Talk:Polyphyly

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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)