View source for Talk:Phylogenetic tree

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==You can merge the two files==
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? [[User:Drobinsonatlaur|Drobinsonatlaur]] 02:31, 8 December 2006 (UTC)

Very stylish. [[User:Wetman|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.[[User:DGG|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. [[User:62.227.165.193|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)[[User:DGG|DGG]] 00:08, 23 September 2006 (UTC) 

==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.  :)  [[User:Barnaby dawson|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?[[User:DGG|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. [[User:Jeffgwatts|Jeffgwatts]] ([[User talk:Jeffgwatts|talk]]) 11:23, 2 April 2010 (UTC)
:: No, but there is a page entitled Straw Man. [[Special:Contributions/174.20.246.198|174.20.246.198]] ([[User talk:174.20.246.198|talk]]) 04:37, 3 October 2016 (UTC)

==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? - ''[[User:Samsara|Samsara]]'' 15:37, 2 January 2006 (UTC) 

== "Evolutionary tree" ==
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]] ===
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 [http://www.backyardnature.net/evotrees.htm 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. [[User:SpectrumDT|SpectrumDT]] 11:33, 9 February 2006 (UTC)
: '''Agree''' --[[User:KimvdLinde|KimvdLinde]] 14:30, 9 February 2006 (UTC)
:<s>Also agree. I'll take a stab at it. - [[User:Samsara|Samsara]] <sub><span style="text-decoration:none">[[Special:Contributions/Samsara|contrib]]</span></sub> <sup><span style="position: relative; left: -36px; margin-right: -36px; text-decoration:none;">[[User talk:Samsara|talk]]</span></sup> 23:29, 9 February 2006 (UTC)</s>
::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)]]? - [[User:Samsara|Samsara]] <sub><span style="text-decoration:none">[[Special:Contributions/Samsara|contrib]]</span></sub> <sup><span style="position: relative; left: -36px; margin-right: -36px; text-decoration:none;">[[User talk:Samsara|talk]]</span></sup> 23:40, 9 February 2006 (UTC)

::And how about [[origin of life]]? - [[User:Samsara|Samsara]] <sub><span style="text-decoration:none">[[Special:Contributions/Samsara|contrib]]</span></sub> <sup><span style="position: relative; left: -36px; margin-right: -36px; text-decoration:none;">[[User talk:Samsara|talk]]</span></sup> 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. --[[User:KimvdLinde|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. [[User:SpectrumDT|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... --[[User:KimvdLinde|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 <small>—The preceding [[Wikipedia:Sign your posts on talk pages|unsigned]] comment was added by [[User:131.162.134.163|131.162.134.163]] ([[User talk:131.162.134.163|talk]] • [[Special:Contributions/131.162.134.163|contribs]]) {{{2|}}}.</small><!-- [Template:Unsigned] -->

::::::That is no argument against having the tree of life as an example of applied phylogenetics in this article. - [[User:Samsara|{{{2|Samsara}}}]] ([[User talk:Samsara|talk]] • [[Special:Contributions/Samsara|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  [[User:DGG|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.  [[User:Barnaby dawson|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 :) [[User:DGG|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. --[[User:Rajah|Rajah]] 21:45, 19 October 2006 (UTC)

=== 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.

[[User:RickReinckens|RickReinckens]] 15:41, 4 September 2006 (UTC)

===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.[[User:DGG|DGG]] 00:08, 23 September 2006 (UTC)

===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 [[User:RickReinckens|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.
-[[User:Safay|Safay]] 03:54, 13 November 2006 (UTC)

===Why was there a merger?===

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.  [[User:Peter coxhead|Peter coxhead]] ([[User talk:Peter coxhead|talk]]) 12:39, 14 March 2010 (UTC)

==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.
-[[User:Safay|Safay]] 03:54, 13 November 2006 (UTC)

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

==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. --[[User:Estelahe|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 ==

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????? [[Special:Contributions/24.11.53.10|24.11.53.10]] ([[User talk:24.11.53.10|talk]]) 22:24, 20 November 2007 (UTC)

==Why Darwin was wrong about the tree of life==

"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."
http://www.newscientist.com/article/mg20126921.600-why-darwin-was-wrong-about-the-tree-of-life.html?page=1

"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."
http://www.newscientist.com/article/mg20126923.000-editorial-uprooting-darwins-tree.html  <span style="font-size: smaller;" class="autosigned">—Preceding [[Wikipedia:Signatures|unsigned]] comment added by [[Special:Contributions/213.158.199.83|213.158.199.83]] ([[User talk:213.158.199.83|talk]]) 21:22, 3 February 2009 (UTC)</span><!-- Template:UnsignedIP --> <!--Autosigned by SineBot-->

==Classification==
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  <span style="font-size: smaller;" class="autosigned">—Preceding [[Wikipedia:Signatures|unsigned]] comment added by [[Special:Contributions/81.246.162.121|81.246.162.121]] ([[User talk:81.246.162.121|talk]]) 06:38, 6 April 2009 (UTC)</span><!-- Template:UnsignedIP --> <!--Autosigned by SineBot-->

== The stupid and insulting phrase ==

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. --[[User:Desertphile|Desertphile]] ([[User talk:Desertphile|talk]]) 17:50, 4 November 2009 (UTC)

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

== Recent changes to lead ==

'''Rogue-pilot''' recently changed the opening sentence from:
::''A '''phylogenetic tree''' or '''evolutionary tree''' is a [[tree (graph theory)|tree]] showing the [[evolution]]ary relationships among various biological [[species]] or other entities that are known to have a [[common descent|common ancestor]]. ''
to
::''A '''phylogenetic tree''' or '''evolutionary tree''' is a [[tree (graph theory)|tree]] that ostensibly shows the [[evolution]]ary relationships among various biological [[species]] or other entities that are modeled as having a [[common descent|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 descent|common ancestor]]."'' "...are known to have a common ancestor" seems unnecessarily wordy to me.) Thoughts? [[User:Dawn Bard|Dawn Bard]] ([[User talk:Dawn Bard|talk]]) 16:50, 6 November 2009 (UTC)

I was confused for more than a month from this phrase: "[[common descent|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. [[User:Leontaurus|Leontaurus]] ([[User talk:Leontaurus|talk]]) 23:58, 21 December 2009 (UTC)

== Problems with History section ==

===Edit 1===
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.  [[User:Peter coxhead|Peter coxhead]] ([[User talk:Peter coxhead|talk]]) 12:13, 14 March 2010 (UTC)

===Edit 2===
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. [[User:Peter coxhead|Peter coxhead]] ([[User talk:Peter coxhead|talk]]) 12:21, 14 March 2010 (UTC)

===Edit 3===
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. [[User:Peter coxhead|Peter coxhead]] ([[User talk:Peter coxhead|talk]]) 12:27, 14 March 2010 (UTC)

== The genetic core of the universal ancestor ==

Useful resources can be drawn from the following journal reference:
* {{cite journal|last=Harris|first=JK|coauthors=Kelley, ST; Spiegelman, GB; Pace, NR|title=The genetic core of the universal ancestor.|journal=Genome research|date=2003 Mar|volume=13|issue=3|pages=407-12|pmid=12618371|doi=10.1101/gr.652803|pmc=430263}}
It contains examples of three-domain and non-three-domain phylogenetic trees from analyses of the COG database protein alignments. <span style="font-family:Segoe script;">[[User:Diptanshu.D|'''<span style="color:#ff0000;">D</span><span style="color:#ff6600;">ip</span><span style="color:#009900;">ta</span><span style="color:#0000ff;">ns</span><span style="color:#6600cc;">hu</span>''']][[User talk:Diptanshu.D|<sup>Talk</sup>]]</span> 05:05, 25 May 2013 (UTC)

== Language use ==

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

== Convergent evolution? ==

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."? – [[User:Elroch|Elroch]]‎ 13:29, 23 November 2014‎

:Consider the central point made in this paper: {{Cite journal | doi = 10.1093/molbev/mss137| title = Ancient Gene Paralogy May Mislead Inference of Plastid Phylogeny| journal = Molecular Biology and Evolution| volume = 29| issue = 11| pages = 3333| year = 2012| last1 = Qiu | first1 = H.| last2 = Yang | first2 = E. C.| last3 = Bhattacharya | first3 = D.| last4 = Yoon | first4 = H. S.}} 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). [[User:Peter coxhead|Peter coxhead]] ([[User talk:Peter coxhead|talk]]) 16:56, 25 November 2014 (UTC)

== Braided river of life ==

[[Hybrid (biology)|hybrid]]isation between species that were not nearest neighbors on the tree before hybridisation takes place, [[convergent evolution]], and [[conserved sequence]]s. 
:: old/| new|/
Inter species hybridization is by definition the reason (if species are defined as population exchanging genes via sexual reproduction) to downgrading such species to subspecies status. Taxonomic reconsideration may by slow down by various [[species concept]]s and pragmatic conservatism in taxonomic namingand and other factors. To overcome limitations of structure of phylogenetic tree is proposed braided river concept. Flowing trough time, bifurcating and merging, surging on obstacles but trying to flow with some branched channels silting to dry. This Braided river reticulate streams of life exchanging genetic information in 4d space is proposed as long overdue [[paradigm change]] in diversity conceptualization  of phylogenetic evolution.<ref>{{doi|10.1002/evan.21787}} [https://osf.io/preprints/africarxiv/y3bp7/download pdf]</ref><ref>{{doi|10.20944/preprints201905.0038.v1}}</ref>

now what ? [[Special:Contributions/99.90.196.227|99.90.196.227]] ([[User talk:99.90.196.227|talk]]) 15:38, 27 September 2019 (UTC)
{{reflist talk}}

:Well, first let's have the correct doi links:
:*{{doi|10.1002/evan.21787}}
:*{{doi|10.20944/preprints201905.0038.v1}}
:Then, when I look at the two papers, it doesn't seem to me that they are primarily concerned with the limitations of phylogenetic trees. There's definitely a need for more sources for the section [[Phylogenetic tree#Limitations of phylogenetic analysis]], particularly the last paragraph that mentions phylogenetic networks, but the above two are not the right papers for this.
:So, apart from the fact that the English in the reverted addition is very hard to understand, and would need a great deal of copy-editing to make sense of it, I don't think the addition is relevantly sourced. [[User:Peter coxhead|Peter coxhead]] ([[User talk:Peter coxhead|talk]]) 17:46, 27 September 2019 (UTC)

== Cladograms (special tree types) ==

The article, in describing a cladogram, says that ''its internal nodes do not represent ancestors.'' As written, this seems nonsensical. It is at the very least contrary to the article on cladograms. It may be an attempt to say that ancestors represented by nodes in a cladogram are not necessarily already identified, but possibly are inferred. If howls of protest do not arise, I'll probably return sometime soon and edit accordingly. [[User:Aboctok|Aboctok]] ([[User talk:Aboctok|talk]]) 17:18, 3 June 2020 (UTC)
:A perennial difficulty is describing cladograms is the vagueness of terminology. When trees (neutral wording) are generated by almost all current programs, the internal nodes show the branching, and do not show ancestors, real or hypothetical. Whatever data you input, all units end up as leaves. Some programs infer the states of the internal nodes, but if you then add a unit with such a state to the input data, it will end up as a leaf. So it is far from nonsensical. Some authors have tried to use terms like "phylogram" for trees with 'real' internal nodes as opposed to "cladograms" in which only branching is indicated, but this hasn't caught on. [[User:Peter coxhead|Peter coxhead]] ([[User talk:Peter coxhead|talk]]) 19:09, 3 June 2020 (UTC)

== Add reference to Pace ==

This article references Woese, but not Norman R. Pace. Here is an earlier good reference for both: Pace, N.R., G.J. Olsen, and C.R. Woese. (1986). Ribosomal RNA phylogeny and the primary lines of evolutionary descent. Cell 45:325-326. [[User:Charles Juvon|Charles Juvon]] ([[User talk:Charles Juvon|talk]]) 19:00, 19 August 2020 (UTC)

== Trees being "speculative" ==

I removed the word "speculative" from the "rooted tree for rRNA genes" figure legend, as this word is misleading. Phylogenetic trees are NOT "speculative" when they are based on DNA (or RNA) data (as in this case). One can argue that phylogenetic relationships are flawed by an erroneous algorithm or too little data, but a phylogenetic tree is simply a representation of similarities and thus a hypothesis about phylogenetic relationships. The figure legend was used by a creationist on Quora to "demonstrate" the "speculative" nature of evolution. Given that there is nothing speculative about evolution itself, I removed the word "speculative" as it (wrongly) indicates that a phylogenetic tree is just guesswork, which it is not. [[User:Peteruetz|Peteruetz]] ([[User talk:Peteruetz|talk]]) 02:49, 3 October 2020 (UTC)
:{{ping|Peteruetz}} no, this is not the issue. The original caption said "A speculatively rooted tree ...". As the section [[Phylogenetic tree#Rooted tree]] states, but doesn't explain, to <em>root</em> a tree with certainty requires an outgroup, but there is no outgroup for life as a whole. So the position of the root is speculative: the caption is correctly read as "A speculatively-rooted tree" not "A speculative rooted-tree"; the adverb "speculatively" has to qualify the adjectival "rooted", not the noun "tree". Remove "rooted" and you get nonsense: "A speculatively tree". I've now tried a longer qualification to avoid the possibility of this misreading. [[User:Peter coxhead|Peter coxhead]] ([[User talk:Peter coxhead|talk]]) 06:15, 3 October 2020 (UTC)
:Also the tree should be sourced; there's more than one hypothesis available for the relationship between bacteria, archaeans and eukaryotes. (See, e.g., [[Neomura#Two domains view]].) [[User:Peter coxhead|Peter coxhead]] ([[User talk:Peter coxhead|talk]]) 06:25, 3 October 2020 (UTC)
::The "original caption" said " A phylogenetic tree of living things ..." -- just look at the figure file. I don't know where the "speculative" comes from but it's NOT from the original caption. [[User:Peteruetz|Peteruetz]] ([[User talk:Peteruetz|talk]]) 18:08, 6 October 2020 (UTC)
:::But Peter_coxhead just explained this.  The "speculative{{em|ly}}" applies to the rootedness of the tree. <span style="white-space:nowrap;font-family:'Trebuchet MS'"> — [[User:SMcCandlish|'''SMcCandlish''']] [[User talk:SMcCandlish|☏]] [[Special:Contributions/SMcCandlish|¢]] 😼 </span> 11:49, 18 October 2020 (UTC)

== Order of branches ==

Is my understanding correct that the order of branches (that is the order resulting from the sum of decisions at each branching point which branch to depict to the left and which to the right – in a tree that shows time on a vertical axis) is arbitrary? Are there any conventions for these individual decisions? Is there any special tree type for which the order is not arbitrary? ◅&nbsp;[[User:SebastianHelm|Sebastian]] 10:54, 10 February 2022 (UTC)
If it helps, one can limit the question to trees that show only extant species. The order, then, would simply be the order of the branches at the crown of the tree. ◅&nbsp;[[User:SebastianHelm|Sebastian]] 11:09, 10 February 2022 (UTC)

== The Three Domain Hypothesis ==

This is an article about phylogenetic trees&mdash;what they are and how to construct them. It is not an article about the tree of life and various models about the relationships between prokaryotes and eukaryotes. 

The history section needs a lot of work. It should describe the first trees based on the sequences of molecules from the early 1960s and why such trees are possible (the Neutral Theory). It should NOT say that that Woese's ribosomal RNA tree (Three Domains) is the first molecular tree and it should certainly not imply that this is the modern view especially since the main Wikipedia article ([[Three-domain system]]) specifically points out that it is no longer the preferred model of eukaryote evolution. 

I have reverted the recent edits that misrepresent the history of molecular trees and the current consensus model of the origin of eukaryotes. [[User:Genome42|Genome42]] ([[User talk:Genome42|talk]]) 16:38, 26 March 2024 (UTC)

:It is not justified to remove the three-domain tree. Of course all scientific theories are hypotheses remaining a topic of debate. Anyhow, the three-domain system has become textbook knowledge (e.g. up to now in the recent ''Brock Biology of Microorganisms'', 2022, Unit 3, p.434, 435).
:Where are the references for '''trees''' based on molecular phylogenetics from the early 1960ies? The history of research on microbial evolution and of different tree concepts has been documented comprehensively by evolutionary biologist and scientific historian Jan Sapp (''The New Foundations of Evolution: On the Tree of Life''. Oxford University Press, 2009). His book is also cited in Wikipedia article “Three-domain system” you mentioned. The so called Neutral Theory does not deal with phylogenetic trees, but with “the evolution of proteins and nucleic acids without selection” (see Jan Sapp, p.130).
:The figure of the tree for blind people (in chapter “rooted tree”) shows exactly the structure of the three-domain tree from [[Carl Woese|Woese]] et al. 1990. It is not correct to ignore the original. [[User:Maya Kandler|Maya Kandler]] ([[User talk:Maya Kandler|talk]]) 19:19, 3 April 2024 (UTC)
::The current consensus view on the origin of eukaryotes is that they arose from a fusion of an alphaproteobacterium and an archaebacterium from the Asgard superphylum. What this means is that the Archaea ancestor of eukaryotes comes from WITHIN the Archaea domain so that eukaryotes are NOT a separate domain. What it also means is that the ancestor of at least half of the genes in eukaryotes is bacterial, not Archaeal. 
::The Three Domain Hypothesis is refuted on both grounds. It has been replaced by a Two Domain tree with the formation of eukaryotes making a ring of life. This is not particularly controversial among knowledgeable scientists who study the origin of eukaryotes.
::The two key papers on molecular phylogenies from the early 1960s are Margoliash (1963) and Zuckerkandl & Pauling (1965) although, admittedly, Margoliash didn't draw a tree in that paper. The essential paper on constructing molecular phylogenetic trees is Fitch and Margoliash (1967).  
::The Neutral Theory is absolutely crucial for understanding the molecular clock. You can't explain molecular phylogenetic trees if you don't understand why there's an approximate molecular clock. 
::The Three Domain figure for blind people is also incorrect and should be removed from an encyclopedia article on phylogenetic trees unless it's just there for historical purposes to show what people used to think before better data became available. [[User:Genome42|Genome42]] ([[User talk:Genome42|talk]]) 15:28, 5 April 2024 (UTC)
:::The “current consensus view on the origin of the eucaryotes” is just another hypothesis. It has to be taken into account that the so-called Asgard superphylum belongs to a group of as yet uncultured phyla “so far identified only through PCR-based and metagenomic surveys” (Brock, 2022, p.703, see also p. 607).
:::“Knowledgeable scientists” use the term Archaea, not the preceding term archaeabacteria. [[User:Maya Kandler|Maya Kandler]] ([[User talk:Maya Kandler|talk]]) 19:56, 20 April 2024 (UTC)
::::Check out the Wikipedia article on [[Archaea]]. You'll see that the Asgard superphylum (Asgardaeota) is nested well within the Archaea domain so that even if you eliminate all the genomes from uncultured species the Archaeal portion of eukayotic genomes still falls WITHIN Archaea. What this means is that one of the ancestors of eukaryotes was not part of a separate eukaryote domain.  
::::The other half of eukaryotic genomes still falls within [[Bacteria]], specifically alphaproteobacteria. The Wikipedia article on Bacteria has a nice phylogenetic tree showing the relationship of Archaea, Bacteria, and Eukaryota. Look in the section on [[Bacteria#Classification_and_identification]]. [[User:Genome42|Genome42]] ([[User talk:Genome42|talk]]) 15:08, 21 April 2024 (UTC)

== What is a "site pattern"? ==

The article on the [[Hadamard transform]] says that phylogenetic trees have corresponding [[site pattern]] vectors or matrices.  Here, [[site pattern]] is currently a red link, and this article mentions no such term. Search engines do reveal that there are lots of academic papers that use the phrase "site pattern" in relation to phylogenetic trees, but I am finding it impossible to guess what this is. Second-order question is how a site pattern could be a "vector or matrix": in math, the distinction between vector and matrix is very sharp: things are one or the other but not both, so what the heck is going on here? Third-order question: a mapping between trees and vectors sounds like it would be generically useful e.g. in linguistics (how languages and dialects are related to each other) and sociology (how cultures and customs are related, how shipping, trade, migration between Phonecia, Egypt, Anatolia interacted in the ancient world.) and law (how court cases build on and refine upon earlier court cases, drawing distinctions where previously there were none.) I imagine other phylogenetic correspondences can be made. e.g. in software. So the underlying relation between trees and "site pattern vectors" seems like it could be generically important.  [[Special:Contributions/67.198.37.16|67.198.37.16]] ([[User talk:67.198.37.16|talk]]) 21:42, 28 March 2025 (UTC)