DOI: 10.5061/dryad.mw6m9065d
title: Patterns of girdle shape and their correlates in Australian limb-reduced skinks

description: The evolution of limb reduction in squamates is a classic example of
 convergence, but the internal morphological patterns associated with it
 are unexplored. To provide insights into the biomechanical and
 developmental consequences of transitions to limb reduction, we use
 geometric morphometrics to examine the morphology of pectoral and pelvic
 girdles in 90 species of limb-reduced skinks and their fully limbed
 relatives. Clavicle shapes converge towards an acute anterior bend when
 forelimbs are lost but hindlimbs are retained — a morphology typical of
 sand swimmers. This may either indicate functional adaptations to
 locomotion in fine substrates, or a developmental consequence of complete
 limb loss. The shape of limb-bearing elements of both girdles (coracoid
 and pelvis) instead closely mirrors limb reduction, becoming more
 simplified as undulation replaces limbed locomotion. Integration between
 girdles decreases in taxa lacking elements of the forelimbs but not
 hindlimbs, indicating differential selection on each girdle in response to
 distinct locomotory strategies. However, this pattern becomes less clear
 when considering phylogenetic history, perhaps because it is limited to
 one specific clade (Lerista). We show how the functional demands of
 locomotion, as well as developmental mechanisms, can induce changes at
 different levels of organismal organisation, including both external and
 internal structures.
description: # Patterns of girdle shape and their correlates in Australian limb-reduced
 skinks
 [https://doi.org/10.5061/dryad.mw6m9065d](https://doi.org/10.5061/dryad.mw6m9065d) ## Description of the data and file structure This R pipeline and associated files were written by Marco Camaiti (and coauthors). It is meant to extract shape information from landmark coordinates of lizard (skink) girdles. The specific usage of the associated files is included and explained in the pipeline itself. The tree file for the phylogenetic tree used for these analyses can be accessed at [https://doi.org/10.1016/j.ympev.2015.10.009](https://doi.org/10.1016/j.ympev.2015.10.009 "Persistent link using digital object identifier"). The full citation for that paper is Zheng, Y., & Wiens, J. J. (2016). Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species. *Molecular phylogenetics and evolution*, 94, 537-547. ### Files and variables #### File: Clav\_c.txt **Description:** a file containing landmark coordinates for the clavicle-scapulocoracoid integration analyses ##### Variables * landmark coordinates (x, y, z) #### File: Pelvic\_pls.txt **Description:** a file containing landmark coordinates for the full pelvis shape analyses ##### Variables * landmark coordinates (x, y, z) #### File: Clav\_reflected\_pls.txt **Description:** a file containing landmark coordinates for the full clavicle shape analyses ##### Variables * landmark coordinates (x, y, z) #### File: Clav\_reflected.txt **Description:** a file containing landmark coordinates for the clavicle-pelvis integration analyses ##### Variables * landmark coordinates (x, y, z) #### File: Pelvic\_pls\_c.txt **Description:** a file containing landmark coordinates for the pelvis-scapulocoracoid integration analyses ##### Variables * landmark coordinates (x, y, z) #### File: Pelvic\_pls\_b.txt **Description:** a file containing landmark coordinates for the clavicle-pelvis integration analyses ##### Variables * landmark coordinates (x, y, z) #### File: SCP\_c.txt **Description:** a file containing landmark coordinates for the scapulocoracoid-pelvis integration analyses ##### Variables * landmark coordinates (x, y, z) #### File: SCP\_ref.txt **Description:** a file containing landmark coordinates for the scapulocoracoid shape analyses ##### Variables * landmark coordinates (x, y, z) #### File: SCP\_ref\_b.txt **Description:** a file containing landmark coordinates for the scapulocoracoid-clavicle integration analyses ##### Variables * landmark coordinates (x, y, z) #### File: SCP\_test.csv **Description:** a file containing the output of the scapulocoracoid shape definition analyses, in the form of Principal Components of shape ##### #### File: cix\_clav\_side.csv **Description:** Morphological and ecological data for clavicle analyses ##### Variables * Species: Species  binomials * FL_extension: forelimb extension (index) * HL_extension: hindlimb extension (index) * Limb_status: degree of limb reduction (index) * LimbN: number of limb pairs (integer) * Comp1: PC1 scores * Comp2: PC2 scores * Comp3: PC3 scores * Clade * Substrate category * HdL: Head length (mm) * SVL: Snout-vent length (mm) * FLL: Forelimb length (mm) * HLL: Hindlimb length (mm) * PSVn: Presacral vertebrae number (integer) * logPSV: log of presacral vertebrae number (log of integer) * FLprop: forelimb proportion (percentage of SVL) * HLprop: hindlimb proportion (percentage of SVL) * Disparity: Limb disparity (index) * Man: Number of fingers (integer) * Pes: Number of toes (integer) * measured from scan: whether measurements were taken from a scan or not; 'presacral vertebrae' indicates that only presacral vertebrae counts were taken from scans * habitat source: The source of habitat data for each species #### File: clav\_test.csv **Description:** a file containing the output of the clavicle shape definition analyses, in the form of Principal Components of shape #### File: gix\_pelv.csv **Description:** morphological and ecological data for pelvis analyses ##### Variables * Species: Species binomial * HL_extension: Hindlimb extension (index) * Limb_status: status of limb reduction * LimbN: Number of limb pairs * Comp1: PC1 scores * Comp2: PC2 scores * Comp3: PC3 scores * Substrate category * Clade * SkW: skull width (mm) * HdL: Head length (mm) * SVL: Snout-vent length (mm) * FLL: Forelimb length (mm) * HLL: Hindlimb length (mm) * PSVn: Presacral vertebrae number (integer) * FLprop: Forelimb proportion (percentage of SVL) * HLprop: Hindlimb proportion (percentage of SVL) * Disparity: Limb disparity (index) * Man: Number of fingers (integer) * Pes: Number of toes (integer) * FL_extension: Forelimb extension (index) * measured from scan: whether measurements were taken from a scan or not; 'presacral vertebrae' indicates that only presacral vertebrae counts were taken from scans * habitat source: The source of habitat data for each species #### File: rex\_SCP\_side.csv **Description:** morphological and ecological data for scapulocoracoid analyses ##### Variables * Species: Species binomial * FL_extension: Forelimb extension (index) * HL_extension: Hindlimb extension (index) * Limb_status: degree of limb reduction * LimbN: Number of limb pairs (integer) * Comp1: PC1 scores * Comp2: PC2 scores * Clade * Substrate category * HdL: Head length (mm) * SVL: Snout-vent length (mm) * FLL: Forelimb length (mm) * HLL: Hindlimb length (mm) * PSVn: Presacral vertebrae number (integer) * logPSV: Log presacral vertebrae number (log of integer) * FLprop: Forelimb proportion (percentage of SVL) * HLprop: Hindlimb proportion (percentage of SVL) * Disparity: Limb disparity (index) * Man: Number of fingers (integer) * Pes: Number of toes (integer) * measured from scan: whether measurements were taken from a scan or not; 'presacral vertebrae' indicates that only presacral vertebrae counts were taken from scans * habitat source: The source of habitat data for each species #### File: sliding\_SCP\_side.txt **Description:** a list of sliding semilandmarks for scapulocoracoid #### File: sliding\_clav\_side.txt **Description:** a list of sliding semilandmarks for clavicle ## Code/software The pipeline was written in R. The packages and versions thereof can be accessed and are described within the submission. ## Access information Other publicly accessible locations of the data: * [https://github.com/Ravaat/Girdle--pipeline](https://github.com/Ravaat/Girdle--pipeline)