Damien Actually I think a number of tools including geomorph/RRPP and MCMCglmm allow you to fit arbitrarily complex linear models while incorporating a phylogeny or pedigree. I could be wrong about this functionality in geomorph though. So I don't think you are limited to single species means while doing such fits. While this makes some strong evolutionary assumptions (BM), it is at least something. Effectively this is just structured error covariance matrix, (i.e. not iid), so a number of tools can in principal handle it (if you know how to set up the covariance matrix), but geomorph is an obvious choice for landmark data (you would need to use a subset of PCs that retain all trait variation for MCMCglmm, and then there are some issues with fitting the various covariance matrices).
In any case, I believe it is via the Cov = argument in lm.rrpp, while in MCMCglmm you would use the pedigree argument (it accepts a phylogeny as I understand it). Let me know if I am wrong about this. I am not 100% sure if it is all tidy yet, but I know they have been working on this for lme4 (here is sort of a rough sketch, https://bbolker.github.io/mixedmodels-misc/notes/phylog.html), and you can also trick lme4 to fit multivariate mixed models (but I have not tried it for very high dimensional data). Here are the notes for the lecture and tutorial I did with Ben Bolker ( https://mac-theobio.github.io/QMEE/MultivariateMixed.html). This is definitely a role your own approach though (you would need to do a lot of tinkering), so I am not sure I would start here. Indeed geomorph is almost certainly the easiest I think. Ian On Tue, 14 Jul 2020 at 21:32, Damien Esquerre <[email protected]> wrote: > Dear all, > thanks for the excellent feedback. I need to maybe clarify some things: > > I am definitely aware and agree that interspecies comparisons need to be > done in a phylogenetic context. However, when you have multiple individuals > per species, and are comparing intraspecific vectors such as allometric > slopes between species (I know it sounds contradictory but hopefully you > know what I mean) I am not aware of any method that can incorporate > phylogenetic information (these usually rely on species means, or one value > per species). We sort of explored a bit of that issue in the attached > paper. I guess I can think of ways around it, like including 'clade' as a > factor in the model, but that doesn't fully account for the relationships > between species. I think Dean and Mike have been working on this? > > I like Ian's suggestion of using species means at a comparable size. > However, that wouldn't work when we are talking about species with orders > of magnitude in size difference. > > Something I can think of, even if ontogenetic trajectories are different > between species, one could compute the evolutionary allometric trajectory > of the mean adult shape of a group of species, and then extract the > residuals from that regression. I guess there could be many arguments > against doing this if those species have different ontogenetic > trajectories, but would love to open a discussion about this. > > Another option is just not performing any allometric corrections and > accept there will be a confounded allometric component to variation with > the evolutionary (interspecific variation). > > In the end, what would you do if you wanted to detect mode of evolution, > convergence and or adaptation (effect of environment) in a clade that > displays heterogeneous allometric slopes? In particular, when you dont have > comprehensive ontogenetic series and that is not the focus of your question. > > This is something I've been thinking about for years, and it fascinates > me, but have never arrived at a satisfactory answer. > > Thanks again! > Damien > > On Wed, Jul 15, 2020 at 6:04 AM Mauro Cavalcanti <[email protected]> > wrote: > >> Dear Hugo, >> >> >shape of one particular species. Now regarding the Ian example in >> Drosophila, I tested allometry into 60 species across the genus and there >> is definitely a >pattern (indeed a beautiful one across the genus looking >> into the different clades) but looking into one particular group of species >> the "size" is indeed a very >> >> Have you already published this work? If so, could you please provide a >> reference? It looks truly great. >> >> With best wishes, >> >> Em ter., 14 de jul. de 2020 às 16:57, Hugo Benítez < >> [email protected]> escreveu: >> >>> Fantastic line of discussion >>> >>> I'm absolutely agree with Joe, when there is not a Phylogenetic context >>> maybe the allometric correction would not have very much sense, because we >>> are looking into only one generation so we really don't know very well if >>> the shape we are looking for is product of environmental condition (that >>> can be connected with plenty of variables like nutrition, stress, etc...) >>> now as you asked there is multiple group of species so definitely in your >>> idea there is some "historic factor" that provide the shape of one >>> particular species. Now regarding the Ian example in Drosophila, I tested >>> allometry into 60 species across the genus and there is definitely a >>> pattern (indeed a beautiful one across the genus looking into the different >>> clades) but looking into one particular group of species the "size" is >>> indeed a very good trait to explain differences (like species from island, >>> marsh or the typical cosmopolitan) cosmopolitan Drosophila have the simple >>> small wing (very small). On the other hand, where maybe "makes sense" is >>> in one single species after doing some quantitative genetics experiments >>> and controlling the factors that could influence the size depending on your >>> question... But I think if there is a simple species in the game the >>> factors in one generation are indeed just the real biological meaning of >>> your differences and I dont think a correction will have a very biological >>> meaning... Now of course could be some exception to the rule and a >>> Biogeographical question like bergmann rule, or another rule like that >>> where the relationship is directly related to size maybe a correction could >>> be ok to see how big there are the differences when the factor is >>> included... >>> >>> I would love to see more replies, nice topic to discuss Damien >>> >>> Best >>> Hugo Benítez >>> >>> >>> El mar., 14 jul. 2020 a las 14:55, Damien Esquerre (< >>> [email protected]>) escribió: >>> >>>> Dear morpho community, >>>> I have a philosophical question on size correction that should start an >>>> interesting discussion. >>>> When we are interested in seeing the effects of species or >>>> environmental variables for example, on shape, people often first remove >>>> allometric variation by computing the residuals of a shape ` size >>>> regression. This of course, doesn't make sense if there are heterogeneous >>>> slopes and species have different allometric trajectories (i.e. if the >>>> species*size term is significant). >>>> What do you think would be the most appropriate way to deal with this >>>> situation then, if you are interested in environmental effects on shape? >>>> Best regards, >>>> Damien Esquerré >>>> >>>> -- >>>> 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/CAJiv7Cw0S2A%3D-kpEmknt-tUp92Vjy0hkiF%3DVF6C77NsFECP%2BMw%40mail.gmail.com >>>> <https://groups.google.com/d/msgid/morphmet2/CAJiv7Cw0S2A%3D-kpEmknt-tUp92Vjy0hkiF%3DVF6C77NsFECP%2BMw%40mail.gmail.com?utm_medium=email&utm_source=footer> >>>> . >>>> >>> >>> >>> -- >>> >>> *Dr. Hugo A. Benítez* >>> Profesor Asociado >>> Centro de Investigación de Estudios Avanzados del Maule >>> Universidad Católica del Maule >>> >>> Research Associate, University of Cambridge Museum of Zoology >>> External Researcher Faculty of Agriculture, University of Zagreb >>> >>> Lab website: http://www.morphoshape.com <http://www.hugoabenitez.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/CACTC4WqeQiyyLW0gGy%3Ds8jr%3DM0pXAJmuEqXGKUCAaxs3%3DOa%2BmA%40mail.gmail.com >>> <https://groups.google.com/d/msgid/morphmet2/CACTC4WqeQiyyLW0gGy%3Ds8jr%3DM0pXAJmuEqXGKUCAaxs3%3DOa%2BmA%40mail.gmail.com?utm_medium=email&utm_source=footer> >>> . >>> >> >> >> -- >> Dr. Mauro J. Cavalcanti >> E-mail: [email protected] >> Web: http://sites.google.com/site/maurobio >> "Life is complex. It consists of real and imaginary parts." >> >> -- >> 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/CAC1JhZYNJdDWqfrsGXGa%2Be0YX8oA5CjoLBTXa67wHuGHaSqJbQ%40mail.gmail.com >> <https://groups.google.com/d/msgid/morphmet2/CAC1JhZYNJdDWqfrsGXGa%2Be0YX8oA5CjoLBTXa67wHuGHaSqJbQ%40mail.gmail.com?utm_medium=email&utm_source=footer> >> . >> > -- > 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/CAJiv7CxV96Zj%2B6Sq793eq%3DB-5EoJ4FbbbOW5K1DsS3ENwYCuDw%40mail.gmail.com > <https://groups.google.com/d/msgid/morphmet2/CAJiv7CxV96Zj%2B6Sq793eq%3DB-5EoJ4FbbbOW5K1DsS3ENwYCuDw%40mail.gmail.com?utm_medium=email&utm_source=footer> > . > -- Ian Dworkin Department of Biology McMaster University Office phone 905 525 9140 ext. 21775 Lab phone 905 525 9140 ext. 20076 [email protected] dworkinlab.github.io -- You received this message because you are subscribed to the Google Groups "Morphmet" group. 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