Talk:PhyloCode

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In actual practice, this has been modified to reflect some phylogenetic concerns, like this (note the addition of domain, subkingdom...

  • "Some" phylogenetic concerns? what phylogenetic concerns?
  • I can't "note the addition of ... subkingdom", because there isn't one. Can someone who knows please add it or remove the reference to it?

-- Mpt 12:55, 6 Aug 2004 (UTC)

Contents

[edit] PhyloCode and nomenclatural chaos

"Filum ariadneum Botanices est Systema, sine quo Chaos es Res herbaria" Carl von Linnaeus. (The Ariadne's thread of Botany is systematics, without which Chaos is a botanical phenomenon).

When innumerable species face a growing risk of extinction in nature, egocentric people meet to create an alternative nomenclatural code!

The PhyloCode will never substitute the Linnaean Taxonomy and ICBN.

Why? Because these (Linnaean Taxonomy and ICBN) are established in all herbaria from worldwide with all the nomenclatural types of all species. Because scientific works, Manuals and Floras and very important identification keys from worldwide, besides works of general reference like this Wikipedia refer to the taxa and not clades.

Clades do not exist in Nature! They are based on erroneous phylogenetic concept: monophyly (see talk:Cladistics#Cladistics as method not compatible with Linnaean Taxonomy); they must not be named, it is preferable to use numbers to not to augment the confusion, that already is great).

Unfortunately, institutions like APG, help to sowing and propagating the Chaos, making drastic and radical changes in taxa (based on analysis of allogenome; that is prokaryote DNA and not plant DNA). Example: Malvales (with apparently simple change moving Sterculiaceae, Tiliaceae and Bombacaceae as subfamilies to family Malvaceae, but they are about 138 genera and about 2500 species, several with economic importance!)

Identification keys are a powerful tools to identify genera and species worldwide, they are utilized for most people, it doesn't matter if they are artificial or natural.

See these comments in Williams, D. M. et al. (2005):Letter to the editor.150 reasons for paraphyly: a response. Taxon 54(4):858.:"The signatories refer to E. O. Wilson’s contribution to the recent symposium on “Linnaean Taxonomy in the 21st Century” held in 2001. The report documenting Wilson’s contribution makes no comment on paraphyly, its preservation or necessity for Linnaean taxonomy. The report does mention that “Wilson recommended that systematists should focus their efforts on discovering life and understanding phylogenetic relationships. He stressed that for taxonomists to be considering a radical makeover of our method of classification at this time would be like ‘rewriting the operating manual for the Titanic’.” (DeFilipps, 2001). Wilson’s words are directed at the PhyloCode—not cladistics, as are also Wheeler’s (2004: 359), whose commentary is also helpful."

See also this very important initiative, like a manifest against PhyloCode and excesses of Cladistics: "Taxon 54(1)(2005): 5-8 LETTERS TO THE EDITOR (Coordinated by: Nordal, I. & Stedje, B.): Paraphyletic taxa should be accepted. available online here (pdf file; page 18), including proposal, but without the 150 signatories, several notable botanists from world-wide, among them: Brumitt, R. K. (from Kew) and Sosef, Mark.

Thus PhyloCode tends to be forgotten.

Berton 14:03, 7 January 2006 (UTC)

[edit] Comments by David Marjanović

"Filum ariadneum Botanicæ est Systema, sine quo Chaos est Res herbaria" (The Ariadne's thread of botany is the system/classification, without which botany (literally: herbal affair[s]) is a chaos). The word order is just for emphasis; Latin word order is extremely flexible.
David Marjanović | david.marjanovic_at_gmx.at | 00:13 CEST | 2006/7/18
I don't want an identification key. I am interested in phylogeny; I actually want to talk about it. I want to talk about clades. That is a lot easier, I'm sure you agree, if they have names.
You and Phylocode followers are interested only in phylogeny. I am interested in life.Berton 15:23, 28 September 2006 (UTC)
"Phylogeny is of only secondary interest to most people including most kinds of biologists. Who needs a crocodile-bird clade when we already have a bird taxon and a crocodile taxon?" from Grant, Verne:INCONGRUENCE BETWEEN CLADISTIC AND TAXONOMIC SYSTEMS. American Journal of Botany 90(9): 1268. 2003. Berton 12:55, 4 October 2006 (UTC)
All clades are taxa. Many taxa are clades.
Taxa prescind entirely of clades. The contrary is not true. Berton 15:33, 28 September 2006 (UTC)
Besides, have you seen the herbarium of the Peabody Museum of Natural History at Yale? It uses phylogenetic nomenclature, and that works quite fine, thank you very much. It simply splits the paraphyletic taxa into clades and doesn't use ranks.
David Marjanović | david.marjanovic_at_gmx.at | 00:19 CEST | 2006/7/18
Bla, bla, bla. Calm down. What's wrong with "an ancestor and all its descendants"?
David Marjanović | david.marjanovic_at_gmx.at | 00:15 CEST | 2006/7/18
All is wrong, cladists (Hennig ahead) and Darwin sow the stupid error of saying that everything should have one common ancestor, if even we have father and mother, like individuals, what saying then of divergent lineages??? Berton 15:30, 28 September 2006 (UTC)
See Mayr, E. & Bock, W. J. 2002. Classifications and other ordering systems. J. Zool. Syst. Evol. Research 40: 169–194. for more details PDF file available here.Berton 13:22, 4 October 2006 (UTC)
Example:"If all the species of a tentatively delimited taxon are the descendants of the nearest common ancestor, the taxon following Haeckel (1866) is called monophyletic (Mayr 1969, Mayr and Ashlock, 1991 pp. 253–255). Hennig (1950) introduced an entirely different concept. The study of phylogeny was for him a forward (to the future) looking process; its starting point was a stem (mother) species. The Hennigian distinguishes a phyletic branch containing the stem species and all its descendants as a taxonomic unit, as a clade, no matter how different the beginning and the ending of a clade may be. Hennig transferred the traditional term monophyly to his new concept of phylogeny, causing great confusion. To terminate it, Ashlock (1971) introduced the term holophyly for Hennig’s new concept. The traditional monophyly concept and the Hennigian holophyly concept have drastically different consequences in taxonomy. A holophyletic clade encompasses a stem species and all of its descendants. A monophyletic taxon consists only of the descendants of the nearest ancestral taxon." from Mayr & Bock 2002 (loc. cit.).Berton 14:55, 4 October 2006 (UTC)
Takhtajan also draws the attention to the difference of the Hennig's concept of monophyly and the one of Haeckel. Takhtajan, A.:Diversity and classification of flowering plants, pp. 2-3, 1997 Berton 15:08, 4 October 2006 (UTC) Example: "The Hennigian concept of monophyly and paraphyly is misleading and, as Cronquist (1988:40) pointed out, 'is destructive to the taxonomic system'. The acceptance of this Hennigian concept would mean the destruction of many of the best-known taxa. It is quite clear that the traditional evolutionary concept of monophyly [in the Haeckelian sense] is entirely unambiguous and creates no difficulties in its application to taxa..." Berton 16:18, 4 October 2006 (UTC)
The APG has nothing whatsoever to do with phylogenetic nomenclature.
Likewise, the question whether chloroplast DNA contains a phylogenetic signal (…erm… of course it does!!!) has nothing whatsoever to do with phylogenetic nomenclature.
David Marjanović | david.marjanovic_at_gmx.at | 00:17 CEST | 2006/7/18
APG has its blame parcel in destroying the stability of Taxonomy and it makes it in the worst way: through molecular research in organelles that are endosymbionts.Berton 15:47, 28 September 2006 (UTC)
"Chloroplast genes have been used extensively in plant cladistic studies. Chloroplasts are semi-independent organelles that can become disassociated from their normal nuclear genome (Rieseberg and Soltis, 1991). Consequently, a particular chloroplast gene may or may not be a reliable indicator of the overall genome of the species in which it is found, depending on its history.
Cronn et al. (2002) analyzed molecular characters in diploid species of Gossypium belonging to the various chromosomal genome groups (A, B, D, etc.). They used three types of DNA and one or more genes in each type: ribosomal DNA (one gene), other chromosome segments (11 loci), and cpDNA (four genes). The cladograms for the 12 loci in the two types of nuclear DNA are in agreement with the other evidence concerning phylogeny of Gossypium. But the cladograms for the four chloroplast genes are incongruent with this evidence and give incorrect phylogenetic indications." from Grant, Verne:INCONGRUENCE BETWEEN CLADISTIC AND TAXONOMIC SYSTEMS. American Journal of Botany 90(9): 1266. 2003. Berton 13:09, 4 October 2006 (UTC)

<copyrighted material from Taxon deleted - MPF>

Is this copy-and-paste from Taxon violating copyright? MrDarwin 16:34, 18 March 2006 (UTC)
No, because this is not an article, but letter. Berton 17:18, 18 March 2006 (UTC)
It looks to me that everything in Taxon is copyrighted, and will need a release. Why not make a link? Brya 21:35, 18 March 2006 (UTC)
Brya, nor everything in Taxon is copyrighted, there is a lot of thing available free at the site IngentaConnect.com Berton 22:28, 18 March 2006 (UTC)
First, a letter to the editor can be protected by copyright as much as an article. Second, "free" is not the same as "not protected by copyright". (In fact many botanical articles are now available on the web, but are still copyrighted.) Third, I am unable to read anything in this issue of Taxon online without a subscription, so I'm wondering whether this is indeed "free". I suspect that Taxon's copyright covers everything published in its pages, but do not have any issues of Taxon in front of me so I can't check; that will have to wait until I'm at work on Monday. MrDarwin 23:00, 18 March 2006 (UTC)
MrDarwin, I am not strictly violating anything, because this is a talk page! Berton 23:15, 18 March 2006 (UTC)
Berton, I agree that the Phylocode will never catch on, at least not as an official system. I think as far as the Phylocode is going to go is as an unofficial system of rankless names for clades that are used in parallel with the Linnaean taxonomic system (and let's not forget that Linnaeus got much of his system wrong!). In fact we are already seeing this happen, simply because Linnaean classification and the nomenclatural systems established by the botanical and zoological codes are so useful. It's like the use of common names and botanical names for plants: both systems are useful, and the establishment of the binomial nomenclatural system was not the deathknell for common or vernacular names. On the other hand, cladistic methodology is definitely going to shake up classification, and that's a good thing. Looking at heterogeneous, poorly defined and unnatural families like the traditional "Scrophulariaceae", I simply find it impossible to defend many of the classifications of the 19th and early 20th centuries, which often stressed a small number of characters to define groups, at the expense of evolutionary relationships. In my own area of specialization I have found a combination of molecular and morphological characters to define groupings that make excellent sense, even though they were overlooked by previous researchers on the same group, who often stressed a very small number of characters and often lumped things together into unnatural groups based on plesiomorphic characters. (Interestingly enough, some of the same groupings were recognized by the splitters of the 19th century, who tended to take a much narrower view of genera in particular.) MrDarwin 15:25, 12 January 2006 (UTC)
MrDarwin, classifications are merely suggestions. When you divide Scrophulariaceae (sensu lato) in Calceolariaceae and in other families, you are suggesting that this would be the best taxonomic grouping, however, this (the grouping) it is a mere convention, that is, doesn't exist in Nature. All the classifications have value, at least, historical (they had certain influence in their time), it is so with Linnaeus system. It is not why a classification is of the century XIX or XX that it should not be accepted, this is not the correct criterion of evaluation. There are always the classifications lumper and the splitter, which often stressed the small or large number of characters to it defines groups, however these characters had great phylogenetic connotation (a priori) and therefore they were used to delimit the groups. Taxonomic type classifications have an advantage on Cladistic classifications, they don't necessarily need to reconstitute the phylogeny strictly, because taxa expresses divergence degrees around a central element that defines them (as nomenclatural types) and not phylogenetic levels, like clades, that has necessarily to mirror in totum the evolution (and that is the "Holy Grail" of Biology, always searched but never reached, finally, an utopia!). Berton 17:49, 12 January 2006 (UTC)
I agree with many, perhaps even most, of the sentiments voiced above. Cladistics is a method of analysis, and has its strong points and weak points. Molecular data, analysed by cladistic methods, has proved very useful, especially the information from chloroplast DNA: the very fact that this is prokaryote DNA, not subject to evolutionary pressure, makes it very useful to shed light on higher order relationships. There is a huge field out there, of nuclear DNA sequences, and it as yet unclear how informative this will prove.
Classifications are something else than cladistic analyses.
Nomenclature is not the same as classification.
Linnaeus's main work on plants gives no real taxonomy at any rank higher than genus.
There are interconnections between all of the above, but great care should be taken when talking about these interconnections.
Brya 12:58, 23 January 2006 (UTC)
Brya, if you think that chloroplast DNA is "not subject to evolutionary pressure" (or that being prokaryotic DNA makes it so), then I think you don't correctly understand why it is useful in reconstructing phylogenies. MrDarwin 15:27, 23 January 2006 (UTC)
Those are a lot of statements close together. Let's start with "chloroplast DNA is "not subject to evolutionary pressure"". In what sense do you disagree with this? Brya 19:39, 23 January 2006 (UTC)
I mean it in the sense that you either said something that is wrong, or worded it in such a way as to be subject to misinterpretation. Of course I might be grossly misinterpreting what you mean by "evolutionary pressure" and if so I'm sure you'll tell me: I'm interpreting it to mean "selective pressure that can result in evolutionary change". The chloroplast does not have a genome of junk DNA. cpDNA is in generally highly conserved but different mutations of different chloroplast genes will have different effects on the fitness of the organism under different selective pressures, and given certain conditions some mutations will be more likely to be inherited more than others. (One very simple example: chloroplast genes tend to be more constrained in fully autotrophic plants than they are in parasitic ones.) Chloroplast genes do indeed evolve, some more quickly than others precisely because there are different selective pressures on different genes, which is why different genes (or parts of genes) are useful at different levels of phylogeny. And the fact that it is "prokaryotic DNA" is completely irrelevant.
Or did you mean something different by "evolutionary pressure"? MrDarwin 01:19, 24 January 2006 (UTC)
It looks like we don't disagree all that much. I would agree that evolutionary can be described as "selective pressure that can result in evolutionary change". It looks to me that chloroplasts are not subject to such pressure, or to be more accurate they are subject to it that people are subject to atmosperic pressure: it is there it is inescapable, it is the same for all, and of no practical consequence. Good point about heterotrophic plants. I don't really know what happens with cpDNA there but the pressure to conserve it (and keep the genes functioning) dropped away and this should have some effect, but is unlikely to lead to a chloroplast that will photosynthesize more effectively.
It would be hard to explain really accurately what the significance is of the fact that cpDNA is prokaryote DNA but
  1. it is factually so
  2. it is a fact that is widely overlooked
  3. it is not a coincidence that a) chloroplasts are to a high degree independent of the rest of the cell and b) cpDNA is prokaryote DNA
  4. no way you look at it can the fact that of the three genes that the APG system is based on there are no less than two cpDNA genes (prokaryote) while the other is a ribosomal gene (although residing in the nucleus still with a somewhat comparable history) be discounted as accidental. IIRC Mark Chase argued that it was the very reason of the succes of molecular methods in plant systematics (and thus the APG system) over comparable efforts in animal systematics. You will note that the animal people are going for mitochondrial DNA rather than the nuclear DNA. Brya 09:39, 25 January 2006 (UTC)
Depends on what taxonomic level we're working at. Also, mtDNA will sometimes cause problems in analysis due to hybridization events. COI barcoding does definitely not work as announced (the speed of molecular evolution varies in the Amniota alone by an order of magnitude). I added a major part on Rieppel's rather lucid philosophical analysis, expand as needed. Suffice to say that it seems that PhyloCode is dead but not forgotten, or rather: that it is shelved as a taxonomical tool of own standing, but that its points are well taken (Another point: it takes at least 2 known and sufficientyl closely related taxa to make a meaningful clade. Point in case: It is not possible to define Archaeopteryx under PhyloCode, because there is nothing known about its immediate evolutionary relationship. You will find that Archie is rather popular as an outgroup for precisely the same reason). Dysmorodrepanis 18:31, 17 May 2006 (UTC)
Of course it is possible to define Archaeopteryx. You only need to invest some thought about the possible consequences. For example you could use a node-based definition: "the MRCA of the 10 specimens [exhaustive list of museum numbers] and all its descendants". This would, however, risk excluding the next discovery that would look almost the same as the currently known 10 specimens. Or you could use a stem-based definition: "everything closer to the London specimen than (to) Velociraptor, Dromaeosaurus, Microraptor, Troodon, Mei, Jinfengopteryx, Scansoriopteryx, and Rahonavis". This would, however, risk becoming larger than intended (though an emendation of that definition would be simple). Or you could use an apomorphy-based definition: "the first organism that has [all autapomorphies you can find for Archie, or the ones you consider most important…], and all its descendants".
Rieppel's analysis is anything but lucid! I actually wonder if Rieppel has read the whole PhyloCode.
DNA barcoding has nothing whatsoever to do with the PhyloCode. The only thing the two proposals have in common is being new. I happen to dislike DNA barcoding because it requires a phenetic species concept, but I digress.
David Marjanović | david.marjanovic_at_gmx.at | 00:31 CEST (edit 00:44) | 2006/7/18
By introducing phylogenetic definitions the PhyloCode will make splitting & lumping impossible (except for species). In other words, when people agree on the phylogeny, they will have to use the same names for the same clades. Under the current codes you can do as you damn well please, for example by introducing phenetic arguments or "level of evolution" arguments or whatever. In yet other words, the PhyloCode will remove one of the two sources of instability – of chaos – in biological nomenclature.
David Marjanović | david.marjanovic_at_gmx.at | 00:37 CEST | 2006/7/18

[edit] Chaos

The word chaos appears appropriate! Berton, it is messy to break up previous text. It affects readability very badly. Also, it is counter to wikipedia policy. Furthermore, reverting a good faith edit is not a nice thing to do.

Making a text available on a Talk-page is a form of making it available on the web. In this case of copyrighted material (see my Talk page).

Note to MrDarwin: you should be able to access this particular letter (download the pdf-file) from any computer, provided cookie settings etc are in order: access is free of charge. Brya 10:00, 19 March 2006 (UTC)

I have tried several different times to get to this article from my computer, and I cannot. As far as I can get on the Ingenta connect website is to the "Letters to the Editor" section and then it tells me "The full text article is available for purchase" I have been unable to find it at any other website. Nevertheless, I am quite certain that copying the letter here is violating copyright and I will notify an administrator. MrDarwin 13:48, 19 March 2006 (UTC)
I suppose I got confused by the title. The Letter to the editor in 54(4) "150 reasons for paraphyly: a response" is available free. The original "Paraphyletic taxa should be accepted" in Vol 54(1) is not free. Probably sloppy reading on my part. There is a whole series of these things and most are free. Sorry about that. Brya 17:54, 19 March 2006 (UTC)
I agree with MrDarwin - we have no right to post material from Taxon here, so I have removed it. Even if it is published on their website, that does not make it copyright-free, unless they clearly and specifically indicate that copyright is waived. Some of the text is available here (pdf file; page 18), where it is clearly stated "reprinted with permission" - permission that we do not have at the moment. - MPF 14:13, 19 March 2006 (UTC)
Nothing to do Michael, you are far, but the letter and its proposal is there (and I recommend emphatically the reading of this proposal)! I bought this in the mentioned site. And I will ask the editors for expressed permission, if it is the case, because I find this letter of highest importance. Berton 17:06, 19 March 2006 (UTC)
Good idea, it is worth asking the editors for permission to reproduce it (you will need to point out to them that placing it on wikipedia will make it available under GFDL, so it is likely to be copied on from here) - MPF 17:28, 19 March 2006 (UTC)
Thank you for the explanation. Berton 17:35, 19 March 2006 (UTC)
The new material is also copyrighted. Brya 18:57, 19 March 2006 (UTC)

[edit] Important note

Please note that Berton has been editing his comments in this discussion after others have already replied to them, sometimes weeks or months after posting his initial comments. MrDarwin 22:35, 19 March 2006 (UTC)

[edit] Controversies

I removed the explanation of Rieppel 2006 because I found it overly long and impossible to follow. (Also, the example definition is actually impossible under PhyloCode.) That said, I strongly think there should be a "Controversies" section presenting both sides of various issues. Would someone like to do this for Rieppel 2006? (I'd do it if I had the paper handy.) --TMKeesey

[edit] Major edit

Just wanted to mention that the changes made half an hour ago are by me. In the future I'll add more literature and write the article on phylogenetic nomenclature.

David Marjanović | ISPN member (like TMKeesey) | david.marjanovic_at_gmx.at | 00:15 CEST | 2006/7/18

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