Dear Jacqueline You say that you “agree it was the nail in the coffin for the coding of X, Y, and Z coordinates as independent characters”. Actually, the simulations in the paper by Varón-González et al. are based on lineages/taxa evolving in multidimensional spaces without specifying anything about the nature of the dimensions of those spaces. So they may be the x, y, and/or z coordinates of landmarks, or they may be the dimensions of a shape tangent space based on landmarks (following Kendall etc.) or different shape tangent spaces (e.g. based on outlines or surfaces; see Srivastava & Klassen, Functional and Shape Data Analysis, Springer, 2016) or perhaps a morphospace obtained by entirely different considerations altogether. The key assumptions of that study were a multidimensional morphospace and evolution characterised as a random walk by some sort of Brownian motion, possibly with additions for morphological integration (Brownian motion with different evolutionary rates in different directions of the morphospace) and/or for stabilising selection (via Ornstein-Uhlenbeck process).
These assumptions are rather general, and should therefore be reasonable for many situations where one might consider using morphometric data for inferring phylogenies. This generality was intentional when we designed the simulations, in the hope that the paper by Varón-González et al. would be able to provide a decisive answer to the question we set out to address. As the simulation results turned out, this answer is rather discouraging. As far as I am aware, most attempts to explain why it should be possible to use morphometric data for inferring phylogenies have referred, in one way or another and sometimes more explicitly and sometimes more implicitly, to just such Brownian motion processes or their variants. Therefore, the simulations in the paper by Varón-González et al. should apply to those discussions and also to the question you recently raised in this forum. 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] *********************************** -----Original Message----- From: [email protected] <[email protected]> on behalf of Jacqueline Silviria <[email protected]> Date: Monday, 5 February 2024 at 16:51 To: andrea cardini <[email protected]> Cc: [email protected] <[email protected]> Subject: Re: [MORPHMET2] Compiling metadata on all methods of phylogenetic inference using GM data Good morning I have the impression that the SB paper by Varón-González et al. was almost the nail in the coffin on the usefulness of morphometric data in phylogenetic inference. I agree it was the nail in the coffin for the coding of X, Y, ZjQcmQRYFpfptBannerStart This Message Is From a New External Sender You have not previously corresponded with this sender. Please exercise caution when opening links or attachments included in this message. ZjQcmQRYFpfptBannerEnd Good morning I have the impression that the SB paper by Varón-González et al. was almost the nail in the coffin on the usefulness of morphometric data in phylogenetic inference. I agree it was the nail in the coffin for the coding of X, Y, and Z coordinates as independent characters, which to my knowledge was never justified to being with, even in a resistant-fit context (correct me if I’m wrong). I am not saying that they're totally useless, but are difficult to model and, more importantly, even when they carry a signal, cases in which the signal is so strong to retrieve an accurate phylogeny are probably the exception. I suspect this is partly because most published phylogenetic morphometric studies only sample one configuration without testing for modularity or including additional configurations, which is the antithesis of the total evidence requirement (see reviews by Catalano, et al. 2015 [academic.oup.com] <https://urldefense.com/v3/__https://academic.oup.com/sysbio/article/64/2/294/1632736__;!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiAH5g85lQ$<https://urldefense.com/v3/__https:/academic.oup.com/sysbio/article/64/2/294/1632736__;!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiAH5g85lQ$>>; Catalano & Torres 2017 [onlinelibrary.wiley.com] <https://urldefense.com/v3/__https://onlinelibrary.wiley.com/doi/full/10.1111/zsc.12186__;!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiDiPPynQg$<https://urldefense.com/v3/__https:/onlinelibrary.wiley.com/doi/full/10.1111/zsc.12186__;!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiDiPPynQg$>>). But the practical difficulties in modeling remain (e.g., logical interdependence between vertices within a configuration; interdependence between configurations; the appropriateness of squared vs. linear displacements; superimposition at “interspecific” vs. “intraspecific” levels; quantifying affine shape changes along branches; static vs. dynamic homology/transitivity for pseudo-landmark data; the tree-length flattening problem reported by Bardin et al., 2013 [onlinelibrary.wiley.com] <https://urldefense.com/v3/__https://onlinelibrary.wiley.com/doi/full/10.1111/1749-4877.12076__;!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiDt3NXKWA$<https://urldefense.com/v3/__https:/onlinelibrary.wiley.com/doi/full/10.1111/1749-4877.12076__;!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiDt3NXKWA$>>), and I don’t know what the solutions are. There are inaccuracies (for instance, we might have stated PCs were good as they're indep., when used in ML, but it is wrong) and I don't think those are particularly good methods. Also agreed, don’t have much to add. Thank you in advance for your time. Jacqueline S. Silviria The Last King of the Jungle Department of Earth & Space Science University of Washington Seattle, WA, USA [email protected]<mailto:[email protected]>, [email protected]<mailto:[email protected]> ResearchGate profile [researchgate.net] <https://urldefense.com/v3/__https://www.researchgate.net/profile/J_Silviria__;!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiDtPP7GeA$<https://urldefense.com/v3/__https:/www.researchgate.net/profile/J_Silviria__;!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiDtPP7GeA$>> Twitter: @JSilviria Sent from my iPhone On Feb 5, 2024, at 12:52 AM, andrea cardini <[email protected]<mailto:[email protected]>> wrote: Dear Jacqueline, I have the impression that the SB paper by Varón-González et al. was almost the nail in the coffin on the usefulness of morphometric data in phylogenetic inference. I am not saying that they're totally useless, but are difficult to model and, more importantly, even when they carry a signal, cases in which the signal is so strong to retrieve an accurate phylogeny are probably the exception. I may be wrong! There are a few papers in which we used ML and NJ (attached). There are inaccuracies (for instance, we might have stated PCs were good as they're indep., when used in ML, but it is wrong) and I don't think those are particularly good methods. I see them as relatively simple tools to explore similarities with some less constraints compared to UPGMA and the like. It would be really nice to have a review on this topic. Keep us updated on what you find! Good luck Andrea PS An interesting issue few have explored (Caumul & Polly and some of my papers) is the effect of sampling error on species means when those species are used to reconstruct phenetic or phyletic relationships: it can be large especially where differences are smaller (say, species within a genus). On 02/02/2024 06:30, Jacqueline Silviria wrote: Good morning, I have been investigating the utility of parsimony and likelihood methods of phylogenetic inference using GM data, specifically for specimen-level analyses of mammalian postcanine dentition. I am compiling a list of all published phylogenetic morphometric methods, to determine which ones would be feasible for evaluation within the constraints of my current research goals and the processing power of my M2 Max MacBook Pro. Below is a list of undiscretized methods (i.e., those that attempt to analyze continuously varying data “as such”, without a priori discretization) I’ve encountered in the literature thus far, with abbreviations modified from Catalano & Torres (2017) <https://onlinelibrary.wiley.com/doi/full/10.1111/zsc.12186><https://onlinelibrary.wiley.com/doi/full/10.1111/zsc.12186%3e> [onlinelibrary.wiley.com] <https://urldefense.com/v3/__https://onlinelibrary.wiley.com/doi/full/10.1111/zsc.12186<https://urldefense.com/v3/__https:/onlinelibrary.wiley.com/doi/full/10.1111/zsc.12186>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiAffEUUwg$>: - LAUP (Landmark Analysis Under [Wagner-like] Parsimony), PM (Phylogenetic Morphometrics in capital letters), “Simultaneous mapping": Catalano et al. (2010) <https://onlinelibrary.wiley.com/doi/full/10.1111/j.1096-0031.2010.00302.x><https://onlinelibrary.wiley.com/doi/full/10.1111/j.1096-0031.2010.00302.x%3e> [onlinelibrary.wiley.com] <https://urldefense.com/v3/__https://onlinelibrary.wiley.com/doi/full/10.1111/j.1096-0031.2010.00302.x<https://urldefense.com/v3/__https:/onlinelibrary.wiley.com/doi/full/10.1111/j.1096-0031.2010.00302.x>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiC-a0eHpQ$>, Goloboff & Catalano (2011) <https://onlinelibrary.wiley.com/doi/full/10.1111/j.1096-0031.2010.00318.x><https://onlinelibrary.wiley.com/doi/full/10.1111/j.1096-0031.2010.00318.x%3e> [onlinelibrary.wiley.com] <https://urldefense.com/v3/__https://onlinelibrary.wiley.com/doi/full/10.1111/j.1096-0031.2010.00318.x<https://urldefense.com/v3/__https:/onlinelibrary.wiley.com/doi/full/10.1111/j.1096-0031.2010.00318.x>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiAdF179NQ$>, Catalano & Goloboff (2012) <https://academic.oup.com/sysbio/article/61/3/392/1669518><https://academic.oup.com/sysbio/article/61/3/392/1669518%3e> [academic.oup.com] <https://urldefense.com/v3/__https://academic.oup.com/sysbio/article/61/3/392/1669518<https://urldefense.com/v3/__https:/academic.oup.com/sysbio/article/61/3/392/1669518>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiDH-0mRtA$>, Perrard et al. (2016) <https://onlinelibrary.wiley.com/doi/full/10.1111/cla.12138><https://onlinelibrary.wiley.com/doi/full/10.1111/cla.12138%3e> [onlinelibrary.wiley.com] <https://urldefense.com/v3/__https://onlinelibrary.wiley.com/doi/full/10.1111/cla.12138<https://urldefense.com/v3/__https:/onlinelibrary.wiley.com/doi/full/10.1111/cla.12138>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiABnuNlkw$>, etc. This is the most widely applied method I’ve seen in the literature after neighbor-joining, and the one I’m most familiar with, but Adams et al. (2013) <http://www.italian-journal-of-mammalogy.it/A-field-comes-of-age-geometric-morphometrics-in-the-21st-century,77238,0,2.html><http://www.italian-journal-of-mammalogy.it/A-field-comes-of-age-geometric-morphometrics-in-the-21st-century,77238,0,2.html%3e> [italian-journal-of-mammalogy.it] <https://urldefense.com/v3/__http://www.italian-journal-of-mammalogy.it/A-field-comes-of-age-geometric-morphometrics-in-the-21st-century,77238,0,2.html<https://urldefense.com/v3/__http:/www.italian-journal-of-mammalogy.it/A-field-comes-of-age-geometric-morphometrics-in-the-21st-century,77238,0,2.html>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiAVbmCuDA$> and Ascarrunz et al. (2019) <https://peerj.com/articles/7476/><https://peerj.com/articles/7476/%3e> [peerj.com] <https://urldefense.com/v3/__https://peerj.com/articles/7476/<https://urldefense.com/v3/__https:/peerj.com/articles/7476/>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiBAW8CpqQ$> have expressed reservations. No ML or Bayesian equivalents exist. - LC-P (Landmark coordinates under [Wagner-like] parsimony), “Linear parsimony": Gold et al. (2014) <https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0105793><https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0105793%3e> [journals.plos.org] <https://urldefense.com/v3/__https://journals.plos.org/plosone/article?id=10.1371<https://urldefense.com/v3/__https:/journals.plos.org/plosone/article?id=10.1371>*journal.pone.0105793*3E__;LyU!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiB9ygWBIA$>, Ascarrunz et al. (2019) <https://peerj.com/articles/7476/><https://peerj.com/articles/7476/%3e> [peerj.com] <https://urldefense.com/v3/__https://peerj.com/articles/7476/<https://urldefense.com/v3/__https:/peerj.com/articles/7476/>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiBAW8CpqQ$>. Heavily criticized by Varón-González et al. (2020) <https://academic.oup.com/sysbio/article/69/5/863/5716339><https://academic.oup.com/sysbio/article/69/5/863/5716339%3e> [academic.oup.com] <https://urldefense.com/v3/__https://academic.oup.com/sysbio/article/69/5/863/5716339<https://urldefense.com/v3/__https:/academic.oup.com/sysbio/article/69/5/863/5716339>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiCEQCruZw$>, though their rationale was in turn criticized by other skeptics of this method (see review by Goloboff, 2022 <https://www.routledge.com/Refining-Phylogenetic-Analyses-Phylogenetic-Analysis-of-Morphological-Data/Goloboff/p/book/9780367420277><https://www.routledge.com/Refining-Phylogenetic-Analyses-Phylogenetic-Analysis-of-Morphological-Data/Goloboff/p/book/9780367420277%3e> [routledge.com] <https://urldefense.com/v3/__https://www.routledge.com/Refining-Phylogenetic-Analyses-Phylogenetic-Analysis-of-Morphological-Data/Goloboff/p/book/9780367420277<https://urldefense.com/v3/__https:/www.routledge.com/Refining-Phylogenetic-Analyses-Phylogenetic-Analysis-of-Morphological-Data/Goloboff/p/book/9780367420277>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiAtwfKFKA$>) - LC-SCP (Landmark coordinates under square-change parsimony): If understand correctly, this is what Ascarrunz et al. (2019) <https://peerj.com/articles/7476/><https://peerj.com/articles/7476/%3e> [peerj.com] <https://urldefense.com/v3/__https://peerj.com/articles/7476/<https://urldefense.com/v3/__https:/peerj.com/articles/7476/>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiBAW8CpqQ$> had to write an R script for to replicate methods proposed elsewhere (e.g., McArdle & Rodrigo, 1994 <https://academic.oup.com/sysbio/article/43/4/573/1686245><https://academic.oup.com/sysbio/article/43/4/573/1686245%3e> [academic.oup.com] <https://urldefense.com/v3/__https://academic.oup.com/sysbio/article/43/4/573/1686245<https://urldefense.com/v3/__https:/academic.oup.com/sysbio/article/43/4/573/1686245>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiCRonIJVg$>, Rohlf, 2001 <https://onlinelibrary.wiley.com/doi/abs/10.1111/j.0014-3820.2001.tb00731.x><https://onlinelibrary.wiley.com/doi/abs/10.1111/j.0014-3820.2001.tb00731.x%3e> [onlinelibrary.wiley.com] <https://urldefense.com/v3/__https://onlinelibrary.wiley.com/doi/abs/10.1111/j.0014-3820.2001.tb00731.x<https://urldefense.com/v3/__https:/onlinelibrary.wiley.com/doi/abs/10.1111/j.0014-3820.2001.tb00731.x>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiCdr5xp6g$>, Klingenberg & Gidaszewski, 2010 <https://academic.oup.com/sysbio/article/59/3/245/1699888><https://academic.oup.com/sysbio/article/59/3/245/1699888%3e> [academic.oup.com] <https://urldefense.com/v3/__https://academic.oup.com/sysbio/article/59/3/245/1699888<https://urldefense.com/v3/__https:/academic.oup.com/sysbio/article/59/3/245/1699888>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiBMpeMYEw$>). I suspect it originates in part from Maddison (1991) <https://academic.oup.com/sysbio/article/40/3/304/1627756><https://academic.oup.com/sysbio/article/40/3/304/1627756%3e> [academic.oup.com] <https://urldefense.com/v3/__https://academic.oup.com/sysbio/article/40/3/304/1627756<https://urldefense.com/v3/__https:/academic.oup.com/sysbio/article/40/3/304/1627756>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiDm9t8IBw$>, but feel free to point out an earlier justification. - LC-ME (Landmark coordinates under [Cavalli-Sforza & Edwards, 1967 <https://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.1967.tb03411.x><https://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.1967.tb03411.x%3e> [onlinelibrary.wiley.com] <https://urldefense.com/v3/__https://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.1967.tb03411.x<https://urldefense.com/v3/__https:/onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.1967.tb03411.x>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiD7MJ9uAg$>] minimum evolution), “Euclidean parsimony”: Oldest use I can find is Varón-González et al. (2020) <https://academic.oup.com/sysbio/article/69/5/863/5716339><https://academic.oup.com/sysbio/article/69/5/863/5716339%3e> [academic.oup.com] <https://urldefense.com/v3/__https://academic.oup.com/sysbio/article/69/5/863/5716339<https://urldefense.com/v3/__https:/academic.oup.com/sysbio/article/69/5/863/5716339>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiCEQCruZw$>, who ultimately criticize it. Also heavily criticized by Goloboff (2022 <https://www.routledge.com/Refining-Phylogenetic-Analyses-Phylogenetic-Analysis-of-Morphological-Data/Goloboff/p/book/9780367420277><https://www.routledge.com/Refining-Phylogenetic-Analyses-Phylogenetic-Analysis-of-Morphological-Data/Goloboff/p/book/9780367420277%3e> [routledge.com] <https://urldefense.com/v3/__https://www.routledge.com/Refining-Phylogenetic-Analyses-Phylogenetic-Analysis-of-Morphological-Data/Goloboff/p/book/9780367420277<https://urldefense.com/v3/__https:/www.routledge.com/Refining-Phylogenetic-Analyses-Phylogenetic-Analysis-of-Morphological-Data/Goloboff/p/book/9780367420277>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiAtwfKFKA$>). - LC-ML (Landmark coordinates under maximum likelihood): Oldest use I can find is Ascarrunz et al. (2019) <https://peerj.com/articles/7476/><https://peerj.com/articles/7476/%3e> [peerj.com] <https://urldefense.com/v3/__https://peerj.com/articles/7476/<https://urldefense.com/v3/__https:/peerj.com/articles/7476/>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiBAW8CpqQ$>, though I swear there was at least one previous application. - LC-BI (Landmark coordinates under Bayesian inference): Parins-Fukuchi (2018 <https://academic.oup.com/evolut/article/72/9/1801/6882142><https://academic.oup.com/evolut/article/72/9/1801/6882142%3e> [academic.oup.com] <https://urldefense.com/v3/__https://academic.oup.com/evolut/article/72/9/1801/6882142<https://urldefense.com/v3/__https:/academic.oup.com/evolut/article/72/9/1801/6882142>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiDkq73Z-w$>), Zhang et al. (2023 in press) <https://academic.oup.com/sysbio/advance-article/doi/10.1093/sysbio/syad067/7470783><https://academic.oup.com/sysbio/advance-article/doi/10.1093/sysbio/syad067/7470783%3e> [academic.oup.com] <https://urldefense.com/v3/__https://academic.oup.com/sysbio/advance-article/doi/10.1093/sysbio/syad067/7470783<https://urldefense.com/v3/__https:/academic.oup.com/sysbio/advance-article/doi/10.1093/sysbio/syad067/7470783>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiAUCIgrkQ$>. - PC-P (Principal components under [Wagner-like] parsimony): González-José et al. (2008) <https://www.nature.com/articles/nature06891><https://www.nature.com/articles/nature06891%3e> [nature.com] <https://urldefense.com/v3/__https://www.nature.com/articles/nature06891<https://urldefense.com/v3/__https:/www.nature.com/articles/nature06891>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiBdNYOfjQ$>. Heavily criticized Adams et al. (2011) <https://www.sciencedirect.com/science/article/pii/S0047248410000278><https://www.sciencedirect.com/science/article/pii/S0047248410000278%3e> [sciencedirect.com] <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0047248410000278<https://urldefense.com/v3/__https:/www.sciencedirect.com/science/article/pii/S0047248410000278>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiCmOckTLg$>, which prompted a response from González-José et al. (2011) <https://www.sciencedirect.com/science/article/pii/S0047248410002356><https://www.sciencedirect.com/science/article/pii/S0047248410002356%3e> [sciencedirect.com] <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0047248410002356<https://urldefense.com/v3/__https:/www.sciencedirect.com/science/article/pii/S0047248410002356>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiDm9zDGVg$>; see also criticisms by Catalano et al. (2010) <https://onlinelibrary.wiley.com/doi/full/10.1111/j.1096-0031.2010.00302.x><https://onlinelibrary.wiley.com/doi/full/10.1111/j.1096-0031.2010.00302.x%3e> [onlinelibrary.wiley.com] <https://urldefense.com/v3/__https://onlinelibrary.wiley.com/doi/full/10.1111/j.1096-0031.2010.00302.x<https://urldefense.com/v3/__https:/onlinelibrary.wiley.com/doi/full/10.1111/j.1096-0031.2010.00302.x>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiC-a0eHpQ$>, Goloboff, 2022 <https://www.routledge.com/Refining-Phylogenetic-Analyses-Phylogenetic-Analysis-of-Morphological-Data/Goloboff/p/book/9780367420277><https://www.routledge.com/Refining-Phylogenetic-Analyses-Phylogenetic-Analysis-of-Morphological-Data/Goloboff/p/book/9780367420277%3e> [routledge.com] <https://urldefense.com/v3/__https://www.routledge.com/Refining-Phylogenetic-Analyses-Phylogenetic-Analysis-of-Morphological-Data/Goloboff/p/book/9780367420277<https://urldefense.com/v3/__https:/www.routledge.com/Refining-Phylogenetic-Analyses-Phylogenetic-Analysis-of-Morphological-Data/Goloboff/p/book/9780367420277>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiAtwfKFKA$>. - PC-ML (Principal components under maximum likelihood): Caumul & Polly (2005) <https://academic.oup.com/evolut/article/59/11/2460/6756964><https://academic.oup.com/evolut/article/59/11/2460/6756964%3e> [academic.oup.com] <https://urldefense.com/v3/__https://academic.oup.com/evolut/article/59/11/2460/6756964<https://urldefense.com/v3/__https:/academic.oup.com/evolut/article/59/11/2460/6756964>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiBUQ7GWGA$>, González-José et al. (2008) <https://www.nature.com/articles/nature06891><https://www.nature.com/articles/nature06891%3e> [nature.com] <https://urldefense.com/v3/__https://www.nature.com/articles/nature06891<https://urldefense.com/v3/__https:/www.nature.com/articles/nature06891>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiBdNYOfjQ$>, Parins-Fukuchi (2021) <https://royalsocietypublishing.org/doi/full/10.1098/rsbl.2020.0754><https://royalsocietypublishing.org/doi/full/10.1098/rsbl.2020.0754%3e> [royalsocietypublishing.org] <https://urldefense.com/v3/__https://royalsocietypublishing.org/doi/full/10.1098/rsbl.2020.0754<https://urldefense.com/v3/__https:/royalsocietypublishing.org/doi/full/10.1098/rsbl.2020.0754>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiBQRtSWww$>. Criticized by Adams et al. (2011) <https://www.sciencedirect.com/science/article/pii/S0047248410000278><https://www.sciencedirect.com/science/article/pii/S0047248410000278%3e> [sciencedirect.com] <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0047248410000278<https://urldefense.com/v3/__https:/www.sciencedirect.com/science/article/pii/S0047248410000278>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiCmOckTLg$>. So far, I haven’t encountered a Bayesian equivalent. - PD-NJ (Procrustes distances under neighbor-joining): Used in many studies since at least Lockwood et al. (2004) <https://www.pnas.org/doi/abs/10.1073/pnas.0306235101><https://www.pnas.org/doi/abs/10.1073/pnas.0306235101%3e> [pnas.org] <https://urldefense.com/v3/__https://www.pnas.org/doi/abs/10.1073/pnas.0306235101<https://urldefense.com/v3/__https:/www.pnas.org/doi/abs/10.1073/pnas.0306235101>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiBoHra0PA$>, not necessarily phylogenetic. Most recently favorably compared to LAUP in terms of performance by Weisbecker et al. (2023) <https://royalsocietypublishing.org/doi/full/10.1098/rstb.2022.0085><https://royalsocietypublishing.org/doi/full/10.1098/rstb.2022.0085%3e> [royalsocietypublishing.org] <https://urldefense.com/v3/__https://royalsocietypublishing.org/doi/full/10.1098/rstb.2022.0085<https://urldefense.com/v3/__https:/royalsocietypublishing.org/doi/full/10.1098/rstb.2022.0085>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiDB0PSggg$>. - PD-ML (Procrustes distances under maximum likelihood): I’m most familiar with Waddell’s (2014 <https://arxiv.org/abs/1501.00019><https://arxiv.org/abs/1501.00019%3e> [arxiv.org] <https://urldefense.com/v3/__https://arxiv.org/abs/1501.00019<https://urldefense.com/v3/__https:/arxiv.org/abs/1501.00019>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiBPXICKpQ$>, 2015 <https://arxiv.org/abs/1512.09115><https://arxiv.org/abs/1512.09115%3e> [arxiv.org] <https://urldefense.com/v3/__https://arxiv.org/abs/1512.09115<https://urldefense.com/v3/__https:/arxiv.org/abs/1512.09115>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiBsg68_7A$>, 2018 <https://direct.mit.edu/books/edited-volume/3632/chapter/121314/The-Phylogenomic-Origins-and-Definition-of-Homo><https://direct.mit.edu/books/edited-volume/3632/chapter/121314/The-Phylogenomic-Origins-and-Definition-of-Homo%3e> [direct.mit.edu] <https://urldefense.com/v3/__https://direct.mit.edu/books/edited-volume/3632/chapter/121314/The-Phylogenomic-Origins-and-Definition-of-Homo<https://urldefense.com/v3/__https:/direct.mit.edu/books/edited-volume/3632/chapter/121314/The-Phylogenomic-Origins-and-Definition-of-Homo>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiCg0BBoFg$>) application, though I’m sure it’s been used before. So far, I haven’t encountered any parsimony or Bayesian equivalents. - PF-ML (Polynomial fits under maximum likelihood): If I understand correctly, this is the method currently being developed by J. Felsenstein and F. L. Bookstein referenced by Catalano & Goloboff (2012) <https://academic.oup.com/sysbio/article/61/3/392/1669518><https://academic.oup.com/sysbio/article/61/3/392/1669518%3e> [academic.oup.com] <https://urldefense.com/v3/__https://academic.oup.com/sysbio/article/61/3/392/1669518<https://urldefense.com/v3/__https:/academic.oup.com/sysbio/article/61/3/392/1669518>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiDH-0mRtA$>. But it’s only vaguely alluded to in their recent works (e.g., Bookstein, 2016 <https://link.springer.com/article/10.1007/s11692-016-9382-7><https://link.springer.com/article/10.1007/s11692-016-9382-7%3e> [link.springer.com] <https://urldefense.com/v3/__https://link.springer.com/article/10.1007/s11692-016-9382-7<https://urldefense.com/v3/__https:/link.springer.com/article/10.1007/s11692-016-9382-7>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiDAwGWlYg$>, 2023 <https://link.springer.com/article/10.1007/s11692-023-09607-2><https://link.springer.com/article/10.1007/s11692-023-09607-2%3e> [link.springer.com] <https://urldefense.com/v3/__https://link.springer.com/article/10.1007/s11692-023-09607-2<https://urldefense.com/v3/__https:/link.springer.com/article/10.1007/s11692-023-09607-2>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiDGTTvMCw$>), which otherwise aren’t focussed on phylogenetics. - EFD-P (Elliptical Fourier descriptors under under [Wagner-like] parsimony): Carlo et al. (2011) <https://www.journals.uchicago.edu/doi/full/10.1086/BBLv220n3p224><https://www.journals.uchicago.edu/doi/full/10.1086/BBLv220n3p224%3e> [journals.uchicago.edu] <https://urldefense.com/v3/__https://www.journals.uchicago.edu/doi/full/10.1086/BBLv220n3p224<https://urldefense.com/v3/__https:/www.journals.uchicago.edu/doi/full/10.1086/BBLv220n3p224>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiAhs58O5w$>. - ES-P (Eigenaxis scores [from elliptical Fourier descriptors] under [Wagner-like] parsimony): Smith & Hendricks (2013) <https://academic.oup.com/sysbio/article/62/3/366/1650286><https://academic.oup.com/sysbio/article/62/3/366/1650286%3e> [academic.oup.com] <https://urldefense.com/v3/__https://academic.oup.com/sysbio/article/62/3/366/1650286<https://urldefense.com/v3/__https:/academic.oup.com/sysbio/article/62/3/366/1650286>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiCfS3eILw$>. So far, I haven’t encountered ML or Bayesian equivalents of this one or of EFD-P. I’d like to know which of the above methods (if any) have been used by MORPHMET subscribers, and if there are additional techniques and publications I’ve missed (especially those either offering or addressing criticism). Note that although all of the above methods are tied to issues of character optimization/ancestor-state reconstruction, I’m primarily interested in generating original topologies, not mapping GM data onto pre-existing topologies as in phylogenetic comparative methods. I’m currently uninterested in discretizing GM data, but I’d still like to hear if any MORPHMET subscribers have used discretization methods (e.g., gap-coding, gap-weighting, simple-gap, ANOVA-MRT). Thank you all in advance for your time. Jacqueline S. Silviria The Last King of the Jungle Department of Earth & Space Science University of Washington Seattle, WA, USA [email protected]<mailto:[email protected]> <mailto:[email protected]<mailto:[email protected]>>, [email protected]<mailto:[email protected]> <mailto:[email protected]<mailto:[email protected]>> ResearchGate profile <https://www.researchgate.net/profile/J_Silviria><https://www.researchgate.net/profile/J_Silviria%3e> [researchgate.net] <https://urldefense.com/v3/__https://www.researchgate.net/profile/J_Silviria<https://urldefense.com/v3/__https:/www.researchgate.net/profile/J_Silviria>*3E__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiA54n1rmQ$> Twitter: @JSilviria -- Andrea Cardini E-mail address: [email protected]<mailto:[email protected]>, [email protected]<mailto:[email protected]> WEBPAGE: https://sites.google.com/view/alcardini/ [sites.google.com] <https://urldefense.com/v3/__https://sites.google.com/view/alcardini/__;!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiBQlqLm_w$<https://urldefense.com/v3/__https:/sites.google.com/view/alcardini/__;!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiBQlqLm_w$>> -- 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:[email protected]> <mailto:[email protected]<mailto:[email protected]>>. To view this discussion on the web visit https://groups.google.com/d/msgid/morphmet2/A86A5E31-3CDF-4011-A3F9-715B5B8DE099%40gmail.com [groups.google.com] <https://urldefense.com/v3/__https://groups.google.com/d/msgid/morphmet2/A86A5E31-3CDF-4011-A3F9-715B5B8DE099<https://urldefense.com/v3/__https:/groups.google.com/d/msgid/morphmet2/A86A5E31-3CDF-4011-A3F9-715B5B8DE099>*40gmail.com?utm_medium=email&utm_source=footer__;JQ!!PDiH4ENfjr2_Jw!D2EJN_USzQEsuvfmpLnmDV0EXkoC6OAkg6RvxodLuZl2iQdm2JUmdYluqpHpgQIyGiaPF9eRXGIGpiZIYiB16thENw$>. -- 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:[email protected]> <mailto:[email protected]<mailto:[email protected]>>. 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