Dear morphometricians I think most of us agree that analyses of landmarks one at a time are not a good idea. We've all been told this over and over and, if we are teaching morphometrics, we routinely tell it to our students. But it is actually not that easy to justify why not.
I think one important point is to think about the language. When we say we are interested "what landmark X does" or want to know "how landmark Y varies", I think we are using a linguistic shortcut. Actually, I think we really do not care at all what landmarks do or how they vary per se. What we are interested in is what they do in relation to the surrounding morphological structures or how their positions vary in relation to the anatomical axes of the structure to which they belong. What we are interested in for most morphological studies is the locations of landmarks and variation in those locations after we have stripped away the information of where the specimen is and which way it points. It is not quite accidental that this is essentially the definition of form (conformation, size-shape, size-and-shape, or whatever name you may prefer). Whether we are interested in this or in shape, after size information has also been stripped away, is a question that depends on the particular research question. For shape variables (the same is true with some differences for form/conformation etc.) it is also possible to show formally that it's not possible for just one landmark in a configuration to change so that the resulting change is just a shape change. Whatever change you might make to any landmark, there is always some change in the non-shape components of size, position and/or orientation. In my (obviously biased) view, the most accessible explanation for this is Figure 3 in the paper freely available via this link: https://link.springer.com/article/10.1007/s11692-020-09520-y Even the suggestions of Pietro and Paolo are not about the variation of a landmark on its own. A distance measurement inevitably involves *two* landmarks and for each of them is relative to the other one. The local measures of deformation all are based on calculations involving all the landmarks and a method for interpolating between them, so again is inherently relative to the whole configuration. As a consequence, we can't ever really separate, either logically or technically via morphometric analyses, how each landmark varies on its own. It is always the landmark of interest relative to all others. And as a result, we should not do analyses of morphometric data (superimposed or not) landmark by landmark, as Andrea and the others in this discussion have agreed. Of course, there are analyses like this out there (including a particular table in an old paper of mine -- I wish I could 'unpublish' that table...). If you encounter them in the literature, ignore them and look at those parts of the respective studies that do not rely on them. And of course we should not add new analyses of that kind. And because language has a role in this, we should also pay attention (as authors, reviewers or editors of morphometrics papers) to how shape changes are described in relation to landmarks. Shifts of landmarks are always relative shifts, and this should be mentioned for all of them. This may require repeating the word 'relative' rather a lot in some passages, but as this discussion shows, it is something that can help everyone in the field. I hope this helps. Best wishes Chris -- *********************************** Christian Peter Klingenberg School of Biological Sciences University of Manchester Michael Smith Building Oxford Road Manchester M13 9PT United Kingdom Web site: https://morphometrics.uk E-mail: [email protected] Phone: +44 161 2753899 Skype: chris_klingenberg *********************************** -----Original Message----- From: <[email protected]> on behalf of Diego Astua de Moraes <[email protected]> Date: Thursday, 13 May 2021 at 02:09 To: andrea cardini <[email protected]> Cc: "[email protected]" <[email protected]> Subject: Re: [MORPHMET2] WE AGREE IT IS STILL WRONG TO DO analyses of landmarks one at a time in Procrustes shape data Dear AndreaRegarding your last paragraph, but it also concerns your problem (1), I am under the impression, totally a guess, I admit that these mistakes are not necessarily more frequent now, but probably are (and will be) a recurrent issue that is likely to resurface from time to time. I guess when less people were in the field, it was easy for everyone to reach out to everyone and discuss dos and don'ts. The more there are people using GM, and we can now consider it is a fairly widespread approach, the more it is likely that one or another error/mistake/misinterpretation will occur again. More people means more literature, meaning more to read to be actually up to date on everything. I know some problems lie within the basics of the method, and should be solved simply by reading the basic literature and textbooks, but more people also mean more people approaching the method by themselves without any guidance. One thing is what we teach our own students, another is what can be expected from a wide variety of students/professionals using the methods and learning by themselves. If some basic issues in other long established fields (let's say, the use of proper terms in phylogenetic systematics, or proper approaches in basic taxonomy) that should be settled for good keep resurfacing here and there, I guess these problems also will in GM. However, why they are made by experienced researchers in top journals is beyond my guess! Cheers, Diego Diego Astúa, D.Sc. Professor Associado & Curador da Coleção de Mamíferos UFPE Associate Professor & Curator of Mammals UFPE _____________________________________________ e-mail: [email protected] / [email protected] Personal: CV Lattes <http://lattes.cnpq.br/3461530401338795> | ResearchGate <https://www.researchgate.net/profile/Diego_Astua> | Publons/ResearcherID <http://www.researcherid.com/rid/A-3583-2010> | ORCID <http://orcid.org/0000-0002-9573-6437> | Google Scholar <https://scholar.google.com/citations?user=KOaSIDEAAAAJ> Lab: Website <https://www.ufpe.br/mastozoologia> | Facebook <https://www.facebook.com/mastozoologiaufpe/> | Instagram <http://www.instagram.com/labmasto.ufpe> Em qua., 12 de mai. de 2021 às 11:35, andrea cardini <[email protected]> escreveu: Dear All, many thanks for your replies and thoughts. I'd split the problem in two (I talk about landmarks but it's similar with semilandmarks): 1) There are things that simply cannot be done (they're wrong and deeply misleading at least in biology): interpreting the variance of single landmarks after a common superimposition with the aim of telling whether this or that landmark varies more than others; computing the evolutionary rate of single landmarks one at a time etc. etc. This is something on which all morphometricians, who developed the methods we're using and whom I bothered with questions since the end of '90s, agree and have agreed for a very long time. I am glad to see there's no change on this issue and simply one should avoid making those mistakes or following those who keep making them (including in very prestigious journals). 2) There might be methods that help to guess whether a specific region (not a single landmark!) is particularly affected by change. Pietro, Philipp and Paolo mentioned some possibilities. There might be problems and difficulties here too, but there could be solutions or at least approximations. I am agnostic on this (with apologies to Paolo, whose paper has been on my reading list for quite a while: I'll get there, I promise!). Right now, however, my worry was about the first issue and those who answered confirm that nothing revolutionary happened: those were and still are big mistakes. Carmelo raised an interesting question about whether this is more or less common than in the past. Hard to say without a huge review of the literature. But 30 years after the "revolution" in morphometrics, those mistakes should not happen at all. Yet, they occur and, when made by experienced morphometricians and published in top journals, set a very bad example. Thanks again for your comments. Cheers Andrea On 12/05/2021 15:11, Paolo Piras wrote: > "Of course, there can be exceptions and a biological signal can be local > and be represented well by a single landmark or a single interlandmark > distance." > > I think that a proper evaluation of local deformation could be effective in > interpreting the "localness" of both shape and deformation differences... > > *Piras P.*, Profico A., Pandolfi L., Raia P., Di Vincenzo F., Mondanaro > A., Castiglione S., Varano V. (2020). Current options for visualization of > local deformation in modern shape analysis applied to paleobiological case > studies. *Frontiers in Earth Science*, 8:66. doi: 10.3389/feart.2020.00066 > IF: 2.689 > ATB > Paolo > > > > > Il giorno mer 12 mag 2021 alle ore 14:10 [email protected] < > [email protected]> ha scritto: > >> Dear Andrea, >> >> In principle, I agree that one should avoid interpreting single landmarks >> or shape coordinates because >> >> - landmarks are not geometrically independent after GPA (loss of degrees >> of freedom) >> >> - landmark displacement vectors depend on the superimposition and, hence, >> the other landmark positions (Pinocchio effect) >> >> - often the shape features are not that local but involve a joint shift of >> multiple landmarks; in this case, the actual shape patterns cannot be >> inferred from looking at each landmark separately. >> >> Formal statistical analyses (e.g., regressions, significance tests) of >> each landmark or shape coordinate separately can hardly be interpreted and >> are subject to the multiple comparison problem. This is why we have >> multivariate stats and GMM. With proper visualizations, such as TPS >> deformation grids or series of reconstructed shapes, the Pinocchio effect >> does not apply and one can observe even complex shape or form differences. >> >> Of course, there can be exceptions and a biological signal can be local >> and be represented well by a single landmark or a single interlandmark >> distance. But one cannot know about this before analyzing all the landmarks >> jointly! >> >> Best, >> >> Philipp Mitteroecker >> On Tuesday, May 11, 2021 at 6:18:33 PM UTC+2 [email protected] wrote: >> >>> Dear Dr. Andrea, Fruciano, and Pietro, >>> >>> I asked a question on integration/modularity in geomorph google forum. I >>> benefit hugely from Mike's reply. >>> >>> That post is somewhat related to the current post. So I am here to let >>> you aware and please feel free to comment further there if you have >>> interest. >>> >>> Link to my question: >>> https://groups.google.com/u/3/g/geomorph-r-package/c/VKpAxHnVW1U >>> >>> On Tuesday, May 11, 2021 at 7:52:05 PM UTC+8 Carmelo Fruciano wrote: >>> >>>> Dear Andrea, >>>> I've seen this from time to time, but I am not too sure there's been a >>>> recent increase in this. >>>> >>>> Some of the most striking cases in my own literature searches and >>>> reading involve genetic mapping of one coordinate at a time (post-GPA) - >>>> as if each coordinate were a separate trait, which is (IMHO) nonsensical. >>>> This is obviously biased because of my own research interests (i.e., I >>>> have seen more in this area because I've read a bit more in this area >>>> than in others, not because they are more frequent in genetic mapping >>>> than in other areas). But these papers are fairly spread over time and I >>>> didn't catch any particular increase in their frequency as of late. >>>> >>>> I understand this does not exactly address what you were asking but I >>>> still hope it helps, >>>> Carmelo >>>> >>>> >>>> -- >>>> ================== >>>> Carmelo Fruciano >>>> Italian National Research Council (CNR) >>>> IRBIM Messina >>>> http://www.fruciano.org/ >>>> ================== >>>> >>>> >>>> On 10 May 2021 14:49, andrea cardini <[email protected]> wrote: >>>> >>>> Dear All, >>>> I have the impression that studies analyzing one landmark at a time >>>> after a Procrustes superimposition (plus a possible sliding of >>>> semilandmarks) are beginning to pop up here and there in the biological >>>> literature. >>>> I wonder whether there's some revolutionary evidence, which was >>>> published and I missed, that contradicts a most basic principle of >>>> Procrustes shape analysis: never to analyze Procrustes shape variables >>>> one at a time, including especially the case of pairs or triplets of >>>> 2D-3D landmark Procrustes shape coordinates. This is nicely summarized >>>> by Paul in J. Anat. (2000) 197, pp. 103–120; exemplified in Fig. 9 of >>>> doi:10.1371/journal.pone.0025630; related to the problem of analyzing >>>> one PW at a time discussed by Jim (Syst. Biol. 47(1):147± 158, 1998); >>>> and most likely known since the early days of Procrustes GMM. >>>> I would be astonished to find that this is not longer true but I am >>>> happy to be surprised. >>>> >>>> Many thanks in advance for refs and feedback. >>>> Please, if you reply directly to me, let me know if I can share your >>>> answer. >>>> >>>> Cheers >>>> >>>> Andrea >>>> >>>> >>>> >>>> >>>> -- >>>> Dr. Andrea Cardini >>>> Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di >>>> Modena e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy >>>> tel. 0039 059 4223140 >>>> >>>> Adjunct Associate Professor, Centre for Forensic Anthropology, The >>>> University of Western Australia, 35 Stirling Highway, Crawley WA 6009, >>>> Australia >>>> >>>> E-mail address: [email protected], [email protected] >>>> WEBPAGE: https://sites.google.com/view/alcardini2/ >>>> or https://tinyurl.com/andreacardini >>>> >>>> FREE Yellow BOOK on Geometric Morphometrics: >>>> https://tinyurl.com/yellowmorphobook >>>> >>>> ESTIMATE YOUR GLOBAL FOOTPRINT: >>>> http://www.footprintnetwork.org/en/index.php/GFN/page/calculators/ >>>> SUPPORT: secondwarning.org <http://secondwarning.org> >>>> >>>> -- >>>> You received this message because you are subscribed to the Google >>>> Groups "Morphmet" group. >>>> To unsubscribe from this group and stop receiving emails from it, send >>>> an email to [email protected] <mailto:morphmet2%[email protected]>. >>>> To view this discussion on the web visit >>>> https://groups.google.com/d/msgid/morphmet2/7e5da2bd-3026-12df-522e-a17eed006d24%40gmail.com. >>>> >>>> >>>> >>>> -- >> You received this message because you are subscribed to the Google Groups >> "Morphmet" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected] <mailto:morphmet2%[email protected]>. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/morphmet2/c1b99d79-5ada-44ef-abd3-3068675d23a9n%40googlegroups.com >> <https://groups.google.com/d/msgid/morphmet2/c1b99d79-5ada-44ef-abd3-3068675d23a9n%40googlegroups.com?utm_medium=email&utm_source=footer> >> . >> > -- Dr. Andrea Cardini Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di Modena e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy tel. 0039 059 4223140 Adjunct Associate Professor, Centre for Forensic Anthropology, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia E-mail address: [email protected], [email protected] WEBPAGE: https://sites.google.com/view/alcardini2/ or https://tinyurl.com/andreacardini FREE Yellow BOOK on Geometric Morphometrics: https://tinyurl.com/yellowmorphobook ESTIMATE YOUR GLOBAL FOOTPRINT: http://www.footprintnetwork.org/en/index.php/GFN/page/calculators/ SUPPORT: secondwarning.org <http://secondwarning.org> -- You received this message because you are subscribed to the Google Groups "Morphmet" group. 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