One long term problem is that there are things that seemogical and would be very interesting biolocally. Very tempting to look at and try to interpret Procrustes plots. I have long told people not to look at and interpret them to much (they are still useful for spotting a specimen that had gross errors in digitization). Perhaps my fault for making it easy to display them. Purpose is just to be able to project data into shape space where one can perform multivariate analyses. The variables of course no longer correspond to what single landmarks do. Jim__________________F. James Rohlf, Distinguished Prof. Emeritus Dept. Anthropology and Ecology & Evolution Stonybrook University -------- Original message --------From: Leandro Monteiro <[email protected]> Date: 5/13/21 6:11 PM (GMT-05:00) To: Morphmet <[email protected]> Subject: [MORPHMET2] Re: WE AGREE IT IS STILL WRONG TO DO analyses of landmarks one at a time in Procrustes shape data I would like to follow on Chris' line about the importance of language in papers, and the responsibility of writers, reviewers, and editors to enforce it. I think that in many applications of GM, there is a disconnection between the biological structure being measured, the theoretical context, and the biological meaning of the measurements. There is sometimes emphasis on covering a structure with reference points, but no biological hypothesis linked to the interpretation of observed shape changes. Investigators need to be more concerned with the biological meaning of a shape change. Which underlying processes are responsible for the differences? It might be easier to do it with interlandmark measurements related to bone growth, but is just as important to keep it in mind when interpreting shape changes. The incorrect interpretation of shape changes might be a symptom of a bigger problem that affects many more areas than GM, which is the lack of theoretical context and biological meaning in measurements, leading to a kind of "data dredging". As a reviewer, I seem to be coming across this more often, or might be more concerned with it than I was before.Best regards,##################################################Leandro R. MonteiroLaboratorio de Ciencias AmbientaisUniversidade Estadual do Norte FluminenseE-mail: [email protected] Lattes: http://lattes.cnpq.br/4987216474124557WS: https://sites.google.com/uenf.br/ecol-evolucao-de-mamiferos/English WS: https://sites.google.com/uenf.br/mammalecologyandevolution/##################################################Em quarta-feira, 12 de maio de 2021 às 11:35:20 UTC-3, [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 >>>> >>>> -- >>>> 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]. >>>> 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]. >> 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 -- 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]. To view this discussion on the web visit https://groups.google.com/d/msgid/morphmet2/eb7ebe05-94e2-4376-a749-68bbeaf50362n%40googlegroups.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]. To view this discussion on the web visit https://groups.google.com/d/msgid/morphmet2/609dc118.1c69fb81.b8ff0.8cd3%40mx.google.com.
