DOI: 10.5061/dryad.1jwstqk46
title: Conservation of rib skeleton regionalization in the homoplastic evolution of the snake-like body form in squamates

description: Squamates have independently evolved an elongate, limb-reduced body form
 numerous times. This transition has been proposed to involve either
 changes to regulatory gene expression or downstream modification of target
 enhancers to produce a homogeneous, deregionalized axial skeleton.
 Analysis of vertebral morphology has suggested that regionalization is
 maintained in snake-like body forms, but morphological variation in the
 other primary component of the axial skeleton, the dorsal ribs, as not
 been previously examined. We quantified rib morphology along the
 anterior-posterior axis in limbed and limbless squamates to test different
 regionalization models. We find that the relative position of regional
 boundaries remains consistent across taxa of differing body types,
 including in the homoplastic evolution of snake-like body forms. The
 consistent retention of regional boundaries in this primaxial domain is
 uncorrelated with more plastic abaxial region markers. Rather than loss of
 regions, rib shape at the anterior and posterior of the axis converges on
 those in the middle, resulting in axial regions being distinguishable by
 allometric shape changes rather than by discrete morphologies. This
 complexity challenges notions of deregionalization, revealing a nuanced
 evolutionary history shaped by shared functions.
description: # Conservation of rib skeleton regionalization in the homoplastic
 evolution of the snake-like body form in squamates
 [https://doi.org/10.5061/dryad.1jwstqk46](https://doi.org/10.5061/dryad.1jwstqk46) ## Description of the data and file structure These files provide the raw data that formed the basis for all analyses in this manuscript. Each file contains the 3D landmark data for a given sampled species. Landmarks were placed for geometric morphometric analysis. For more details on the landmark scheme, please refer to the manuscript and its associated electronic supplement, where the 3D landmarking scheme is figured and described in detail.  ### Files and variables Each of these files contains the landmark coordinates before superimposition of all sampled ribs for each taxon sampled in our analysis. The experimental efforts involved collecting and analyzing whole-body computerized tomography (CT) scans from adult specimens of 56 species, covering all major squamate clades and *Sphenodon punctatus*. Data segmentation and rendering were conducted using Thermo Scientific Avizo Software (v9.3 lite), and pre-cloacal free dorsal ribs from one bilateral half of each specimen were exported as un-smoothed PLY files. These files were used for landmarking in the Institute for Data Analysis and Visualization (IDAV) Landmark software (v3.6). A three-dimensional landmarking configuration was applied to every rib from specimens with fewer than 50 ribs, and at 4% intervals along the axis for more elongate species (with the exception of *Pantherophis guttatus* where a version was created where all ribs were sampled, seen in the file 'Pantherophis.Full.txt'). For each species, the landmark coordinates from each rib were consolidated into these TPS files. Each file therefore is labelled with the species name, and has a series of coordinate matrices for each landmarked rib. Each matrix is labelled with the rib number that the landmarks capture. #### File: Urostrophus.undulatus.txt #### File: Subdoluseps.txt #### File: Hypsiscopus.txt #### File: Laudakia.txt #### File: Afrotyphlops.txt #### File: Teius.txt #### File: Podarcis.txt #### File: Typhlosaurus.txt #### File: Xantusia.txt #### File: Dibamus.txt #### File: Sphenodon.txt #### File: Urostrophus.vautieri.txt #### File: Rieppeleon.txt #### File: Candoia.txt #### File: Loxocemus.txt #### File: Rhineura.txt #### File: Gekko.txt #### File: Crocodilurus.txt #### File: Helminthophis.txt #### File: Echinosaura.txt #### File: Varanus.txt #### File: Tropidophis.txt #### File: Pantherophis.Full.txt **Description:** this file contains the landmark coordinates from all ribs of the snake* Pantherophis guttatus.* #### File: Exiliboa.txt #### File: Pantherophis.Subsampled.txt #### File: Epicrates.txt #### File: Cnemidophorus.txt #### File: Cylindrophis.txt #### File: Shinisaurus.txt #### File: Leioheterodon.txt #### File: Boedon.txt #### File: Teratoscincus.txt #### File: Chameleo.txt #### File: Anolis.txt #### File: Bipes.txt #### File: Callophis.txt #### File: Cachryx.txt #### File: Chalicides.txt #### File: Blanus.txt #### File: Fimbrios.txt #### File: Aplopeltura.txt #### File: Calotes.txt #### File: Calabaria.txt #### File: Bolyeria.txt #### File: Cadea.txt #### File: Anilius.txt #### File: Amphisbaenia.txt #### File: Acontias.txt #### File: Anniella.txt #### File: Cordylus.txt #### File: Amblyrhynchus.txt #### File: Daboia.txt #### File: Agamodon.txt #### File: Acrochordus.txt #### File: Anguis.txt #### File: Xenosaurus.txt #### File: Chrysopelea.txt ## Code/software The landmark coordinates can be input and analyzed in R (v3.6.3), using packages ‘Morpho’ (Schlager, 2017) and ‘regions’ (Jones, et al., 2018). The code for this, and all subsequent analyses is included in full in the file EJHillan_Code.R  ## Access information Data was derived from the following sources: * These landmark data were generated from CT scan data which can be found on [www.MorphoSource.org](http://www.MorphoSource.org), Duke University. Links to each individual sampled can be found in Supplement Table 1