Talk:Apomorphy and synapomorphy/Archive 1

The Compleat Cladist
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The workbook "The Complete Cladist" (Compleate is spelled "eate" - its an old English word) defines synapomorhies as "shared derived characters" (page 2). It notes that Aves, Crocodylia, and Squamata are all considered to be relatives because they share synapomorphic characters "thought to have originated in their common ancestor" (page 2).

The citation for the workbook is

Wiley, EO, D Siegel-Causey, DR Brooks, and VA Funk. 1991. The Compleat Cladist: A Primer of Phylogenetic Procedures. University of Kansas Museum of Natural History Special Publication 19.

Can be read online at http://www.archive.org/stream/compleatcladistp00wile#page/n3/mode/2up

or downloaded at

http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.77.2670&rep=rep1&type=pdf

this is a vary large, scanned PDF file

Brouwern (talk) 00:01, 31 October 2010 (UTC)

Apomorphy
"Apomorphy" currently redirects to this page, which seems less than helpful given that this page never defines "apomorphy" and in fact uses the word in a definition as if the reader should be expected to know what it means (the second sentence of this article reads in part that "A synapomorphy is thus an apomorphy visible in multiple taxa" ("apomorphy" in the sentence is a wikilink, but since, again, it simply redirects back to this page, it's not a particularly useful one)). This means that anyone trying to look up "apomorphy" in Wikipedia is out of luck. I see from the page history of "apomorphy" that it used to redirect to cladistics, where "apomorphy" was defined, but was changed two years ago. I'm not sure why the change; it seems that it makes more sense to redirect "apomorphy" to a page where the concept is defined and discussed, rather than one in which it's simply mentioned in passing. I propose that either "apomorphy" be made to redirect back to "cladistics" again, or that "apomorphy" be discussed and defined in this article, rather than just mentioned in passing as it is now. I haven't made the change myself only because I'm not knowledgeable about the subject and don't know that there might have been a good reason for making the change in the redirect, and thus don't know which course of action would be preferable. (I infer that perhaps most apomorphies of interest are in fact synapomorphies, and thus the broader use of the word "apomorphy" is relatively rare? If so, that should be made clear in the article.)  --Smeazel (talk) 20:18, 1 February 2012 (UTC)
 * Hello smeazel. I will refrain from calling you my usual "buddy" or some such thing, as some people do not seem to like it. It seems to me you've gone out of your way to come to my attention. You've been on since 2007, at least this time, and you know enough to hide your IP address under a user name. You're not telling us anything about yourself. I'm not a sysadmin so I can't track you. Five years is a long time, yet there is almost no history on your discussion page. You pick out an obscure point in an article you claim to know nothing about and send me a message. However, there seems to be no record of me ever working on that article. Yet, you cite a figure of two years. I would say you are trying to come to my attention. All right, you have my attention. What do you want? For the point you mention, well, I have no memory of working on that article, senator (joke). It is of course wrongly linked, as you say. One does not link to the same article and I believe there is or was an error message associated with it. You put yourself forward as needing my blessing on changing it. That isn't necessary as it is a manifest error. Again, after 5 years I might have assumed you'd know that, but maybe not. So, I'm changing it. You can too! (to get poetic). Anything else? You want to converse? WP is against conversation but you could probably slip a few things through. Just don't use it to denounce tyranny, as I have in the past. By the way I got no plans to get back on the cladistics articles. The specialized vocabulary didn't "take" among linguists. I see "shared common innovation" a lot, I never see synapomorphy. I do not think the linguists are going to follow the geneticists into the twists and turns of essentially mathematical language. I know I wouldn't, but then I'm a technical writer trying to be user-friendly. You find me more on the language side. Ciao (oops! Does that offend you?)Dave (talk) 01:21, 2 February 2012 (UTC)

User:Smeazel was quite right that the article is confusing. I've done a little bit of work on it, but it needs more. The relationship between "derived character", "apomorphy" and "synapomorphy" needs careful explanation. Peter coxhead (talk) 17:42, 6 December 2015 (UTC)

External links modified
Hello fellow Wikipedians,

I have just added archive links to 1 one external link on Synapomorphy. Please take a moment to review my edit. If necessary, add after the link to keep me from modifying it. Alternatively, you can add to keep me off the page altogether. I made the following changes:
 * Added archive https://web.archive.org/20080828192820/http://www.ebrary.com/ to http://www.ebrary.com

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Title
User:Oranjelo100 moved the page to "Synapomorphy and Apomorphy". I moved it to "Synapomorphy and apomorphy" as per WP:LOWERCASE – sentence case is used in article titles.

More generally, the use of "and" in this way in article titles is frowned on – see WP:AND. The article could be moved back to "Synapomorphy" or could be moved to "Apomorphy" on the grounds that this is the more general term. It would be useful to have some views on this. Peter coxhead (talk) 06:29, 19 June 2018 (UTC)

Novelty
Do I understand the concept?
 * An apomorphy is a novelty that a species/genus/clade has relative to the particular ancestor being considered (where novelty = genetic divergence).

We could call the particular ancestor to which the consideration is relative the apex ancestor, AA, and call such a novelty an apex novelty.
 * A synapomorphy is an apex novelty that is 1. shared by (some not necessarily all) members the species/genera/clades being considered and 2. shared by their most recent common ancestor, MRCA.
 * A homoplasy is an apex novelty that is 1. shared by members of the species/genera/clades being considered and 2. NOT shared by their most recent common ancestor, MRCA.
 * A plesiomorphy is trait that a species/genus/clade shares with the particular ancestor being considered. (It is an apex trait.)
 * A symplesiomorphy is an apex trait that is 1. shared by (some not necessarily all) members the species/genera/clades being considered and 2. shared by their most recent common ancestor
 * A pseudoplesiomorphy is a trait that cannot be classified as an apex novelty or an apex trait. (Things are unclear!)
 * An autapomorphy is an apex novelty that is unique to a particular group.

So first 1. decide which ancestor is to be the apex ancestor, AA Then 2. decide if the trait is an apex novelty or an apex trait relative to the apex ancestor, AA. Then 3. decide whether or not the groups showing the apex novelty or apex trait share it with their most recent common ancestor MRCA, or 4. (in the case of an autapomorphy) decide if the apex novelty is shared with other groups. --Burraron (talk) 09:59, 6 June 2021 (UTC)
 * well, it's better to discuss these concepts in relation to an example tree, I think. The article says "The concept of synapomorphy is relative to a given clade in the tree of life", but this is true of the concept of plesiomorphy as well, as the immediately following sentence shows. Some points I would make:
 * Apomorphies are, as you say, novelties, distinctive features of a clade that separate the clade from its sister(s). Thus it's important that they are not shared by members of the surrounding clade, a proviso which needs to be stressed. Apomorphies separate one clade from another.
 * Neither (syn)apomorphies nor (sym)plesiomorphies need to be shared by all members of the clade; both can be lost in some members. (Thus parasites, such as species of the parasitic plant Rafflesia, typically lack many of the distinctive characters/synapomorphies of the larger clades to which they belong, but that doesn't stop them being synapomorphies of those clades.)
 * Almost all modern phylogenetic studies of extant organisms are based on molecular evidence, not characters, so some of the 'traditional' cladistic terminology is not now relevant. Incomplete lineage sorting is common, so the gene trees and the species/population tree are different; an apomorphy of a gene tree may be a plesiomorphy of species tree. Hemiplasy is probably the norm; species trees are a kind of average over gene trees.
 * Peter coxhead (talk) 06:15, 7 June 2021 (UTC)
 * Thank you. I tried not to phrase things in terms of genes or physical characteristics. I edited what I wrote above and added "(some not necessarily all)", but I am still not sure I have given in accurate account of the use of the terms. In general I don't find these piles of words helpful in thinking about living things. --Burraron (talk) 10:14, 9 June 2021 (UTC)
 * I entirely agree that "piles of words" are not helpful in the case of these terms concepts, which is why I would always prefer to discuss in the context of an example tree. However, I would say that you can't discuss apomorphy and plesiomorphy without explicitly considering physical characteristics, since they emerged as concepts in the context of early (Hennig-based) cladistics which was concerned with observable characters, and now you can't discuss any kind of phylogeny without considering genetic and/or genomic data. The direction of discussion in papers reporting phylogenetic studies is typically: (1) find a tree based on molecules (2) based on this tree look for (syn)apomorphies.
 * What we can agree, I think, is that these concepts are tricky to explain! Peter coxhead (talk) 07:45, 10 June 2021 (UTC)

“Refers to” vs. “Are”
Perhaps you could kindly explain to me why you think “refers to” is more accurate than “are.” As far as I can see, this is more of a stylistic preference than anything else. danielkueh (talk) 11:05, 13 October 2021 (UTC)
 * I'm reaching out to you again in an effort to resolve this issue. You recently reverted my edit, claiming that synapomorphy and apomorphy "are not the actual characters" but instead "refer to the presumed evolutionary history, the patterns of the characters on the cladogram ," which I have just reverted . They are not patterns of traits on a cladogram. That would be a phylogenetic tree. And yes, they are characters or traits, specifically derived characters or traits, and here are three reliable sources that say so:
 * Hillis, David M.; Sadava, David; Hill, Richard W.; Price, Mary V.. Principles of Life, Second Edition
 * Synapomorphy: A trait that arose in the ancestor of a phylogenetic group and is present (sometimes in modified form) in all of its members, thus helping to delimit and identify that group. Also called a shared derived trait.
 * Futuyma, Douglas J.; Kirkpatrick, Mark (2017). "Evolutionary Biology". Evolution (4th ed.)
 * Apomorphic: Having a derived character or state, with reference to another character or state. See synapomorphy.
 * Synapomorphy: A derived character state that is shared by two or more taxa and is postulated to have evolved in their common ancestor.
 * Kitching, Ian J.; Forey, Peter L.; Williams, David M. "Cladistics". In Levin, Simon A. (ed.). Encyclopedia of Biodiversity (2nd ed.)
 * Apomorphy: A derived character or character state; if two or more taxa share apomorphies, these are referred to as synapomorphies.
 * Homology: Two characters passing the similarity, conjunction, and congruence tests are termed homologous; in cladistics, homology is synonymous with synapomorphy.
 * And according to one of WP's policy document WP:NOTDIC, it describes "poorly written dictionary-style introductory sentences" as ones that use "refer to" such as '"Dog is a word that refers to a domesticated canine" (WP:ISATERMFOR).' The policy document goes even further to say that "opening sentences like the above ought to be cleaned up in accordance with our Guide to writing better articles. Editors should boldly replace these cumbersome phrasings ("is a term for", "is a word that means", "refers to") with the more direct "is" construction, for example: "A dog is an animal of the species Canis lupus.", or "A dog is a domesticated canine." (See: Writing better articles: Avoid using "refers to")"
 * So if there are no further objections, I think the lead sentence should make it clear that synapomorphy is indeed a derived a character or trait that is shared by two or taxa and is thought to have evolved from a common ancestor, consistent with how it is described in reliable sources (WP:V). danielkueh (talk) 12:25, 13 October 2021 (UTC)
 * the terms can be used differently. "(Syn)apomorphy" can be used in a concrete, countable sense to mean a particular character state, which is what the definitions you quote capture. It's also the original Henig sense. In this sense, you can substitute "(shared) derived character state" for "(syn)apomorphy" in a use and it will make sense. But the terms can also be used in a more abstract, mass sense, as in this paper, for example. When the authors write "synapomorphy and monophyly are not the same", "synapomorphy is the evidence", "synapomorphy in turn is merely the organizing principle used to arrive at monophyletic groups", you can't just replace "synapomorphy" by "shared derived character". They are abstracting a concept from concrete examples.
 * So to return to our article. I, wrongly I now think, read the original wording as meaning the concept – because it didn't say " an apomorphy" or "apomorph ies " to make clear the concrete sense intended. I agree with you about "refers" vs. "is". So I think the first sentence should be changed to something like "In phylogenetics, an apomorphy is a derived character of a clade; a synapomorphy is a shared apomorphy." Peter coxhead (talk) 06:16, 14 October 2021 (UTC)
 * I agree with that suggested definition. In fact, I was thinking along the same lines since this articles has two names. danielkueh (talk) 07:16, 14 October 2021 (UTC)