Reptile & Amphibian Forums

Hypothetical taxon: frogs birds

Is this a polyphyletic group, or is it paraphyletic?

Thanks.

According to my copy of "The Compleat Cladist", that grouping would be polyphyletic. But I think the distinction is can get fuzzy is some circumstances, therefore I prefer to simply distinguish between monophyletic and non-monophyletic. You can download a copy of "The Compleat Cladist" (that is the correct spelling) if you want more info. Just use the google.

>>According to my copy of "The Compleat Cladist", that grouping would be polyphyletic. >>

That is not surprising because the birds have a different nearest common ancestor than the frogs. Lumping these two groups would create a polyphyletic group.

>>But I think the distinction is can get fuzzy is some circumstances, therefore I prefer to simply distinguish between monophyletic and non-monophyletic>>

Actually, there is no circumstance in which a group that consists of only birds and frogs (and nothing else) could be considered paraphyletic, so it is not necessary to be ambiguous. Cladists use the term "non-monophyletic" to hide the fact that the taxon they are dismantling is paraphyletic instead of polyphyletic. Since most biologists do not discriminate against paraphyletic taxa, cladists could not usually persuade others to go along with their taxonomic proposals without concealing their true intentions of dismantling paraphyletic taxa. Cladists who use the term "non-monophyletic" in their taxonomic proposals are therefore dishonest. If the taxon/taxa they propose to disqualify is paraphyletic, then they should say so, instead of hiding behind an ambiguous term like "non-monophyletic." Hennig invented the term paraphyletic; his followers should use it if it is so important to them that they have no qualms with generating taxonomic chaos in their unending quest to rid this world of paraphyletic taxa.

>>. You can download a copy of "The Compleat Cladist" (that is the correct spelling) if you want more info. Just use the google.>>

If one wants to be a "compleat cladist" then this is a good source of information. If one wants to be a scientist, then there are better sources of information for the aspiring systematist.

>>Actually, there is no circumstance in which a group that consists of only birds and frogs (and nothing else) could be considered paraphyletic, so it is not necessary to be ambiguous.

The other circumstances I suggested would include OTHER TAXA. This particular case is clear. But sometimes it is unclear whether a grouping is paraphyletic or polyphyletic. Under those circumstances the use of the term non-monophyletic is completely appropriate, not "dishonest".

You sure have a big ship on your shoulder, CKing.

>>>>Actually, there is no circumstance in which a group that consists of only birds and frogs (and nothing else) could be considered paraphyletic, so it is not necessary to be ambiguous.
>>
>>The other circumstances I suggested would include OTHER TAXA.>>

In this case, it is clear from the beginning that no other taxa are involved.

>> This particular case is clear.>>

Absolutely, and that is what I said. There is no circumstance in which a group that consists of only birds and frogs (and nothing else) could be considered paraphyletic.

>> But sometimes it is unclear whether a grouping is paraphyletic or polyphyletic.>>

That is hard to believe. A group is paraphyletic if it shares a nearest common ancestor. If it does not share a nearest common ancestor, then it is polyphyletic. If you do not know whether it is polyphyletic or paraphyletic, then you also do not know whether it is monophyletic or not. Hence a cladist cannot claim that he/she knows anything in such a case. To then suggest that such a group is "not monophyletic" is to assert what is not actually known.

>> Under those circumstances the use of the term non-monophyletic is completely appropriate, not "dishonest".>>

I disagree. It is not only dishonest, but also unscientific because science is based on the available evidence. To go ahead and disqualify taxa on the basis of such lack of evidence would be tragic and also not scientific.

>>You sure have a big ship on your shoulder, CKing.>>

To assert that I have a chip on my shoulder is to assert the unknown. That is again not scientific.

CKing, Let me try to explain this to you again...There are situations when it is clear whether a group is para or polyphyletic. There are other situations when it is not so clear (see example in my other post). Get it?

>>CKing, Let me try to explain this to you again...There are situations when it is clear whether a group is para or polyphyletic. There are other situations when it is not so clear (see example in my other post). Get it?>>

You are not getting it. There are of course situations (lots of them in fact) when not enough is known to determine whether a group is monophyletic or polyphyletic. For example, many paleontologists believe that Dinosauria is monophyletic. Some of their critics, however, point out that the characters used to define Dinosauria may well be convergent similarities. In fact, the late paleontologist Romer considers dinosaurs a polyphyletic group.

These ambiguous situations have nothing to do with the ambiguous term "not monophyletic". Some cladists use this term to deceive the uninitiated of their true intentions. A cladist may want to dismantle an existing taxon because it is paraphyletic, because it is contra to cladistic dogma. But because many biologists do not subscribe to cladistic dogma, they do not distinguish between holophyletic and paraphyletic taxa. Therefore some cladists have no luck with their taxonomic proposals. By calling a taxon "not monophyletic," some cladists are trying to mislead the uninitiated into thinking that the taxon under consideration is polyphyletic. But since it is in fact not polyphyletic, a cladist cannot claim that it is without outright lying. So some of them resort to the ambiguous term "not monophyletic" to conceal their true intentions of dismantling paraphyletic taxa, which are considered monophyletic by most biologists, all pheneticists and all Darwinian systematists.

Therefore, the term "not monophyletic" is unnecessary and it cannot be used in cases when not enough is known about the phylogenetic status of a putative taxon. If it is not known whether a group is polyphyletic or not, then how can one assert that it is "non-monophyletic?" For example, how can we apply the term "non-monophyletic" to a group like Dinosauria, which may be paraphyletic or polyphyletic, depending on which authority is referenced? If a group is paraphyletic, then just say so. Hennig invented the term. Cladists cannot stand paraphyletic taxa because of their dogma. If they hate paraphyletic taxa so much, then why not let the world know the real reason (a determined effort to rid this world of paraphyletic taxa) behind a vast majority of the taxonomic proposals made within the last decade? What are the cladists afraid of? Rejection of their taxonomic proposals? If so, then they have a very good reason for hiding their true intentions because a vast majority of biologists still recognize such paraphyletic taxa as Reptilia and Prokaryota.

I recognize reptiles and I use the word all the time. It's an adjective... The word "reptile" means "all amniotes that did not evolve feathers or fur". That's a meaningful definition in certain contexts (like in a pet shop), but it is phylogenetically meaningless and it's subjective.

Do non-venomous snakes comprise a clade? The term is ubiquitous and useful... but it's utter nonsense in the phylogenetic sense.

What does "reptile" mean to you?

>>I recognize reptiles and I use the word all the time. It's an adjective... The word "reptile" means "all amniotes that did not evolve feathers or fur". That's a meaningful definition in certain contexts (like in a pet shop), but it is phylogenetically meaningless and it's subjective.>>

Reptilia is a monophyletic taxon. Reptile is not just "an adjective." It is a noun. It is a basal group, what cladists call a paraphyletic group. The cladists do not like paraphyletic groups because of their dogma. But that is their problem, not ours. They have a problem, but the rest of us don't.

Reptile is not meaningless. It is useful. One can discuss reptilian physiology quite easily because this basal group has more in common with each other physiologically than they do with birds, which some cladists include in their "Reptilia." The cladists' Reptilia is also a taxon, but it is a mess because of the inclusion of birds and the exclusion of such reptilian groups as the synapsids and therapsids. If birds and mammals never evolved, Reptilia would have been a perfectly homogeneous taxon, just like Mammalia or Aves. You are letting cladistic dogma color your views.

>>Do non-venomous snakes comprise a clade?>>

Probably not. That is because some coral snakes may have undergone reversal and become non-venomous.

>>The term is ubiquitous and useful... but it's utter nonsense in the phylogenetic sense. >>

The term non-venomous snakes is not nonsense. Invertebrates is another term that makes sense, not nonsense. If no venomous snake has descendants that have undergone a reversal, then it is possible to have a clade that comprises of all non-venomous snakes. Whether non-venomous snakes form a clade or not is irrelevant. Scientists need to communicate with each other, and they have to refer to groups that are not holophyletic. In fact, they often have to refer to paraphyletic groups. They use terms like non-avian reptiles, but that is less useful than the term reptiles. Even after Romer proposed that Dinosauria is an invalid polyphyletic taxon, he still uses the term dinosaur. So, not every name that systematists use has to refer to a holophyletic group.

>>What does "reptile" mean to you?>>

Reptiles is a clade, a monophyletic group. A clade does not have to include all of the descendants of its common ancestor. Reptile is very meaningful to me. And it is a useful taxon, far more useful than the cladists' reptile. Besides, even the cladists find the name Reptilia indispensable, but their redefined "Reptilia" is not very useful because it excludes some reptiles like the synapsids and therapsids, and it includes some endothermic, highly derived species known collectively as the birds.

You think amniotes become more homogenous if birds and mammals are removed?

By what criteria do you judge snakes and crocodiles to be more similar to each other than crocodiles are to birds? Nucleotide sequence? Morphometrics? Embryology? Behavior?

>>You think amniotes become more homogenous if birds and mammals are removed? >>

Of course I think so. And I am not alone. Other than some dogmatic cladists, a vast majority of biologists consider Reptilia (excluding birds) a natural group and a valid taxon.

>>By what criteria do you judge snakes and crocodiles to be more similar to each other than crocodiles are to birds? Nucleotide sequence? Morphometrics? Embryology? Behavior?>>

Morphologically crocs and snakes are more similar because their scales are more similar to each other. Biochemically snake scales and crocodilian scales are made of the same kind of protein. Feathers, however, are made of a unique protein not found in reptiles.

Physiologically, snakes and crocodilians have more in common with each other and with other reptiles than any reptiles do with birds. All reptiles are ectotherms. They rely on external heat sources and they do not generate a lot of metabolic heat internally. Birds are different. Birds are endotherms and they rely on metabolic heat to maintain a more or less constant body temperature.

If a classification is to be natural, then it must take evolution into account. Since birds have evolved into a different sort of animal than their reptilian ancestor, removing them from their ancestral group Reptila is perfectly consistent with evolutionary theory.

But of course similarity has never been the sole criterion for a natural classification. Snakes and crocodilians do form a monophyletic (paraphyletic if you insist) group with other reptiles. Hence reptiles form a natural group. Their similarities with one another also make such a group far more homogeneous and useful than a "Reptilia" that includes the birds.

Cking wrote: "A clade does not have to include all of the descendants of its common ancestor."

I think it is clear that Cking has little understanding of modern phylogenetics.

I disagree. He clearly understands phylogeny. The thing is that this person supports the infusion of subjectivity in order to preserve historical mistakes. He promotes banishing the birds and mammals from the reptiles because they are "different". All reptiles are different. To me, turtles are more divergent from the other amniotes than birds. The turtle shell is as different and strange as fur or feathers, but I keep my opinions out of my science. I also think whales and bats are fantastically different from other mammals, but I don't feel the need to make a taxon out of the non-whale and non-bat mammals to satisfy my ignorant gut feeling that all land mammals seem to be more similar to each other than any of them are to whales or bats. I allow the whales and bats to remain in the mammal taxon dispite their odd adaptations, and I allow birds to remain in the reptile taxon despite their odd adaptations.

Seriously, I think this discussion has been enlightening. It shows that some of us can get past our primitive tendency to group things based on superficial similarity. We use objective criteria and we accept the results even if the results go against what our middle-school science teachers told us.

Bottom line: is phylogeny the pursuit of groups defined by relatedness or perceived similarity?

>>Bottom line: is phylogeny the pursuit of groups defined by relatedness or perceived similarity?

Phylogeny is absolutely the pursuit of groups defined by relatedness (i.e. monophyly, not paraphyly or polyphyly).

Phenetics (a dead science) is based on similarity with no regard for relatedness.

Frankly this is a silly debate. If you want to understand this stuff, read the literature. I entered this discussion to direction some to that literature, not debate an issue that is essentially dead.

Cheers folks!

I know plenty about phenetics... and the rest of the literature on phylogeny, for that matter. I studied morphometrics and biometry with Bob Sokal, actually. I'm not a dumb as I let on. I just wanted to hear the best an individual like Cking had to offer, and so far it's what I expected... blind adherence to the groups he learned about in elementary school.

I'm glad we no longer have mushrooms in the plantae, and it's nice to see the protists breaking up. If I could just get the textbook publishers to quit printing chapters on "invertebrates". They ignore my comments every time I serve as a reviewer.

He will not beat your challenge, by the way. Nice one.

Hey apeltes, I did not mean to give you a hard time about knowing the literature. That was not really meant to be as harsh as it sounded. I get annoyed with people like Cking and I can be pretty blunt at times. Sokal eh? Very good. I think you and I basically agree on this stuff. Thanks for the complement on the "challenge". Looks like Cking completely missunderstood the example. Do you think it was not clear? I wonder sometime if that is a problem in these forums.

No offense taken! It's my fault for being in "stealth mode" or something like it.

I'm outta here. I got what I needed from CKing. He actually admitted that he clings to the "reptilia" because Linnaeus told him to. I honestly didn't hope for such a satisfying conclusion, but there it is. I also delighted in his flailings about how taxonomy isn't science and that phylogeny is purely about utility... I guess I'll just start categorizing animals by color, then. Sure, evolution is history, but that doesn't mean it's not accessible to science for Pete's sake. He's worse than my creationist students.

The funny thing is after all his claims about how the proposal for including aves within repltilia was rejected by most, I decided to pull a couple of my old herp texts off the shelf and see what the experts think. According to Zug (1993) aves is ranked within reptilia, same with Pough (1998). So who are the people who have rejected placing aves within reptilia?

Pet shops, zoos, and middle schools.

>>Pet shops, zoos, and middle schools.>>

Pet shops and zoos may have both reptiles and birds in their collection. I am not sure why middle schools are included in your list. Is it the highest level of science education you have achieved? Based on your posts, that appears to be the case.

>>The funny thing is after all his claims about how the proposal for including aves within repltilia was rejected by most, I decided to pull a couple of my old herp texts off the shelf and see what the experts think. According to Zug (1993) aves is ranked within reptilia, same with Pough (1998). So who are the people who have rejected placing aves within reptilia?>>

Ever heard of ornithology? Ever heard of Ernst Mayr, an ornithologist, among other things? Most ornithologists still consider Class Aves separate from Class Reptilia, for example. Find me an article or book in which S. J. Gould classifies birds as reptiles. There isn't any.

Have you ever read any articles within Copeia, Herpetologica or Journal of Herpetology? I don't see any article about "avian reptiles" within the covers of these journals. If birds are indeed reptiles, then bird biology should be taught by herpetologists in universities. The most recent edition of the fiel guide "Reptiles and Amphibians of Western North America" excludes birds. Have you ever heard of Dr. Robert C. Stebbins, herpetologist?

Did Pough or Zug include birds or any aspect of bird biology in their texts? If you don't have a copy of R. L. Carroll's "Vertebrate Paleontology and Evolution," then please go to the library. Turn to page 624; it reads "Class Aves". Turn to page 615; it reads "Class Reptilia."

Ignorance is not power.

Looks like you were right about the challenge. Check out the latest post. He does not like the example so he claims that the data are garbage, even though the example is completely contrived. No one ever has data that good.

>>>>Bottom line: is phylogeny the pursuit of groups defined by relatedness or perceived similarity?
>>
>>Phylogeny is absolutely the pursuit of groups defined by relatedness (i.e. monophyly, not paraphyly or polyphyly).>>

Phylogeny is not the pursuit of grouping organisms. Phylogeny is the pursuit of determining evolutionary history. Grouping organisms on the basis of similarity is the pursuit of the taxonomist. Ever since Darwin, however, only those groups (which are delimited on the basis of similarity) that are demonstrably monophyletic (i.e. a group that share a recent common ancestor) are recognized. Groups that are found to be polyphyletic have been removed from the taxonomy ever since Darwin.

Phylogenetics is a separate branch of science than classification, which is itself not actually science. There are many biochemical phylogeneticists who are only interested in determining phylogeny but they are either not interested or not qualified to be taxonomists. They may publish a paper on phylogeny but they may not make any taxonomic proposals. Of course there are people who are interested in both phylogeny and classification as well, but phylogeny is not the same as classification.

>>Phenetics (a dead science) is based on similarity with no regard for relatedness. >>

Absolutely not! Pheneticists argue that evolutionary history is unknowable. Therefore the best way (to them) to find groups that are closely related to each other is to use overall similarity. Their reasoning was that if a group of organisms share a large number of similarities, then that group is likely to be closely related evolutionarily. Curiously, some cladists are making the same argument, yet they claim they are not pheneticists.

Of course, since convergence, reversal and parallelism are rampant, the pheneticist approach is demonstrably false. 2 organisms (such as the wolf and the thylacine (or marsupial wolf) can be remarkably similar because of convergence upon a similar lifestyle. In fact, many cladists are unwittingly practicing phenetics when they lump a group of organisms together on the basis of superficial similarities without critically analyzing the goodness of their taxonomic characters. A. Feduccia of the Univ. of North Carolina calls such practice "clado-phenetics."

So while few systematists call themselves pheneticists nowadays, many of them still carry on the practice, albeit unwittingly. Nevertheless the methods developed by pheneticists can be useful when determining disparity. And many of the procedures pheneticsts followed have now been adopted by the cladists. Sometimes one wonders whether some pheneticists merely morphed themselves into cladists in their never-ending assault on Darwinian taxonomy.

>>Frankly this is a silly debate. If you want to understand this stuff, read the literature. I entered this discussion to direction some to that literature, not debate an issue that is essentially dead.
>>
>>Cheers folks!

It appears that misunderstanding of phylogeny, systematic methodology and classification is rampant.

>>I disagree. He clearly understands phylogeny.>>

Thank you for your objectivity.

>>The thing is that this person supports the infusion of subjectivity in order to preserve historical mistakes.>>

Historical mistakes, if it means polyphyletic taxa, should not be condoned. I do not condone such mistakes. If a taxon is polyphyletic, as Pachdermata was clearly so, then such a taxon would need to be disqualified. There are of course many taxa that have been delimited historically that are perhaps not to the liking of the cladists or their fans, but these taxa are by no means mistakes if the Darwinians and a vast majority of biologists world wide continue to recognize them. Besides, cladists make mistakes constantly. One of the biggest ones is the bird-theropod lexus. It is a polyphyletic group, but the cladists recognize it as a clade. In sum, I do not support the recognition of polyphyletic taxa, whether they are historical mistakes or current ones.

>>He promotes banishing the birds and mammals from the reptiles because they are "different".>>

Do you have a problem with excluding mammals and birds from Reptilia? You have a problem. You are also in the minority. Besides, if you do not exclude organisms that have evolved disparity from an old taxon, you end up with a single genus for all life on earth because nothing can be deserving of being removed from the old genus. Clearly, if we are going to have more than one genus, more than one family, more than one order, more than one class, and more than one phylum, then we need to remove organism from one genus, family, order, class or phylum and put it in another. The question then, is not whether, but which. Which organisms should be removed from Reptilia and placed in another Class? Most biologists have decided that Mammals and Birds are sufficiently different from Reptiles to be excluded from Reptilia. I happen to agree with them, not because their decision is historical, but because their decision results in a more useful classification than the alternative proffered by some cladists.

>> All reptiles are different. To me, turtles are more divergent from the other amniotes than birds. >>

You are entitled to your opinion of course. Turtles, though quite different morphologically from other reptiles in some ways, are nevertheless morphologically similar to other reptiles in other ways. They are also not physiologically different from most other reptiles.

>> The turtle shell is as different and strange as fur or feathers, but I keep my opinions out of my science. >>

The turtle shell is indeed quite unique among vertebrates. But it is still morphologically simply modified bone and reptilian scales. Fur and feathers, OTOH, are fundamentally different than reptilian scales. Hair grows out of follicles. Feathers are biochemically different from reptilian scales. In fact, feathers are so different from scales that no one has yet figured out how feather evolved.

>> I also think whales and bats are fantastically different from other mammals>>

I, too, agree that whales are quite morphologically disparate. I support classifying whales in the Order Cetacea, instead of classifying them in the same order as the Artiodactyla, even though it has been demonstrated that whales evolved from an artiodactyl and that the closest living relative of whales is the hippopotamus. Nevertheless, whales still retain mammalian characteristics such as lactation and endothermy. Therefore whales are not as different from a typical mammal as mammals are to the reptiles. Do whales deserve to be removed from Mammalia? A vast majority of taxonomists would say no. Bats, although they have achieved flight, are still very much mammal-like in their biology. Hence a vast majority of biologists have not classified bats in a different class from Mammalia. Again, you are probably thinking that everbody else are wrong but you are right.

>>but I don't feel the need to make a taxon out of the non-whale and non-bat mammals to satisfy my ignorant gut feeling that all land mammals seem to be more similar to each other than any of them are to whales or bats.>>

Scientists do not rely on ignorant gut feelings. They rely on data.

>>I allow the whales and bats to remain in the mammal taxon dispite their odd adaptations, and I allow birds to remain in the reptile taxon despite their odd adaptations. >>

We do not need your permission to recognize a Mammalia that includes both bats and whales. We also disagree with your idea that birds should be placed in Reptilia.

>>Seriously, I think this discussion has been enlightening. It shows that some of us can get past our primitive tendency to group things based on superficial similarity.>>

That is a strawman. No one is grouping organisms by superficial similarity, except perhaps those taxonomists who do not critically analyze their characters but rely on superficial similarities. That is why some scientists are dismayed by the cladistic practice of ignoring the goodness of taxonomic characters.

>> We use objective criteria and we accept the results even if the results go against what our middle-school science teachers told us. >>

So far I see no sign that you have any objectivity except for your opening remark. LOL.

>>Bottom line: is phylogeny the pursuit of groups defined by relatedness or perceived similarity?>>

Phylogeny is a science dealing with the evolutionary relationship of living organisms. I think you are confusing phylogeny with classification. Classification is not phylogeny and classification is not science. However, classification must take into account phylogeny. It means that taxa must reflect phylogenetic relationships, but it does not mean that classification is phylogeny and phylogeny only. Classification must be useful because classification exists to serve scientists in their communication. Any classificatory practice that makes communication difficult would therefore be contradictory to the goals of classification. When scientists communicate with each other and refer to reptiles, it is nearly universally understood that they mean a group of basal amniotes that are not endothermic. It is very simple and elegant and it has served us well for centuries. If we include birds in Reptilia and exclude the synapsids and therapsids from Reptilia, then the term reptiles has lost its meaning. Communication is more difficult. Now, when cladists want to communicate with each other, they need to use the term non-avian reptiles. They don't need to do that if they would just leave Aves alone instead of making a mess of their "Reptilia."

Okay Cking, I have a final challenge for you. Tell me whether B and C form a paraphyletic or polyphyletic group in this example:

The relationships among the taxa are ((A,B)C)(D,E). The character matrix is:

A - 000
B - 111
C - 111
D - 000
E - 000

Lets assume that 1000 other characters support the above relationships perfectly (i.e. no homoplasy), so the relationships are not ambiguous. Using a character based definition of para and polyphyly (which you appear to prefer), I argue that there is no way to distinguish between between para or polyphyly, but it is clear that these two species do not form a monophyletic (i.e. ancestor and all descendents) group. This is what I suggested could happen, while you denied it is possible. In this case it is clearly correct to state that B and C are not monophyetic (unless you and I disagree on the definition of monophyly), but it is not clear whether they are para or polyphyletic. Hence the appropriate use of the term non-monophyltic. If you can prove that there is a way to tell whether B and C are para or polyphyletic, I am very interested to see this proof.

For those who are not familiar with character state optimization, all three characters in the above example show the same number of steps on the tree whether they are optimized as plesimorphies for the clade ((A,B)C) or as convergent on B and C. Either optimization requires 2 steps (a gain in the ancestor and a loss in A, or a gain in B and C independently). The only way to "decide" whether the above arrangement is para or polyphyletic is to decide a priori that the ancestor to B and C either has or does not have the character state 1. There is no evidence one way or the other so this decision would be subjective and not scientific. Let's see how Cking solves this one.

>>Okay Cking, I have a final challenge for you. Tell me whether B and C form a paraphyletic or polyphyletic group in this example:
>>
>>The relationships among the taxa are ((A,B)C)(D,E). The character matrix is:
>>
>>A - 000
>>B - 111
>>C - 111
>>D - 000
>>E - 000
>>
>>Lets assume that 1000 other characters support the above relationships perfectly (i.e. no homoplasy), so the relationships are not ambiguous.>>

Those 1000 characters are meaningless without knowing what they are. They could be symplesiomorphs, or they could be synapomorphs or they could be homoplasies (convergences, parallelism or reversal) or a mixture of different combinations of these types. A naive cladist may be impressed by the claim of 1000 similarities, but I am not.

A similar claim has been made concerning birds and dinosaurs. The cladists like to impress their followers and the uninitiated as to how many similarities there are between birds and dinosaurs. The real deciding character, however, is feathers. The oldest known reptile with feathers is Longisquama insignis, a Triassic organism. On the other hand, there is no known dinosaur that has feathers. All the so-called "feathered dinosaurs" come from a period long after birds have diversified into many different types, and none of them predated the oldest known bird, Archaeopteryx. Some of the "feathered dinosaurs" have proven to be forgeries. Other "feathered dinosaurs" have filamentous structures that are similar to the collagen fibers found in the skin of vertebrates that do not have any trace of feathers. Yet other "feathered dinosaurs" are actually secondarily flightless birds.

>>Using a character based definition of para and polyphyly (which you appear to prefer),>>

How else can you identify paraphyletic and polyphyletic groups unless you examine the taxonomic characters of the members of a particular group, be they molecular or morphological characters?

>>I argue that there is no way to distinguish between between para or polyphyly,>>

If that is the case, then you don't know enough to make a taxonomic proposal. The prudent thing to do is to leave the existing taxonomy as is but investigate further.

>> but it is clear that these two species do not form a monophyletic (i.e. ancestor and all descendents) group.>>

That does not bother me. I am not obsessed with holophyletic groups. Paraphyletic groups are perfectly fine. Polyphyletic groups, however, should not be recognized as valid taxa. In fact, holophyletic groups are kind of boring because nothing much new has evolved from them to warrant the erection of a new higher taxon. If life never evolved beyond the bacterial stage on earth, then we have a rather uninteresting holophyletic group, and neither you nor I would be typing at a keyboard or going out herping. We would all be extracting energy from some inorganic source and be single celled organisms. Evolution produces paraphyletic groups, therefore the cladists should stop destroying paraphyletic taxa.

>>This is what I suggested could happen, while you denied it is possible.>>

I never said that it is not possible to be unable to figure out the truth. I only said that if there is not sufficient information, then do not make a hasty taxonomic proposal. If a taxonomist claims that a taxon is not monophyletic, then he should exlain to us whether he/she means the taxon is paraphyletic or polyphyletic. If he/she does not know, then say so. Don't hide behind the term "not monophyletic."

>>In this case it is clearly correct to state that B and C are not monophyetic (unless you and I disagree on the definition of monophyly), but it is not clear whether they are para or polyphyletic. Hence the appropriate use of the term non-monophyltic. If you can prove that there is a way to tell whether B and C are para or polyphyletic, I am very interested to see this proof.>>

I am not interested in your example, because a hypothesis of relationships is only as good as the taxonomic characters used to support such a relationship. Without knowing the goodness of the taxonomic characters, even 1000 similarities does not impress me and these similarities do not prove anything. If there is not enough information to determine whether a group is paraphyletic or polyphyletic, then just say that there is not enough data. Don't declare the group "not monophyletic."

>>Okay Cking, I have a final challenge for you. Tell me whether B and C form a paraphyletic or polyphyletic group in this example:
>>
>>The relationships among the taxa are ((A,B)C)(D,E). The character matrix is:
>>
>>A - 000
>>B - 111
>>C - 111
>>D - 000
>>E - 000
>>
>>Lets assume that 1000 other characters support the above relationships perfectly (i.e. no homoplasy), so the relationships are not ambiguous.>>

>Those 1000 characters are meaningless without knowing what they are. They >could be symplesiomorphs, or they could be synapomorphs or they could be >homoplasies (convergences, parallelism or reversal) or a mixture of different >combinations of these types. A naive cladist may be impressed by the claim of >1000 similarities, but I am not.

They could NOT be symplesiomorphies because symplesiomorphies are not informative about relationships and I clearly stated that the characters support the relationships above (i.e. they are informative). Did you miss the phylogeny above?
Also they could NOT be homoplasies, I told you there are no homoplasies, see above. That only leaves 1000 synapomorphies, not just similarities. You do know that it means for a character to "support" a phylogeny don't you?

I won't waste time commenting on the rest of your response because you could not even understand the example. Feel free to try again though. I'll try to make it easier to understand: of the 1000 synapomorphies, 10 are autapomorphies, 2 for each OTU (I had not thought to have any in the original example but we can add them now. Frankly it does not really matter if they are here or not but I don't want you to try to weasel out of this on some technicality) . The rest are evenly distributed on the more basal branches on the tree. For example 330 support A as sister to B, 330 support A B as sister to C, and 330 support D sister to E. We can assume A-E form a monophyletic group. Again there is no homoplasy, all the characters actually support the relationships as described (except the autapomorphies which are uninformative about the phylogeny). There are no symplesiomorphies. Here is a diagram of the tree in case you are having trouble understanding what ((A,B)C)(D,E) means.

A B C D E
|__| | |__|
|___| |
|_____|

You can clearly see that A B and C form a monophyletic (or holophyletic if you please) group. Please tell us how to determine if B and C form a para or polyphyletic group.

Just to referesh your memory this challenge is in response to a statement you made.

Cking wrote: " If you do not know whether it is polyphyletic or paraphyletic, then you also do not know whether it is monophyletic or not. Hence a cladist cannot claim that he/she knows anything in such a case. To then suggest that such a group is "not monophyletic" is to assert what is not actually known. "

I believe I have clearly proven you wrong, but if I am mistaken please explain.

Not sure how to make the figure work in this format, so I will just describe the tree. A and B are sister taxa. A B is sister to C. D is sister to E. A B C is sister to D E.

In my second paragraph

"of the 1000 synapomorphies, 10 are autapomorphies,"

should read

"of the 1000 characters, 10 are autapomorphies"

There is a very simple answer to your question. It is: garbage in, garbage out. IOW, a tree is only as good as the characters that are used to construct it. Evolution is history, and history can only be inferred, but not directly observable. Sometimes there just isn't enough available evidence to infer history with any degree of certainty. You can draw any tree you want and use it as a riddle of some sort, but at the end of the day, it makes no difference. If you cannot determine whether a group is polyphyletic or paraphyletic using the available evidence, then you cannot claim that it is "not monophyletic". Asserting what is not actually known is perhaps a favorite past time of the cladists and their supporters, but that is not what scientists do. If you want to speculate on the phylogenetic status of a particular group of organisms, then feel free to do so. Just don't call it science.

>>There is a very simple answer to your question. It is: garbage in, garbage out. IOW, a tree is only as good as the characters that are used to construct it.

This hypothetical data set is better (more robust, contains less homoplasy, and has evenly distributed characters and therefore even branch lengths) that any real data set that has ever been published. So what is your point about garbage?

>>Evolution is history, and history can only be inferred, but not directly observable. Sometimes there just isn't enough available evidence to infer history with any degree of certainty.

Not in this case.

>>You can draw any tree you want and use it as a riddle of some sort, but at the end of the day, it makes no difference.

The difference it makes is proving you were wrong, which turned out to be pretty easy.

>>If you cannot determine whether a group is polyphyletic or paraphyletic using the available evidence, then you cannot claim that it is "not monophyletic".

Can and did. Do you think B and C form a monophyletic (holophyletic if you please) group? I don't. Can you tell me if they are para or polyphyletic? Nope.

>>Asserting what is not actually known is perhaps a favorite past time of the cladists and their supporters, but that is not what scientists do.

Not known?!? Its an example that I made up. I told you what the relationships were.
If you can't figure out what the monophyletic groups are then you don't know how to read a tree.

>>If you want to speculate on the phylogenetic status of a particular group of organisms, then feel free to do so. Just don't call it science.

Speculate? LOL. So now it is speculation to identify taxa as monophyletic or not by looking at the tree and applying the definition. LOL.

>>>>There is a very simple answer to your question. It is: garbage in, garbage out. IOW, a tree is only as good as the characters that are used to construct it.
>>
>>This hypothetical data set is better (more robust, contains less homoplasy, and has evenly distributed characters and therefore even branch lengths) that any real data set that has ever been published. So what is your point about garbage?>>

It is garbage because your hypothetical data set has nothing to do with any real world cases in which the term "not monophyletic" were used. In these cases, the cladists did not use the simpler, more elegant, more powerful term polyphyletic because that is simply not true. They could have used the term paraphyletic but that is likely to reveal their true intentions. So, many cladists hide behind the ambiguous term "not monophyletic" because their sledgehammer is being aimed at taxa that few people other than the dogmatic cladists will likely disqualify.

If you are claiming that your hypothetical case has anything to do with real world cases in which the term "not monophyletic" have actually been used, then please cite such cases. Otherwise you are simply making an entirely unsupported, fraudulent claim.

After re-reading this thread it is clear to me that once again we have a disagreement that stems in semantics. I think Cking and I agree on the definitions of para and polyphyly, but he thinks paraphyly is a form of monophyly, where I equate the terms holophyly and monophyly. While I believe my use of these terms has historical precedence and is more widely accepted in the literature, I'd rather not argue semantics. If Cking were smarter he might have caught this before I did, but it looks like he instead resorted to claiming my example had "garbage" for data and never really took the time to examine the challenge. It is this type of dogma that prevents any progress from being made in these discussions.

I believe we still disagree on whether paraphyletic groups should be recognized in formal taxonomy, but that is a matter of opinion. I have shown that the distinction between para and polyphyly can be impossible sometimes even when the tree is fully resolved. This provided an excellent example of why non-monophyletic (or non-holophyletic if you please) is useful sometimes. It is also useful if you don't care whether the grouping is para or polyphyletic, only if the grouping is monophyletic (or holophyletic). So in the end much of the difference is opinion on two fronts (the meaning of the term monophyly and the acceptance of paraphyletic groups in formal taxonomy). But claiming that cladists are dishonest whenever they use the term non-monophyletic is clearly bull.

Allow me to elaborate a little on the potential for ambiguity. Consider the phylogeny (A,B)(C,D). What would the grouping of A and C as one taxon be? Paraphyletic or Polyphyletic? Difficult for me to tell, but I know the taxon is not monophyletic. There are also multiple definitions of para and polyphyly that depend on different criteria including whether the homoplasy used to group the non-monophyletic taxon is the result of convergent or parallel evolution. Distinguishing between convegent and parallel evolution can also be difficult and there continues to be debate about this. On the other hand, whether a taxon in monophyletic or not is easy to determine while looking at the phylogeny.

I guess I'll respond to my own post, since no one else did. In the example phylogeny the character that groups the taxa A and C would require 3 steps if it were plesiomorphic, but only 2 steps if it were convergent. If we use a parsimony approach to reach a conclusion then the group A C would be considered polyphyletic. This example was actually easier to resolve than I first thought. I'll have to try to recall an example where the hypotheses of plesimorphy or convegence are ambiguous and this renders the distinction between para and polyphyly ambiguous too. I think have come across these at times when optimizing characters in MacClade, but it may take a little time to actually come up with one. Under a statistical model it is possible that the two alternatives are equally likely (using maximum likelihood or bayesian techniques) even in this case. I will work on this a little in my spare time and if I come up with an example that is ambiguous under parsimony, I'll post it. If anyone else can think on one please post it. Otherwise I might have been proven wrong.

As a side note, definitions of para and polyphyly based on the inclusion or exclusion of common ancestors would not be able to distinguish between para and polyphyly the example I provided above. Maybe that was what I was thinking about when I came up with it. So again things come back to defining what you are writing about. Whew, this is a good brain workout. Haven't thought about these details in quite some time.

>>Hypothetical taxon: frogs birds
>>
>>Is this a polyphyletic group, or is it paraphyletic?
>>
>>Thanks.

If this taxon consists only of frogs and birds, then it is considered polyphyletic by any systematist, whether he/she is a cladist, a pheneticist or a Darwinian.

The closest living relatives of frogs are salamanders and caecilians. Thus frogs, salamanders and caecilians have a nearest common ancestor that is different than the common ancestor of the birds and frogs. The closest living relatives of birds are the crocodilians, and of course birds are also more closely related to the reptiles and even the mammals than they are to the frogs. The common ancestor of the birds, mammals and reptiles is the common ancestor of the amniotes. The common ancestor of the frogs, salamanders and caecilians is the common ancestor of the lissamphibians.

Therefore a taxon consisting or birds and frogs only would consist of one group from the amniotes and one group from the lissamphibians. That taxon would of course be unambiguously polyphyletic, no ifs, ands, or buts about that.

The common ancestor of the frogs and birds is also the common ancestor of the tetrapods. If one removes frogs (a crown group) from the tetrapods and puts them in a new higher taxon, the remaining tetrapods (excluding frogs) is a basal group that lacks some of the crown groups. Such a group (i.e. the basal tetrapods) would be considered paraphyletic by the cladists. The Darwinians and pheneticists, however, do not make a distinction between paraphyletic and monophyletic groups. Therefore the basal tetrapods (excluding the frogs) would be considered monophyletic by Darwinians and pheneticists. If one then removes birds (also a crown group) from the remaining tetrapods and classify the birds as another higher taxon, then the remaining tetrapods (excluding frogs and birds) would again be paraphyletic according to the cladists but monophyletic according to the Darwinians. But if one lumps frogs and birds (2 different crown groups with different common ancestors) into a single taxon, the such a taxon would be polyphyletic according to the Darwinians, the cladists, or the pheneticists.

I thought a paraphyletic group was a group of species that share a common ancestor, but with some of the descendents of that common ancestor excluded. Woudn't that be the case for a group consisting of birds and frogs?

>>I thought a paraphyletic group was a group of species that share a common ancestor, but with some of the descendents of that common ancestor excluded. Woudn't that be the case for a group consisting of birds and frogs?>>

Birds and frogs do not form a paraphyletic group because they do not share a single nearest common ancestor. All birds share a nearest common ancestor, which is the first archosaurian reptile that evolved feathers. All frogs also share a nearest common ancestor, which is a lissamphibian. The nearest common ancestor of all frogs and all birds are different. So these two groups cannot be lumped into a single monophyletic group. Lumping them would result in a polyphyletic group.

When you start with a group that consists of the descendants of a single nearest common ancestor, then systematists of all schools (Darwinian, cladistic, or phenetic) would agree that such a group is monophyletic. When you remove species from a monophyletic group, you end up with at least 2 different groups. The tetrapods form a monophyletic group because all members share a single common ancestor. If you remove the frogs from the tetrapods, you end up with 2 different groups: "frogs" and "all the other tetrapods but frogs". "All other tetrapods but frogs" (even though this group is now missing some of the descendants of their common ancestor) still share a nearest single common ancestor. Therefore "all other tetrapods but frogs" would be monophyletic according to the Darwinians and pheneticists. This same group is considered paraphyletic by the fastidious cladists.

If you then remove the birds from the group "all other tetrapods but frogs", then you end up with three different groups: birds, frogs, and "all other tetrapods but frogs and birds". The group "all other tetrapods but frogs and birds" would still share a nearest common ancestor (namely the first tetrapod that evolved). Therefore the group of "all other tetrapods but frogs and birds" would be monophyletic according to the Darwinians and pheneticists but it would be paraphyletic according to the fastidious cladists.

Since frogs share a nearest common ancestor, it is also a monophyletic group. The same is true of the birds. Birds also form a monophyletic group. However, if you then lump the birds and the frogs into a single group, you end up with a group with 2 different nearest common ancestors. Such a group would of course be polyphyletic.

Hence you are correct that a paraphyletic group is a group that is missing some of the descendants of a common ancestor. However, a paraphyletic group is also a monophyletic group according to the Darwinians and the pheneticists because this group shares a nearest common ancestor. A polyphyletic group, however, does not share a single nearest common ancestor. Since birds and frogs do not share a single nearest common ancestor, birds plus frogs would be considered polyphyletic, not paraphyletic or monophyletic.

As you can see, paraphyletic groups and polyphyletic groups are very different, and they should not be lumped into the umbrella term "not monophyletic," as some dishonest cladists have done. In fact, a paraphyletic group is merely one flavor of a monophyletic group, just as red giants, neutron stars and white dwarfs are different flavors of what we call stars. Hence Darwinians and pheneticists consider paraphyletic taxa valid. It is the cladists who have a weird dogma of intolerance of paraphyletic taxa. Such quasi religious dogma really has no place in science, and the cladists' intolerance has resulted in taxonomic chaos for decades to come.

The group containing frogs and birds has one common ancestor and all of the descendents except for three groups of species (i.e., urodeles, gymnophiona, and amniota). Isn't that paraphyletic in the same way reptiles are paraphyletic? Reptiles have one common ancestor and a few groups of descendant species removed (e.g., synapsida and aves).

>>The group containing frogs and birds has one common ancestor and all of the descendents except for three groups of species (i.e., urodeles, gymnophiona, and amniota). Isn't that paraphyletic in the same way reptiles are paraphyletic? Reptiles have one common ancestor and a few groups of descendant species removed (e.g., synapsida and aves).>>

Tetrapods include more than the groups you cite. There are basal amphibians that are included among tetrapods besides the urodeles, and the caecilians. You are incorrect that your group (birds plus frogs) excludes the amniota because birds are included in amniota. If you were to exclude all amniotes from your taxon, that leaves frogs only, which is of course a monophyletic group. Frogs do not even form a paraphyletic group. It is a holophyletic group.

Reptilia is a monophyletic group (paraphyletic according to the fastidious cladists) because it shares a nearest common ancestor. Since all life on earth share a single common ancestor, any 2 or more species on earth can therefore form a monophyletic group. Hence there would be no such thing as a polyphyletic group using such a broad definition of monophyletic.

Biologists have agreed that a monophyletic group should be defined as a group in which all members must share a nearest common ancestor. Reptilia is a paraphyletic group (according to the fastidious cladists) because it is a stem group within Amniota. The lineages of all of the members of Reptilia can be traced directly to the ancestral stem species of Amniota. Reptiles is paraphyletic (instead of holophyletic) because two crown groups of amniotes have been removed: namely the birds and the mammals. Since the birds have been removed from Amniota, the many lineages of the Aves cannot be traced directly to the common ancestor of the amniotes. The nearest common ancestor of Aves is now the first archosaurian reptile with feathers (Longisquama being the oldest known reptile with feathers would be a good candidate as bird ancestor, not withstanding many cladists' denial that Longisquama has feathers because they dogmatically believe that birds are descended from a dinosaur and Longisquama is not a dinosaur). The nearest common ancestor of the mammals is a therapsid reptile that evolved fur from whiskers. Lumping two crown groups like birds and mammals would create a polyphyletic group because these two groups have different nearest common ancestors. Lumping frogs and birds into the same taxon is similar to lumping mammals and birds because they too have different nearest common ancestors.

Yeah... I messed up the amniota there.

Birds and frogs are a monophyletic group with all of the amniotes except birds removed, and all of the anamniote tetrapods except frogs removed.

>>Yeah... I messed up the amniota there.
>>
>>Birds and frogs are a monophyletic group with all of the amniotes except birds removed, and all of the anamniote tetrapods except frogs removed.>>

One way to test monophyly is to use taxonomic characters. Monophyletic groups are united by synapomorphies, or shared derived characters. Example, the monophyletic group called Aves is united by the synapomorphy of feathers. Polyphyletic groups are united by convergent characters. For example, the polyphyletic group Haemothermia is defined on the basis of the convergent character homeothermy. Paraphyletic groups are defined by symplesiomorphs or shared ancestral characters. For example, Anapsida is defined by the shared ancestral state of an unfenestrated skull.

Please propose either a sympleisomorph or a synapomorph, either morphological or molecular, that would define your monophyletic/paraphyletic group "frogs plus birds." Otherwise you have no evidence to assert your claim of monophyly or paraphyly for this group.

Let me start first, your group frogs plus birds form a polyphyletic group because they share the convergent character of fewer than 5 fingers (frogs have 4 and birds have 3). Frogs have fingers 1-2-3-4, whereas birds have fingers 2-3-4. Since the closest relative of birds, the crocs, have five fingers, it follows that the last common ancestor of the frogs, crocs and birds probably had 5 fingers. That means frogs and birds lost their fingers independently after they last shared a common ancestor. Hence birds are only convergently similar to frogs and the two thus form a polyphyletic group.

Frogs and birds share thousands of traits that derive from common ancestry... not convergence. They both have limbs, for example.

I think the disagreement on this issue stems from the definitions used for paraphyly.

Apeltes: I thought a paraphyletic group was a group of species that share a common ancestor, but with some of the descendents of that common ancestor excluded.

This vague definition can render any two taxa, that are not sisters, paraphyletic. While this definition is common in texts, it is not very practical if one is interested in differentiating between the two concepts.

CKing: Paraphyletic groups are defined by symplesiomorphs or shared ancestral characters {(note: and exclude taxa with relevant apomorphies)}. Polyphyletic groups are united by convergent characters.

This allows for differentiating between the two scenarios in many circumstances, but perhaps not always, because sometimes we don't know whether traits are convergent or plesiomorphic (see my post on Sept 29).

Hopefully this helps.

I think I get it. A paraphyletic group is defined by shared ancestral characters (not convergent similarities), and the lack of certain apomorphies found in the excluded sub-taxa.

For example: reptiles are defined by an amniotic egg and scales not modified as hair or feathers.

Looks like you get it.

So, would this be a valid paraphyletic clade?

The "Notaves"
This clade is united by amniote development and the lack of feathers. It includes mammals and reptiles.

Well I am one of those people who Cking refers to as Cladists. I see no reason to recognize anything besides monophyletic groups. There are an infinite number of paraphyletic groups that could be recognized, but they don't really tell me much about phylogeny. So the short answer is: No.

Not sure what you mean by "valid paraphyletic clade". It is paraphyletic, but I don't think it is taxonomically valid.

I have read many posts here about how paraphyletic clades are valid, but Cladists are trying to get rid of them. I thought I'd start by making sure I know what a paraphyletic clade is.

Here's what I've learned. It seems pretty easy. All you have to do is:
1)Choose a bunch of organisms you percieve to be similar and put them in a group together (Reptiles: turtles, snakes, lizards, crocodiles, and tuataras)
2)Identify the nearest common ancestor and define your group with synaplesiomorphies (e.g., flat scales and endothermy)
3)Justify the removal of the other descendants of the same common ancestor by identifying apomorphies that are inappropriate for the group you created.

I assume you mean ectothermy rather than endothermy and symplesiomorphies instead of synaplesiomorphies. If so, then you are on the right track. Personally I can't figure out why anyone would want to recognize either para or polyphyletic taxa. Neither reflects phylogeny, and I find that taxonomy based on phylogeny is the most informative. Cking seems to think there is something "natural" about paraphyletic taxa, but I don't see it.

Here is an example of what can happen when you consider paraphyletic groups to be valid taxa. Let's say there are 4 species in genus X, and each member of the genus possesses some autapomorphy in a different character (while the other species are plesiomorphic). Let's use an example based on DNA for simplicity.

For gene X:
Position 10: species A has the nucleotide T
Position 11: species B has the nucleotide A
position 12 species C has the nucleotide G
position 13 species D has the nucleotide C

Let's assume the real relationships among the species are (A,B)(C,D). We could exclude any of the species from the group by their autapomorphy, just like birds are excluded from reptiles for their autapomorphies. So what is the "best" paraphyletic taxonomic grouping based on plesiomorphies.

A,B,C as one taxon?
How about A,C,D?
Maybe A,B,D?

I see no objective answer. If I asked you to name every monophyletic group, anyone who understands the definition of monophyly can do that. So besides the fact that peraphyletic goups do not reflect phylogeny, they can also be quite arbitrary.

What is the point?

I would say the point is that paraphyletic taxa preserve mistakes and traditions. Paraphyletic taxa only make sense if people wish to base phylogeny on subjective perceptions. For example: many can accept a taxon made up of species with bony shells, hollow venomous fangs, rattles, hemipenes, and heat-sensing facial pits... but not fur or feathers.

>>I would say the point is that paraphyletic taxa preserve mistakes and traditions.>>

Paraphyletic taxa are not "mistakes." Polyphyletic taxa are mistakes. When uncovered, polyphyletic taxa are removed from the classification. For example, Pachydermata, a polylphyletic taxon consisting of elephants, hippos and rhinos, is no longer recognized even though it is an old taxon. Paraphyletic taxa are actually the inevitable result of the process of evolution. If you don't understand it, that is okay. I will explain.

Turn the clock back to an early stage in the history of life, when there is only a single genus and a few related species, all of them not very different from one another. Move forward a couple of million years, and we see a new species which is different from all the other species existing at the time. A taxonomist is now faced with the decision of whether to continue recognizing only a single genus or place the new distinct species in a second genus. Recognizing a second genus automatically causes the old genus to become paraphyletic. Is the erection of a new genus "subjective?" Yes, certainly. Is it bad? If you are a cladist, you would probably think it is a bad decision because you don't like paraphyletic taxa.

So, what should be done? One genus or two genera? Of course, whether taxonomists call these groups of species one genus or two genera has no effect on the welfare of these species. The only reason why we even bother to consider the question of one genus or two genera is because of convenience. It is far more convenient to refer to all the species found in one genus using the name of the genus, instead of having to refer to all of the species by name. Hence, the reason we classify is that it helps us communicate with each other. So, what does the dogmatic belief that paraphyletic taxa are not acceptable has to do whether a classification is useful or not? Yes it does. That is because if we do not recognize paraphyletic taxa, then we cannot recognize a second genus at all. All life on each therefore cannot be classified in more than one all encompassing genus without violating the no paraphyletic taxa rule.

>> Paraphyletic taxa only make sense if people wish to base phylogeny on subjective perceptions.>>

Certainly. One must rely on subjectivity when judging amounts of differences between any 2 species. But how else can we decide whether and how to classify organisms unless we rely on judgment? Should we flip a coin or play a game of musical chairs to decide whether one species should be classified in one genus or another? How is coin flipping going to result in a better classification? Flipping coins is very objective, because there is a 50-50 chance of tail or head. So, you worship objectivity. Unfortunately, objectivity is not a cure all.

>>For example: many can accept a taxon made up of species with bony shells, hollow venomous fangs, rattles, hemipenes, and heat-sensing facial pits... but not fur or feathers.>>

As I said, taxonomy is a democracy. If you think it is stupid to recognize a taxon that shares the synapomorphy of fur or a taxon sharing the synapomorphy of feathers, then you can certainly publish a taxonomic proposal to disqualify these taxa. BTW, hollow fangs have evolved independently in the elapids and the crotalids. So, it is a convergent character that cannot be used to define a taxon. Thought you may want to exclude hollow fangs from your argument the next time you make it. Also, fangs are not themselves venomous, but they are used to inject secretions from the venom gland that is located next to the teeth.

>>Frogs and birds share thousands of traits that derive from common ancestry... not convergence. They both have limbs, for example.>>

Yes they both have limbs, but that begs many questions. On what basis does "limbs" allow birds and frogs to form a monophyletic or paraphyletic group? After all, lots of animals have limbs. For example, insects (e.g. butterflies), molluscs (e.g. octopus), arachnids (e.g. spiders), crustaceans (e.g. crabs) and of course many tetrapods (e.g. alligators) have limbs. So, why use "limbs" to separate frogs and birds from all these other animals? How does limbs exclude these other animals from this group? It doesn't. In fact, limbs is a convergent character between molluscs and tetrapods. Therefore, a group consisting of animals with limbs would be polyphyletic because "limbs" is a convergent character. I know of no practicing systematist who would consider "limbs" a valid taxonomic character. However, some natural groups can be identified by the number of limbs that they possess. Spiders have 8. Insects have 6, and of course tetrapods have 4. But even eight limbs is not itself a good taxonomic character by itself, because octopuses also have 8 limbs.

So, unfortunately, you have not provided a single synapomorphy that could be used to unite frogs and birds as either a monophyletic or a paraphyletic group. If I were a professor, I would give you an F. You flunked. LOL.

Sorry for being vague. By "limb", I mean a limb comprised of a humerus, radius, ulna, etc... with or without some parts fused or lost. If we are grouping things using symplesiomorphies, this should work fine. Please re-evaluate my grade.

>>Sorry for being vague. By "limb", I mean a limb comprised of a humerus, radius, ulna, etc... with or without some parts fused or lost. If we are grouping things using symplesiomorphies, this should work fine. Please re-evaluate my grade.>>

Sorry, your new answer is not any better. The limb bones of tetrapods are derived from fish, so your "limb" now would include the fins of some fishes. "Limb" (per your definition) is now a symplesiomorph of a more inclusive group than tetrapods. Even if we restrict your new definition of "limb" to tetrapod limbs, we end up with Tetrapoda, not your nameless taxon of frogs plus birds. That is because a paraphyletic group must include all organisms that possess that symplesiomorph, not just some. You can exclude snakes and legless lizards and other limbless vertebrates from a paraphyletic group, defined as having "limb comprised of a humerus, radius, ulna, etc..." because the limbless vertebrates have evolved a new character state: loss of limb. But you cannot exclude other tetrapods from this group because they still have limbs. "Limb comprised of a humerus, radius, ulna, etc..." is not a symplesiomorph or synapomorph of frogs plus birds. It is the sympleisomorph of a more inclusive group.

Therefore even if you were allowed to retake the test, your grade remains an F.

Got it. We need to have a symplesiomorphy in our paraphyletic group that is not present in the excluded taxa. Fine.

I hereby create the "Nonchelonia". This taxon includes all organisms that posess a sacrum not covered by a carapace of fused ribs.

>>Got it. We need to have a symplesiomorphy in our paraphyletic group that is not present in the excluded taxa. Fine.
>>
>>I hereby create the "Nonchelonia". This taxon includes all organisms that posess a sacrum not covered by a carapace of fused ribs.>>

Taxonomy is a democracy. Anyone can propose any taxon for any reason, including of course the hatred of paraphyletic taxa among cladists. What you need is to publish your taxonomic proposal. Good luck.

I don't think I'll publish a phylogeny as stupid as the one I proposed... which is identical in its logic, construction, and merit to the reptiles. Just replace "sacrum covered with ribs" with "fur or feathers". The difference between the two: opinion. You think feathers don't belong in the reptilia because you don't feel like they belong, and someone else could just as well remove the turtles for equally subjective and absurd reasons. The difference, therefore, is actually historic. Generations ago, ignorant people felt like birds were different from reptiles, but people felt like turtles were not.

>>I don't think I'll publish a phylogeny as stupid as the one I proposed... >>

You are entitled to your opinion. I would not call it "stupid" but I would consider it not very useful. Taxonomy is all about utility. It is not science although taxonomists do agree that taxonomy must reflect phylogeny and therefore evolution.

>>which is identical in its logic, construction, and merit to the reptiles. >>

I disagree. Reptilia is a more logical and meritorious taxon than your proposed taxon "Nonchelonia." That is not only my opinion but also the opinion of a vast majority of taxonomists through history. Linnaeus, who knows quite a bit about classification, did not recongize a "Nonchelonia" but he did recognize Reptilia.

>>Just replace "sacrum covered with ribs" with "fur or feathers".>>

It is not that simple. Carapace are identifiable as scales, and fused ribs are still identifiable as bone. Feathers and furs originated from scales, but they are very different from scales morphologically. To this date, no one knows exactly how scales evolved into feathers, and some of the hypotheses of feather evolution proposed by some cladists to conform to their dogma of a dinosaurian origin of birds are demonstrably silly. Feathers is also chemically different from reptilian scales.

>>The difference between the two: opinion. >>

Not at all. Your opinion is that feathers or fur do not differ very much from scales, but your opinion is simply wrong. It is contradicted by scientific fact and by the opinion of a large number of the greatest scientific minds that have lived throughout history.

>>You think feathers don't belong in the reptilia because you don't feel like they belong, and someone else could just as well remove the turtles for equally subjective and absurd reasons.>>

Of course I don't think feathered animals should be classified in Reptilia. That is not just my "feeling", but the consensus of many of the greatest minds of the past and present. Most biologists would agree that Class Aves is a separate taxon from Class Reptilia.

>>The difference, therefore, is actually historic. >>

That is your opinion. And of course my opinion is that you have made a logical error.

>>Generations ago, ignorant people felt like birds were different from reptiles, but people felt like turtles were not.>>

If ignorance = lack of knowledge, then indeed many people in the past lack the knowledge that birds were derived from reptiles. However, they do know that birds are different from Reptiles. Reptiles, for example, are ectotherms. Birds, OTOH, are endotherms. Sure, some ignorant people claim that dinosaurs are endotherms, but it has been shown by those who are knowledgeable that all of the evidence that have been proposed for endothermic dinosaurs are either erroneous or equivocal.

Reptiles and birds do share the sympleisomorph of egg laying, but then monotremes also lay eggs. So, the cladists are absolutely incorrect to group the birds with reptiles and then exclude the monotremes from their "Reptilia." In fact, physiologically monotremes have more in common with reptiles than birds do. Of course the therapsids and anapsids, which the cladists exclude from their "Reptilia," are even more reptile like than the birds and the monotremes. The cladistic "Reptilia" therefore is not very useful and it is silly.

Ever since the discovery of Archaeopteryx, there is no doubt that birds are descended from a reptile. Nevertheless, until recently, no one tried to classify birds as reptiles. And even after some cladists proposed including birds in Reptilia, most biologists have ignored that ridiculous proposal and continue to recognize a paraphyletic Reptilia. So, it is demonstrably not the lack of knowledge about bird ancestry that have resulted in the continued recognition of a paraphyletic Reptilia. In fact, it is not knowledge, but cladistic dogma (which is intolerant of paraphyletic taxa), that is the motivation behind the cladists' proposal to include birds in Reptilia. Unfortunately for the cladists, their dogma has not been adopted by a vast majority of biologists world wide, who continued to accept paraphyletic taxa such as Reptilia and Prokaryota.

Finally, if you think that feathers are not very different from scales, then you are just ignorant.

"Linnaeus, who knows quite a bit about classification, did not recongize a "Nonchelonia" but he did recognize Reptilia."

I rest my case. This is the confession I've been seeking.

See y'all. I'll be busy moving science forward while others light candles for Linnaeus. Best regards. I have a reptile collection to attend to!

>>"Linnaeus, who knows quite a bit about classification, did not recongize a "Nonchelonia" but he did recognize Reptilia."
>>
>>I rest my case.>>

Good. I was getting tired of your antics.

>>This is the confession I've been seeking.>>

Not a confession, but a statement of fact. Linnaean classification is still used throughout the world. Some cladists have proposed that we abandon the Linnaean system because there just aren't enough taxonomic ranks to satisfy the cladists' needs. It appears that instead the world has decided to abandon cladistic classificatory practice instead. Reptilia is alive and well and most people do not include birds within Reptilia. BTW, Ernst Mayr probably thinks that Linnaeus is a better taxonomist than many cladists.

>>See y'all. I'll be busy moving science forward while others light candles for Linnaeus. Best regards. I have a reptile collection to attend to!>>

You, moving science forward? How? I see no evidence of that capabilitiy from you.

Good luck with your reptile collection. I hope that your "reptile" collection does not include birds because birds have a much higher basal metabolism than reptiles and they require daily feeding as well as daily cleaning of the cages, unlike traditional reptiles. Those who clean bird cages and reptile cages know the difference between birds and reptiles, even if the cladists do not. LOL.

>>See y'all. I'll be busy moving science forward while others light candles for Linnaeus.>>

I got it. You are going to propose new names for old taxa. That is what the cladists have been doing for the past couple of decades. If that is your idea of scientific progress, then I submit that putting old wine in a new bottle is also scientific progress.