Evolutionary Morphology - Science topic

The horn is absolutely not for defense. I’ve tried super hard to get hurt on the horn but the horn does nothing at all. It’s too floppy to do anything defense-related. I’m guessing it has something to do with sensory functions or tricking predators. This would be a cool capstone research project for anyone interested!

This is not a simple question to answer because the methods you mention are very different. Neither should be used without a thorough understanding of how it works and (more importantly) of what it assumes about the evolutionary mode(s) of your lineages. The compare.evol.rates function in geomorph compares Brownian rates. If considered simply in terms of statistical performance, it's a sound method. But it assumes that your data fit a one- or multi-rate Brownian model. If those models do not fit, you won't find out by running the function. You will get a comparison of the Brownian rates and a statistical test to determine if the rates differ. The function does not warn you that the rates are incorrectly estimated, as they would be if the mode is not Brownian. So, before using it, you need to determine whether a Brownian model (single or multiple-rate) fits your data better than alternative models that would call for a different rate formula. I have not used AUTEUR because it was (and may still be) limited to univariate data. If you have 10 morphological traits, you will need to think about how to analyze them in light of the correlations among the traits.

I just found a study of leporid lagomorphs that tackles a similar problem and uses 3D landmarks for morphometrics and phylo-morphospace plots:

Kraatz B, Sherratt E. 2016. Evolutionary morphology of the rabbit skull. PeerJ 4:e2453 https://doi.org/10.7717/peerj.2453

Mathematics, computer programs, &c., while certainly very useful in many situations, have - like any other "rigorous" methodology - two immanent Achilles' heels. First is what computer specialists often formulate as "garbage in, garbage out": to start a procedure we must put some data in, and if these data are wrong, wrongly interpreted or wrongly selected, then the results would have usually rather little in common with the truth; selection, formulation and interpretation of the data to be put in must be done based on the observable "external" (ecological, geographical, or any, but in taxonomy most frequently morphological) evidence, so our morphological knowledge and intuition is in most cases primarily responsible for the "input" not being "garbage". Second is the fact that complicated (and sometimes even relatively simple) mathematical or computerized procedures are almost invariably (at least for the "average": not specially trained in mathematics and/or computer programming) biologist something like a "black box": we put something (garbage or not) in and receive something out, but typically are not able to check (and understand!) step-by-step what happens in between, so we cannot easily (if at all) discover potential "bugs" (e.g. analogical to those on which the popular mathematical or logical "tricks" - "proofs" that 3 is less than 2, that swift-footed Achilles would never overcome a turtle, &c. - are based, or resulting from the application of the procedure in a situation where the preconditions of its reliable functioning are not met); such pitfalls are not always easy to see, and formalized procedures are typically not "self-verifying": they will not by themselves warn us if the result is wrong, here again the help of observable facts are needed. So, even if we recourse (as we must frequently do) to mathematics or computer-program, the external, directly observable (typically morphological) evidence remains the "alpha and omega" of our study: this assures that input is not "garbage", and this enables us to check whether the output makes biological (ecological, geographical, and especially morphological) sense. Only in this way we can avoid acceptation of such "rigorously derived" results as those obtained by Giribet & Ribera [2000. A review of arthropod phylogeny: new data based on ribosomal DNA sequences and direct character optimization. Cladistics 16: 204-23] where any of the 7 versions of molecular-phylogenetic reconstruction consistently placed e.g. Daphnia among Myriapods or Onychophora, or in BUHAY’s (2009. “COI-like” sequences are becoming problematic in molecular systematic and DNA barcoding studies. J. Crust. Biol. 29, 1: 96-110) somewhat surrealistic but highly symptomatic experiment “I used a subset of” a dataset from a published phylogenetic analysis “and added my favourite recipe for pumpkin pie (imagine it is a numt sequence or junk DNA) to the nexus file ... executed the file and”... “demonstrated” (with 100% bootstrap support!) that her pumpkin pie belongs to the genus Orconectes (Crustacea: Decapoda: Cambaridae) and is the sister species of O. burri! [that, of course, neither Buhay nor Giribet & Ribera have accepted the result of "rigorously performed analyses", was just because the morphological control ["The polyphyletic status of hexapods is certainly unacceptable from a morphological point of view, although it has been repeatedly obtained in molecular analyses of ribosomal sequence data ... [Giribet & Ribera: 222]"]. Not only taxonomy, but science in general, is - as it was for Goethe and Saint-Hilaire - "art and science at the same time", and it must remain so if we do not wish to reduce it to a kind of formal game in which (to use the famous mathematician, Kornél Lánczos words) "interesting is not what the world is, but what it should be" - I am biologist, not mathematician, for me interesting is what the world is, not what it (according to somebody or some rigorous formula) "should" be!