Talk:Phylogenetic tree

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You can merge the two files, as long as you include a separate definition inside of it. Phylogenetic trees are stated as relationship hypotheses; evolutionary trees should include time and fossil information. Anonymous, 22:50 18 Jun 2006

Don't we have evidence that the eukariotes are formed by branches merging? What does that do to the neat figure? Drobinsonatlaur 02:31, 8 December 2006 (UTC)

Very stylish. Wetman 10:07, 19 Nov 2003 (UTC)~

but do we have refs?
and not quite accurate, as the evolutionary trees, however based on evidence, are also hypotheses, which will be corrected or confirmed by firther evidence. For example, the very topmost node of fig.1, properly labeled "speculative" is probably wrong, as the fungi+animals form a separate branch from the plants → Fungus .
is it considered acceptable to draw a tree with a three-way split to indicate lack of knowledge? A non-biologist might think it represented something that coud happen.DGG 00:08, 23 September 2006 (UTC)

Some information on how phylogentic trees are computed from genome sequences would be nice. There doesn't seem to be awfully much material on that on the web. 62.227.165.193 20:34, 10 Apr 2004 (UTC)

there is more now, and all the sequences on Entrez, and it should be added. At the least a stub shoud be written so it can be linked to. The page DNA sequencing treats it as a biochemical technique only. What shall we call it, though? (btw, I do not have the knowledge to write the page)DGG 00:08, 23 September 2006 (UTC)

Contents

[edit] Invitation

Work is currently in progress on a page entitled Views of Creationists and mainstream scientists compared. Also currently being worked upon is Wikipedia: NPOV (Comparison of views in science) giving guidelines for this type of page. It is meant to be a set of guidelines for NPOV in this setting. People knowledgable in many areas of science and the philosophy of science are greatly needed here. And all are needed to ensure the guidelines correctly represent NPOV in this setting.  :) Barnaby dawson 22:09, 29 Dec 2004 (UTC)

not just beween creationists and evolutionists, but also different theories of the creationists, The "young earth" people are the ones in the news, but the "old earth" people, who consider supernatural influence only at key points (such as the origin of the phyla) have a much more elaborate arguement. I almost wrote "much more sophisticated."
Has an work been done on this page since 2005?DGG 00:08, 23 September 2006 (UTC)

[edit] Extinct species in trees?!

From the article, "Trees that do not include extinct species must also be interpreted with care." (emphasis mine)

I think this should read "Trees that include extinct species must also be interpreted with care." This is because extinct species may or may not be terminal nodes, the likelihood that they are terminal nodes, however, is very high (see coalescence (genetics)); however, they have often been placed on internal nodes in the past. These are the trees one should be wary of. Anyone differ? - Samsara 15:37, 2 January 2006 (UTC)

Largely semantics but I do not think there is such a thing as an evolutionary tree (entirely possible I could be wrong) as such I feel like searching for an 'evolutionary tree' should return a phylogenetic tree. Ho


[edit] Merge this with Evolutionary tree

As far as I can determine by googling the subject, an "evolutionary tree" is the same as a "phylogenetic tree". Therefore, I suggest that we merge the two pages.

According to this article, "phylogenetic tree" is the more technical term. Therefore, I suggest that we merge the evolutionary tree article into this one (although the reverse is also possible. SpectrumDT 11:33, 9 February 2006 (UTC)

Agree --KimvdLinde 14:30, 9 February 2006 (UTC)
Also agree. I'll take a stab at it. - Samsara contrib talk 23:29, 9 February 2006 (UTC)
Actually, I'm sitting on the fence now. It seems that evolutionary tree concerns itself with the current consensus tree, whereas phylogenetic tree is about the theory behind trees in general, and the tree of life in particular. So, evolutionary tree should really be called tree of life, but that article is already taken; perhaps tree of life (biology)? - Samsara contrib talk 23:40, 9 February 2006 (UTC)
And how about origin of life? - Samsara contrib talk 00:49, 10 February 2006 (UTC)
I think still merge. The images at this page are phylogenetic trees matching the worked out tree of evolutionay tree. --KimvdLinde 01:40, 10 February 2006 (UTC)
The origin of life page is not very much overlapping with neither this nor evolutionary tree. Origin of life is about the processes that create life, not about the exact evolutionary "path" taken by the various species. SpectrumDT 21:33, 24 February 2006 (UTC)
Ok, this question is out there for already 2 weeks, so if there is not overriding objection, I wll merge them somewhere during the weekend... --KimvdLinde 03:54, 25 February 2006 (UTC)
Phylogenetic trees are not restricted to evolutionary links. It can also represent a heirarchal taxonomy tree. I suggest leaving the two seperate —The preceding unsigned comment was added by 131.162.134.163 (talk • contribs) .
That is no argument against having the tree of life as an example of applied phylogenetics in this article. - Samsara (talk • contribs) 17:13, 12 May 2006 (UTC)
Looking at the articles, the major difference at present is that the PT article explains the theory (or at least one view of the theory) and the ET is a somewhat simplified presentation. The names unfortunately do not make this clear. I am not sure there is agreement on all the theoretical positions take in the PT article, including the one below. Further , the PhyloCode article very properly says "The PhyloCode is controversial. The number of supporters for official adoption of the PhyloCode is still small, and it is uncertain, as of 2006, when the code will be implemented and how widely it will be followed." It's a rather technical article, and probably should be kept separate, just as the articles on the separate codes are. It mentions "The Second International Phylogenetic Nomenclature Meeting took place June 28 – July 2, 2006." I don't know what was said there, but it would be relevant. As a non-specialist in nomenclature, just a biologist, I feel it is better to have a single code, but my feelings won't determine the outcome. If we don't merge we are presenting each party to the arguments in a separate article--quite regardless of NPOV, it is in this case confusing to the user of WP. The information he will get is determined by what term he happens to start with. The separate articles are not long, aand many of the references shoud be the same.

Even the single "don't merge" comment by RickReinckens can be taked as supporting the merger DGG 02:26, 13 September 2006 (UTC)

Disagree The evolutionary tree article needs to deal with issues about the actual history of life including lateral gene transfer. The phylogenetics article is about a tool which we use to analyse data concerning the history of life which does not deal well with all possibilities (for example lateral gene transfer). These two things should not be confused and ought to have separate articles. The evolutionary tree article needs to include more information concerning the subtleties of the subject matter. Barnaby dawson 07:47, 13 September 2006 (UTC)
I don't think the phylogenetics article can possibly be about the actual history of life. To the extent that it discusses particlar groups, even broad groups like kingdoms, the information goes with the stuff being discussed. To the extent is deals with spcific processes, it goes with the process. There's an article on horizontal gene transfer Phylogenetics isn't a tool, it a field of study, not a single method or tool. As applied in a rough outline, suitable for an elementary article in an encyclopedia, it is well illustrated by the evolutionary tree in more or less its customary form, with horizontal gene transfer seen as an overlay, possibly accounting for some of the drastic changes that didn't make much sense otherwise. If everything at the root evolutionary level is a melange of genomes, then we do not have a tree overall, and need another metaphor, and more complicated diagrams. We might still have a tree for phyla, or within phyla, at least until more sequencing gets done. The "subtleties of the subject matter" go with the organisms or the processes.

I accept there's been a long discussion on this. I also accept that there is no single way of doing it, but it does have to be done either one way, or the other. Perhaps the way to go is to try writing it both ways and see what's possible and helpful. (This is not an offer to do it myself just now :) DGG 01:50, 14 September 2006 (UTC)

Ok, I was bold and merge evolutionary tree into this article before I read the talk page. my bad. I agree that they are separate entities, but I think one article would suffice. I guess we can undo my changes if people think otherwise. --Rajah 21:45, 19 October 2006 (UTC)

[edit] Don't merge

  • From the Phylogenic Tree article (hi-lited):
"By their very nature, phylogenetic trees cannot represent actual evolutionary patterns and are in fact distorted by any lateral gene transfer[5] or hybridisation between species that are not nearest neighbors on the tree before hybridisation takes place. For these reasons, the proposed PhyloCode . . . does not assume a tree structure."
  • They are saying that this is a different way of thinking about the material being examined. It would be like merging articles on Quantum gravity and M-Theory.
  • These articles should cross-reference each other, not be merged.
  • The Evolutionary Tree article should be expanded.
  • Many people have heard of "evolutionary tree". Few have heard of phylogenetic tree. If anything, "phylogenetic tree" should be merged into evolutionary tree and not vice versa.

RickReinckens 15:41, 4 September 2006 (UTC)

[edit] overall view

As the layman will not know the precise distinction, perhaps it is more important to have a single article, than worry about the name. I agree with the comment above that the best-known term is evolutionary tree. The various detailed meanings & implications can be explained in the article. Equally impt would be to have a single presentation for all the kingdom, etc. pages, as there is no agreement among them. The existence of different hypotheses can also be discussed once, with the refs, and then referred to. NPOV should be possible, as the disagreements are fundamentaly over which set of genes is the more important, and this is still mainly a matter of opinion. What I think we should avoid is going over the same ground repeatedly, with the same arguments and examples and variant views. that's confusing rather than neutral. Neutral is expressing the different hypotheses clearly and accurately; that's hard enough, bit we should only have to deal with it once.DGG 00:08, 23 September 2006 (UTC)

[edit] Yet another opinion

Initially, I thought they should be merged. As an evolutionary biologist who uses phylogenetic methods to infer evolutionary history, I definitely blur the distinction between "evolutionary tree" and "phylogenetic tree." But there is a fundamental difference, as pointed out by RickReinckens. I think we do indeed have a problem if laypeople search for "evolutionary tree" and end up with this largely technical article about phylogenetics. I suggest we move a lot of this material over to phylogenetics, where it belongs, and change this article to evolutionary tree, if that is truly the term that laypeople will be familiar with. -Safay 03:54, 13 November 2006 (UTC)

[edit] First use of a tree to represent evolutionary history?

Does anyone know of the first use of a tree to represent evolutionary history? Darwin has his diagram in On the Origin..., but does anyone know of another before that? This would make an interesting historical addition to an article about evolutionary trees. -Safay 03:54, 13 November 2006 (UTC)

[edit] category renaming

Discussion about renaming Category:Tree of life to Category:Organisms: Wikipedia:Categories for discussion/Log/2007 January 10.--ragesoss 23:49, 10 January 2007 (UTC)

[edit] Limitations category lacking

There aren't any references cited for the limitations of phylogenetic trees. Also, calling ancient DNA "little useful" is a little vague and misleading. I can root around for some references if necessary. --Estelahe 16:37, 9 October 2007 (UTC)

[edit] When extinct species are included in a tree, they should always be terminal nodes, as it is unlikely that they are direct ancestors of any extant species

When extinct species are included in a tree, they should always be terminal nodes, as it is unlikely that they are direct ancestors of any extant species

Why is that? It makes absolutely no sense to me, that the direct ancestor of a living species is most likely to also be a living species. I would think that would actually be quite rare. Can someone point me to a multi-celled living species whose direct ancestor is also living????? 24.11.53.10 (talk) 22:24, 20 November 2007 (UTC)