Talk:Basal (phylogenetics)

Examples

"it has had more time to evolve" - that phrase needs reworking. I don't have the time now, but it needed mentioning. I think this is a good start. I came here from the page on Mockingbirds. Your examples relating humans and plants may make perfect sense to a professional, but this layman's mind has to stretch way too far to place plants and humans on the same clade. Couldn't you choose a clade within vertebrates, or synapsids or something? Who's basal in human evolution? I am merely a bird loving artist who stumbled upon this article--but I feel it's an important bit of info that could be better explicated to the layman. And, as a luxury, perhaps having links to creatures that are considered basal would be illuminating.Francis Smith (talk) 01:31, 12 April 2009 (UTC)

Wow, you said that rather nicely. Please, in the future, feel free to just edit out anything you see that is that bad and confusing for the general reader. --KP Botany (talk) 03:33, 12 April 2009 (UTC)

The abuse of "basal"

Okay, so we've all done it (even I've done it), but this notion of a terminal taxon being "basal" in a tree is a common terminological abuse. The base of a tree is its root. None of the terminal species in a cladogram can be said to be basal, that's why they are terminal. The term "basal" simply means towards the root of the tree. Consider the cladogram used in the example:

	Basal group
	Non-basal group Non-basal group Non-basal group Non-basal group

Suppose we simply collapse the "Non-basal" terminals and add an outgroup. We get:

	Outgroup
	Basal group Non-basal group

Which side of the tree is basal now? Neither. That's because all nodes in a cladogram are rotatable. In both cases, the correct way to report the topology is that "Basal group" is the sister group of "Non-basal group". The reason is because we're not actually justified in calling it "basal" any more than we are justified in calling it "primitive". In fact, both terms implie exactly the same thing anyway—that the taxon in question is somehow exhibiting more ancestral features. This is certainly not the case. It simply happens to be a smaller clade and may or may not have a greater number of apomorphic states.

Please see: Krell, F.-T. and Cranston, P. (2004). "Which side of the tree is more basal?". Systematic Entomology 29 (3): 279–281. doi:10.1111/j.0307-6970.2004.00262.x. The Braz (talk) 12:06, 2 November 2009 (UTC)

I totally agree, although I don't see "basal" ever going away. I've yet to see a situation where the meaning of a sentence including "basal" could not be expressed more precisely with "is the sister group to", "is the outgroup to", "is not a member of the clade X + Y", "has the plesiomorphic state of character Z", and so forth.--Curtis Clark (talk) 14:30, 2 November 2009 (UTC)

Indeed, these are all better and more precise alternatives to "basal". I also agree that the terminological abuse is unlikely to go away soon. Perhaps the article could be re-written to explain what "basal" actually means, and the present text used as an addendum to explain what people often mean by it. —Preceding unsigned comment added by The Braz (talk • contribs) 14:57, 2 November 2009 (UTC)The Braz (talk) 15:29, 2 November 2009 (UTC)

Feel free to edit.--Curtis Clark (talk) 03:29, 3 November 2009 (UTC)

I'm not a biologist, but it's my understanding that basal describes a relationship of three or more clades that together comprise another clade. In the case

	A B C D

we say that A is basal to C and D. Saying A is basal to B isn't really that useful, though I guess it means they are sister groups, along with an imprecise implication that B is composed of multiple groups itself. Bennetto (talk) 00:25, 8 March 2010 (UTC)

Last example question

I'm confused about the meaning of the last example involving the family Hominidae and orangutans. Is this diagram illustrating a clade? If so, are orangutans the basal member? Brycehughes (talk) 04:23, 31 May 2013 (UTC)

Every tree diagram in the article represents a clade, and yes, the orangutan genus Pongo is the basal genus in Hominidae. WolfmanSF (talk) 23:11, 16 April 2014 (UTC)

Thank you! Brycehughes (talk) 23:22, 16 April 2014 (UTC)

Article intro

States: A basal clade can be described as the earliest clade (of a given taxonomic rank[a]) to branch within a larger clade. Can anyone please clarify what, if anything, this means? The Braz (talk) 12:28, 16 April 2014 (UTC)

Look at the cladogram of family Hominidae in the article, drawn to show only genera. Which genus branches off first? Hominidae has an obvious basal genus (Pongo), although there is no basal species. WolfmanSF (talk) 18:38, 16 April 2014 (UTC)

More generally, taxon A can be described as basal within clade B if every other taxon within B having the same rank as A is a subset of the sister group of A. WolfmanSF (talk) 20:52, 16 April 2014 (UTC)

Right, but how do we determine that Pongo is a basal genus? Why isn't (Homo + Pan + Gorilla) the basal group? Excepting, of course, the following reasons: 1) it is the clade containing humans; 2) it is the more species-rich side of the (imbalanced) cladogram. When the term "basal" is used to describe terminals in a tree, it is almost invariably in an imbalanced cladogram. If Gorilla is made the sister group of Pongo, then which genus is most basal?

None of what you say answers the question, however. In a given rank, how can one branch be earlier than the other? Any pair of sister branches in a cladogram split at precisely the same time. Neither is branched before or earlier than the other. Only splits in a tree (i.e. the nodes themselves) can be ordered from most to least basal, with the root being most basal. This is impossible for terminals. Why should we insist on perpetuating an abuse of terminology that is technically wrong and misleading. We teach students over and over to not read cladograms across the tip, to not read them as ladders of progress. How is it any better to employ equivocal usages for a term that refers to the actual base (root!) of the tree and the sister group order of terminals?

Regarding the more general example, A is the sister group of the rest of B. Simple as that. I don't think we need engender an equivocal and misleading meaning for "basal" when there already exists adequate, precise, and less misleading terminology. I don't think we should be using a term to describe terminals that we already use to describe the order of internal nodes. I think this undermines the most basic principles of tree thinking: that taxa are ordered by degrees of relatedness, not chains of ancestors and descendants. The Braz (talk) 15:04, 27 May 2014 (UTC)

I don't disagree with most of what you're saying. Homo + Pan + Gorilla is a basal group within Hominidae - a basal subfamily, not a basal genus. There's only one basal genus in this case, and three nonbasal genera. There are two basal subfamilies (Homininae and Ponginae), and no nonbasal subfamilies, so there isn't much point in applying the term to either of the subfamilies. There must always be at least two basal clades. How basal any clade is is just a function of the node in the cladogram that represents its root.

Your recommendations for use of terminology are sensible, but our power to highlight sweeping proposals to change usage is limited. We can at least try to show how this deeply ingrained usage of the term can be logically consistent. WolfmanSF (talk) 08:17, 4 October 2014 (UTC)

The intro is excessively technical. A naive reader will be lost. I know something about clades and I am overwhelmed by the technicality. I know it is possible to explain this better. Please, someone help. Zaslav (talk) 06:23, 9 January 2020 (UTC)

Why don't you help us by listing the sentences that you don't think are clear? WolfmanSF (talk) 07:50, 9 January 2020 (UTC)

Very Basal

The phrase "Very Basal" just sounds wrong to me, yet a search shows it used 67 times in Wikipedia.

Question: Is this a real term, in which case can it be defined here in the article please, or should this be edited to a simple "Basal" in the referencing articles? Thank you Kiore (talk) 05:39, 15 March 2015 (UTC)

Strictly speaking, it doesn't make sense, since a taxon is either basal or it isn't. Loosely speaking, when applied to large groups, "basal" is often used to mean 'more basal than the great majority of'; in this situation, it does make sense, and this has been noted in the article. WolfmanSF (talk) 16:24, 15 March 2015 (UTC)

Thankyou WolfmanSF. This answered my question perfectly. Kiore (talk) 19:07, 15 March 2015 (UTC)

Basal lineages

While the term "basal lineage" is often used, this is a loose way of saying the lineage possesses ancestral character(s). Every lineage within a given clade can be traced traced back to the root of the clade, so all of them are equally "basal". Every lineage in biology (with the possible exception of those for viruses) can be traced back to the origin of life. Thus, the term "basal lineage", taken literally, is nonsensical. This is in contrast to the situation with clades, where whether or not a clade is basal within a larger clade depends on its topological position within that clade, independent of any consideration of characters. "Lineage" is also sometimes used loosely to mean "clade". WolfmanSF (talk) 18:36, 2 November 2017 (UTC)

Total redo

Based on the comments above, and various other published works, I completely redid this article, specifically to try and discourage the "misuse" of the word "basal" to represent sister groups. I deleted most of the examples, and nearly all should be moved to the sister group article if they should even be kept at all. It is not clear to me what the correct usage should be other than talking about deep nodes (not taxa deriving from those nodes) but perhaps someone else could add this. Wrfrancis (talk) 09:46, 9 September 2018 (UTC)

The result, I fear, is not an article that follows WP:NPOV by neutrally explaining actual usage, but one that attempts to teach a particular view. The description of a taxon with many pleisomorphic characters that is sister to taxa with many apomorphic characters as "basal" is widespread.

On reflection, I think the best step would be to restore the previous version and start again. I'll wait for comments first, though. We are explicitly not here to teach, but to report. Peter coxhead (talk) 15:28, 9 September 2018 (UTC)

As applied to lineages, the term "basal" is nonsensical. As applied to clades, basal has a specific, unambiguous and useful meaning (as the previous version of the article should have made clear) and the term is deeply enough entrenched that it is unlikely to ever go away (nor arguably, should it). Note that "lineage" is sometimes used as a sloppy way of saying "clade". WolfmanSF (talk) 16:52, 9 September 2018 (UTC)

I agree, but what you or I think isn't the point, it's what is in sufficiently widespread use to be included.

WP:STRUCTURE cautions against explicit Criticism sections; I think it would be better to work this material into the article. Peter coxhead (talk) 17:13, 9 September 2018 (UTC)

Regarding the (now deleted) example comparing humans to turtles, that is seriously compromised by the ambiguity and confusion surrounding the term "reptile". Also, I think we should avoid examples of trees which are highly misleading by virtue of very selective presentation of nodes. WolfmanSF (talk) 17:28, 9 September 2018 (UTC)

The new account is clear and helpful, but frankly the term "basal" appears in it as magnificently obscure and difficult; further, it is clear that some (many?) scientists have at times applied it very loosely if not "wrongly".

I think Peter coxhead's comment is key here: we as editors should analyse the literature and report on what is there, not on what we believe. If 80% of scientists think one thing and 20% another, then we should report both the majority and the minority views, making clear their relative frequency. If a term has multiple meanings in such different usages, it is a bit awkward in an article as this isn't a dictionary: we may need to include See alsos or otherwise cross-refer to related articles (such as on sister clades). On the choice of examples, it will be much the best if we can use examples published in the literature, so they can be cited directly. Chiswick Chap (talk) 06:53, 10 September 2018 (UTC)

I agree with the latter comment in general, but whether that is equally true of the most basic illustrative examples is debatable. As far as relative frequency statistics go, they may vary by field and so be difficult to come by. WolfmanSF (talk) 03:32, 11 September 2018 (UTC)

This is a classic example of the problem we've often run into before with more theoretical biological topics. When you study the literature, you find that biologists simply don't use some of their terminology in a clear and consistent way, and it's often easy to show that terms are actually being used in inconsistent ways. However, there are few if any reliable secondary sources that discuss the variability in a neutral way (as opposed to saying that the other uses are wrong). This makes it difficult to write a Wikipedia article keeping to WP:NPOV.

As an example, I've just been working on some spider articles using a major 2017 article on the spider tree of life (the Wheeler et al. 2017 ref at e.g. Entelegynae). "Basal" is used many times; mostly 'correctly' to refer to tree topology ("basal branches/branching") but sometimes related to pleisomorphic characters (e.g. "a basal placement in the family seems plausible, as it is the only genus ... that retains [a particular character accepted as ancestral]"). A Google Scholar search for "basal character" OR "basal characteristic" OR "basal trait" throws up large numbers of papers using such terms.

So I remain very concerned about In phylogenetics, the term basal can be correctly applied to clades of organisms, but not to lineages or to individual traits possessed by the organisms—although it may be misused in these ways in technical literature. It's simply a fact that "basal" is widely applied to mean or to relate to "possessing ancestral rather than derived characters", and we should not be saying flatly that this is a misuse: I might well agree with those who claim that it is, we shouldn't say this in an editorial voice in a Wikipedia article. Peter coxhead (talk) 08:26, 11 September 2018 (UTC)

That can be reworded in a less "preachy" fashion. The present wording is in part a concession to parties that wanted it to be even more preachy. WolfmanSF (talk) 06:39, 12 September 2018 (UTC)

So can you reword it, please? Peter coxhead (talk) 14:26, 12 September 2018 (UTC)

Yes, in time, but please see my email to you. WolfmanSF (talk) 21:06, 12 September 2018 (UTC)

I really do not like the direction this has gone. I felt like my redo was mostly objective, reflecting the usage and the criticism of that usage. Given that, I would STRONGLY ADVISE AGAINST starting the article stating that a basal lineage is a sister group to the remaining diversity in that group. This is imprecise usage, and the fact that it is used in some papers does not justify the definition. As mentioned above, usage of terms is not always consistent, but the criticisms of such inconsistency have been presented in primary literature before. I would advise reverting to my version.Wrfrancis (talk) 17:08, 3 February 2019 (UTC)

One objection regarding your "redo version" is that you made arguments based on fragmentary, and thus deceptive, cladograms. A cladogram used in discussion of which clade(s) might be basal should be expected to show all the taxa of a given rank (or at least present a reasonably objective depiction of the amount of diversification that has occurred in various branches). In general, it seems like you were trying to eliminate the normative usage of the term. WolfmanSF (talk) 17:59, 3 February 2019 (UTC)

There are obviously many examples out there, such as Amborella, where a clade described as basal really is sister to the rest of the larger group. WolfmanSF (talk) 17:24, 4 February 2019 (UTC)

The normative usage is inconsistent and disagrees with textbooks, so imprecise terminology should be corrected. The inconsistency in the common usage is probably exacerbated by this very article by stating that "basal" means sister group, or the amount of diversity in some branch. Both of these usages are incorrect. Those unfamiliar with phylogenetics will read this page, and use "basal" incorrectly in their papers. This may result in many papers using the term incorrectly or inconsistently. It is clearly problematic to then report on the incorrect usage of the majority in the interest of a "neutral point of view". My version did not remove all mention of the idea. I had stated in the intro that the usage is inconsistent and has been criticized more than once. The example cladograms were given to illustrate this inconsistency. The perspective of which group is "basal" changes depending on what branches are on the tree, therefore the term is clearly misapplied. However, nodes are not equally basal, so it makes sense to refer to some nodes as basal, but not branches.Wrfrancis (talk) 19:42, 3 February 2019 (UTC)

In the strict sense, and in our examples, "basal group" does indeed mean "sister group to the rest of the clade". In a looser sense, it need not, but context should make the difference clear. I don't think there's much confusion out there around the concept of sister group. As for the amount of diversity of a branch, this is where things get interesting. It has nothing to do with whether a clade is basal (which the article should make clear), but may have a lot to do with what kind of basal clade it is. Is it a basal clade with 250,000 species, or a basal clade of just one (a "basal species")? What, exactly, does the level of diversity imply about the probability of having ancestral traits? I'm not sure this has been adequately studied. WolfmanSF (talk) 05:48, 6 February 2019 (UTC)

It's pretty awkward to have an article about a term that mainly discusses it's potential for misuse, and does not really describe how it should be used. You don't really address the one-to-one correspondence between nodes and clades. WolfmanSF (talk) 07:18, 4 February 2019 (UTC)

@Wrfrancis: it's not our job in an encyclopedia to correct wrong usages, but to report what reliable secondary sources say. The term is used inconsistently, and in a way that I too think is incorrect. But what I think and what you think is irrelevant, and must not influence our editing. Peter coxhead (talk) 09:51, 4 February 2019 (UTC)

It may also be true that by focusing on the potential for misusage, we are presented a distorted picture. That is, maybe no one feels a need to investigate the extent to which less diverse basal clades do indeed tend to posses ancestral characters, as in the ase of Amborella. WolfmanSF (talk) 17:20, 4 February 2019 (UTC)

@Peter coxhead: that's a fair point, yet even in this case, there are several sources that define basal in a particular way (I think I cited Krell 2004). @WolfmanSF: I agree that it was focused too much on misusage. The edits you made recently are an improvement (I think the definition of basal groups as having relative subgroups is fine), but I think there is still a problem with the example tree. This issue is somewhat theoretical and semantic, that it could be possible for a branch/leaf to be more or less basal than its sister lineage. All splits are bifurcations, meaning any two sister groups are by definition equally basal, thus it is inappropriate to call either one basal. If the example tree labeled the nodes (say, vertebrates, amniotes, mammals, primates), I would agree it is correct, but it is instead shown with the labels on the leaves. For my above 4 clades, vertebrates are then basal to mammals, that is, the LCA of vertebrates is closer to the base than the LCA of mammals. However, any given species of fish is not basal to mammals, even if they have fewer species or retain ancestral characters. Otherwise it really still implies that one modern taxon could somehow be "more basal" than another, which is precisely the inconsistent usage in the literature that Krell had criticized.Wrfrancis (talk) 20:22, 4 February 2019 (UTC)

I think you can call either or both clades from the first split in a tree basal when you might be comparing them with clades originating from later splits. It would be pointless if you were comparing them just to each other. Also, if the branches of a cladogram are labelled as clades, it shouldn't matter where you put labels, because clades and nodes correspond exactly. The article as written should make clear that if "basal" can applied to a clade as a whole, it does not then apply to any subset of the clade. WolfmanSF (talk) 01:40, 6 February 2019 (UTC)