Talk:Polyphyly

Image:Polyphyletic.png

The "lower land vertebrates" are a polyphyletic group.

This is a nice image, but I don't think it actually describes a polyphyletic group. The common ancestor of amphibians and mammals was a land vertebrate, and although the illustration does not show this, the lower land vertebrates are usually meant to include it. As such, this is a paraphyletic group, comprising all its descendants except the mammals (and I would think the birds). Might a better illustration might be the warm-blooded animals, highlighting Mammalia and Aves separately? Josh

Well, are you sure that the warm-blooded animals are a polyphyletic group? Was the most recent common ancestor of birds and mammals warm-blooded or cold-blooded? I think this picture actually shows a paraphyletic group, doesn't it? Because the yellow curve includes the fork between Mammaila and Aves? I don't know, I'm no biologist. Keenan Pepper 19:50, 21 July 2005 (UTC)

I'm not sure what to make of that picture. It's generally understood that the ancestral amniotes were cold-blooded, and crocodylians are too. Also, although it technically falls under the definition we give for paraphyletic, that group would still be polyphyletic since it leaves out connecting forms - the difference is whether the tree is topologically connected. I'm not entirely sure how to word this. Josh

How about this text? A picture highlighting mammals and birds separately would go great with it. Keenan Pepper 23:12, 22 July 2005 (UTC)

That sounds fair. The image would be easy to adapt, but it's on the commons and I don't know where the update should go. Josh

New image, based on the discussion here. There is also an svg source for the image on commons, so it should be very easy to correct. Zeimusu | Talk page 15:40, 30 September 2005 (UTC)

Examples of Polyphyly

These examples aren't clear to me. The definition of polyphyly here requires not including the common ancestor, but these examples don't state whether the nearest common ancestor is a member of the group or not. Rather, these examples say that the descendants of the common ancestor are not all included. Isn't that just paraphyly? Octavo (talk) 20:10, 26 November 2007 (UTC)

Yeah, it sure seems that way. Let me think about that. — the Sidhekin (talk) 17:11, 6 February 2008 (UTC) Meanwhile ...

Last example is misleading... seems to imply that primates are the descendants of birds and bats. This is not true - the MRCA was a non-flying reptile of some sort. 75.110.136.111 (talk) 16:18, 6 February 2008 (UTC)

Seems to me it's saying birds and bats are descended from primates ... but then, the second example seems to say plants and bacteria are descended from animals. Seems a few "descendents of" have gone missing ... hang on ... fixing ... better now?

Of course Octavo's objection still stands. — the Sidhekin (talk) 17:11, 6 February 2008 (UTC)

"However, the number of paraphyletic groups and polyphyletic groups is exponentially larger than that, on the order of N²" - Not an expert, so don't want to modify this page, but N² isn't exponentially larger -than N -Gargletheape (talk) 14:49, 7 December 2008 (UTC)

Added citation needed on the birds and mammals stuff. Very controversial, with a lack of longstanding scientific consensus. Things like algae are clear good examples; birds and mammals are a maybe... depending on your point of view. I'll wait for citations first. If none show up, then this example can be removed. If citations do show up, then we can move to POV issues regarding conflicting cites, and if it is better to remove the controversial example, or note the controversy.2001:470:1F04:3DF:0:0:0:2 (talk) 19:03, 6 January 2014 (UTC) I see both the "lower land vertebrates" and Protista to be paraphyletic, but Protozoa is poly. — Preceding unsigned comment added by 69.195.57.54 (talk) 17:33, 26 October 2014 (UTC)

Wrong definitions of polyphyly

Polyphyly is defined by characters: A polyphyletic group is a taxon defined by convergent characters (homoplasies), while a paraphyletic group is defined by primitive characters (plesiomorphies), and monophyletic groups by shared derived characters (apomorphies) (ref: Hennig, 1950). The definition and examples given here are instead *tree-based*, but in tree-based definitions there is only monophyly and non-monophyly, as there is no difference between paraphyly and polyphyly. This is why there is confusion above whether the cited examples are para- or polyphyletic. —Preceding unsigned comment added by 130.242.24.193 (talk) 10:19, 26 May 2010 (UTC)

There IS a difference between paraphyly and polyphyly in tree-based definitions, as these terms are currently used. Taking monophyly to be synonymous with holophyly (as it is in current use), then a paraphyly is a monophyly minus one or more (usually one) sub-monophylies. A polyphyly is any other kind of non-monophyly other than a paraphyly. In other words there is the classification of classifications:

• monophyly
• non-monophyly

• paraphyly
• polyphyly

Now it can well be argued that this rather distorts the derivation of the words: something which is 'not mono' should be 'poly', but we have to describe consensus usage, whether or not this is what we would wish it to be. Peter coxhead (talk) 15:46, 6 December 2010 (UTC)

"A polyphyletic group is a taxon defined by convergent characters (homoplasies)" — I'm with 130.242.24.193 that far. When a group is alleged to be polyphyletic, isn't an argument for a convergence standardly produced? Is this not consensus usage? Peter Brown (talk) 22:50, 30 July 2013 (UTC)

Why have three articles?

Please see Talk:Monophyly#Why_have_three_articles where I have asked why there should be separate articles on monophyly, paraphyly and polyphyly. Please leave comments there. Peter coxhead (talk) 15:57, 6 December 2010 (UTC)

Incorrect definition

The definition currently given in the first sentence ("A polyphyletic ... group is one whose members' last common ancestor is not a member of the group") is obviously incorrect. Imagine that in the very first diagram the blue-purple area were extended to include the region around the word "Amniota". In other words a group was defined as "all amniotes up to but not including Sauropsida + all mammals and their ancestors + all Aves". This group would not be polyphyletic according to this definition, whereas it clearly is.

The problem is that a short but correct definition can, as far as I can see, only be negative: a polyphyletic group is one that is neither monophyletic nor paraphyletic. A longer but correct definition is "a polyphyletic group is one that excludes some of the descendants of the nearest common ancestor of the members of the group and also excludes at least one of the members of the sister groups of the excluded members" (based on Oosterbroek, Pjotr (1987), "More Appropriate Definitions of Paraphyly and Polyphyly, with a Comment on the Farris 1974 Model", Systematic Biology, 36 (2): 103–108). However, this definition is incomprehensible without a lot of explanation.

I still believe that attempting to have separate articles on monophyly, paraphyly and polyphyly is a serious mistake; the three terms cannot be properly understood except in terms of each other. Peter coxhead (talk) 12:46, 4 October 2011 (UTC)

Peter I disagree, I think almost everything in wikipedia requires the context of other linked articles to be properly understood. Lumping them together is silly because the vast majority of people who end up here will come in through a link from something that is mono-, para-, or polyphylic. They may or may not be interested in the others, but the others are not the likely point of interest. Nobody is going to "properly" understand anything. They are hopefully going to get from an encyclopedia a basic understanding, no more. 2001:470:1F04:3DF:0:0:0:2 (talk) 19:12, 6 January 2014 (UTC)

However, there are some topics which are more connected than others. The only consistent definition of "polyphyly" in its modern sense is that it isn't either a monophyly or a paraphyly. So anyone who really wants to understand this term has to read the other two articles. Peter coxhead (talk) 22:51, 6 January 2014 (UTC)

To say that a group is polyphyletic if some defining characteristics evolved convergently is pretty close to being accurate. One who takes that as the meaning of "polyphyletic" will not go far wrong even if he or she has no idea what monophyly or paraphyly is. Understanding all three -phylies is not necessary for most purposes. Peter Brown (talk) 23:25, 6 January 2014 (UTC)

Well, we've had this discussion before, Peter. Yes, this is the original Hennig definition and can be understood more-or-less independently of the other two. However, almost all modern usages of the three terms are different; they relate purely to the geometry of computer-derived cladograms and cannot easily be understood in isolation. I accept that I'm in the minority here and three articles will remain for the present – although I still think I'm right! Peter coxhead (talk) 08:41, 7 January 2014 (UTC)

Like standard dictionaries, Wikipedia is primarily for the general reader, not for anyone familiar with computer-generated cladograms. These dictionaries, The Free Dictionary for example, all define "polyphyly" in the Hennigian sense, and I would argue that Wikipedia should follow their example. Agreed, there is another sense, one known only to specialists, and perhaps it should be mentioned in the Polyphyly article. Peter Brown (talk) 18:59, 7 January 2014 (UTC)

I don't think that it is now only relevant to specialists. When editors add information to plant articles (these are what I mainly follow, so know best), based on recent research, saying that such-and-such a group has been shown to be polyphyletic or paraphyletic and so has been divided into other taxa, that research is virtually always based on molecular phylogenetics, and so relies on purely geometric definitions of the "phylies". For example, if you look at the use of "polyphyly" in Liliaceae#Modern APG classification (an article which is currently being expanded), it refers primarily to cladograms produced by molecular phylogenetic analyses. Some of the taxa into which the old Liliaceae have been split, such as the APG's broad Asparagaceae, have few if any common morphological characteristics. (Stevens says "This is a highly unsatisfactory family. Nothing characterises it, and while some of the subfamilies have several distinctive apomorphies and are also easy to recognise, others are difficult to recognise.") The modern APG classification in this area of the tree of life relies on the geometry of molecular cladograms.

General dictionaries aren't usually a good guide to current biological thinking. The Kew Plant Glossary of 2010 defines polyphyletic as "of mixed evolutionary origin, sharing more than one common ancestor" which is clearly an attempt at a purely geometric definition, with no mention of characters. However, although I see what this definition is trying to say, it doesn't seem to me that it is accurate: any group has more than one common ancestor. I believe the modern use of "polyphyly", which is now the dominant one, is extremely difficult to define except negatively. Peter coxhead (talk) 10:14, 8 January 2014 (UTC)

What's wrong with polyphyly?

Wikipedia currently provides two explanations of the near-universal rejection of polyphyletic groups. In both cases, the contrast is with monophyletic groups. In the article Polyphyly, it is noted that:

Because polyphyletic groups can frequently be defined as a sum of clades, some consider them less fundamental than monophyletic (single, whole) clades.

Also, Phylogenetic nomenclature#Philosophy cites Hennig:

[Polyphyletic groups] are distinguished from the monophyletic ones essentially by the fact that they have no independent history and thus possess neither reality or individuality.

— Hennig, Phylogenetic systematics (1966)

As to the first reason, the fact that polyphyly is "less fundamental" than monophyly is an inadequate reason for the widespread rejection of polyphyletic groups in most areas of biology. In this sense, monophyly is less fundamental than ancestry (monophyly is defined in terms of ancestry), but there is no parallel rejection of monophyly. As to the second reason, I am not aware of a widespread conviction among biologists that anything real must have "an independent history", whatever that is. Finally, any force these arguments have against polyphyly tells also against paraphyly. Many biologists are quite willing to accept well-supported paraphyletic groups but few would countenance polyphyletic groups as formal taxa.

I have my own ideas as to why polyphyletic groups are so totally unacceptable while paraphyletic groups are often thought useful. To expound them, however, would be OR. Is there any discussion in the literature as to why polyphyletic groups are such a bad idea? Peter Brown (talk) 22:34, 30 July 2013 (UTC)

As we've found before, finding modern sources which discuss these concepts isn't easy! You have to go back to the purposes of classification and then ask whether polyphyletic groups meet them. My problem in finding sources for this is that many of them are highly polemical and primarily interested in attacking each other; they generally don't discuss areas of agreement at all. Stace, Clive A. (2010), "Classification by molecules: What's in it for field botanists?" (PDF), Watsonia, 28: 103–122 has a nice discussion which I think is relevant, although not specifically put in terms of polyphyly. It's to do with predictability. Linnaeus' Diandria (plants with 2 stamens) is a polyphyletic group. Knowing that a plant belongs to the Diandra doesn't allow you to predict anything much else about the plant: grasses, speedwells and slipper orchids are in this group. Having 2 stamens is simply a convergence. On the other hand, if you know that a plant is in Araceae sensu Stace (which is paraphyletic because it excludes Lemnaceae) it allows you to make many predictions; e.g. that the inflorescence will consist of a spathe and spadix. His Araceae possess these characters through shared inheritance, not through convergence. Peter coxhead (talk) 07:20, 31 July 2013 (UTC)

Thanks! Just what was needed. Peter Brown (talk) 18:22, 31 July 2013 (UTC)

I really like the way you've worded the addition. There's much more along these lines by Mayr, but he's too polemical, I think. Peter coxhead (talk) 18:26, 31 July 2013 (UTC)

Is there are fourth category besides monophyly, paraphyly, and polyphyly?

What if a taxon had some apomorphies (novel traits) that persisted for a very long time in some lineages, rapidly disappeared in others, and persisted for a moderate amount of time in yet others. For example, labyrinthodonts. They inherited a suite of 5 traits from their tetrapodomorph fish ancestors, along with a 6th (relating to the skull table) from a basal tetrapod. These traits persisted for tens of millions of years in those lineages that remained bigger than a breadbox. In those lineages where size dropped to below the size of a breadbox, the halflife of the traits was inversely proportional to the size of the animals. The result is like a starburst pattern, with a single starting point (the first tetrapod) but many ending points. I don't think it even counts as an evolutionary grade. Ripidista (by the old definition) had a similar problem. Zyxwv99 (talk) 22:49, 14 June 2015 (UTC)

Never mind, I found it. It's polyparaphyletic. Zyxwv99 (talk) 22:53, 14 June 2015 (UTC)

Definition, again

I've read the discussion in #Incorrect definition (and understand the difference between polyphyly and paraphyly) but I still think the current [polyphyletic grouping is] based on characteristics that do not imply that they share a common ancestor that is not also the common ancestor of many other taxa is completely unparsable. While I understand Peter coxhead's concern that the simpler "("A polyphyletic ... group is one whose members' last common ancestor is not a member of the group")" is not 100% correct, I think we ought to do better and be less technical in the lead sentence, and perhaps explain fine points later in the lead or body. After all, that sort of wording is accurate in most real-life cases, and the examples where the last common ancestor is part of the polyphyletic group are (IMO) mostly theoretical.

For my part, I propose something like A group is said to be polyphyletic if its members belong to disjoint branches of the phylogenetic tree. No such user (talk) 08:59, 16 September 2022 (UTC)

@No such user: it's very difficult to give a verbal definition of "polyphyly" that is unambiguously correct, if you want to allow multiply paraphyletic groups (i.e. monophyletic groups minus two or more monophylies) to be considered distinct from polyphylies. I do agree that the existing text is hard to understand, but I think any change needs to be discussed here first. The absence of the last common ancestor is also not so useful now, because modern programs that generate phylogenetic trees treat all the inputs as leaves, so the interior nodes don't actually represent ancestors, but rather give an indication of the branching order. We've spent a lot of time discussing this and related topics in the past, so please suggest changes here first. Peter coxhead (talk) 09:23, 16 September 2022 (UTC)

I did, above. Merged talk page sections for clarity. Although, on second reading, "disjoint branches" is not unambiguously accurate either. It seems that there's no sharp distinction between "polyphyly" and "paraphily"?
But then, I'd prefer a readable definition that is merely "good enough" to the one which is unreadable and unambiguously correct. Fine points can be discussed later. No such user (talk) 09:31, 16 September 2022 (UTC)

[polyphyletic grouping is] based on characteristics that do not imply that they share a common ancestor that is not also the common ancestor of many other taxa may or may not be unparsable – it seems ok to me – but it is correct on a character-based approach (the original Hennigian approach). I don't think that an encyclopedia should give incorrect definitions, whether or not refined later.

Actually, on reflection, I don't think it does correctly distinguish a polyphyletic group from some kinds of paraphyletic group. Sigh... See below. Peter coxhead (talk) 06:41, 17 September 2022 (UTC)

If defined in character terms, polyphyly and paraphyly can be given a sharp distinction: the former reflects a group based on independent evolution of a character, the latter a group based on persistence of an ancestral character. I agree that if defined in terms of the geometry of the group in a cladogram, they can shade together if "multiply paraphyletic" is allowed.
I've long thought that having separate articles on Monophyly, Paraphyly and Polyphyly is a mistake: the terms are to a large extent defined relative to each other, and there's common material that shold be in all three articles (e.g. the move from Hennig's character-based approach centred on phylograms to the more modern geometry-based approach centred on cladograms). Peter coxhead (talk) 06:09, 17 September 2022 (UTC)

Suggestion

I think the definition in The Kew Plant Glossary has the merit of being simpler and clearly sourced: "polyphyletic, (of a taxon) of mixed evolutionary origin, sharing more than one common ancestor". (A paraphyly does have only one common ancestor, because geometrically it starts from a monophyly and has one or more sub-monophylies removed, so the common ancestor of the starting monophyly is the common ancestor of the paraphyly.) Made into a sentence, the opening definition could be

"A polyphyletic group or assemblage is a set of organisms, or other evolving elements, that is of mixed evolutionary origin, sharing more than one common ancestor."

Or if using the title of the article is preferred, then

"A polyphyly is a group or assemblage of organisms, or other evolving elements, that is of mixed evolutionary origin, sharing more than one common ancestor."

Peter coxhead (talk) 06:41, 17 September 2022 (UTC)

Thank you, Peter. Much easier to understand, and it does not delve into gory details. Let's incorporate it in the article. No such user (talk) 08:38, 19 September 2022 (UTC)

@No such user: well, I've added it to the article, and it is well sourced, but there is an interpretation issue with "sharing more than one common ancestor". The blue group has one common ancestor at its base and the red group another one at its base, and these are different. But this would equally be true if the green group is removed altogether.

A correct geometry-based definition might be something like this, I think. A monophyletic group has a lowest common ancestor that is the ancestor of every taxon in the group and of no other taxa. A non-monophyletic group has a lowest common ancestor that is also the ancestor of taxa not in the group. Non-monophyletic groups that are made up from a monophyletic group with N monophyletic subgroups removed are N-paraphyletic. This corresponds to the definition at Paraphyly. Non-monophyletic groups that cannot be made up in this way are polyphyletic. However, the difference between an Nly-paraphyletic group and a polyphyly when N>1 is problematic, in my view. If you describe the group "lorises+tarsier" as made up from the monophyletic primates minus the monophyletic lemurs and the monophyletic simians, then "lorises+tarsiers" is doubly paraphyletic, not polyphyletic. But this is WP:OR without a reference. Peter coxhead (talk) 17:06, 19 September 2022 (UTC)

Well, I've found references that make a clear distinction between paraphyly and polyphyly, but it's very hard to explain in words. Consider the red leaf nodes in the two cladograms below.

	A B C D E F G

	A B C D E F G

According to Platnick's 1977 explanation of Farris's 1974 definitions, in the first cladogram, B+C+D form a paraphyly, whereas in the second cladogram, B+C+E form a polyphyly. Platnick explains Farris's algorithm that can be used to make the decision. Farris's formal definition is a "group is said to be polyphyletic if its group membership character appears non-uniquely derived". In the first cladogram, whatever unites B+C+D appears derived from their common ancestor without any reversals. In the second cladogram, whatever unites B+C+E does not, because if it did, then it should also unite D into the group. But to really understand the definition, I think you have to apply the algorithm, which is worked out in detail in Platnick (1977).
Note that there's nothing about the common ancestor having to be in the group or not. Nor are any explicit characters considered – the "group membership character" is simply the condition of belonging or not belonging to the group in question. Peter coxhead (talk) 13:40, 30 November 2022 (UTC)

I should add that Farris's "appears" has the implicit qualification "assuming parsimony", which is what his algorithm uses. The parsimonious interpretation of the second cladogram is that a change occurred in the line leading to the ancestor of A+B+C which was reversed in the line leading to A, and a change occurred separately in the line leading to E – three changes in total; polyphyly because the two changes producing group membership were independent. A less parsimonious interpretation is that a change occurred in the line leading to the ancestor of the whole cladogram and was reversed three times (in the lines leading to A, to D, and to F+G) – four changes in total; paraphyly because the change creating group membership occurred once.

I conclude that although sources make distinctions between paraphyly and polyphyly, their definitions are neither consistent, completely satisfactory or easy to explain. Sigh... Peter coxhead (talk) 15:05, 2 December 2022 (UTC)

References

Additional sources

The following source was once in the article but is no longer cited as of the current version:

• Beentje, Henk (2010). The Kew Plant Glossary. Richmond, Surrey: Royal Botanic Gardens, Kew. p. 91. ISBN 978-1-84246-422-9.

 — SMcCandlish ☏ ¢ 😼  21:16, 10 September 2023 (UTC)