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.

README: Conservation of rib skeleton regionalization in the homoplastic evolution of the snake-like body form in squamates

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, Duke University. Links to each individual sampled can be found in Supplement Table 1

Conservation of rib skeleton regionalization in the homoplastic evolution of the snake-like body form in squamates

Data files

Abstract