Talk:Monophyly

message: 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)
thread_title:  NPOV?  Accuracy? 

message: 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)
replies: text: 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)
thread_title:  definition of polyphyletic as distinct from paraphyletic 

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

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

message: 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)
replies: text: 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)
replies: text:  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)
thread_title:  Iragopogen miscellus 

message: Is a monophyletic group basically the same as a clade?23:59, 21 December 2006 (UTC)
replies: text: Identical.Dave (talk) 03:54, 23 January 2010 (UTC)
thread_title: Clades

message: 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)
thread_title: Edit planned

message: 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)
thread_title: Translational English

message: 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)
thread_title:  Rewritten lead paragraphs 

message: 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)
thread_title:  Why have three articles? 

message: 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)
replies: text: 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)
thread_title:  Those "other systematists" who are content 

message: the word Reptilia's modern definition in zoology books includes bird (see the wikipedia article on Reptiles, definition section), making it a monophyletic group. this definition is not 100% agreed upon as can be seen by that page's talk page. therefore i think that this is maybe not the best example to use
maybe we should have a different example, then, instead of the one that we have here, or add a note to the the diagram's text that Reptiles and Reptilia should not be confused ?
my source for the modern definition of Reptilia is Integrated Principles of Zoology, 16th international edition, Hickman et al.(2014)
Playmobil111 (talk) 15:03, 27 December 2016 (UTC)
thread_title:  Supposed problem with the 3rd diagram usage of 'Reptilia' 

message: The article is confused, in my view, because of inconsistent definitions of the three "phylies". Each can be defined in two ways: via the geometry of a cladogram/phylogram, or via the origin of shared characteristics. What's wrong is to define monophyly in terms of geometry, and then contrast it with polyphyly defined in terms of characteristics. Peter coxhead (talk) 03:05, 17 August 2017 (UTC)
thread_title:  Still confused 

message: A monophyly is  “an arrangement” …. Q>  What kind of arrangement? ..what specifics of “arrangement”?     
A> .. A monophyly is an arrangement of the members of a “monophyletic”  group,
..or, to illustrate the problem:
A> ..A monophyly is an arrangement of the members of a “monophyly-like”  group;
---here a modifier (an adjective) of the root word is used in describing the root word; it’s the same ‘loop’ error as when using the root word to define a root word. 
Further, even as “monophyletic group” is (previously) described, the reader is still left with:  ..a monophyly (the label of this article) is some sort of an “arrangement”---an unexplained arrangement ---that is described by calling upon the adjective form of the root word. This is not ok for Wp!
…Ah, but let me try again. I shall return here---but not before Irma is done with me.Jbeans (talk) 10:48, 8 September 2017 (UTC)
replies: text: But that's not what the article says or does. First it defines monophyletic group, with the core requirement that it "consists of all the descendants of a common ancestor". Then it says that the arrangement of the members of a monophyletic group is called a monophyly. So it's not circular at all; "monophyletic group" is defined independently of "monophyly". Peter coxhead (talk) 12:11, 8 September 2017 (UTC)
thread_title:  Presently, the Wp description of monophyly is ..