Talk:Phylogenetics

message: 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)
replies: text: 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)
thread_title:  Phenetics and cladistics as methods 

message: would sympathtic editors consider a positive vote here? Slrubenstein   |  Talk 15:18, 23 August 2006 (UTC)
thread_title:  embryology 

message: (Moved to talk:clade). Richard001 06:58, 4 November 2007 (UTC)
replies: text: See the explanation of the concepts in Envallhttp://www3.interscience.wiley.com/journal/119394227/abstract Envall, M. 2008. On  the difference between mono-, holo- and paraphyletic groups - a consistent distinction of process and pattern. Biol. J. Linn. Soc. 94:217-220.]  —Preceding unsigned comment added by 83.254.20.53 (talk) 23:23, 21 September 2008 (UTC)
thread_title: [[Monophyly]], [[paraphyly]] and [[polyphyly]] merge

message: 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)
replies: text: 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)
thread_title:  Cladistics a synonym for phylogenetics? 

message: 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)
thread_title:  Who is this Williamson? 

message: 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)
thread_title: Obsolete sentence

message: 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)
thread_title:  Is this article about phylogenetics or cladistics? 

message: 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)
replies: text: 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)
replies: text: No, not in this case since user:Consist is permanently blocked for pushing his own research.Sjö (talk) 15:10, 23 September 2008 (UTC)
thread_title:  Am I allowed to change this article 

message: 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)
thread_title:  Can cladists ever make phylogenetics synonymous to cladistics? 

message: Expert opinions on the notability of this topic would be appreciated. Tim Vickers (talk) 16:58, 15 February 2009 (UTC)
thread_title: [[Wikipedia:Articles for deletion/Genetic equidistance]]

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

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

message: 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)
thread_title:  Edit 23 September 2012 

message: 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)
thread_title:   "1st evolutionary tree", Ernst Haeckel (1866) 

message: Domain of crocodile 216.247.81.103 (talk) 22:55, 23 January 2023 (UTC)
thread_title:  Earth and life 

message: 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)
replies: text: has been fixed. Peter coxhead (talk) 09:45, 27 April 2023 (UTC)
thread_title:  Basic grammar 

message: 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)
thread_title:  Plagiarism Issue