clade defined by H. sapiens and H. neanderthalensis, i.e. all descendants of their LCA. If we had fossils corresponding to points all over the grey areas of the diagram, then the different PhyloCode definitions would put some of them in different clades. Peter coxhead (talk) 22:27, 18 April 2012 (UTC)

──────────────────────────────────────────────────────────────────────────────────────────────────── This stuff is difficult to explain clearly without example diagrams to refer to (and I accept that some of my verbal explanations, including my use of "branching order", aren't very good). Since I don't want to upload to Commons diagrams which will only be of transient interest, please see here for my attempt to explain more clearly the nature of what Podani (2010) calls "phylogenetic trees" and "cladograms" and how clades can be defined in them.

The difference between "phylogenetic trees" and "cladograms" (or whatever names you call them) is not, in my view, properly explained at present in our set of articles about phylogenetics. Peter coxhead (talk) 10:56, 19 April 2012 (UTC)

Those "other systematists" who are content[edit]

I have deleted from the end of the Monophyly#Definitions section a paragraph reading:

Other systematists are content to confine their classifications to observed taxa and to not become preoccupied with ancestors, stem lineages and other hypothetical entities, and for these, it is straightforward to circumscribe genera and other higher taxa so that they are monophyletic. For example, we can say that Hominini (chimpanzees and humans) form a monophyletic group with respect to gorillas and orangutans, based on morphological and DNA characters, even though we do not know everything about all of the extinct predecessors of these extant taxa.

This fails in several ways to meet Wikipedia standards.

  • It is unsourced.
  • No examples of the "other systematists" are provided. Surely, the writer had a group of systematists in mind, but it could be a fringe group.
  • Monophyly is defined in terms of ancestry, so it's impossible to be concerned with the one without the other. While clades could be defined as sets of specimens, thereby eliminating "hypothetical entities" like ancestors, that's nonstandard and contrary to the definitions in Clade and many other Wikipedia articles.
  • Circumscribing genera and higher taxa is never "straightforward".
  • The clause "Hominini (chimpanzees and humans) form a monophyletic group with respect to gorillas and orangutans" expresses an unexplicated relation between one group (Homonini) and another (gorillas and orangutans). As defined in the lead, monophyly is a property, not a relation. I can guess what "monophyletic with respect to" means (Google scholar turns up many instances) but that would be OR.

All the same, I do not want to delete all reference to a bona fide research tradition. Is there one? Peter Brown (talk) 23:34, 17 July 2013 (UTC)

I think there is, but it's difficult to source (which is part of why it was absolutely right to remove this material). Biologists seem reluctant to write about definitions and theory! Part of the problem is that Podani's useful distinction between "-phylies" and "-cladies" hasn't been taken up. In his terminology, a monophyly is defined as in the article, whereas a monoclady is made up only of the terminals. Many papers using "monophyly" and "monophyletic" really refer only to the taxa in a cladogram, which are necessarily all terminal, and so the strict definition doesn't apply. Peter coxhead (talk) 08:27, 18 July 2013 (UTC)