Talk:Phylogenetic tree

message: 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)
thread_title: Extinct species in trees?!

message: * 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)
thread_title:  Don't merge 

message: 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)
thread_title: Overall view

message: 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)
thread_title: Yet another opinion

message: 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)
thread_title: Why was there a merger?

message: 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)
thread_title: First use of a tree to represent evolutionary history?

message: 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)
thread_title: Category renaming

message: 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)
thread_title: Limitations category lacking

message: 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)
thread_title:  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 

message: "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  —Preceding unsigned comment added by 213.158.199.83 (talk) 21:22, 3 February 2009 (UTC)
thread_title: Why Darwin was wrong about the tree of life

message: 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 81.246.162.121 (talk) 06:38, 6 April 2009 (UTC)
thread_title: Classification

message: 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)
thread_title:  The stupid and insulting phrase 

message: 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. 
to
::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)
thread_title:  Recent changes to lead 

message: ===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.  Peter coxhead (talk) 12:13, 14 March 2010 (UTC)
replies: text: 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)

text: 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)
thread_title:  Problems with History section 

message: 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)
thread_title: Edit 1

message: 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)
thread_title: Edit 2

message: 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)
thread_title: Edit 3

message: 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)
thread_title:  The genetic core of the universal ancestor 

message: 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)
thread_title:  Language use 

message: 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:  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)
thread_title:  Convergent evolution? 

message: 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. Aboctok (talk) 17:18, 3 June 2020 (UTC)
replies: text: 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. Peter coxhead (talk) 19:09, 3 June 2020 (UTC)
thread_title:  Cladograms (special tree types) 

message: 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. Charles Juvon (talk) 19:00, 19 August 2020 (UTC)
thread_title:  Add reference to Pace 

message: 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. Peteruetz (talk) 02:49, 3 October 2020 (UTC)
replies: text: 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 root 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. Peter coxhead (talk) 06:15, 3 October 2020 (UTC)

text: 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.) Peter coxhead (talk) 06:25, 3 October 2020 (UTC)
replies: text: 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. Peteruetz (talk) 18:08, 6 October 2020 (UTC)
replies: text: But Peter_coxhead just explained this.  The "speculative" applies to the rootedness of the tree.  — SMcCandlish ☏ ¢ 😼  11:49, 18 October 2020 (UTC)
thread_title:  Trees being "speculative" 

message: 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? ◅ Sebastian 10:54, 10 February 2022 (UTC)
thread_title:  Order of branches