Monophyletic, Paraphyletic and Polyphyletic

Having covered the basics of taxonomy and how to read phylogenetic trees it is long past the time I should have dealt with the concept of monophyly and it’s ‘ugly sisters’, paraphyly and polyphyly. While the terms might be unfamiliar, the concepts behind them are simple and practical and I suspect at least a few readers will actually know them even if they couldn’t actually say what they were (so to speak). The three terms all describe different ways of grouping taxa together and are most easily demonstrated on a phylogentic tree (though they don’t need one as such).

Monophyly, paraphyly, polyphyly

Monophyletic groups and lineages are the fundamental basis of taxonomy and evolution as a whole really. Everything within a monophyletic group is the descendent of a single common ancestor and thus are the clades we typically talk about in biology and palaeontology. Here the clade comprising taxa A, B, C and D is monophyletic. Everything that descends from the ancestral lineage or organism that existed at the point marked by the red arrow belongs in that clade and thus it is a monphyletic group. Should we later discover any new relatives that fit anywhere in the tree above that point then they would also by definition be part on that monophyletic clade. Obviously the clade A-D is not the only monphyletic one in this tree, one could name a clade of just A & B, or A-F and this would still be monophyletic.

Paraphyletic groups do not include all of the descendents of a single common ancestor. This means that while the group has a common ancestor, we are artificially ignoring a subset of its descendents. Here the green arrows indicate first the monophyletyic group which we are considering (A-F) and then the second monophyletic group (A & B) that we are not considering, thus leaving us with the paraphyletic clade of C-F. As before, there are other ways of creating a paraphyletic group on this tree and I am merely illustrating one.

This might sound odd, but paraphyletic groups are still used as they have a practical value for describing some groups. The most obvious ones to readers here are the dinosaurs. Birds are dinosaurs, that is, they are the direct descendents of an ancestor that spawned the dinosaurs, yet palaeontologists typically refer to dinosaurs while explicitly not referring to birds. Thus one should formally call them non-avian dinosaurs (basically all dinosaurs except birds) and this does happen quite regularly, thought not always, and certainly not in the press. Two others are worth of mention, one as it relates to this blog regularly and another as a striking example of a paraphyletic group. First off the rhamphorhynchoid pterosaurs (or more properly ‘rhamphorhynchoids’ as the quotes denote it as paraphyletic) which often come up here in my frequent posts on pterosaurs. As with non-avian dinosaurs, the term persists as one of convenience as basically it’s easier to write than “non-pterodactyloid pterosaurs” (or a more extreme example, one can call Plaetosaurus a ‘prosauropod’, or a “non-sauropodan sauropodomorph”). Finally there is the most obvious group of all – fish, or rather ‘fish’. Yes fish are obviously paraphyletic since all vertebrates have a single common ancestor, but tetrapods descended from them but no-one calls mammals or birds fish do they?

Polyphyletic groups are those which have multiple origins and thus do not share a common ancestor or indeed much in common at all aside from whatever trait holds them together. Here the various blue highlighted taxa have been pulled together into a polyphyletic group, and again one could do this in a great many ways on even this small tree. Polyphyletic groups are rarely mentioned (for obvious reasons), but they do come up occasionally when a revision has led to a previously monopyletic or even paraphyletic group being declared polyphyletic as a result of some systematic rearrangement (e.g. ‘we have found that taxa X and Y are not members of clade Q and actually belong to two different clades, thus the clade Q under its current definition is polophyletic and a new definition is required that excludes X and Y’). One obvious example from history is the pachyderms (elephants, rhinos and hippopotamuses) which of course all belong in different mammalian families and were put together based on a few minor characters of their skin.

Hopefully that makes everything clear and explains the fixation with the term monophyletic that often springs up on dinosaur forums (and indeed evolutionary ones in general). Monophyletic groups are the only taxonomically and systematically viable ones – that is they represent evolutionary history. As stated paraphyletic ones are useful for rhetorical simplicity, provided everyone is clear that they are paraphyletic and in what sense they are being applied. Polyphyletic ones are never used, except when referring to changes in taxonomic status, or of course in the most general terms (‘bipeds’ are polyphyletic).



Just a small and very late addition – I’ve noticed this one page gets a hell of a lot of traffic which is never brought in from search engines or linked from other sites and seems to boom and bust on certain days. I’m sure that’s because this is being used as a teaching resource and lecturers are pointing out the url to students. If so, great!, but I’d love to know if that’s the case. If you’ve been sent here by your professor, please put a comment in below and let me know which college / uni you are at. Thanks.

31 Responses to “Monophyletic, Paraphyletic and Polyphyletic”

  1. 1 Allen Hazen 19/12/2008 at 1:46 pm

    On the dinosaur example… There is a textbook– I can’t remember the authors– designed for a one-semester undergraduate unit called something like “Dinosaurs– the textbook.” (American undergraduates take a broader smorgasbord of courses OUTSIDE their majors than British or Australian, and many university departments have special units designed for non-majors: “Physics for poets,” etc. I ***think*** this book was designed for such a unit: something that would attract non-geology, non-biology students as well as a small number of actual budding paleontologists.)

    Anyway, said book has a section explaining the ideas of monophyly and polyphyly, and makes the point that BIRDS ARE DINOSAURS, and then goes on to say that, for convenience of communication, in the rest of the book the word “dinosaur” will be used as an abbreviation for the phrase “non-avian dinosaur.”

  2. 2 David Hone 19/12/2008 at 2:47 pm

    Yeah, and that’s fine and the right way to do it (there is more coming on this, give it a coupel of days) but often that *doesn’t* happen and that’s when problems start arising or confusion sets in. Generally it’s not an issue and the context is clear, but not always, and hence it is a problem.

  3. 3 Mike Taylor 19/12/2008 at 8:25 pm

    > Polyphyletic clades are rarely mentioned

    That’s because they are an oxymoron!

    > e.g. ‘we have found that taxa X and Y are not members of clade Q and actually belong to two different clades, thus the clade Q under its current definition is polophyletic and a new definition is required that excludes X and Y’).

    Sorry, Dave, this would be Just Plain Wrong. If Q is a clade then it’s monophyletic; if it’s polyphyletic, then it’s not a clade. That’s what the word clade _means_. (Which is also why I nurse a pet hate for the tautological but surprisingly common phrase “monophyletic clade”.) You hypothetical authors should have said “we have found that taxa X and Y are not members of clade Q” and left it at that, since any definition of clade Q (e.g. “all taxa closer to A than to B”) constrain it to be monophyletic under all topologies.

    (That’s why I am always frustrated by statements like “… confirms the monophyly of Diplodocoidea”.)

    • 4 jmc 09/12/2012 at 10:05 pm

      Please excuse this non-scientist for his confusion. My understanding is that most (all?) life forms are nested together–that is, say mitochondria (with their own dna) used to be free bacteria but are now embedded within animal cells–I could cite other examples of endosymbiogeniesis. Of course, the metarelationships among assemblages must be taken into account also when attempting to separate identities for the purpose of naming. The new sciences of chaos, strange attractors, and emergence must also be taken into account when considering the art of naming things.

      Meanwhile, certain creatures are capable of direct (horizontal) transfer and exchange of genetic information. What does this do to the concept of identity–what does it do when coupled with the above? Does our current nomenclature simply break down, but we refuse to see it because we don’t have anything else to hold on to?

      So my confusion is this:
      Given this information, how can we assign such assemblages and consortia a name like species. How can we further associate such clusters as CLADES–Aren’t we all in the same metaclade? How can we talk of something like a tree of life at all. The metaphor seems to be an anthropocentric and theocratic convenience and a scientific misnomer. What does all this do the work of taxonomy itself? Is the explosion of information pushing scientific reductionism out into the light of day?

      • 5 David Hone 10/12/2012 at 10:34 am

        The short answer is taxonomy itself in purely as convenience (I’ve said so myself on here plenty of times), but a necessary artificial construct if we don’t want to get trapped into just talking about individuals. Horizontal transfer obvious is an issue for various groups, but is not a major problem for many (plants) or at all for some (vertebrates) and is only really an issue where things are already highly plastic and definitions may be rough (bacteria).

    • 6 jakc 01/11/2013 at 4:50 am

      Thank you Mike (5 years later)

      I came to this site due a recent interest in how cladistics are used. I’m not a professional but due have a reasonable academic background in the area, and from time to time, dive back in the material again. I have been amazed and dismayed to find out how casually parapheltic groups are used. For example, if you search for the relationship between sharks and fish, you will time and time again see sharks called a kind of fish, with perhaps some distinction made that they differ from ray finned fish, and at most a note that the group is parapheltic and a defense of the use of the term (such as fish has no strict taxonomic meaning or that it makes sense a researcher who likes to look at ray finned fish also likes to look at sharks).
      My general objection to this sort of usage is that it is misleading. Ask a bright 12 year old, and he or she will probably tell you that squids and whales aren’t fish. And yet in fact, a whale is more closely related to a tuna, and the tuna to the whale, than either is to a shark. Is it any wonder that the general public has such great problems with understanding evolutionary relationships (“if humans evolved from monkeys, why are there still monkeys?”) when professionals speak in such a way that implies incorrect relationships? I understand that a professional biologist knows the true relationship between a shark, a whale and a tuna, but the general public does not. The average person hearing a biologist call sharks a kind of fish will leave with a misconception about these relationships.

  4. 7 David Hone 20/12/2008 at 9:55 am

    Sorry Mike, you are quite right. After last week’s discussion it does appear that the term ‘clade’ is by definition monophletic, though plenty of people (including me) do not (or did not in my case) use it as such all the time. I’ll kick the habit, honest, and in the meantime I’ll fix it here.

  5. 8 euel benet 27/06/2009 at 1:16 am

    the discussion was good.. and thanks to Mr. Mike Taylor for sharing what a clade really means.. I’ll try fix my taxonomic vocabularies also… thanks for the info!

  6. 9 leys 04/10/2010 at 4:29 pm

    Thanks, I’m studying fishes at my university, and this is helpful in understanding all the -phyly’s.

  7. 10 suhail ahmad wagay 05/12/2011 at 5:02 am


  8. 11 Chanel 12/12/2011 at 4:11 am

    Interesting article. I am so used to the use of monophyly, that I have a libral and radical outlook on taxinomy. I consider humans to literally be apes. Birds are not just dinosaurs, but also reptiles. Paraphyly can be a bit shocking for me, and polyphyly can be really mindblowing. The pachyderms is one bizare group. Elephants, rinos and hippos are all placental mammals, but they are otherwize compleatly unrelated. The rinos closest relatives are horses and tapirs. Hippos are related to deer, cows, pigs and especialy whales. Using a more inclusive group would help unify them. Yet it wouldn’t be compleate whithout a variety of other animals, like dogs, cats, pangolins, bats and hedghogs. Despite this elephants don’t belong in this general group. They don’t really have any close relatives. When placed in a general group they go with aardvarks, manatees and hyrax. In order to cover about all placental mammal species, there only needs to be a third general group. This group has creatures like mice, rabbits and monkeys. I think the traditional group of plants may also count as polyphylic. Plants are nice and exclusive now. It seems like the old definition for them is any multicellular organism that is not an animal. Algea used to be considered to be plants. Green algea is closely related to true plants, so they have more justification. Even fungi used to be considered plants. It is really wierd considering that are much more closely related to animals.

  9. 12 R.Y. 29/01/2012 at 9:25 pm

    thanks so much for this, i’m studying for my evolution class and you really helped me understand monophyly, polyphyly and paraphyly. thanks again.

  10. 13 Taxi priser med Find Taxa 11/03/2012 at 9:50 pm

    After I initially left a comment I seem to have clicked on the -Notify me when new comments are added- checkbox and now each time a comment is added I get 4 emails with the exact same comment. Perhaps there is a means you can remove me from that service? Cheers!

  11. 15 anjali bisht 18/04/2012 at 11:16 am

    it is good but if you also give diagram with example then it will be more meaningful any thanks for infomation.

  12. 16 Meredith 01/02/2013 at 7:14 pm

    I’m still having a difficult time understanding why one starts at the newest divergent species to define a clade… seems to me that to be monophyletic one could start at a lower level and include all those below itself and that would include all the decedents of a common ancestor…I need help

    • 17 David Hone 01/02/2013 at 11:17 pm

      Sorry, I really don’t understand the question here. I can’t follow what you’ve asked and thus can’t spot what misunderstanding you have and so how to try and correct it.

  13. 18 ZackH 08/03/2013 at 12:11 am

    Thanks for the great explanation and the cladogram that went with it. I think I’m starting to really understand the differences between mono, para, and poly-phyletic groups. I’m trying to apply it to botanical lineages in my study of plant taxonomy, but many textbooks and online definitions are a little ambiguous. The dinosaur example really explains it. Thanks

  14. 19 Yousaf 30/04/2013 at 4:59 am

    Using this for my Biodiversity class at UCSD. Thanks for the info!

  15. 20 Zivanai T 15/05/2013 at 8:11 am

    Thanks for the explanations. I wasn’t sent by a professor, but was a reading paper for our lab group discussion and came across terms I had forgotten about. The search engine took me to this site.

    • 21 David Hone 15/05/2013 at 10:50 am

      Thanks for letting me know. I’m just curious as this page is flooded with hits all the time but most seem to be directly typed URLs and I’m intrigued to see where they are coming from. It’s great people are using this as a resource, but I’d like to know who.

      • 22 Anne Keegan 23/05/2013 at 2:35 am

        Thank you for thorough, detailed information. Am a non-biologist avid cactus and succulent grower. While researching Rebutia, Sulcorebutia, Weingartia, came across term “polyphyletic”. Got URL from search engine when querried for meaning.

  16. 23 jakc 17/09/2013 at 1:40 pm

    Came here from duckduckgo. I’m not a biologist and was surprised when reading several articles on line to see paraphyletic groups treated as legitimate, being under the impression that only monophyletic groups ought to be considered so. Your explanation is much better than that of wikipedia, at least as I understand your explanation: paraphylitec groups can be convenient but lack the legitimacy of monophyletic groups if considered from rigorous taxonomic viewpoint.

  17. 24 Manoj 19/09/2013 at 5:19 am

    can u please give an example of polyphyletic.

  18. 26 Jess 22/09/2013 at 2:22 am

    Hi! Im a student from University of New England NSW Australia.
    I found this Googling “Monophyletic, Paraphyletic and Polyphyletic” to help me clarify these terms.
    I wasn’t sent here from a lecturer, my lecturer is actually quite horrible and this site explained it WAY better than he ever could.
    Kudos to you! :)

  19. 27 Diarmuid Hayes 09/10/2013 at 4:47 pm

    Student of University College Cork (Ireland), on exchange to National University of Singapore, was linked this on the class facebook page for Principles of Taxonomy and Systematics (4th year). Thanks very much, did not actually know there was a strict difference between paraphyletic and polyphyletic. Nice page =D

  20. 28 Caleb D. 09/11/2013 at 10:36 pm

    My teacher didn’t assign this, but I was searching differences between these types of organizations of phyla. I’m from Virginia and I go to Virginia Commonwealth University. Great chart and easy to read material. Thank you so much!

  21. 29 Crocodile Dressing table 14/11/2013 at 2:34 am

    Awesome! Its in fact awesome post, I have got much clear idea about
    from this piece of writing.

  22. 30 samah hallumi 25/01/2014 at 3:10 pm

    I’ve checked this link as a preparation for my exam (course: evolution) to understand the difference between all of the 3 groups.
    I’m from Israel, College: Technion.
    thank you

  1. 1 Terminology time « Dave Hone’s Archosaur Musings Trackback on 24/12/2008 at 9:03 am

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