Talk:Phylogenetic tree

From Wikipedia, the free encyclopedia
Jump to: navigation, search
WikiProject Tree of Life (Rated B-class, Top-importance)
WikiProject icon This article is within the scope of WikiProject Tree of Life, a collaborative effort to improve the coverage of taxonomy and the phylogenetic tree of life on Wikipedia. If you would like to participate, please visit the project page, where you can join the discussion and see a list of open tasks.
B-Class article B  This article has been rated as B-Class on the project's quality scale.
 Top  This article has been rated as Top-importance on the project's importance scale.
WikiProject Computational Biology (Rated B-class, Top-importance)
WikiProject icon This article is within the scope of WikiProject Computational Biology, a collaborative effort to improve the coverage of Computational Biology on Wikipedia. If you would like to participate, please visit the project page, where you can join the discussion and see a list of open tasks.
B-Class article B  This article has been rated as B-Class on the quality scale.
 Top  This article has been rated as Top-importance on the importance scale.

You can merge the two files[edit]

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. 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)


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)

Is there a page entitled Views of Flat Earthers and mainstream scientists compared? Or one called Views of People Who Think Disease Is Causes By Ill Humours and mainstream scientists compared? Wake up people and move on. Jeffgwatts (talk) 11:23, 2 April 2010 (UTC)

No, but there is a page entitled Straw Man. (talk) 04:37, 3 October 2016 (UTC)

Extinct species in trees?![edit]

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

Merge this with Evolutionary tree[edit]

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 (talkcontribs) .
That is no argument against having the tree of life as an example of applied phylogenetics in this article. - Samsara (talkcontribs) 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)

Don't merge[edit]

  • 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)

overall view[edit]

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)

Yet another opinion[edit]

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)

Why was there a merger?[edit]

Looking at the history of this article and the discussion, I can't see why the merger took place, i.e. I can't see that there was a consensus among editors to do this.

  • An 'evolutionary tree' represents a hypothesis about the evolutionary relationships among the taxonomic units shown in the tree. The evidence for the tree/hypothesis may be morphological or genetic or some mixture. Evolutionary trees for long extinct species are necessarily based only on morphology, since genetic analysis is not possible.
  • A 'phylogenetic tree' is a particular kind of 'evolutionary tree' in which genetic analysis provides all or most of the evidence for the tree/hypothesis. In recent usage, it almost always means a tree produced by an automated method (i.e. by one of a number of available computer packages).

It doesn't seem to me that the article conveys this at all. I'm reluctant to add anything without understanding the views of previous editors. Peter coxhead (talk) 12:39, 14 March 2010 (UTC)

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

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)

category renaming[edit]

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)

Limitations category lacking[edit]

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)

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[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

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????? (talk) 22:24, 20 November 2007 (UTC)

Why Darwin was wrong about the tree of life[edit]

"For much of the past 150 years, biology has largely concerned itself with filling in the details of the tree. "For a long time the holy grail was to build a tree of life," says Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, France. A few years ago it looked as though the grail was within reach. But today the project lies in tatters, torn to pieces by an onslaught of negative evidence. Many biologists now argue that the tree concept is obsolete and needs to be discarded. "We have no evidence at all that the tree of life is a reality," says Bapteste. That bombshell has even persuaded some that our fundamental view of biology needs to change."

"Most biologists now accept that the tree is not a fact of nature - it is something we impose on nature in an attempt to make the task of understanding it more tractable." —Preceding unsigned comment added by (talk) 21:22, 3 February 2009 (UTC)


Acoording to the Department of Biology, University of Oslo, the eukaryots are divided in

  • plants
  • ophistokonts
  • excavates
  • SAR (newly added branch; used to be chromoalveolates and rhizaria)

Dont see this classification anywhere, please inlclude —Preceding unsigned comment added by (talk) 06:38, 6 April 2009 (UTC)

The Stupid and Insulting Phrase[edit]

The main article states in part "... various biological species or other entities that are believed to have a common ancestor." The word "believed" is not appropriate: common descent is an observed fact, and it requires no belief. I have corrected the article. --Desertphile (talk) 17:50, 4 November 2009 (UTC)

So you were there to observe it? And "fact." My aren't we good a hyperbole.--TDurden1937 (talk) 00:24, 15 October 2011 (UTC)

Recent changes to lede[edit]

Rogue-pilot recently changed the opening sentence from:

A phylogenetic tree or evolutionary tree is a tree showing the evolutionary relationships among various biological species or other entities that are known to have a common ancestor.


A phylogenetic tree or evolutionary tree is a tree that ostensibly shows the evolutionary relationships among various biological species or other entities that are modeled as having a common ancestor.

The edit was undone by 3 different users, but it keeps being restored. I don't want to get into an edit war (though Rogue-pilot is already in violation of 3RR), but the original version has been stable indicating a de-facto consensus, and the change has not been sourced (not to mention that it seems specious), so I'm just checking here to see if there is consensus to go back to the previous version. Rogue-pilot, it would be great if you could discuss it here instead of changing the article repeatedly without sources or explanation. (I think I would change the end of the sentence to ...biological species or other entities that have a common ancestor." "...are known to have a common ancestor" seems unnecessarily wordy to me.) Thoughts? Dawn Bard (talk) 16:50, 6 November 2009 (UTC)

I was confused for more than a month from this phrase: "common ancestor". I had to look at numerous sources (too bad I cannot site any one here) and I had to verify this with a genetics professor. I concluded that we can talk about ancestry (not only common ancestor, but also the higher node as ancestor to lower nodes or leaves), only in rooted trees. In unrooted trees, we can only say that the leaves are ancestors to no other node. We can make no other assumption about ancestry in unrooted trees. Leontaurus (talk) 23:58, 21 December 2009 (UTC)

Problems with History section[edit]

Edit 1[edit]

Before my edit, this sentence appeared in the History section: "Over a century later, evolutionary biologists still use tree diagrams to depict evolution because the floral analogy effectively conveys the concept that speciation occurs through the adaptiveand random splitting of lineages." At first I had no idea what was meant by "the floral analogy" (and the links to "flora" and "analogy" didn't help me). I think it was meant to mean that tree diagrams are a 'floral analogy'. Well, they are an 'analogy' but not a 'floral' one in the usual meaning of 'floral', i.e. they have nothing to do with flowers. I've changed 'the floral analogy' to 'such diagrams', which I think is much clearer. Peter coxhead (talk) 12:13, 14 March 2010 (UTC)

Edit 2[edit]

Before my edit, this paragraph appeared in the History section:

Adolf Engler (1844 - 1930) and Karl A. E. Prantl (1849 - 1893) published a system of plant classification in their monograph Die Natürlichen Pflanzenfamilien. In it, they arranged the families and orders of flowering plants on the basis of complexity of floral morphology. Characters like a perianth with one whorl, unisexual flowers and pollination by wind were considered primitive as compared to perianth with two whorls, bisexual flowers and pollination by insects.[1]

This is undoubtedly true, but not, as far as I can see, of any relevance. The Engler system is not primarily an evolutionary tree and certainly not a phylogenetic tree. It's a 'Chain of Being' type view, based on ideas of what characters are 'primitive' and what are 'advanced'. Hence I've removed this paragraph entirely. Peter coxhead (talk) 12:21, 14 March 2010 (UTC)

Edit 3[edit]

This paragraph:

The plant kingdom is further divided into divisions, sub-divisions, classes, orders and families. According to this system, monocotyledons are considered more primitive than dicotyledons. It also considers evolution of angiosperms from a single source and the sequence of orders and families show parallel evolution.

was, I think, meant to follow on from the paragraph about the Engler system (assuming that the "It" in the second sentence refers to the Engler system). As I don't think that the previous paragraph is relevant, I've removed this too. Peter coxhead (talk) 12:27, 14 March 2010 (UTC)

The genetic core of the universal ancestor[edit]

Useful resources can be drawn from the following journal reference:

It contains examples of three-domain and non-three-domain phylogenetic trees from analyses of the COG database protein alignments. DiptanshuTalk 05:05, 25 May 2013 (UTC)

Language use[edit]

I fixed the article per MOS:ANDOR. It's better to avoid its use in articles. Χρυσάνθη Λυκούση (talk) 20:12, 26 March 2014 (UTC)

Convergent evolution?[edit]

In the section on limitations, it claims that "convergent evolution" can be a confounder for creating phylogenetic trees based on genome sequencing. This seems unlikely, as convergent evolution is in almost all cases the evolution of similar features with a distinct genetic basis. To reproduce the exact same sequence of mutations is a quite different matter. Am I right in suggesting "convergent evolution" should really be deleted from the sentence: "The data on which they are based is noisy; the analysis can be confounded by genetic recombination, horizontal gene transfer, hybridisation between species that were not nearest neighbors on the tree before hybridisation takes place, convergent evolution, and conserved sequences."? – Elroch‎ 13:29, 23 November 2014‎

Consider the central point made in this paper: Qiu, H.; Yang, E. C.; Bhattacharya, D.; Yoon, H. S. (2012). "Ancient Gene Paralogy May Mislead Inference of Plastid Phylogeny". Molecular Biology and Evolution. 29 (11): 3333. doi:10.1093/molbev/mss137.  The genes for photosystem II appear to have undergone parallel reductions to a single copy in the plastids of different lineages of plants. So the genetic sequences are misleadingly similar. This is certainly a kind of "convergent evolution", although deeper analysis may show that the genetic changes were not precisely the same (since different copies may have been lost). Peter coxhead (talk) 16:56, 25 November 2014 (UTC)