Patterns of girdle shape and their correlates in Australian limb-reduced skinks
Data files
Aug 22, 2024 version files 1.14 MB
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cix_clav_side.csv
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Clav_c.txt
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Clav_reflected_pls.txt
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Clav_reflected.txt
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gix_pelv.csv
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Pelvic_pls_b.txt
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Pelvic_pls_c.txt
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Pelvic_pls.txt
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README.md
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rex_SCP_side.csv
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SCP_c.txt
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SCP_ref_b.txt
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SCP_ref.txt
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sliding_clav_side.txt
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sliding_SCP_side.txt
Abstract
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.
README: Patterns of girdle shape and their correlates in Australian limb-reduced skinks
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. 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
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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: