Dear Hadi,

see some definition :

study.com/.../monophyletic-groups-definition-examples-quiz.html

www.thefreedictionary.com/Monophyletic+group

www.nature.com/.../a-monophyletic-group-sometimes-called-a-cla...

A monophyletic group can be separated from the root with a single cut, whereas a ... Reading a Phylogenetic Tree: The Meaning of Monophyletic Groups.

P.s. in my practice it not exist polyphyletic groups! Not good study - yes.

for Homoplasy:

science.sciencemag.org/content/331/6020/1032.full

A monophlyetic group is one that has evolved from a single ancestor, and doesn't exclude any other taxa that also evolved from that ancestor; that is, an entirely 'natural' evolutionary branch.

Reconstructing the trees can be done through various methods, including morphological cladistic analyses. These can be easily misled by homoplasy, which leads to taxa being grouped together by the analysis but which do not lie close together in their phylogenetic history. The result is a polyphyletic group, which includes members of two or more separate branches within the same taxon.

The term "monophyletic" is being currently used in two different meanings. It was originally coined by HAECKEL in early 1860-s to simply denote common ancestry: a group is monophyletic if all included taxa have a common ancestor (or, more exactly, if it includes “the last common ancestor of all members of the group and all intermediate taxa between them and the common ancestor” - quoted from my "Fallacies and false premises..." - Hołyński 2016), it is polyphyletic if there is no single common ancestor. For the next hundred years it was universally so interpreted, and so is also now by followers of the "synthetic" (="evolutioary") "school" of taxonomy (Mayr, Ashlock, Stuessy, Hörandl, and many others including me). Unfortunately later HENNIG (1950) and his followers ("cladistic" school) have introduced enormous confusion making a meaningful dispute very difficult, by restricting the meaning to only those monophyletic groups which contain all the descendants of the last common ancestor. For such groups Ashlock (1984) proposed the unambiguous term "holophyletic", but cladists, wishing to present their rejection of paraphyletic (= monophyletic but not holophyletic) taxa and reduce classification to simple "translation" of cladograms, stick to the confusing terminology and persistently try to present it as the only, universally accepted one (as, unfortunately, Joseph also does)...

Interesting, Roman. It seems that Hennig's redefinition is now extremely widely used, and it is (at least in the UK, so far as I can make out) almost universally taught as the 'correct' definition. Perhaps it is because this was the first definition that I learned, but I do not find the usage confusing, and do think it is very useful to separate monophyly from paraphyly. Ultimately, it doesn't matter whether we use monophyletic and holophyletic or monophyletic and paraphyletic - so long as we stick to one of them, or specify which we're using.

I'd be interested to know whether other people are still using Haeckel's definition widely? (I've noticed that it is still used in some US university teaching, but I thought this was the exception...).

"I do not find the usage confusing" - hmmm, Joseph, do you really not find confusing if some people say "monophyletic" in the sense "holophyletic" and others use the same term for "holophyletic + paraphyletic"? This makes frequently our discussions like the proverbial "discourse of a goose with a piglet", as if we were speaking different languages - especially if one or both parts disregards the fact that the other may understand the same word differently! It is nice to receive a gift from an Englishman, but gift from a German may be... dangerous ("gift" in German = poison)! So, why not use the exact and unambiguous terms (holophyly, paraphyly, polyphyly), making the reinterpretation of "monophyly" superfluous?

I don't find the usage confusing because in my area the Haeckel / Ashlock terminology just isn't used any more. As I said, though, of course we need to have a single system of definitions in order to avoid confusion where it still occurs. There's no requirement that that first definition should be the one that is used, however, and ideas are constantly changing. Searching recent papers on Google Scholar, for example, shows a huge preponderance of 'monophyletic' over 'holophyletic.' Since by far the most widely-used definitions happen to be Hennig's ones, I see no reason why the minor usages should not be the ones to be dropped. An explicit statement from, for example, the ICZN/ICBN would be helpful, of course - I don't know whether any has been issued?

Hadi, the message to take from this is that there are some alternative definitions out there, and occasionally still being used - so be aware of them in case you encounter some confusing usage!

I would further stir this pot by noting that from an epistemological perspective, the existence of common ancestors is an inference based on phylogenetic analysis of empirical data.  Monophyletic groups are discovered by assessing patterns of synapomorphy, which is the evidence that allows us to recognize them.  Homoplasy, in this regard, is simply patterns of character distribution that add extra steps to the most parsimonious tree because the features appear to arise more than once, or to be gained and then lost, in various taxa.  Common ancestors are hypothetical entites that reside at the internal nodes of the cladogram.

"I see no reason why the minor usages should not be the ones to be dropped" - i see one, in my opinion decisive, reason: the term "holophyletic" is unambiguous, while "monophyletic" in cladistic sense confuses two different situations (holophyly and paraphyly). Additional point is a kind of "principle of priority": it is generally harmful (and not quite honest...) to change the meaning of important terms for "marketing" purposes - this practice leads only to the situation where often do not know what in fact are we speaking about!. As to the "majority" vs. "minority", this is a relative assessment: in the publications ruled by near-monopolistic profit-oriented molochs like Elsevier, Brill, Taylor & Francis &c., it is indeed practically impossible (editorial censorship is too strict...) to publish a paper based on "synthetic" "philosophy", but please check taxonomical papers in the less "fashionable" journals and see how many of them follow in practice the cladistic dogmas! And anyway, scientific questions should not be solved by voting!

It seems to me that every scientific view has a dogma - a set of principles by which the methodology operates. Whether cladistic or non cladistic, this is also true of phylogeny construction. While holophyly may be unambiguous, I get the impression that in current usage that I have seen, monophyly is a term applied in the same context and is not confusing at all, especially when used in relation to a phylogenetic tree that shows inclusiveness of all clade members. The distinction here is that a paraphyletic assemblage can be specified, but has no real existence as a lineage other than by exclusion - a bit like saying my family comprises my parents and my siblings with the exception of sibling 'y'. So the grouping of living 'great apes' for example, is only monophyletic if it includes humans. Otherwise it is not monophyletic in any meaningful sense.

I would add to the comments on homoplasy to say that homoplasy can only be recognized after the preferred tree is selected. There are no inherently homoplasous characters. Homoplasy is as applicable to molecular characters as it is to morphology. The difference is that character states of morphological characters can be identified before constructing the tree.

While I would agree in principle that scientific questions should not be solved by voting, in practice there are majority views and minority views. This is just a fact of life. Sometimes the majority view can be restrictive or repressive. Again, that's just how science works as a social process. David Hull wrote on that quite  extensively for systematics, especially on cladistics and traditional systematics. There was also a very good book on how this occurred in the science of geology called the 'Dark Side of the Earth'

John:

“every scientific view has a dogma – a set of principles by which the methodology operates” – well, if you prefer to call set of operative principles a dogma, let’s be! But if so, as regards phylogenetic reconstruction, the only justified “dogma” is the fact of evolution: if we do not accept evolution, there is no phylogeny to be reconstructed. But terminology is not a “principle by which the methodology operates”: it can operate equally well whether we use the unambiguous terms [“monophyly” = “holophyly” + “paraphyly”] or misleadingly apply the first one in the sense of the second.

“I get the impression that ... monophyly is a term applied in the same context and is not confusing at all” – if you read only papers of cladists, you may indeed get such impression: cladists do not say honestly “monophyletic (or non-monophyletic) in cladistic sense”, but always try to show their terminology (and generally cladistic “philosophy”) as the only acceptable and universally accepted – but just therefore such usage of the term is particularly confusing: if you read any discussion paper on, e.g., acceptability of paraphyletic taxa, you will see how frequently the disputants (especially just cladists) “fight the strawmen” having (or shamming to have..) not understood what did the opponent really say!

“paraphyletic assemblage can be specified, but has no real existence as a lineage other than by exclusion - a bit like saying my family comprises my parents and my siblings with the exception of sibling 'y'“ – if that sibling established his own family, lives separately, has his own children and grandchildren, &c., then in a quite meaningful sense he is indeed no more a member of your family. But the family analogy in your formulation is generally not informative (the criteria of in- vs. exclusion not applicable) in the context of this discussion: I would rather ask, do you really think that I am my Mother (according to cladists birds are dinosaurs...), or on 9 I 1937 (my birth date) my Mother suddenly “ceased to have real existence”???

“the grouping of living 'great apes' for example, is only monophyletic if it includes humans. Otherwise it is not monophyletic in any meaningful sense” – it is monophyletic in the very meaningful sense: “grouping the descendants of single [mono-] ancestor”, even if not embracing the entire [holo-] clade. In fact, it is illogical to call “non-monophyletic” (i.e. literally “not sharing a single ancestor”) a group defined as sharing a single ancestor!

“While I would agree in principle that scientific questions should not be solved by voting, in practice there are majority views and minority views. This is just a fact of life”. The existence of “majority views” is indeed the fact and this is OK. But attempts to impose one’s (even if “majority”) views on others is either good or bad. If good, then of course we should agree and follow them, but if bad (as you apparently evaluate them [“I would agree in principle that scientific questions should not be solved by voting”]) then our, as scientists, duty is to oppose and refuse to accept: as Carvalho & al. (2008) justly point out “systematists must bear some blame ... as well – qui tacet consentire videtur (‘he who keeps silent is assumed to consent’). ... the climate of opinion depends upon who speaks and who keeps quiet, ... editors, peers, administrators, and policy-makers become enforcers of a vox populi vox dei ... leading to a ‘new kind of superficiality ... where technological advance is equated with conceptual progress”!

Roman,

Well, I understand your perspective. But to me terms are just terms - unambiguous to some, not to others. Monophyly - again, understand your perspective. But when I do a cladistic analysis or offer a cladistic interpretation I do not feel it necessary to specify monophyletic in a ‘cladistic sense’. 

Family - oh heck, should have avoided the temptation for an analogy.

Birds and dinosaurs – not so worried about whether they are or not, but what is the sister group of birds.

Great apes – agree to disagree.

Science, like any other human endeavor, is a very imperfect process for sure.

Cheers,

John G.

The conflation of pedigrees of individual organisms with phylogenetic relationships is a favorite semantic obfuscation of lovers of paraphyly.  For an excellent discussion of these mattrers, see

Schmidt-Lebuhn, A. N. 2012. Fallacies and false premises - a critical assessment of the arguments for the recognition of paraphyletic taxa in botany. Cladistics 28, 174-187.

Schmidt-Lebuhn, A. N. 2014. "Evolutionary" classifications do not have any information content - a reply to Stuessy and Horandl. Cladistics 30, 228-231.

To get back to the homoplasy issue in the original question, it is my view that homoplasy does not obscure relationships in any way since homoplasy cannot be identified until a tree is selected. What might 'obscure' relationships is when more than one set of characters result in very similar or even identical alternative relationships. There are various techniques for making choices (such as minimising steps etc.) and once a choice is made the excluded characters become, by default, homoplasies. One could say that every synapomorphy is a potential homoplasy, or vice versa, and all at the click of a button. Some relationships may forever remain 'obscure' or unresolved since there is no evolutionary imperative that I am aware of that necessitates that every cladistic event will be tracked by an unambiguous character set.

Andrew

"The conflation of pedigrees of individual organisms with phylogenetic relationships is a favorite semantic obfuscation of lovers of paraphyly" - no, at least not mine: I only reactd to John's analogy! But conflation of phylogenetic reconstruction with taxonomic classification is the favourite obfuscation of enemies of paraphyly. To those who will read Schmidt-Lebuhn (2012) I would suggest to read also my reply (Hołyński 2016: Fallacies and false premises downloadable from RG) - audiatur et altera pars!

I agree with Roman and Andrew, use of pedigrees as an analogy is not a good idea, just results in unnecessary distractions.

In science there are always, by definition, 'enemies' so long as there is more than a single supported viewpoint. In that sense, enemies are a scientist's best friend. Good science needs enemies in my opinion.

If you use "enemy" in the sense of "who disagrees with one's conclusion", that's OK, such "enemies" are, indeed, useful - but only as long as both parts behave honestly, i.e. neither view is presented as universally accepted when in fact it is accepted by only some scientists (no matter: "majority" or "minority") and each part accepts (not only in words!) the right of the other to freely express its views. Unfortunately, in the last decades the "discussions", with increasing frequency and to increasing extent, remind of Fred Hoyle's observation that "a scientist whose views differ from those currently dominating, will quickly see that his/her papers are not published in scientific periodicals and grant applications are outright rejected by the governmental fund disposers. ... scientific circles do not, in fact, aim at the scientific truth, but at the situation where all their members would think the same" - and those who try to "promote" their preferences in such way are true enemies certainly not "best friends" of either honest scientists or of serious Science!

No we don't need enemies! How can you say that, possibly because you don't have any!

Would it make any difference if I did or did not? Some researchers published (in Systematic Biology) a call editors to reject publication of work of a viewpoint supported by myself and colleagues. In a sense those researcher may be considered 'enemies' and certainly of the kind that science can do well of without, but others who oppose and even condemn such works may also be considered 'enemies' but at the same time they raise issues and viewpoints and for that everyone benefits. These are good enemies, and well worth having - in my opinion.