Talk:Phylogenetics

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On 28 Mar 2005, this article was nominated for deletion. See Wikipedia:Votes for deletion/Phylogenetics

The Picture

The picture on this article is technically a cladogram, not a phylogeny. This is because it does not incorporate environmental or temporal information. —The preceding unsigned comment was added by 12.217.236.33 (talk) 23:04, 18 February 2007 (UTC).

There is an understood temporal component in all cladograms. The deeper branches are older. The term phylogeny is appropriate here as well as cladogram.

I should like to attract attention to the colouring of the diagram: what does the connection in red between the birds (where is actually turns orange: why is the overlay area between blue and yellow not green????????) and the mammalians stand for? There is no common ancestor to these branches who was warm blooded and we have an independant evolution of this feature: so what does this connection try to suggest here? Or does it simply attempt to confuse and render incomprehensible what is essentially straightforward??? —Preceding unsigned comment added by 80.132.203.205 (talk) 13:23, 6 February 2008 (UTC)

Oh dear, oh dear... How are we ever to get out of Hennig's confusion (i.e., cladism)? A phylogenetic tree illustrates a 4D reality in 2D, thus by necessity confusing two dimensions, namely time and space. A phylogenetic tree traditionally conveyed information about either relationship or properties (the two phenomena that was confused in the dimensional reduction), consistently joined in a conceptualization of the Linnean kind (i.e., categories of categories). Now, Hennig's comprehension boldly confused the 4D reality with the 2D illustration thus introducing a new kind of dichotomous illustration that he (or his successors) called a 'cladogram'. This kind of illustration, or rather this kind of interpretation of this kind of illustration is thus a conceptual confusion confusing the concepts time and space.

The picture on this article is thus not "technically a cladogram, not a phylogeny". It is an illustration of the relationship between the terminal units. However, its definitions of poly-, mono- and paraphyletic groups is biased towards cladistics by deeming paraphyletic groups to be non-monophyletic and excluding holophyletic groups (see Envall). The problem with its partitioning of reality into these different kinds of groups is that it it based on this 2D-illustration of a 4D phylogeny. It does in practice not partition reality into different kinds of things, but instead classifies this dimensional reduction into different kinds of things. It classifies a classification. The problem with it is thus not what it is, but what it is interpreted as. Including the partitioning into kinds of groups, it is not an illustration of phylogenetics, but of cladistics. It is thus an erroneous confusion of the concept 'cladistics' with the concept 'phylogenetics'. These two concepts are not equal or even synonymous. The former (i.e., cladistics) is actually a specific kind of conceptualization of phylogenies, which Envall explains is inconsistent, self-contradictory and (empirically) wrong. —Preceding unsigned comment added by 83.254.20.53 (talk) 23:08, 21 September 2008 (UTC)

Phenetics and cladistics as methods

The article's statement that "The most commonly used methods to infer phylogenies include cladistics, phenetics, maximum likelihood, and MCMC-based Bayesian inference." is a bit puzzling. (This is part of what I think is a general muddle over the term "cladistics"). The declaration that one method for inferring phylogenies is "phenetics" is strange, since phenetics as a philosophy of classification is positively uninterested in phylogenies and interprets its branching diagrams as classifications but not as phylogenies. What is going on here is to label parsimony methods "cladistics" and distance matrix methods "phenetics". In my view these latter two terms are best reserved as labels for approaches to classification, not methods for inferring phylogenies. The two get middled together all the time. (But keep in mind that in systematics this view of mine is considered by most people as dubious and marginal -- when it comes to this view I'm regarded as a fringe crackpot.) Felsenst

I made these changes to the wording of that section. It's a drop in the bucket compared to what's needed with this article. --Aranae 17:15, 5 July 2006 (UTC)

User Felsenst is correct. Neither cladistics nor phenetics are "methods to infer phylogenies". This statement is instead a symptom of the cladistic confusion. I am a personal friend to Swofford, and I can assure Felsenst and everyone else that neither Felsenstein not Swofford would ever accept this confusion. The problem is Hennig's confusion of reality and our illustration of it. I am prepared to write a comprehensive explanation of what phylogenetics is, but since I explain that cladistics is inconsistent, self-contradictory and wrong, I constantly get deleted and blocked. A consistent explanation of phylogenetics will show cladistics to be wrong, and cladists therefore delete and block phylogeneticists (like me). Consist (presently at 83.254.20.53 (talk) 23:21, 21 September 2008 (UTC)).

embryology

would sympathtic editors consider a positive vote here? [1]Slrubenstein | Talk 15:18, 23 August 2006 (UTC)

Monophyly, paraphyly and polyphyly merge

(Moved to talk:clade). Richard001 06:58, 4 November 2007 (UTC)

See the explanation of the concepts in Envall —Preceding unsigned comment added by 83.254.20.53 (talk) 23:23, 21 September 2008 (UTC)

Lumping and splitting

Would a discussion of "lumping" and "splitting"—what the terms mean, and how authorities come to such decisions—be warranted here? MeegsC | Talk 15:40, 20 May 2007 (UTC)

At present this article is rather short, and such a new item might be out of proportion. But do take a look at Lumpers and splitters. The topic is explored there in some depth. EdJohnston 16:15, 20 May 2007 (UTC)

"Lumping and splitting" in biological systematics is actually extremely interesting on the most fundamental (generic) level, and therefore should not be discussed in this article. Basically, it concerns the fact that reality can be comprehended in terms of yes's and no's, which cannot sum up to one (exactly the opposite to what the probability for each does). This fact occurs in statistics in the form of Type 1 and Type 2 errors, that is, falsifying a true hypothesis respectively accepting an erroneous hypothesis, and in cartography by the different aspects on accuracy, that is, the probability that a randomly chosen position on the map is correctly classified respectively the probability that a randomly chosen position in reality is correctly classified. In the case of "lumpers and splitters" in biological systematics, this fact means that partitioning reality according to similarities or differences simply cannot give the same result. Getting the same result is just as impossible as that Type 1 and Type 2 errors is the same; if they had been, they wouldn't have been different. At the most fundamental level, it is the fact of the impossibility that a difference can be a similarity.

Now, cladists think that this fact is just a consequence of conceptualization itself, thus claiming that a confusion of conceptualization is "natural", but it is wrong. This fact actually has roots in reality, as witnessed by the fact that time is relative. It suggests that this fact is the reason for process itself by meaning that reality simply cannot find a stable configuration per definition. Whatever the reason for the fact is, it means that our conceptualization of reality in terms of generics and specifics is a consistent handling of this fundamental fact. Cladists are thus totally wrong. They obviously do not recognize this fact, much less understand the complicated relation between concepts and reality. They actually appear to be totally ignorant of everything that preceded, or exist in parallell, to cladism. They are true extremists: don't discuss anything in other terms or conceptual frameworks than you self decide. In the light of cladism, "lumpers and splitters" do not even exist. They are burried in its coding of characters and character states. The fundamental ambiguity is swept under the mat pretending that it does not exist. I am this fact trying to get out from under the mat, and they, led by Sjö, constantly pushes me back under the mat.

After this comment, I will probably be blocked till at least the 10th of December, and probably by Sjö. I will, however, be back either when the blocked is lifted or under another ip-adress. Typical for cladists is that they think that things have a mandatory connection to their addresses (i.e., properties), and thus cannot escape them. I will show them that they are wrong. —Preceding unsigned comment added by 83.254.20.59 (talk) 01:15, 7 November 2008 (UTC)

Cladistics a synonym for phylogenetics?

Ernst Mayr would be rolling in his grave. I think this should be reverted. Cladistics is the Hennig school, and their view of how things go in phylogeny is far from universally shared. One of the problems is that the different authors give their own meanings to the words, and then assume that those meanings are universal. Phylogeny comes from the 18th century, before cladistics was thought of. All we should do is cover the controversy, without picking winners and losers. EdJohnston 19:43, 14 November 2007 (UTC)

Phylogenetic Systematics and Cladistics are two different approaches to interpretations of evolutionary relationships. They should not be used synonymously as phylogentic systematics takes in consideration of ALL homologous characters, whereas cladistics considers specifically chosen derived characters to reach generalizations of evolutionary relationships. This process results in a development of a phylogenetic chart showing relationships through time with hypothesized ancestor-descendant links (phylogenetic systematics) or a cladogram with no ancestor-descendant links hypothesis AND without a time dimension. Timothy Michael Earwood 04:40, 27 January 2008 (UTC) —Preceding unsigned comment added by Poethical (talk • contribs)

EdJohnston is right, not because "Ernst Mayr would be rolling in his grave", he was pretty incomprehensible himself, but because phylogenetics is not a synonym to cladistics. Phylogenetics denotes a science that discusses dichotomously branching processes, whereas cladistics denotes a confusion of reality and our illustration of it concerning dichotomously branching processes. Phylogenetics is thus the science, whereas cladistics is an inconsistent, self-contradictory and (empirically) erroneous comprehension of phylogenies. —Preceding unsigned comment added by 83.254.20.53 (talk) 23:38, 21 September 2008 (UTC)

Who is this Williamson?

Williamson believes that larvae and embryos represent adults in other taxa that have been transferred by hybridization (the larval transfer theory)

Who is Williamson, why is he important, why should we care about his ideas, what exactly are his ideas anyway and what does hybridization or larval transfer mean in this context? Some of the readers are not as familiar in the field of developmental biology as you are, please try to keep that in mind. Shinobu 12:57, 4 December 2007 (UTC)

I have no idea why this passage about Williamson is included. At best, it is a wild conjecture that is far outside of mainstream evolutionary biology! — Preceding unsigned comment added by 141.217.188.92 (talk) 21:17, 17 October 2011 (UTC)

The "Williamson" mentioned is this guy. Saying his views are a wild conjecture is a great understatement -- they are totally off the wall. See the "Controversy" section of that Wikipedia page. Felsenst (talk) 21:47, 30 November 2011 (UTC)

Cladistics is a method to do ... what?

The article currently says:

Cladistics provides a simplified method of understanding phylogenetic trees. .... The most commonly used methods to infer phylogenies include parsimony, maximum likelihood, and MCMC-based Bayesian inference. Distance-based methods construct trees based on overall similarity which is often assumed to approximate phylogenetic relationships.

So is "cladistics" a method of "understanding" trees, or constructing them? Are parsimony, ML, and Bayesian methods examples of "cladistics"? Or not? Or do they reconstruct the trees which are then "understood" by cladistics? Also, why are distance methods "assumed to approximate phylogenetic relationships" but likelihood and Bayesian methods, which are based on the same models, not making that assumption? (Don't mind me, I am just harassing folks in this field because I think the standard descriptions of what is going on are totally muddled, and this article reflects that). Felsenst (talk) 20:28, 19 March 2008 (UTC)

Hello, Professor F! We do have an article on Cladistics, but I believe it is an imaginative reconstruction of what the field ought to be, not referenced to reliable sources. (The content of Wikipedia articles may ironically reflect the popular understanding of certain topics, even when it diverges from the sources). I have a sense that it would be easier to reform our article on Maximum parsimony if anyone had the patience to begin. There is probably a real story to be told there, for which strong references could be found. Since that article at present has no inline citations, the rationale for re-writing is evident. EdJohnston (talk) 21:03, 19 March 2008 (UTC)

The article is written by a cladist. I (Envall) have explained that cladism is inconsistent, self-contradictory and (empirically) wrong. Cladism is actually the ultimate conceptual confusion, confusing all concepts. I claim that Wikipedia have to discard cladists to make an encyclopedia. Cladists do not distinguish concepts, but confuse concepts. Allowing them to influence Wikipedia is like letting the fox into the hen-house. Cladists are confused. They are actually paranoic. They ought to be in treatment rather than in scientific discussions. Consist (presently at 83.254.20.53 (talk) 23:48, 21 September 2008 (UTC))

Wikipedias' problem is just to shut off believers from being administrators. Belief does not agree with knowledge per definition. Wish cannot be combined with skepticism.

An encyclopedia has to rest on skepticism to fulfill its aims. Distinguishing belief from skepticism is the grand problem for Wikipedia's administrators. If they succeed, Wikipedia will be a good encyklopedia, but of they fail, Wikipedia will split into several encyclopedias. Consist, presently at 83.254.20.59 (talk) 00:38, 8 November 2008 (UTC)

Obsolete sentence

The intro contains the sentence "The problem posed by phylogenetics is that genetic data are only available for the present", and cites a 1967 journal, but this is no longer true. DNA sequencing has been performed on ancient organisms, including mammoths frozen in permafrost, and insects embedded in amber. This is not my field and I don't have readily available references, so please accept this request for an update. --Blainster (talk) 16:02, 4 July 2008 (UTC)

Is this article about phylogenetics or cladistics?

When reading the page, I get confused by the constant inflictions of references to cladism. Why is the same picture included in this article as in the article about cladistics? Envall has recently shown in Biol J Linn Soc that cladistics actually denies both facts and science, why should it be allowed to confuse itself with the science of phylogenetics? Can't it stick to its own article (where it, by the way, refuses to include criticism of it). Is cladism allowed to infect all articles discussing evolution? Consist (talk) 23:32, 8 July 2008 (UTC)

Am I allowed to change this article

Am I allowed to change this article without being deleted or blocked? Consist (presently at 83.254.20.53 (talk) 23:53, 21 September 2008 (UTC))

Anyone can make constructive contributions. If they are made in good faith and constructive but wrong they may be deleted, but you won't be blocked unless they are clearly vandalism or construed as such. Plantsurfer (talk) 07:54, 22 September 2008 (UTC)

No, not in this case since user:Consist is permanently blocked for pushing his own research.Sjö (talk) 15:10, 23 September 2008 (UTC)

Phylogenetic systematics or cladism?

How come an explanation of the concept phylogenetics in the beginning contains the expression "phylogentic systematics or cladism", thus equalizing the two? What on earth does a science has to do with an extremism of that science? Phylogenetics does not require acknowledgement of the inconsistent, self-contradictory, empirically erroneous and ambiguous concept "clades". This acknowledgement is actually a bold confusion of process and pattern, that is, only an extremism kind of phylogenetics. Is islam equal to alQuiada? Consist, presently at 83.254.20.122 (talk) 00:19, 6 November 2008 (UTC)

First of all, might I suggest you calm down a bit? You analogies are bad and you come across confrontational. Always assume good faith. There are plenty of references where "phylogenetic systematics" and "cladistics" are referred to very nearly synonymously (see the references at the end of the Cladistics article). Note that it is "phylogenetic systematics" and not "phylogentics"; there is a difference. I am not sure where you find clades to be "self-contradictory" or "empirically erroneous". Obviously, it is a changing science. We are constantly revising the Tree of Life. However, if you can prove something to be wrong, feel free to add it to the article. It is easy to throw around claims and criticisms, but you must back them up (and not with your own research, as I suspect is the case). --Thorwald (talk) 19:37, 6 November 2008 (UTC)

I am calm. My analogy focuses on the fact that both are confusions of a generic with one of its specifics. The fact that there are many people in biological systematics that presently make this confusion doesn't mean that it isn't a confusion. Thorwald also appears to understand that it is a confusion, as judged by his expression "very nearly synonymously". It actually means not synonymous, because a close hit is not a hit. Cladistics does, of course, rest on the concept clades, and Envall has explained exactly how this concept is inconsistent (i.e., self-contradictory) and empirically erronous. It does, however, not mean that phylogenetics, or even phylogenetic systematics is afflicted with these errors. The errors resides solely in the distinction of clades, manifested in the "denial" of paraphyletic groups. The truth is that "clades" ought to be called holophyletic groups (as also Ashlock explained long ago), and that both holo- and paraphyletic groups are monophyletic groups. Cladism "sinks" (or drags) holophyletic groups into monophyletic groups thus making them "very nearly synonymous". To really nail their synonymonity (is that correctly spelled?), it actually defines that they are synonymous, thus inconsistently (meaning self-contradictory) and empirically erroneously. They are not, I repeat not, nor can be, synonymous. I beg the administrators of Wikipedia to pull this confusion apart. Cladism can't be made synonymous to phylogenetics (or phylogenetic systematics) by any definition(s) in the universe. They are as different as fruits and pears are. Cladism is actually applied conceptual confusion. Let it play in its own sandbox. Its inherent inconsistency means that it will split into thousands of pieces as time passes. It is the donkey's chase for the carrot in front of his eyes and thus, incidently, also golden pants in science. Does anyone see the problem? Consist, presently at 83.254.20.59 (talk) 00:15, 7 November 2008 (UTC)

I apologise. I misunderstood what you were arguing (originally). I understand now and very much agree that there is a common confusion, even among those doing phylogenetics. And, yes, that is why I wrote "very nearly synonymous". I didn't know how much the reader would understand the concepts of holo-, para-, and mono-phyletic. This comes up very often when I TA a class for students learning MrBayes. As we are always looking for the "optimal" tree, the students constantly think of clades. We really should switch to using mono- and para-phyletic when ever someone tries to use "clade". Note that you don't need to be an administrator of Wikipedia to help re-write this article and present it more as it would appear in the field (but, of course, always remembering that a layperson might be reading it). Thanks for taking the time to explain. I suppose I should have taken more time to read your original post. --Thorwald (talk) 01:36, 7 November 2008 (UTC)

Finally reaching common ground. However, when you wrote that "We really should switch to using mono- and para-phyletic when ever someone tries to use "clade", I suppose you mean holo- and paraphyletic groups. My original reason for pursuing this battle against cladism is that it unlegitimately "denies" reconstruction of phylogenetic units "from the inside and out", that is, in terms of less inclusive units forming more inclusive units (for example populations forming species), although it has developed into an existential matter, that is, a matter about facts. I have gradually reached a deeper understanding of the problem and have thereby understood that it is actually very simple, although very difficult to understand.

The simple explanation is on an existential level that "pattern isn't process", and on a conceptual level that "we conceptualize reality in terms of opposites, and white can't be black".

The complicated explanation is that we may comprehend the problem only as a conceptual problem, like cladists do, and claim that there are two opposite possibilities to discuss reality, both of which are just as consistent given their premises. However, the same "opposite" also exists as a reality (i.e., a fact) in the form of process and pattern, thus suggesting that both of the opposite possibilities to discuss reality is correct at the same time, although they can't be. This is an inconsistency in the concept "correct" between its implications on reality and on conceptualization that we cannot possibly accept, since "correct" has to unify reality and conceptualization. The synthesis of these two meanings of "correct" is accomplished by Aristotle's conceptualization, that is, organizing concepts into genera (genos), specifics (eide) and specific differences (diaphora), that is, differences in similarities. This conceptualization paved the way for science, and is presently attacked by cladism.

The fundamental difference between science and cladism is that science is objective and cladism subjective. Science is ambiguous concerning categorization of reality by the simple fact that categorization is ambuguous per definition, and cladism is ambiguous by the fact that it is personal (and thus different between us) Cladism can, however, attract the narrow-minded, like nazism did, and thereby create big problems for science, as well as for humanity. As I see it, there is no room for respect towards cladists, since they do not show any respect towards non-cladists per definition, since cladism is a belief. Non-cladists simply have to continue explaining that cladism is inconsistent (that is, self-contradictory) and empirically erroneous till they have pushed cladists inside a cladistic fence. Non-cladists have to understand that cladists will never abandon their denial of science, since it, for them, would mean denying cladism. (Anyway, thanks Thorwald). Consist, presently at 83.254.20.59 (talk) 22:49, 7 November 2008 (UTC)

I can also inform Thorwald that I'm not allowed to make any changes in any article about either cladism or phylogenetics. Instead, I'm constantly blocked by a user named Sjö (appearantly a cladist) and a user named C.Fred (probably not a cladist), although I was passed by a user named Ed.Johnston (appearantly not a cladist). Ed does thus appear to have been transferred from (or voluntarily left)these matters (or this matter). I thus can't change anything in the article. I actually will probably be blocked from this discussion page soon by Sjö. That's how cladists act. Consist, presently at 83.254.20.59 (talk) 23:09, 7 November 2008 (UTC)

Can cladists ever make phylogenetics synonymous to cladistics?

In the beginning of this article about phylogenetics, cladists have sneaked in a sentence synonymizing phylogentics with cladism, which opens for a continuous confusion of these concepts. As explained above, this insneaked synonymonity is just "very nearly". It is just as "very nearly" as apples are "very nearly" synonymous to fruits. This closeness is, indeed, very close. Apples are indeed fruits, but..., are they synonymous to fruits? If they are, what about pears? Aren't they fruits? Cladists "solve" this conceptual problem by "denying" pears. What does this mean? Does it mean that pears aren't fruits, or that they aren't acceptable fruits? Whatever it means, they claim that "evolutionary biologists use the methods and the tools that are useful to laying the evolutionary puzzle, and that in this category [?] does cladism fit" (see Thomas e on the Swedish page on phylogenetics). What category? The evolutionary puzzle is layed by many persons, some of them cladists and some of them non-cladists. How does Thomas e (and the rest of the cladists) mean that non-cladists should react to Thomas e's (and the rest of the cladists') "denial" of us? Shall we just accept it or "deny" cladists? The answer is that facts deny cladism. Cladism is actually an insensible simplification just like nazism or any other -ism is. We don't have to "acknowledge" or "deny" any of them (just as we don't have to choose side in Bush's battle against terrorism), but can instead demonstrate that cladism is inconsistent (thus self-contradictory), and empirically wrong. We don't have to answer their questions, because they simply are insensible. We can continue explaining that their approach is an -ism, that is, one of all possible subjective approaches to reality. We can continue explaining that science differs from all these approaches by being objective. We can admit that objectivity does not allow a single, true classification of reality, but at the same time emphasize the fact that only it agrees with facts. Utopia isn't possible, but science is at least correct. It means that cladists can make phylogentics synonymous to cladistics to the extent that they can make pattern synonymous to process, that is, not. Consist, presently at 83.254.20.59 (talk) 00:20, 8 November 2008 (UTC)

Wikipedia:Articles for deletion/Genetic equidistance

Expert opinions on the notability of this topic would be appreciated. Tim Vickers (talk) 16:58, 15 February 2009 (UTC)

How many nucleotides?

In the section "Taxon sampling and phylogenetic signal" there's a number given as "~16,00". Is this a typo, and what would be the sensible number? Expert needed, please! --Stfg (talk) 21:31, 2 June 2010 (UTC)

That should be around ~16,000 nucleotides. I've fixed it, and added a reference-- Simon (talk) 00:57, 4 June 2010 (UTC)

proposed addition

I would like to propose the following addition:

Phylogeny in Psychoanalysis

Phylogeny in psychoanalysis is the study of the whole family or species of an organism in order to better understand the pre-history of it, because it might have an unconscious influence on a patient,according to Sigmund Freud. After the possibilities of ontogeny, the development of the whole organism viewed from the light of occurrences during the life, have been exhausted phylogeny might shed more light on the pre-history of an organism.

However, it would also require a minor edit of the general introduction; into this:

General Introduction

The term phylogenetics derives from the Greek terms phyle (φυλή) and phylon (φῦλον), denoting “tribe” and “race”; and the term genetikos (γενετικός), denoting “relative to birth”, from genesis (γένεσις) “origin” and “birth”. Phylogenetics /faɪloʊdʒɪˈnɛtɪks/ is the study of evolutionary relatedness among groups of organisms (e.g. species, populations), In biology this is discovered through molecular sequencing data and morphological data matrices, while in Psychoanalysis this is discovered by analysis of the memories of a patient and the relatives.

References

I will leave this proposal here for a little while. If I will see no comments, I will follow through on it. If I do, I will gladly discuss any changes.

--Fan Singh Long (talk) 20:30, 19 February 2012 (UTC)

That looks fine. I would just go ahead and add it; we generally encourage people to make bold improvements to pages. ItsZippy ^{(talk • contributions)} 20:40, 19 February 2012 (UTC)

Willdo!

--Fan Singh Long (talk) 06:01, 20 February 2012 (UTC)

Phylogenetics/Phylogeny

Are phylogenetics and phylogeny synonymous terms? I have entered the term phylogeny, and have been redirected to phylogenetics, but in the article there is no reference to phylogeny. It all came as I was reading this page http://www.mobot.org/mobot/research/apweb/welcome.html, that uses the term Phylogeny.

Comparison with other Wikipedias:

Catalan W. distinguishes the terms "filogènesi" that is a process, and "filogènia", that is a study or science.

Spanish W. uses the term "filogenia".

French W. uses the term "phylogènie".

Italian W. states that "filogenesi", "filogenetica", "filogenia" are equivalent terms.

I tend to think that "phylogenetics" and "phylogeny" are synonymous, if it is so, it would be useful to include this in the article.--Auró (talk) 19:04, 5 August 2012 (UTC)

"Biology online" is clear. Phylogenetics is a science, and phylogeny is the result of this science.--Auró (talk) 20:58, 20 August 2012 (UTC)

Edit 23 September 2012

This article overlapped a lot with Cladistics and Clade, and it still overlaps with Cladogram and probably several others. Having edited Clade and Cladogram, I've tried to make this article more independent of them and more focused on its own topic.

• Phylogenetic systematics (which redirects to cladistics) isn't a science, it's the application of the science of phylogenetics to systematics by means of the principle that only clades should be named.
• "Cladism" is pejorative. Bizarrely, it redirected to Phylogenetic nomenclature; this is wrong several times over, so I've changed that redirect to Cladistics.
• I've replaced the entire sentence that contains the above two points, and which was grammatically a mess, with a sentence that fits better with the preceding one: "The degree to which taxonomy depends on phylogenies differs between schools of taxonomy: numerical taxonomy ignored phylogeny altogether, trying to represent the similarity between organisms instead; phylogenetic systematics tries to reproduce phylogeny in its classification without loss of information; evolutionary taxonomy tries to find a compromise between them in order to represent stages of evolution."
• I've put "main article: Computational phylogenetics", "main article: Cladogram" and "see also: Molecular phylogenetics" under the headline "Construction of a phylogenetic tree". It's ridiculous, but the cladogram article contains a much more detailed explanation of phylogenetics than the phylogenetics article! I don't have time to move all that stuff now, though. – I seriously wonder whether there should even be a separate article for "cladogram". Doesn't "dendrogram that is the outcome of a phylogenetic analysis" say everything?
• Do not equate cladogenesis with speciation. They are usually not the same, except under one or two species concepts that (almost?) nobody uses. I have replaced "speciate" by "split".
• "The problem posed by phylogenetics"... and then a quote about alleged problems with fossils in phylogenetics, from 1967, by two molecular biologists who had almost certainly never tried to do scientific phylogenetics with fossils – AFAIK, nobody did that before the mid-1980s. It was just ridiculous to keep that quote in. There's been a lot of research on that topic in the last 45 years. I've deleted that sentence, which was completely out of context there anyway.
• Cladistics isn't one method – unless you restrict it to maximum parsimony, which you shouldn't.
• I've rewritten that paragraph.
• Phenetics now has its own paragraph. It is, after all, not phylogenetics; it shouldn't be in the middle of a paragraph about methods of phylogenetics!
• The "Grouping of organisms" section was off topic, and now better explained in the Cladistics article (where it fits just a little better), so I've deleted it.
• The first paragraph "molecular phylogenetics" section was entirely redundant, so I've deleted it. The second is now in the middle of the introduction, though it should be rewritten for style a bit.
• Haeckel was completely out of place. I've moved him to the bottom of the article into a new "history of phylogenetics" section and rewritten accordingly.
• Williamson was completely out of place even within the Haeckel paragraph! Give me a reason to put him back in, and I'll do that...
• The new "Limitations and workarounds" section contains "homoplasy" (formerly "homoplasy weighting"), "horizontal gene transfer", "taxon sampling", "phylogenetic signal" and "missing data" as subsections.
• The paragraph about Woese was wrong – rRNA is as prone to long-branch attraction as anything else, and is no longer relied upon to the extent that it once was, so I've deleted the paragraph. Besides, the three domains weren't a theory, but a classification! Woese just elevated the subkingdoms Archaebacteria and Eubacteria to domain status, changing their names to Archaea and Bacteria, because he found them to be so distinct from each other. And a molecular clock is something for divergence dating, not for phylogenetics.
• "microorganisms, to which the species concept does not apply" – there isn't one species concept, there are 147 (as of February 2008), some of them do apply, and this is irrelevant to phylogenetics anyway! The lack of morphological data that could be used for phylogenetics is real; but because this article already takes molecular data for granted, there's probably no point in stating this. I've deleted the paragraph.
• Taxon sampling: Wiens (2006) isn't a proposal, it's a demonstration of a fact, using simulations. I've rewritten the sentence; it now cites Zwickl & Hillis (2002) and Wiens (2006) in the same place.
• The explanation of phylogenetic signal was wrong. I've fixed it. I've also stated explicitly that tests for phylogenetic signal exist – as the reference says.
• The next sentence, while true, was out of context. I've made the introduction of the limitations section out of it.
• The first paragraph of the section on the role of fossils is fine, it just needed a bit of modification. The second (which looked very confused to me) was about estimations of diversity rates – that's not phylogenetics, it's an application of phylogenetic trees. If you want to resurrect this, do so in the article about phylogenetic trees.
• I've mentioned stratocladistics in the last sentence of the section about the role of fossils.

Most sorely missing are more history – I need to track down the reference (a 1998 book by Pascal Tassy) to "phylopessimism", the last stage before phylogenetics became a science – and more references. I can supply all that, but not soon.

There is still too much overlap with several other articles.

David Marjanović (talk) 22:02, 23 September 2012 (UTC)

Taxonomy logically and necessarily includes phylogenetics

Taxonomy is classification and phylogenetics is phylogenetic classification, so phylogenetics is logically and necessarily a subset of taxonomy. The introduction says otherwise and the quote used doesn't even back it up--it says something else nonsensical. Where in the biological literature does it ever say phylogenetics is distinct from taxonomy?

Whether we take the position that taxonoomy is a subset of systematics or vice-versa, phylogenetics would not be distinct from either. Some even equate phylogenetics with systematics, which would mean phylogenetics is a subset of taxonomy or includes it. No matter how you look at it phylogenetics is certainly not distinct from taxonomy.

I have made the correction twice but it was reverted each time.--Trouveur de faits (talk) 15:28, 4 July 2013 (UTC)

Your statement that "phylogenetics is phylogenetic classification" appears to me to be the heart of this problem. One can derive a phylogeny without creating a classification from it, in fact this is a common approach because (1) a phylogeny is likely to come out differently with the next analysis that is based on different or greater amounts of data and (2) conflicting phylogenies are often produced for the same group of organisms if different loci are used or if organelle DNA is compared with nuclear DNA. Some cladistic practitioners are fond of stating that a phylogeny is a hypothesis, it is always challenged by the next phylogenetic analysis of the same organisms. Classification is a later step, a step that takes into account how the classification is to be used, and makes decisions that compensate for the lack of absolutely complete data (because data are never absolutely complete). Sminthopsis84 (talk) 18:26, 4 July 2013 (UTC)

Precisely my view. However, sources express different opinions as to the meaning and relationship of these topics (phylogenetics, taxonomy, classification, systematics). Our task is to fairly represent all of these opinions where they are sufficiently represented in reliable sources, regardless of whether we think they are right or wrong. It's difficult to do, and tends to produce confusing text unless carefully written, but we cannot simplify or impose our views.

I do agree that the Edwards & Cavalli-Sforza quote doesn't support the sentence in the lead. I don't have access to the source so can't tell if it's just the quote that is poor or the source as a whole. But the sentence "Taxonomy, the classification, identification, and naming of organisms, is usually richly informed by phylogenetics, but remains methodologically and logically distinct" can, I think, be sourced from the literature. I'll see if I can find a better ref. Peter coxhead (talk) 10:21, 5 July 2013 (UTC)

I'd like to comment further on Trouveur de faits's statement above.

• Taxonomy is classification. See Taxonomy (biology)#Definition for sourced alternative definitions. Some support this statement, some do not. In particular, for those who define taxonomy as including description, identification and nomenclature it's clearly not the same as classification. Alpha taxonomy is largely independent of classification.
• phylogenetics is phylogenetic classification. Says who? Many different classifications can be derived from the same phylogenetic tree. They can be based on the traditional rank-based codes, nowadays generally using strictly monophyletic taxa as in the APG systems, but some also using paraphyletic taxa as in Stace's system for the British flora. They can alternatively be based on the Phylocode. So how can phylogenetics and phylogenetic classification be the same thing? Maybe some sources say they are, but others clearly describe a two-step process: first obtain phylogenetic hypotheses (e.g. trees) and then decide on a classification.

Peter coxhead (talk) 10:58, 5 July 2013 (UTC)

You're making artificial and gratuitous distinctions. A phylogeny is a classification, whether or not it is contradicted by another analysis. The 2-step process you describe is the process of phylogenetic classification. You could nitpick and say there's the phylogeny and there's the classification, but if you do, phylogenetics still necessarily includes both.

" 'Phylogenetics is phylogenetic classification' Says who?" Professional taxonomists, that's who. I quote from Cladistics, 1st ed., p. 3:

"In biology, cladistics is a method of systematics (Patterson, 1980), most coherently formulated by Hennig (1950, 1966), which is used to reconstruct geneologies of organisms and to construct classifications. However, it is also a general approach to classification which can be used for comparative information, having been independently discovered in linguistics..." This clearly says classification is part and parcel of phylogenetics. You'll never find any reference that says the 2 are distinct.--Trouveur de faits (talk) 17:13, 6 July 2013 (UTC)

Please give better hints about citations, to save other editors from pointless trips to the bookshelf to check this book Kitching, I.J. (1998). Cladistics: The Theory and Practice of Parsimony Analysis. Oxford University Press. ISBN 9780198501381. {{cite book}}: Cite has empty unknown parameter: |1= (help), and possibly others with the same first word in the title.

Now to your point: "method A is used to make classifications" does not mean that method A is itself classification. Your interpretation of the words is incorrect. Counting the number of hairs on the backs of flies is a method that could be used to make classifications, but it is not itself classification in any meaningful sense. Classifying flies only according to the number of hairs on their backs would be neither generally useful to those who want to distinguish different fly species nor a biologically realistic classification. Similarly, constructing a phylogeny from the nuclear gene pCOSAt103 may not give a useful representation of the evolutionary history of the taxa concerned, nor is it likely to indicate where the boundaries should be drawn between the taxa. Drawing the boundaries between taxa is part of classification, but phylogenetic taxonomists either take that as already provided by previous generations of scientists, or impose the boundaries after they have seen the phylogeny. Classification is an aim for which phylogenies are one tool that is used. To use your idiomatic phrase, phylogenetics is part and parcel of classification, not the other way around. Sminthopsis84 (talk) 22:39, 7 July 2013 (UTC)

"phylogenetics is part and parcel of classification," also proves my point that phylogenetics and taxonomy are not distinct. We don't say that oranges are distinct from fruits nor vice versa. Method A is a necessary part of the classification. You can't have a phylogenetic taxonomy without a phylogeny, nor can you have a phylogeny without a phylogenetic taxonomy. Like I say, you are nitpicking and making arbitrary, artificial, and gratuitous distinctions, and disagreeing with professional taxonomists.--Trouveur de faits (talk) 14:36, 8 July 2013 (UTC)

Of course "oranges are distinct from fruits". Oranges are a subset of fruits (using the normal English sense of the word "fruit"). A subset is, by definition, not the same as (i.e. is distinct from) the set of which it is a member.

No-one says that phylogenetics, classification and taxonomy are unrelated, but this doesn't mean that they are the same thing. Classification and taxonomy existed before (formal) phylogenetics; if nothing else the "history of biological classification" and the "history of taxonomy" are not the same as the "history of phylogenetics". You clearly "can't have a phylogenetic taxonomy without a phylogeny", as you say, but you can have a "bare" phylogeny, e.g. a cladogram showing the relationship between species in which none of the other nodes are named and which is not used to inform classification. These are necessary distinctions between three topics which are (today) closely related but which are not identical. Peter coxhead (talk) 19:12, 8 July 2013 (UTC)

To say a phylogeny is not a classification is irrational and you'll have to provide a reference which reflects that view and that has some kind of currency instead of just a small minority view.--Trouveur de faits (talk) 15:24, 15 July 2013 (UTC)

Well, consider this quotation from Mishler (2009), Taxon 58: 61–67: "The major outcome of the evolutionary process is the production of an ever-branching phylogenetic tree of life ... most systematists now feel that the general biological classification system should be used to reflect this tree of life." The classification should reflect the phylogenetic tree of life, but it's not the same thing.

Botanists (biologists generally) have never been very interested in talking about theory (unlike, say, physicists), so you often have to infer meaning from usage. Consider Manning, John C.; Forest, Félix; Devey, Dion S.; Fay, Michael F.; Goldblatt, Peter (2009). "A molecular phylogeny and a revised classification of Ornithogaloideae (Hyacinthaceae) based on an analysis of four plastid DNA regions". Taxon. 58 (1): 77–107. Note that the very title implies that "a molecular phylogeny" isn't a "classification". If you look at p. 82, the phylogeny is the tree on the left; the classification is the set of labels on the right.

I couldn't find anyone who says without qualification that a phylogeny is a classification – do you have a source for this? Peter coxhead (talk) 15:40, 15 July 2013 (UTC)

"1st evolutionary tree", Ernst Haeckel (1866)

I understand that Haeckel's tree is likely the first, out side of Darwin's notebook, meant to imply continuity in the lineage of life but I feel that it is somewhat dishonest to label it the "1st" evolutionary tree. This is primarily because it doesn't include any paleontological data and is not the first to show continuous branching. As outlined [on this page], Haeckel's diagram is preceded by both that of Lamarck, Hitchcock, and Bronn, (of which the latter two paired their trees to paleontological scales). Additional information about each can be found in this essay1, by JD Archibald. I would contend that as both Darwin and Haeckel failed to provide a mechanism by which heredity functioned, we should consider one of the these earlier "trees" as being "the first". Seeing as Hitchcock was vehemently anti-evolution and Bronn explicitly excluded a mechanism for the succession of forms that he documented, I recommend that Bronn replace Haeckel in this sense. In addition, Bronn was correspondent with Darwin and the translator of OOSMNSPFRSL into German 2. Any thoughts or objections to my proposed change? StereoTypo (talk) 04:07, 7 April 2014 (UTC)

Earth and life

Domain of crocodile 216.247.81.103 (talk) 22:55, 23 January 2023 (UTC)

Basic grammar

What's with specie's? It should be species' for both singular and plural possessives, as species is both the singular and the plural. Aboctok (talk) 03:38, 25 April 2023 (UTC)

@Aboctok: has been fixed. Peter coxhead (talk) 09:45, 27 April 2023 (UTC)

Plagiarism Issue

Certain sections of the page, particularly "Phylogenetic screens" and "Phylogenetic tree shapes", seem to have been copied from this paper. I wasn't sure if reporting that section would affect the entire article so I wanted to raise that concern here. — Preceding unsigned comment added by Reputationbiohazard (talk • contribs) 15:25, 15 February 2024 (UTC)