Talk:Monophyly

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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?

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

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

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 the holophyletic link redirects to monophyly. —The preceding unsigned comment was added by Wikiality123 (talk • contribs) 10:45, 24 April 2007 (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 (talk • contribs)

Iragopogen miscellus

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

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

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

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

• "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

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?

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?

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)