Data from: The utility of cranial ontogeny for phylogenetic inference: a case study in crocodylians using geometric morphometrics

Watanabe A, Slice DE

Date Published: March 25, 2014

DOI: http://dx.doi.org/10.5061/dryad.14fn1

 

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title Coordinate data of crocodylian crania (pre-superimposed)
Downloaded 33 times
Description 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.
Download WatanabeSlice_JEB_PreGPA.nts (594.0 Kb)
Details View File Details
Title PermuTree
Downloaded 50 times
Description Python 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.
Download permutree.py (5.315 Kb)
Download README.txt (1.235 Kb)
Details View File Details
Title Tree Comparison Test (SPR)
Downloaded 14 times
Description 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 <matrix.tnt> <tree1.tre> <tree2.tre> <# iterations>" in the command line.
Download comptreeSPR.run (1.626 Kb)
Details View File Details

When using this data, please cite the original publication:

Watanabe A, Slice D (2014) The utility of cranial ontogeny for phylogenetic inference: a case study in crocodylians using geometric morphometrics. Journal of Evolutionary Biology 27(6): 1078–1092. http://dx.doi.org/10.1111/jeb.12382

Additionally, please cite the Dryad data package:

Watanabe A, Slice DE (2014) Data from: The utility of cranial ontogeny for phylogenetic inference: a case study in crocodylians using geometric morphometrics. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.14fn1
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: