DOI: 10.5061/dryad.14fn1
title: Data from: The utility of cranial ontogeny for phylogenetic inference: a case study in crocodylians using geometric morphometrics

description: The degree to which the ontogeny of organisms could facilitate our
 understanding of phylogenetic relationships has long been a subject of
 contention in evolutionary biology. The famed notion that ‘ontogeny
 recapitulates phylogeny’ has been largely discredited, but there remains
 an expectation that closely related organisms undergo similar
 morphological transformations throughout ontogeny. To test this
 assumption, we used three-dimensional geometric morphometric methods to
 characterize the cranial morphology of 10 extant crocodylian species and
 construct allometric trajectories that model the post-natal ontogenetic
 shape changes. Using time-calibrated molecular and morphological trees, we
 employed a suite of comparative phylogenetic methods to assess the extent
 of phylogenetic signal in these trajectories. All analyses largely
 demonstrated a lack of significant phylogenetic signal, indicating that
 ontogenetic shape changes contain little phylogenetic information.
 Notably, some Mantel tests yielded marginally significant results when
 analysed with the morphological tree, which suggest that the underlying
 signal in these trajectories is correlated with similarities in the adult
 cranial morphology. However, despite these instances, all other analyses,
 including more powerful tests for phylogenetic signal, recovered
 statistical and visual evidence against the assumption that similarities
 in ontogenetic shape changes are commensurate with phylogenetic
 relatedness and thus bring into question the efficacy of using allometric
 trajectories for phylogenetic inference.
description: Coordinate data of
 crocodylian crania (pre-superimposed)Coordinate data of 78
 three-dimensional landmarks from 204 cranial specimens of 10 extant
 crocodylian species. All specimens, with the exception of Gavialis and
 Tomistoma, are from non-captive individuals. Raw coordinate data were
 collected with a G2 Microscribe digitzer (Immersion Corporation, CA, USA)
 by the principal author (A.W.). The coordinate data is in NTSYS format, in
 which the digitized specimens have been aligned according to PC axes (x
 axis = anteroposterior; y axis = mediolateral; z axis=dorsoventral), but
 still retain their original size. The coordinate points, therefore, have
 not been subjected to generalized Procrustes superimposition, allowing the
 user to calculate centroid size. Specimens are labeled in the file with
 species ID (first three letters of generic and specific names; e.g.,
 allmis = Alligator mississippiensis) followed by their respective
 institutional specimen number. Please refer to the main article and
 associated supplementary text file for description of landmarks and
 additional information on the acquisition and treatment of
 data.WatanabeSlice_JEB_PreGPA.ntsPermuTreePython program for performing a permutational regression analysis on trees. It takes a NEWICK string file and a CSV file of a single continuous variable and tests for significant correlation between phenotypic and phylogenetic distances. Please note that this script was written in Python version 2.7, thus some commands may not run properly (e.g., print function). In addition, the script requires the tree.py module to run, which can be downloaded through Peter Beerli's website (see README), as well as matplotlib and scipy Python packages.permutree.pyTree Comparison Test (SPR)Script written for the TNT phylogenetic program for testing the significant of topological similarity between two trees relative to randomly generated tree topologies. After placing the script in the same directory as TNT, analysis is performed by running "comptreeSPR &lt;# iterations&gt;" in the command line.comptreeSPR.run